High yield fabrication of fluorescent nanodiamonds

PubMed Central

Boudou, Jean-Paul; Curmi, Patrick; Jelezko, Fedor; Wrachtrup, Joerg; Aubert, Pascal; Sennour, Mohamed; Balasubramanian, Gopalakrischnan; Reuter, Rolf; Thorel, Alain; Gaffet, Eric

2009-01-01

A new fabrication method to produce homogeneously fluorescent nanodiamonds with high yields is described. The powder obtained by high energy ball milling of fluorescent high pressure, high temperature diamond microcrystals was converted in a pure concentrated aqueous colloidal dispersion of highly crystalline ultrasmall nanoparticles with a mean size less than or equal to 10 nm. The whole fabrication yield of colloidal quasi-spherical nanodiamonds was several orders of magnitude higher than those previously reported starting from microdiamonds. The results open up avenues for the industrial cost-effective production of fluorescent nanodiamonds with well-controlled properties. PMID:19451687

Month-to-month and year-to-year reproducibility of high frequency QRS ECG signals

NASA Technical Reports Server (NTRS)

Batdorf, Niles J.; Feiveson, Alan H.; Schlegel, Todd T.

2004-01-01

High frequency electrocardiography analyzing the entire QRS complex in the frequency range of 150 to 250 Hz may prove useful in the detection of coronary artery disease, yet the long-term stability of these waveforms has not been fully characterized. Therefore, we prospectively investigated the reproducibility of the root mean squared voltage, kurtosis, and the presence versus absence of reduced amplitude zones in signal averaged 12-lead high frequency QRS recordings acquired in the supine position one month apart in 16 subjects and one year apart in 27 subjects. Reproducibility of root mean squared voltage and kurtosis was excellent over these time intervals in the limb leads, and acceptable in the precordial leads using both the V-lead and CR-lead derivations. The relative error of root mean squared voltage was 12% month-to-month and 16% year-to-year in the serial recordings when averaged over all 12 leads. Reduced amplitude zones were also reproducible up to a rate of 87% and 81%, respectively, for the month-to-month and year-to-year recordings. We conclude that 12-lead high frequency QRS electrocardiograms are sufficiently reproducible for clinical use.

In Spite of Indeterminacy Many Common Factor Score Estimates Yield an Identical Reproduced Covariance Matrix

ERIC Educational Resources Information Center

Beauducel, Andre

2007-01-01

It was investigated whether commonly used factor score estimates lead to the same reproduced covariance matrix of observed variables. This was achieved by means of Schonemann and Steiger's (1976) regression component analysis, since it is possible to compute the reproduced covariance matrices of the regression components corresponding to different…

Combining high biodiversity with high yields in tropical agroforests.

PubMed

Clough, Yann; Barkmann, Jan; Juhrbandt, Jana; Kessler, Michael; Wanger, Thomas Cherico; Anshary, Alam; Buchori, Damayanti; Cicuzza, Daniele; Darras, Kevin; Putra, Dadang Dwi; Erasmi, Stefan; Pitopang, Ramadhanil; Schmidt, Carsten; Schulze, Christian H; Seidel, Dominik; Steffan-Dewenter, Ingolf; Stenchly, Kathrin; Vidal, Stefan; Weist, Maria; Wielgoss, Arno Christian; Tscharntke, Teja

2011-05-17

Local and landscape-scale agricultural intensification is a major driver of global biodiversity loss. Controversially discussed solutions include wildlife-friendly farming or combining high-intensity farming with land-sparing for nature. Here, we integrate biodiversity and crop productivity data for smallholder cacao in Indonesia to exemplify for tropical agroforests that there is little relationship between yield and biodiversity under current management, opening substantial opportunities for wildlife-friendly management. Species richness of trees, fungi, invertebrates, and vertebrates did not decrease with yield. Moderate shade, adequate labor, and input level can be combined with a complex habitat structure to provide high biodiversity as well as high yields. Although livelihood impacts are held up as a major obstacle for wildlife-friendly farming in the tropics, our results suggest that in some situations, agroforests can be designed to optimize both biodiversity and crop production benefits without adding pressure to convert natural habitat to farmland.

High yield reproducible rat model recapitulating human Barrett’s carcinogenesis

PubMed Central

Matsui, Daisuke; Omstead, Ashten N; Kosovec, Juliann E; Komatsu, Yoshihiro; Lloyd, Emily J; Raphael, Hailey; Kelly, Ronan J; Zaidi, Ali H; Jobe, Blair A

2017-01-01

AIM To efficiently replicate the biology and pathogenesis of human esophageal adenocarcinoma (EAC) using the modified Levrat model of end-to-side esophagojejunostomy. METHODS End-to-side esophagojejunostomy was performed on rats to induce gastroduodenoesophageal reflux to develop EAC. Animals were randomly selected and serially euthanized at 10 (n = 6), 17 (n = 8), 24 (n = 9), 31 (n = 6), 38 (n = 6), and 40 (n = 6) wk postoperatively. The esophagi were harvested for downstream histopathology and gene expression. Histological evaluation was completed to determine respective rates of carcinogenic development. Quantitative reverse transcription-polymerase chain reaction was performed to determine gene expression levels of MUC2, CK19, and CK20, and results were compared to determine significant differences throughout disease progression stages. RESULTS The overall study mortality was 15%. Causes of mortality included anastomotic leak, gastrointestinal hemorrhage, stomach ulcer perforation, respiratory infection secondary to aspiration, and obstruction due to tumor or late anastomotic stricture. 10 wk following surgery, 100% of animals presented with esophagitis. Barrett’s esophagus (BE) was first observed at 10 wk, and was present in 100% of animals by 17 wk. Dysplasia was confirmed in 87.5% of animals at 17 wk, and increased to 100% by 31 wk. EAC was first observed in 44.4% of animals at 24 wk and increased to 100% by 40 wk. In addition, two animals at 38-40 wk post-surgery had confirmed macro-metastases in the lung/liver and small intestine, respectively. MUC2 gene expression was progressively down-regulated from BE to dysplasia to EAC. Both CK19 and CK20 gene expression significantly increased in a stepwise manner from esophagitis to EAC. CONCLUSION Esophagojejunostomy was successfully replicated in rats with low mortality and a high tumor burden, which may facilitate broader adoption to study EAC development, progression, and therapeutics. PMID:28970723

Combining high biodiversity with high yields in tropical agroforests

PubMed Central

Clough, Yann; Barkmann, Jan; Juhrbandt, Jana; Kessler, Michael; Wanger, Thomas Cherico; Anshary, Alam; Buchori, Damayanti; Cicuzza, Daniele; Darras, Kevin; Putra, Dadang Dwi; Erasmi, Stefan; Pitopang, Ramadhanil; Schmidt, Carsten; Schulze, Christian H.; Seidel, Dominik; Steffan-Dewenter, Ingolf; Stenchly, Kathrin; Vidal, Stefan; Weist, Maria; Wielgoss, Arno Christian; Tscharntke, Teja

2011-01-01

Local and landscape-scale agricultural intensification is a major driver of global biodiversity loss. Controversially discussed solutions include wildlife-friendly farming or combining high-intensity farming with land-sparing for nature. Here, we integrate biodiversity and crop productivity data for smallholder cacao in Indonesia to exemplify for tropical agroforests that there is little relationship between yield and biodiversity under current management, opening substantial opportunities for wildlife-friendly management. Species richness of trees, fungi, invertebrates, and vertebrates did not decrease with yield. Moderate shade, adequate labor, and input level can be combined with a complex habitat structure to provide high biodiversity as well as high yields. Although livelihood impacts are held up as a major obstacle for wildlife-friendly farming in the tropics, our results suggest that in some situations, agroforests can be designed to optimize both biodiversity and crop production benefits without adding pressure to convert natural habitat to farmland. PMID:21536873

Projecting crop yield in northern high latitude area.

PubMed

Matsumura, Kanichiro

2014-01-01

Changing climatic conditions on seasonal and longer time scales influence agricultural production. Improvement of soil and fertilizer is a strong factor in agricultural production, but agricultural production is influenced by climate conditions even in highly developed countries. It is valuable if fewer predictors make it possible to conduct future projections. Monthly temperature and precipitation, wintertime 500hPa geopotential height, and the previous year's yield are used as predictors to forecast spring wheat yield in advance. Canadian small agricultural divisions (SAD) are used for analysis. Each SAD is composed of a collection of Canadian Agricultural Regions (CAR) of similar weather and growing conditions. Spring wheat yields in each CAR are forecast from the following variables: (a) the previous year's yield, (b) earlier stages of the growing season's climate conditions and, (c) the previous year's wintertime northern hemisphere 500hPa geopotential height field. Arctic outflow events in the Okanagan Valley in Canada are associated with episodes of extremely low temperatures during wintertime. Principal component analysis (PCA) is applied for wintertime northern hemisphere 500hPa geopotential height anomalies. The spatial PCA mode1 is defined as Arctic Oscillation and it influences prevailing westerlies. The prevailing westerlies meanders and influences climatic conditions. The spatial similarity between wintertime top 5 Arctic outflow event year's composites of 500hPa geopotential height anomalies and mode 3's spatial pattern is found. Mode 3's spatial pattern looks like the Pacific/North American (PNA) pattern which describes the variation of atmospheric circulation pattern over the Pacific Ocean and North America. Climate conditions from April to June, May to July, mode 3's time coefficients, and previous year's yield are used for forecasting spring wheat yield in each SAD. Cross-validation procedure which generates eight sets of models for the eight

Comparison of oilseed yields: a preliminary review

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

Duke, J.A.; Bagby, M.O.

It was assumed that for most oilseed crops, 90% of the oil yield might be considered as profit. To compare oil seeds, pertinent portions of the yield and energy paragraphs from a summary published by Dr. Duke for DOE Grant No. 59-2246-1-6-054-0 with Dr. Bagby as ADODR were reproduced. The seed yields ranged from 200 to 14,000 kg/ha, the low one too low to consider and the high one suspiciously high. The yield of 14,000 kg oil per hectare is equivalent to more than 30 barrels of oil per hectare. The energy species included ambrette, tung-oil tree, cashew, wood-oil tree,more » mu-oil tree, peanut, mustard greens; rape, colza; black mustard, turnip, safflower, colocynth, coconut, crambe, African oil palm, soybean, cotton, sunflower, Eastern black walnut, Engligh walnut, meadow foam, flax, macadamia nuts, opium poppy, perilla, almond, castorbean, Chinese tallow tree, sesame, jojoba, yellow mustard, stokes' aster, and Zanzibar oilvine. 1 table. (DP)« less

Making Early Modern Medicine: Reproducing Swedish Bitters.

PubMed

Ahnfelt, Nils-Otto; Fors, Hjalmar

2016-05-01

Historians of science and medicine have rarely applied themselves to reproducing the experiments and practices of medicine and pharmacy. This paper delineates our efforts to reproduce "Swedish Bitters," an early modern composite medicine in wide European use from the 1730s to the present. In its original formulation, it was made from seven medicinal simples: aloe, rhubarb, saffron, myrrh, gentian, zedoary and agarikon. These were mixed in alcohol together with some theriac, a composite medicine of classical origin. The paper delineates the compositional history of Swedish Bitters and the medical rationale underlying its composition. It also describes how we go about to reproduce the medicine in a laboratory using early modern pharmaceutical methods, and analyse it using contemporary methods of pharmaceutical chemistry. Our aim is twofold: first, to show how reproducing medicines may provide a path towards a deeper understanding of the role of sensual and practical knowledge in the wider context of early modern medical culture; and second, how it may yield interesting results from the point of view of contemporary pharmaceutical science.

Reproducibility and calibration of MMC-based high-resolution gamma detectors

DOE PAGES

Bates, C. R.; Pies, C.; Kempf, S.; ...

2016-07-15

Here, we describe a prototype γ-ray detector based on a metallic magnetic calorimeter with an energy resolution of 46 eV at 60 keV and a reproducible response function that follows a simple second-order polynomial. The simple detector calibration allows adding high-resolution spectra from different pixels and different cool-downs without loss in energy resolution to determine γ-ray centroids with high accuracy. As an example of an application in nuclear safeguards enabled by such a γ-ray detector, we discuss the non-destructive assay of 242Pu in a mixed-isotope Pu sample.

Enhancing reproducibility: Failures from Reproducibility Initiatives underline core challenges.

PubMed

Mullane, Kevin; Williams, Michael

2017-08-15

Efforts to address reproducibility concerns in biomedical research include: initiatives to improve journal publication standards and peer review; increased attention to publishing methodological details that enable experiments to be reconstructed; guidelines on standards for study design, implementation, analysis and execution; meta-analyses of multiple studies within a field to synthesize a common conclusion and; the formation of consortia to adopt uniform protocols and internally reproduce data. Another approach to addressing reproducibility are Reproducibility Initiatives (RIs), well-intended, high-profile, systematically peer-vetted initiatives that are intended to replace the traditional process of scientific self-correction. Outcomes from the RIs reported to date have questioned the usefulness of this approach, particularly when the RI outcome differs from other independent self-correction studies that have reproduced the original finding. As a failed RI attempt is a single outcome distinct from the original study, it cannot provide any definitive conclusions necessitating additional studies that the RI approach has neither the ability nor intent of conducting making it a questionable replacement for self-correction. A failed RI attempt also has the potential to damage the reputation of the author of the original finding. Reproduction is frequently confused with replication, an issue that is more than semantic with the former denoting "similarity" and the latter an "exact copy" - an impossible outcome in research because of known and unknown technical, environmental and motivational differences between the original and reproduction studies. To date, the RI framework has negatively impacted efforts to improve reproducibility, confounding attempts to determine whether a research finding is real. Copyright © 2017 Elsevier Inc. All rights reserved.

Reproducible segmentation of white matter hyperintensities using a new statistical definition.

PubMed

Damangir, Soheil; Westman, Eric; Simmons, Andrew; Vrenken, Hugo; Wahlund, Lars-Olof; Spulber, Gabriela

2017-06-01

We present a method based on a proposed statistical definition of white matter hyperintensities (WMH), which can work with any combination of conventional magnetic resonance (MR) sequences without depending on manually delineated samples. T1-weighted, T2-weighted, FLAIR, and PD sequences acquired at 1.5 Tesla from 119 subjects from the Kings Health Partners-Dementia Case Register (healthy controls, mild cognitive impairment, Alzheimer's disease) were used. The segmentation was performed using a proposed definition for WMH based on the one-tailed Kolmogorov-Smirnov test. The presented method was verified, given all possible combinations of input sequences, against manual segmentations and a high similarity (Dice 0.85-0.91) was observed. Comparing segmentations with different input sequences to one another also yielded a high similarity (Dice 0.83-0.94) that exceeded intra-rater similarity (Dice 0.75-0.91). We compared the results with those of other available methods and showed that the segmentation based on the proposed definition has better accuracy and reproducibility in the test dataset used. Overall, the presented definition is shown to produce accurate results with higher reproducibility than manual delineation. This approach can be an alternative to other manual or automatic methods not only because of its accuracy, but also due to its good reproducibility.

High-biomass C4 grasses-Filling the yield gap.

PubMed

Mullet, John E

2017-08-01

A significant increase in agricultural productivity will be required by 2050 to meet the needs of an expanding and rapidly developing world population, without allocating more land and water resources to agriculture, and despite slowing rates of grain yield improvement. This review examines the proposition that high-biomass C 4 grasses could help fill the yield gap. High-biomass C 4 grasses exhibit high yield due to C 4 photosynthesis, long growth duration, and efficient capture and utilization of light, water, and nutrients. These C 4 grasses exhibit high levels of drought tolerance during their long vegetative growth phase ideal for crops grown in water-limited regions of agricultural production. The stems of some high-biomass C 4 grasses can accumulate high levels of non-structural carbohydrates that could be engineered to enhance biomass yield and utility as feedstocks for animals and biofuels production. The regulatory pathway that delays flowering of high-biomass C 4 grasses in long days has been elucidated enabling production and deployment of hybrids. Crop and landscape-scale modeling predict that utilization of high-biomass C 4 grass crops on land and in regions where water resources limit grain crop yield could increase agricultural productivity. Copyright © 2017 Elsevier B.V. All rights reserved.

Reproducible, high-yielding, biological caproate production from food waste using a single-phase anaerobic reactor system.

PubMed

Nzeteu, Corine Orline; Trego, Anna Christine; Abram, Florence; O'Flaherty, Vincent

2018-01-01

Nowadays, the vast majority of chemicals are either synthesised from fossil fuels or are extracted from agricultural commodities. However, these production approaches are not environmentally and economically sustainable, as they result in the emission of greenhouse gases and they may also compete with food production. Because of the global agreement to reduce greenhouse gas emissions, there is an urgent interest in developing alternative sustainable sources of chemicals. In recent years, organic waste streams have been investigated as attractive and sustainable feedstock alternatives. In particular, attention has recently focused on the production of caproate from mixed culture fermentation of low-grade organic residues. The current approaches for caproate synthesis from organic waste are not economically attractive, as they involve the use of two-stage anaerobic digestion systems and the supplementation of external electron donors, both of which increase its production costs. This study investigates the feasibility of producing caproate from food waste (FW) without the supplementation of external electron donors using a single-phase reactor system. Replicate leach-bed reactors were operated on a semi-continuous mode at organic loading of 80 g VS FW l -1 and at solid retention times of 14 and 7 days. Fermentation, rather than hydrolysis, was the limiting step for caproate production. A higher caproate production yield 21.86 ± 0.57 g COD l -1 was achieved by diluting the inoculating leachate at the beginning of each run and by applying a leachate recirculation regime. The mixed culture batch fermentation of the FW leachate was able to generate 23 g caproate COD l -1 (10 g caproate l -1 ), at a maximum rate of 3 g caproate l -1 day -1 under high H 2 pressure. Lactate served as the electron donor and carbon source for the synthesis of caproate. Microbial community analysis suggested that neither Clostridium kluyveri nor Megasphaera elsdenii, which are

Month-to-Month and Year-to-Year Reproducibility of High Frequency QRS ECG signals

NASA Technical Reports Server (NTRS)

Batdorf, Niles; Feiveson, Alan H.; Schlegel, Todd T.

2006-01-01

High frequency (HF) electrocardiography analyzing the entire QRS complex in the frequency range of 150 to 250 Hz may prove useful in the detection of coronary artery disease, yet the long-term stability of these waveforms has not been fully characterized. We therefore prospectively investigated the reproducibility of the root mean squared (RMS) voltage, kurtosis, and the presence versus absence of reduced amplitude zones (RAzs) in signal averaged 12-lead HF QRS recordings acquired in the supine position one month apart in 16 subjects and one year apart in 27 subjects. Reproducibility of RMS voltage and kurtosis was excellent over these time intervals in the limb leads, and acceptable in the precordial leads using both the V-lead and CR-lead derivations. The relative error of RMS voltage was 12% month-to-month and 16% year-to-year in the serial recordings when averaged over all 12 leads. RAzs were also reproducible at a rate of up to 87% and 8 1 %, respectively, for the month-to-month and year-to-year recordings. We conclude that 12-lead HF QRS electrocardiograms are sufficiently reproducible for clinical use.

Analysis of the trade-off between high crop yield and low yield instability at the global scale

NASA Astrophysics Data System (ADS)

Ben-Ari, Tamara; Makowski, David

2016-10-01

Yield dynamics of major crops species vary remarkably among continents. Worldwide distribution of cropland influences both the expected levels and the interannual variability of global yields. An expansion of cultivated land in the most productive areas could theoretically increase global production, but also increase global yield instability if the most productive regions are characterized by high interannual yield variability. In this letter, we use portfolio analysis to quantify the tradeoff between the expected values and the interannual variance of global yield. We compute optimal frontiers for four crop species i.e., maize, rice, soybean and wheat and show how the distribution of cropland among large world regions can be optimized to either increase expected global crop production or decrease its interannual variability. We also show that a preferential allocation of cropland in the most productive regions can increase global expected yield at the expense of yield stability. Theoretically, optimizing the distribution of a small fraction of total cultivated areas can help find a good compromise between low instability and high crop yields at the global scale.

Highly reproducible and sensitive silver nanorod array for the rapid detection of Allura Red in candy

NASA Astrophysics Data System (ADS)

Yao, Yue; Wang, Wen; Tian, Kangzhen; Ingram, Whitney Marvella; Cheng, Jie; Qu, Lulu; Li, Haitao; Han, Caiqin

2018-04-01

Allura Red (AR) is a highly stable synthetic red azo dye, which is widely used in the food industry to dye food and increase its attraction to consumers. However, the excessive consumption of AR can result in adverse health effects to humans. Therefore, a highly reproducible silver nanorod (AgNR) array was developed for surface enhanced Raman scattering (SERS) detection of AR in candy. The relative standard deviation (RSD) of AgNR substrate obtained from the same batch and different batches were 5.7% and 11.0%, respectively, demonstrating the high reproducibility. Using these highly reproducible AgNR arrays as the SERS substrates, AR was detected successfully, and its characteristic peaks were assigned by the density function theory (DFT) calculation. The limit of detection (LOD) of AR was determined to be 0.05 mg/L with a wide linear range of 0.8-100 mg/L. Furthermore, the AgNR SERS arrays can detect AR directly in different candy samples within 3 min without any complicated pretreatment. These results suggest the AgNR array can be used for rapid and qualitative SERS detection of AR, holding a great promise for expanding SERS application in food safety control field.

High-yield positron systems for linear colliders

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

Clendenin, J.E.

1989-04-01

Linear colliders, such as the SLC, are among those accelerators for which a high-yield positron source operating at the repetition rate of the accelerator is desired. The SLC, having electron energies up to 50 GeV, presents the possibility of generating positron bunches with useful charge even exceeding that of the initial electron bunch. The exact positron yield to be obtained depends on the particular capture, transport and damping system employed. Using 31 GeV electrons impinging on a W-type converter phase-space at the target to the acceptance of the capture rf section, the SLC source is capable of producing, for everymore » electron, up to two positrons within the acceptance of the positron damping ring. The design of this source and the performance of the positron system as built are described. Also, future prospects and limitations for high-yield positron systems are discussed. 11 refs., 5 figs., 3 tabs.« less

Reproducibility of Clathromorphum compactum coralline algal Mg/Ca ratios and comparison to high-resolution sea surface temperature data

NASA Astrophysics Data System (ADS)

Hetzinger, S.; Halfar, J.; Kronz, A.; Simon, K.; Adey, W. H.; Steneck, R. S.

2018-01-01

The potential of crustose coralline algae as high-resolution archives of past ocean variability in mid- to high-latitudes has only recently been recognized. Few comparisons of coralline algal proxies, such as temperature-dependent algal magnesium to calcium (Mg/Ca) ratios, with in situ-measured surface ocean data exist, even rarer are well replicated records from individual sites. We present Mg/Ca records from nine coralline algal specimens (Clathromorphum compactum) from a single site in the Gulf of Maine, North Atlantic. Sections from algal mounds were analyzed using Laser Ablation-Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) yielding individual Mg/Ca records of up to 30 years in length. We first test intra- and intersample signal replication and show that algal Mg/Ca ratios are reproducible along several transects within individual sample specimens and between different samples from the same study site. In addition, LA-ICP-MS-derived Mg/Ca ratios are compared to electron microprobe (EMP) analyzed data on the longest-lived specimens and were found to be statistically commensurable. Second, we evaluate whether relationships between algal-based SST reconstructions and in situ temperature data can be improved by averaging Mg/Ca records from multiple algal specimens (intersample averages). We found that intersample averages yield stronger relationships to sea surface temperature (SST) data than Mg/Ca records derived from individual samples alone. Thus, Mg/Ca-based paleotemperature reconstructions from coralline algae can benefit from using multiple samples per site, and can expand temperature proxy precision from seasonal to monthly.

Strontium and barium iodide high light yield scintillators

NASA Astrophysics Data System (ADS)

Cherepy, Nerine J.; Hull, Giulia; Drobshoff, Alexander D.; Payne, Stephen A.; van Loef, Edgar; Wilson, Cody M.; Shah, Kanai S.; Roy, Utpal N.; Burger, Arnold; Boatner, Lynn A.; Choong, Woon-Seng; Moses, William W.

2008-02-01

Europium-doped strontium and barium iodide are found to be readily growable by the Bridgman method and to produce high scintillation light yields. SrI2(Eu ) emits into the Eu2+ band, centered at 435nm, with a decay time of 1.2μs and a light yield of ˜90000photons/MeV. It offers energy resolution better than 4% full width at half maximum at 662keV, and exhibits excellent light yield proportionality. BaI2(Eu ) produces >30000photons/MeV into the Eu2+ band at 420nm (<1μs decay). An additional broad impurity-mediated recombination band is present at 550nm (>3μs decay), unless high-purity feedstock is used.

Reducing pressure on natural forests through high-yield forestry

Treesearch

W.T. Gladstone; F. Thomas Ledig

1990-01-01

High-yield forestry can make a valuable contribution to the conservation and sustained use of forest ecosystems. Despite the pressing reasons for conserving forest resources, population growth creates pressures for exploiting them. Unless needs for forest products, export credits, and local employment can be met by new devices, such as high-yield forestry, these...

Preparation of reflective CsI photocathodes with reproducible high quantum efficiency

NASA Astrophysics Data System (ADS)

Maier-Komor, P.; Bauer, B. B.; Friese, J.; Gernhäuser, R.; Kienle, P.; Körner, H. J.; Montermann, G.; Zeitelhack, K.

1995-02-01

CsI as a solid UV-photocathode material has many promising applications in fast gaseous photon detectors. They are proposed in large area Ring Imaging CHerenkov (RICH) devices in forthcoming experiments at various high-energy particle accelerators. A high photon-to-electron conversion efficiency is a basic requirement for the successful operation of these devices. High reproducible quantum efficiencies could be achieved with CsI layers prepared by electron beam evaporation from a water-cooled copper crucible. CsI films were deposited in the thickness range of 30 to 500 μg/cm 2. Absorption coefficients and quantum efficiencies were measured in the wavelength region of 150 nm to 250 nm. The influence of various evaporation parameters on the quantum efficiency were investigated.

Spatial Sampling of Weather Data for Regional Crop Yield Simulations

NASA Technical Reports Server (NTRS)

Van Bussel, Lenny G. J.; Ewert, Frank; Zhao, Gang; Hoffmann, Holger; Enders, Andreas; Wallach, Daniel; Asseng, Senthold; Baigorria, Guillermo A.; Basso, Bruno; Biernath, Christian;

International Interlaboratory Digital PCR Study Demonstrating High Reproducibility for the Measurement of a Rare Sequence Variant.

PubMed

Whale, Alexandra S; Devonshire, Alison S; Karlin-Neumann, George; Regan, Jack; Javier, Leanne; Cowen, Simon; Fernandez-Gonzalez, Ana; Jones, Gerwyn M; Redshaw, Nicholas; Beck, Julia; Berger, Andreas W; Combaret, Valérie; Dahl Kjersgaard, Nina; Davis, Lisa; Fina, Frederic; Forshew, Tim; Fredslund Andersen, Rikke; Galbiati, Silvia; González Hernández, Álvaro; Haynes, Charles A; Janku, Filip; Lacave, Roger; Lee, Justin; Mistry, Vilas; Pender, Alexandra; Pradines, Anne; Proudhon, Charlotte; Saal, Lao H; Stieglitz, Elliot; Ulrich, Bryan; Foy, Carole A; Parkes, Helen; Tzonev, Svilen; Huggett, Jim F

2017-02-07

This study tested the claim that digital PCR (dPCR) can offer highly reproducible quantitative measurements in disparate laboratories. Twenty-one laboratories measured four blinded samples containing different quantities of a KRAS fragment encoding G12D, an important genetic marker for guiding therapy of certain cancers. This marker is challenging to quantify reproducibly using quantitative PCR (qPCR) or next generation sequencing (NGS) due to the presence of competing wild type sequences and the need for calibration. Using dPCR, 18 laboratories were able to quantify the G12D marker within 12% of each other in all samples. Three laboratories appeared to measure consistently outlying results; however, proper application of a follow-up analysis recommendation rectified their data. Our findings show that dPCR has demonstrable reproducibility across a large number of laboratories without calibration. This could enable the reproducible application of molecular stratification to guide therapy and, potentially, for molecular diagnostics.

Silver nanowires for highly reproducible cantilever based AFM-TERS microscopy: towards a universal TERS probe.

PubMed

Walke, Peter; Fujita, Yasuhiko; Peeters, Wannes; Toyouchi, Shuichi; Frederickx, Wout; De Feyter, Steven; Uji-I, Hiroshi

2018-04-26

Tip-enhanced Raman scattering (TERS) microscopy is a unique analytical tool to provide complementary chemical and topographic information of surfaces with nanometric resolution. However, difficulties in reliably producing the necessary metallized scanning probe tips has limited its widespread utilisation, particularly in the case of cantilever-based atomic force microscopy. Attempts to alleviate tip related issues using colloidal or bottom-up engineered tips have so far not reported consistent probes for both Raman and topographic imaging. Here we demonstrate the reproducible fabrication of cantilever-based high-performance TERS probes for both topographic and Raman measurements, based on an approach that utilises noble metal nanowires as the active TERS probe. The tips show 10 times higher TERS contrasts than the most typically used electrochemically-etched tips, and show a reproducibility for TERS greater than 90%, far greater than found with standard methods. We show that TERS can be performed in tapping as well as contact AFM mode, with optical resolutions around or below 15 nm, and with a maximum resolution achieved in tapping-mode of 6 nm. Our work illustrates that superior TERS probes can be produced in a fast and cost-effective manner using simple wet-chemistry methods, leading to reliable and reproducible high-resolution and high-sensitivity TERS, and thus renders the technique applicable for a broad community.

Sensitivity Gains, Linearity, and Spectral Reproducibility in Nonuniformly Sampled Multidimensional MAS NMR Spectra of High Dynamic Range.

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

Suiter, Christopher L.; Paramasivam, Sivakumar; Hou, Guangjin

Recently, we have demonstrated that considerable inherent sensitivity gains are attained in MAS NMR spectra acquired by nonuniform sampling (NUS) and introduced maximum entropy interpolation (MINT) processing that assures the linearity of transformation between the time and frequency domains. In this report, we examine the utility of the NUS/MINT approach in multidimensional datasets possessing high dynamic range, such as homonuclear 13C–13C correlation spectra. We demonstrate on model compounds and on 1–73-(U-13C,15N)/74–108-(U-15N) E. coli thioredoxin reassembly, that with appropriately constructed 50 % NUS schedules inherent sensitivity gains of 1.7–2.1-fold are readily reached in such datasets. We show that both linearity andmore » line width are retained under these experimental conditions throughout the entire dynamic range of the signals. Furthermore, we demonstrate that the reproducibility of the peak intensities is excellent in the NUS/MINT approach when experiments are repeated multiple times and identical experimental and processing conditions are employed. Finally, we discuss the principles for design and implementation of random exponentially biased NUS sampling schedules for homonuclear 13C–13C MAS correlation experiments that yield high quality artifact-free datasets.« less

Sensitivity gains, linearity, and spectral reproducibility in nonuniformly sampled multidimensional MAS NMR spectra of high dynamic range

PubMed Central

Suiter, Christopher L.; Paramasivam, Sivakumar; Hou, Guangjin; Sun, Shangjin; Rice, David; Hoch, Jeffrey C.; Rovnyak, David

2014-01-01

Recently, we have demonstrated that considerable inherent sensitivity gains are attained in MAS NMR spectra acquired by nonuniform sampling (NUS) and introduced maximum entropy interpolation (MINT) processing that assures the linearity of transformation between the time and frequency domains. In this report, we examine the utility of the NUS/MINT approach in multidimensional datasets possessing high dynamic range, such as homonuclear 13C–13C correlation spectra. We demonstrate on model compounds and on 1–73-(U-13C, 15N)/74–108-(U-15N) E. coli thioredoxin reassembly, that with appropriately constructed 50 % NUS schedules inherent sensitivity gains of 1.7–2.1-fold are readily reached in such datasets. We show that both linearity and line width are retained under these experimental conditions throughout the entire dynamic range of the signals. Furthermore, we demonstrate that the reproducibility of the peak intensities is excellent in the NUS/MINT approach when experiments are repeated multiple times and identical experimental and processing conditions are employed. Finally, we discuss the principles for design and implementation of random exponentially biased NUS sampling schedules for homonuclear 13C–13C MAS correlation experiments that yield high-quality artifact-free datasets. PMID:24752819

Angiographic core laboratory reproducibility analyses: implications for planning clinical trials using coronary angiography and left ventriculography end-points.

PubMed

Steigen, Terje K; Claudio, Cheryl; Abbott, David; Schulzer, Michael; Burton, Jeff; Tymchak, Wayne; Buller, Christopher E; John Mancini, G B

2008-06-01

To assess reproducibility of core laboratory performance and impact on sample size calculations. Little information exists about overall reproducibility of core laboratories in contradistinction to performance of individual technicians. Also, qualitative parameters are being adjudicated increasingly as either primary or secondary end-points. The comparative impact of using diverse indexes on sample sizes has not been previously reported. We compared initial and repeat assessments of five quantitative parameters [e.g., minimum lumen diameter (MLD), ejection fraction (EF), etc.] and six qualitative parameters [e.g., TIMI myocardial perfusion grade (TMPG) or thrombus grade (TTG), etc.], as performed by differing technicians and separated by a year or more. Sample sizes were calculated from these results. TMPG and TTG were also adjudicated by a second core laboratory. MLD and EF were the most reproducible, yielding the smallest sample size calculations, whereas percent diameter stenosis and centerline wall motion require substantially larger trials. Of the qualitative parameters, all except TIMI flow grade gave reproducibility characteristics yielding sample sizes of many 100's of patients. Reproducibility of TMPG and TTG was only moderately good both within and between core laboratories, underscoring an intrinsic difficulty in assessing these. Core laboratories can be shown to provide reproducibility performance that is comparable to performance commonly ascribed to individual technicians. The differences in reproducibility yield huge differences in sample size when comparing quantitative and qualitative parameters. TMPG and TTG are intrinsically difficult to assess and conclusions based on these parameters should arise only from very large trials.

A reproducible approach to high-throughput biological data acquisition and integration

PubMed Central

Rahnavard, Gholamali; Waldron, Levi; McIver, Lauren; Shafquat, Afrah; Franzosa, Eric A.; Miropolsky, Larissa; Sweeney, Christopher

2015-01-01

Modern biological research requires rapid, complex, and reproducible integration of multiple experimental results generated both internally and externally (e.g., from public repositories). Although large systematic meta-analyses are among the most effective approaches both for clinical biomarker discovery and for computational inference of biomolecular mechanisms, identifying, acquiring, and integrating relevant experimental results from multiple sources for a given study can be time-consuming and error-prone. To enable efficient and reproducible integration of diverse experimental results, we developed a novel approach for standardized acquisition and analysis of high-throughput and heterogeneous biological data. This allowed, first, novel biomolecular network reconstruction in human prostate cancer, which correctly recovered and extended the NFκB signaling pathway. Next, we investigated host-microbiome interactions. In less than an hour of analysis time, the system retrieved data and integrated six germ-free murine intestinal gene expression datasets to identify the genes most influenced by the gut microbiota, which comprised a set of immune-response and carbohydrate metabolism processes. Finally, we constructed integrated functional interaction networks to compare connectivity of peptide secretion pathways in the model organisms Escherichia coli, Bacillus subtilis, and Pseudomonas aeruginosa. PMID:26157642

[Study on High-yield Cultivation Measures for Arctii Fructus].

PubMed

Liu, Shi-yong; Jiang, Xiao-bo; Wang, Tao; Sun, Ji-ye; Hu, Shang-qin; Zhang, Li

2015-02-01

To find out the high yield cultivation measures for Arctii Fructus. Completely randomized block experiment design method was used in the field planting, to analyze the effect of different cultivation way on agronomic characters, phenological phase,quality and quantity of Arctii Fructus. Arctium lappa planted on August 28 had the best results of plant height, thousand seeds weight and yield. The highest yield of Arctii Fructus was got at the density of 1,482 plants/667 m2. Arctiin content was in an increase trend with the planting time delay and planting density increasing. The plant height, thousand seeds weight, yield and arctiin content by split application of fertilizer were significantly higher than that by one-time fertilization. Compared with open field Arctium lappa, plant height, yield, arctiin content and relative water content of plastic film mulching Arctium lappa was higher by 7.74%, 10.87%, 6.38% and 24.20%, respectively. In the topping Arctium lappa, the yield was increased by 11.09%, with 39. 89% less branching number. Early planting time and topping shortened the growth cycle of Arctium lappa plant. The high-yield cultivation measures of Arctii Fructus are: around August 28 to sowing, planting density of 1 482 plants/667 m2, split application of fertilizer for four times, covering film on surface of the soil and topping in bolting.

Accuracy, repeatability, and reproducibility of Artemis very high-frequency digital ultrasound arc-scan lateral dimension measurements

PubMed Central

Reinstein, Dan Z.; Archer, Timothy J.; Silverman, Ronald H.; Coleman, D. Jackson

2008-01-01

Purpose To determine the accuracy, repeatability, and reproducibility of measurement of lateral dimensions using the Artemis (Ultralink LLC) very high-frequency (VHF) digital ultrasound (US) arc scanner. Setting London Vision Clinic, London, United Kingdom. Methods A test object was measured first with a micrometer and then with the Artemis arc scanner. Five sets of 10 consecutive B-scans of the test object were performed with the scanner. The test object was removed from the system between each scan set. One expert observer and one newly trained observer separately measured the lateral dimension of the test object. Two-factor analysis of variance was performed. The accuracy was calculated as the average bias of the scan set averages. The repeatability and reproducibility coefficients were calculated. The coefficient of variation (CV) was calculated for repeatability and reproducibility. Results The test object was measured to be 10.80 mm wide. The mean lateral dimension bias was 0.00 mm. The repeatability coefficient was 0.114 mm. The reproducibility coefficient was 0.026 mm. The repeatability CV was 0.38%, and the reproducibility CV was 0.09%. There was no statistically significant variation between observers (P = .0965). There was a statistically significant variation between scan sets (P = .0036) attributed to minor vertical changes in the alignment of the test object between consecutive scan sets. Conclusion The Artemis VHF digital US arc scanner obtained accurate, repeatable, and reproducible measurements of lateral dimensions of the size commonly found in the anterior segment. PMID:17081860

Repeatability and Reproducibility of Compression Strength Measurements Conducted According to ASTM E9

NASA Technical Reports Server (NTRS)

Luecke, William E.; Ma, Li; Graham, Stephen M.; Adler, Matthew A.

2010-01-01

Ten commercial laboratories participated in an interlaboratory study to establish the repeatability and reproducibility of compression strength tests conducted according to ASTM International Standard Test Method E9. The test employed a cylindrical aluminum AA2024-T351 test specimen. Participants measured elastic modulus and 0.2 % offset yield strength, YS(0.2 % offset), using an extensometer attached to the specimen. The repeatability and reproducibility of the yield strength measurement, expressed as coefficient of variations were cv(sub r)= 0.011 and cv(sub R)= 0.020 The reproducibility of the test across the laboratories was among the best that has been reported for uniaxial tests. The reported data indicated that using diametrically opposed extensometers, instead of a single extensometer doubled the precision of the test method. Laboratories that did not lubricate the ends of the specimen measured yield stresses and elastic moduli that were smaller than those measured in laboratories that lubricated the specimen ends. A finite element analysis of the test specimen deformation for frictionless and perfect friction could not explain the discrepancy, however. The modulus measured from stress-strain data were reanalyzed using a technique that finds the optimal fit range, and applies several quality checks to the data. The error in modulus measurements from stress-strain curves generally increased as the fit range decreased to less than 40 % of the stress range.

Reproducibility patterns of multiple rapid swallows during high resolution esophageal manometry provide insights into esophageal pathophysiology.

PubMed

Price, L H; Li, Y; Patel, A; Gyawali, C Prakash

2014-05-01

Multiple rapid swallows (MRS) during esophageal high resolution manometry (HRM) assess esophageal neuromuscular integrity by evaluating postdeglutitive inhibition and rebound contraction, but most reports performed only a single MRS sequence. We assessed patterns of MRS reproducibility during clinical HRM in comparison to a normal cohort. Consecutive clinical HRM studies were included if two separate MRS sequences (four to six rapid swallows ≤4 s apart) were successfully performed. Chicago Classification diagnoses were identified; contraction wave abnormalities were additionally recorded. MRS-induced inhibition (contraction ≤3 cm during inhibition phase) and rebound contraction was assessed, and findings compared to 18 controls (28.0 ± 0.7 year, 50.0% female). Reproducibility consisted of similar inhibition and contraction responses with both sequences; discordance was segregated into inhibition and contraction phases. Multiple rapid swallows were successfully performed in 89.3% patients and all controls; 225 subjects (56.2 ± 0.9 year, 62.7% female) met study inclusion criteria. Multiple rapid swallows were reproducible in 76.9% patients and 94.4% controls (inhibition phase: 88.0% vs 94.4%, contraction phase 86.7% vs 100%, respectively, p = ns). A gradient of reproducibility was noted, highest in well-developed motor disorders (achalasia spectrum, hypermotility disorders, and aperistalsis, 91.7-100%, p = ns compared to controls); and lower in lesser motor disorders (contraction wave abnormalities, esophageal body hypomotility) or normal studies (62.2-70.8%, p < 0.0001 compared to well-developed motor disorders). Inhibition phase was most discordant in contraction wave abnormalities, while contraction phase was most discordant when studies were designated normal. Multiple rapid swallows are highly reproducible, especially in well-developed motor disorders, and complement the standard wet swallow manometry protocol. © 2014 John Wiley & Sons Ltd.

Reproducibility of WC-C High-Temperature Fixed Point

NASA Astrophysics Data System (ADS)

Grigoryeva, I. A.; Khlevnoy, B. B.; Solodilov, M. V.

2017-05-01

Reproducibility of the tungsten carbide-carbon peritectic (WC-C) fixed point (3021 K) was investigated by comparing six WC-C blackbody-type cells with each other. All the cells were built at VNIIOFI and had the same design with a cell outer diameter of 24 mm and a cavity opening diameter of 3 mm. Four cells were built using tungsten powder supplied by Alfa Aesar, while the other two cells used powder from Zhuzhou KETE (China). The nominal purity of both suppliers was 99.999 %. All the cells were compared in the same furnace. A reference cell in the second furnace was used for monitoring the stability of a radiation thermometer. Melting temperatures (given by the point of inflection) of all six cells agreed within ±45 mK. The reproducibility, as a standard deviation of the measured temperatures, can be estimated as 35 mK. The Zhuzhou KETE cells showed a slightly lower temperature than the Alfa Aesar cells: by 32 mK on average, which is comparable with repeatability of the measurements.

Highly Reproducible Label Free Quantitative Proteomic Analysis of RNA Polymerase Complexes*

PubMed Central

Mosley, Amber L.; Sardiu, Mihaela E.; Pattenden, Samantha G.; Workman, Jerry L.; Florens, Laurence; Washburn, Michael P.

2011-01-01

The use of quantitative proteomics methods to study protein complexes has the potential to provide in-depth information on the abundance of different protein components as well as their modification state in various cellular conditions. To interrogate protein complex quantitation using shotgun proteomic methods, we have focused on the analysis of protein complexes using label-free multidimensional protein identification technology and studied the reproducibility of biological replicates. For these studies, we focused on three highly related and essential multi-protein enzymes, RNA polymerase I, II, and III from Saccharomyces cerevisiae. We found that label-free quantitation using spectral counting is highly reproducible at the protein and peptide level when analyzing RNA polymerase I, II, and III. In addition, we show that peptide sampling does not follow a random sampling model, and we show the need for advanced computational models to predict peptide detection probabilities. In order to address these issues, we used the APEX protocol to model the expected peptide detectability based on whole cell lysate acquired using the same multidimensional protein identification technology analysis used for the protein complexes. Neither method was able to predict the peptide sampling levels that we observed using replicate multidimensional protein identification technology analyses. In addition to the analysis of the RNA polymerase complexes, our analysis provides quantitative information about several RNAP associated proteins including the RNAPII elongation factor complexes DSIF and TFIIF. Our data shows that DSIF and TFIIF are the most highly enriched RNAP accessory factors in Rpb3-TAP purifications and demonstrate our ability to measure low level associated protein abundance across biological replicates. In addition, our quantitative data supports a model in which DSIF and TFIIF interact with RNAPII in a dynamic fashion in agreement with previously published reports. PMID

High Energy Explosive Yield Enhancer Using Microencapsulation.

DTIC Science & Technology

The invention consists of a class of high energy explosive yield enhancers created through the use of microencapsulation techniques. The... microcapsules consist of combinations of highly reactive oxidizers that are encapsulated in either passivated inorganic fuels or inert materials and inorganic...fuels. Depending on the application, the availability of the various oxidizers and fuels within the microcapsules can be customized to increase the

Properties of galaxies reproduced by a hydrodynamic simulation

NASA Astrophysics Data System (ADS)

Vogelsberger, M.; Genel, S.; Springel, V.; Torrey, P.; Sijacki, D.; Xu, D.; Snyder, G.; Bird, S.; Nelson, D.; Hernquist, L.

2014-05-01

Previous simulations of the growth of cosmic structures have broadly reproduced the `cosmic web' of galaxies that we see in the Universe, but failed to create a mixed population of elliptical and spiral galaxies, because of numerical inaccuracies and incomplete physical models. Moreover, they were unable to track the small-scale evolution of gas and stars to the present epoch within a representative portion of the Universe. Here we report a simulation that starts 12 million years after the Big Bang, and traces 13 billion years of cosmic evolution with 12 billion resolution elements in a cube of 106.5 megaparsecs a side. It yields a reasonable population of ellipticals and spirals, reproduces the observed distribution of galaxies in clusters and characteristics of hydrogen on large scales, and at the same time matches the `metal' and hydrogen content of galaxies on small scales.

Ultimate waveform reproducibility of extreme-ultraviolet pulses by high-harmonic generation in quartz

NASA Astrophysics Data System (ADS)

Garg, M.; Kim, H. Y.; Goulielmakis, E.

2018-05-01

Optical waveforms of light reproducible with subcycle precision underlie applications of lasers in ultrafast spectroscopies, quantum control of matter and light-based signal processing. Nonlinear upconversion of optical pulses via high-harmonic generation in gas media extends these capabilities to the extreme ultraviolet (EUV). However, the waveform reproducibility of the generated EUV pulses in gases is inherently sensitive to intensity and phase fluctuations of the driving field. We used photoelectron interferometry to study the effects of intensity and carrier-envelope phase of an intense single-cycle optical pulse on the field waveform of EUV pulses generated in quartz nanofilms, and contrasted the results with those obtained in gas argon. The EUV waveforms generated in quartz were found to be virtually immune to the intensity and phase of the driving field, implying a non-recollisional character of the underlying emission mechanism. Waveform-sensitive photonic applications and precision measurements of fundamental processes in optics will benefit from these findings.

High-resolution mapping of yield curve shape and evolution for high porosity sandstones

NASA Astrophysics Data System (ADS)

Bedford, J. D.; Faulkner, D.; Wheeler, J.; Leclere, H.

2017-12-01

The onset of permanent inelastic deformation for porous rock is typically defined by a yield curve plotted in P-Q space, where P is the effective mean stress and Q is the differential stress. Sandstones usually have broadly elliptical shaped yield curves, with the low pressure side of the ellipse associated with localized brittle faulting (dilation) and the high pressure side with distributed ductile deformation (compaction). However recent works have shown that these curves might not be perfectly elliptical and that significant evolution in shape occurs with continued deformation. We therefore use a novel stress-probing methodology to map in high-resolution the yield curve shape for Boise and Idaho Gray sandstones (36-38% porosity) and also investigate curve evolution with increasing deformation. The data reveal yield curves with a much flatter geometry than previously recorded for porous sandstone and that the compactive side of the curve is partly comprised of a near vertical limb. The yield curve evolution is found to be strongly dependent on the nature of inelastic strain. Samples that were compacted under a deviatoric load, with a component of inelastic shear strain, were found to have yield curves with peaks that are approximately 50% higher than similar porosity samples that were hydrostatically compacted (i.e. purely volumetric strain). The difference in yield curve evolution along the different loading paths is attributed to mechanical anisotropy that develops during deviatoric loading by the closure of preferentially orientated fractures. Increased shear strain also leads to the formation of a plateau at the peak of the yield curve as samples deform along the deviatoric loading path. These results have important implications for understanding how the strength of porous rock evolves along different stress paths, including during fluid extraction from hydrocarbon reservoirs where the stress state is rarely isotropic.

Quantifying potential yield and water-limited yield of summer maize in the North China Plain

NASA Astrophysics Data System (ADS)

Jiang, Mingnuo; Liu, Chaoshun; Chen, Maosi

2017-09-01

The North China Plain is a major food producing region in China, and climate change could pose a threat to food production in the region. Based on China Meteorological Forcing Dataset, simulating the growth of summer maize in North China Plain from 1979 to 2015 with the regional implementation of crop growth model WOFOST. The results showed that the model can reflect the potential yield and water-limited yield of Summer Maize in North China Plain through the calibration and validation of WOFOST model. After the regional implementation of model, combined with the reanalysis data, the model can better reproduce the regional history of summer maize yield in the North China Plain. The yield gap in Southeastern Beijing, southern Tianjin, southern Hebei province, Northwestern Shandong province is significant, these means the water condition is the main factor to summer maize yield in these regions.

A Novel Extraction Method Combining Plasma with a Whole-Blood Fraction Shows Excellent Sensitivity and Reproducibility for Patients at High Risk for Invasive Aspergillosis

PubMed Central

Springer, Jan; Schloßnagel, Hannes; Heinz, Werner; Doedt, Thomas; Soeller, Rainer; Einsele, Hermann

2012-01-01

Diagnosis of invasive aspergillosis (IA) is still a major problem in routine clinical practice. Early diagnosis is essential for a good patient prognosis. PCR is a highly sensitive method for the detection of nucleic acids and could play an important role in improving the diagnosis of fungal infections. Therefore, a novel DNA extraction method, ultraclean production (UCP), was developed allowing purification of both cellular and cell-free circulating fungal DNA. In this prospective study we evaluated the commercially available UCP extraction system and compared it to an in-house system. Sixty-three patients at high risk for IA were screened twice weekly, and DNA extracted by both methods was cross-analyzed, in triplicate, by two different real-time PCR assays. The negative predictive values were high for all methods (94.3 to 100%), qualifying them as screening methods, but the sensitivity and diagnostic odds ratios were higher using the UCP extraction method. Sensitivity ranged from 33.3 to 66.7% using the in-house extracts to 100% using the UCP extraction method. Most of the unclassified patients showed no positive PCR results; however, single-positive PCR replicates were observed in some cases. These can bear clinical relevance but should be interpreted with additional clinical and laboratory data. The PCR assays from the UCP extracts showed greater reproducibility than the in-house method for probable IA patients. The standardized UCP extraction method yielded superior results, with regard to sensitivity and reproducibility, than the in-house method. This was independent of the PCR assay used to detect fungal DNA in the sample extracts. PMID:22593600

Properties of galaxies reproduced by a hydrodynamic simulation.

PubMed

Vogelsberger, M; Genel, S; Springel, V; Torrey, P; Sijacki, D; Xu, D; Snyder, G; Bird, S; Nelson, D; Hernquist, L

2014-05-08

Previous simulations of the growth of cosmic structures have broadly reproduced the 'cosmic web' of galaxies that we see in the Universe, but failed to create a mixed population of elliptical and spiral galaxies, because of numerical inaccuracies and incomplete physical models. Moreover, they were unable to track the small-scale evolution of gas and stars to the present epoch within a representative portion of the Universe. Here we report a simulation that starts 12 million years after the Big Bang, and traces 13 billion years of cosmic evolution with 12 billion resolution elements in a cube of 106.5 megaparsecs a side. It yields a reasonable population of ellipticals and spirals, reproduces the observed distribution of galaxies in clusters and characteristics of hydrogen on large scales, and at the same time matches the 'metal' and hydrogen content of galaxies on small scales.

[Characteristics of phosphorus uptake and use efficiency of rice with high yield and high phosphorus use efficiency].

PubMed

Li, Li; Zhang, Xi-Zhou; Li, Tinx-Xuan; Yu, Hai-Ying; Ji, Lin; Chen, Guang-Deng

2014-07-01

A total of twenty seven middle maturing rice varieties as parent materials were divided into four types based on P use efficiency for grain yield in 2011 by field experiment with normal phosphorus (P) application. The rice variety with high yield and high P efficiency was identified by pot experiment with normal and low P applications, and the contribution rates of various P efficiencies to yield were investigated in 2012. There were significant genotype differences in yield and P efficiency of the test materials. GRLu17/AiTTP//Lu17_2 (QR20) was identified as a variety with high yield and high P efficiency, and its yields at the low and normal rates of P application were 1.96 and 1.92 times of that of Yuxiang B, respectively. The contribution rate of P accumulation to yield was greater than that of P grain production efficiency and P harvest index across field and pot experiments. The contribution rates of P accumulation and P grain production efficiency to yield were not significantly different under the normal P condition, whereas obvious differences were observed under the low P condition (66.5% and 26.6%). The minimal contribution to yield was P harvest index (11.8%). Under the normal P condition, the contribution rates of P accumulation to yield and P harvest index were the highest at the jointing-heading stage, which were 93.4% and 85.7%, respectively. In addition, the contribution rate of P accumulation to grain production efficiency was 41.8%. Under the low P condition, the maximal contribution rates of P accumulation to yield and grain production efficiency were observed at the tillering-jointing stage, which were 56.9% and 20.1% respectively. Furthermore, the contribution rate of P accumulation to P harvest index was 16.0%. The yield, P accumulation, and P harvest index of QR20 significantly increased under the normal P condition by 20.6%, 18.1% and 18.2% respectively compared with that in the low P condition. The rank of the contribution rates of P

Highly uniform and reproducible surface-enhanced Raman scattering from DNA-tailorable nanoparticles with 1-nm interior gap

NASA Astrophysics Data System (ADS)

Lim, Dong-Kwon; Jeon, Ki-Seok; Hwang, Jae-Ho; Kim, Hyoki; Kwon, Sunghoon; Suh, Yung Doug; Nam, Jwa-Min

2011-07-01

An ideal surface-enhanced Raman scattering (SERS) nanostructure for sensing and imaging applications should induce a high signal enhancement, generate a reproducible and uniform response, and should be easy to synthesize. Many SERS-active nanostructures have been investigated, but they suffer from poor reproducibility of the SERS-active sites, and the wide distribution of their enhancement factor values results in an unquantifiable SERS signal. Here, we show that DNA on gold nanoparticles facilitates the formation of well-defined gold nanobridged nanogap particles (Au-NNP) that generate a highly stable and reproducible SERS signal. The uniform and hollow gap (~1 nm) between the gold core and gold shell can be precisely loaded with a quantifiable amount of Raman dyes. SERS signals generated by Au-NNPs showed a linear dependence on probe concentration (R2 > 0.98) and were sensitive down to 10 fM concentrations. Single-particle nano-Raman mapping analysis revealed that >90% of Au-NNPs had enhancement factors greater than 1.0 × 108, which is sufficient for single-molecule detection, and the values were narrowly distributed between 1.0 × 108 and 5.0 × 109.

High pressure intensification of cassava resistant starch (RS3) yields.

PubMed

Lertwanawatana, Proyphon; Frazier, Richard A; Niranjan, Keshavan

2015-08-15

Cassava starch, typically, has resistant starch type 3 (RS3) content of 2.4%. This paper shows that the RS3 yields can be substantially enhanced by debranching cassava starch using pullulanase followed by high pressure or cyclic high-pressure annealing. RS3 yield of 41.3% was obtained when annealing was carried out at 400MPa/60°C for 15 min, whereas it took nearly 8h to obtain the same yield under conventional atmospheric annealing at 60°C. The yield of RS3 could be further significantly increased by annealing under 400 MPa/60°C pressure for 15 min followed by resting at atmospheric pressure for 3h 45 min, and repeating this cycle for up to six times. Microstructural surface analysis of the product under a scanning electron microscope showed an increasingly rigid density of the crystalline structure formed, confirming higher RS3 content. Copyright © 2015 Elsevier Ltd. All rights reserved.

Added-values of high spatiotemporal remote sensing data in crop yield estimation

NASA Astrophysics Data System (ADS)

Gao, F.; Anderson, M. C.

2017-12-01

Timely and accurate estimation of crop yield before harvest is critical for food market and administrative planning. Remote sensing derived parameters have been used for estimating crop yield by using either empirical or crop growth models. The uses of remote sensing vegetation index (VI) in crop yield modeling have been typically evaluated at regional and country scales using coarse spatial resolution (a few hundred to kilo-meters) data or assessed over a small region at field level using moderate resolution spatial resolution data (10-100m). Both data sources have shown great potential in capturing spatial and temporal variability in crop yield. However, the added value of data with both high spatial and temporal resolution data has not been evaluated due to the lack of such data source with routine, global coverage. In recent years, more moderate resolution data have become freely available and data fusion approaches that combine data acquired from different spatial and temporal resolutions have been developed. These make the monitoring crop condition and estimating crop yield at field scale become possible. Here we investigate the added value of the high spatial and temporal VI for describing variability of crop yield. The explanatory ability of crop yield based on high spatial and temporal resolution remote sensing data was evaluated in a rain-fed agricultural area in the U.S. Corn Belt. Results show that the fused Landsat-MODIS (high spatial and temporal) VI explains yield variability better than single data source (Landsat or MODIS alone), with EVI2 performing slightly better than NDVI. The maximum VI describes yield variability better than cumulative VI. Even though VI is effective in explaining yield variability within season, the inter-annual variability is more complex and need additional information (e.g. weather, water use and management). Our findings augment the importance of high spatiotemporal remote sensing data and supports new moderate

Reproducible, high-throughput synthesis of colloidal nanocrystals for optimization in multidimensional parameter space.

PubMed

Chan, Emory M; Xu, Chenxu; Mao, Alvin W; Han, Gang; Owen, Jonathan S; Cohen, Bruce E; Milliron, Delia J

2010-05-12

While colloidal nanocrystals hold tremendous potential for both enhancing fundamental understanding of materials scaling and enabling advanced technologies, progress in both realms can be inhibited by the limited reproducibility of traditional synthetic methods and by the difficulty of optimizing syntheses over a large number of synthetic parameters. Here, we describe an automated platform for the reproducible synthesis of colloidal nanocrystals and for the high-throughput optimization of physical properties relevant to emerging applications of nanomaterials. This robotic platform enables precise control over reaction conditions while performing workflows analogous to those of traditional flask syntheses. We demonstrate control over the size, size distribution, kinetics, and concentration of reactions by synthesizing CdSe nanocrystals with 0.2% coefficient of variation in the mean diameters across an array of batch reactors and over multiple runs. Leveraging this precise control along with high-throughput optical and diffraction characterization, we effectively map multidimensional parameter space to tune the size and polydispersity of CdSe nanocrystals, to maximize the photoluminescence efficiency of CdTe nanocrystals, and to control the crystal phase and maximize the upconverted luminescence of lanthanide-doped NaYF(4) nanocrystals. On the basis of these demonstrative examples, we conclude that this automated synthesis approach will be of great utility for the development of diverse colloidal nanomaterials for electronic assemblies, luminescent biological labels, electroluminescent devices, and other emerging applications.

Rapid and highly reproducible analysis of rare earth elements by multiple collector inductively coupled plasma mass spectrometry

NASA Astrophysics Data System (ADS)

Baker, Joel; Waight, Tod; Ulfbeck, David

2002-10-01

A method has been developed for the rapid chemical separation and highly reproducible analysis of the rare earth elements (REE) by isotope dilution analysis by means of a multiple collector inductively coupled plasma mass spectrometer (MC-ICP-MS). This technique is superior in terms of the analytical reproducibility or rapidity of analysis compared with quadrupole ICP-MS or with thermal ionization mass spectrometric isotope dilution techniques. Samples are digested by standard hydrofluoric-nitric acid-based techniques and spiked with two mixed spikes. The bulk REE are separated from the sample on a cation exchange column, collecting the middle-heavy and light REE as two groups, which provides a middle-heavy REE cut with sufficient separation of the light from the heavier REE to render oxide interferences trivial, and a Ba-free light REE cut. The heavy (Er-Lu), middle (Eu-Gd), and light REE (La-Eu) concentrations are determined by three short (1 to 2 min) analyses with a CETAC Aridus desolvating nebulizer introduction system. Replicate digestions of international rock standards demonstrate that concentrations can be reproduced to <1%, which reflects weighing errors during digestion and aliquotting as inter-REE ratios reproduce to ≤0.2% (2 SD). Eu and Ce anomalies reproduce to <0.15%. In addition to determining the concentrations of polyisotopic REE by isotope dilution analysis, the concentration of monoisotopic Pr can be measured during the light REE isotope dilution run, by reference to Pr/Ce and Pr/Nd ratios measured in a REE standard solution. Pr concentrations determined in this way reproduce to <1%, and Pr/REE ratios reproduce to <0.4%. Ce anomalies calculated with La and Pr also reproduce to <0.15% (2 SD). The precise Ce (and Eu) anomaly measurements should allow greater use of these features in studying the recycling of materials with these anomalies into the mantle, or redox-induced effects on the REE during recycling and dehydration of oceanic lithosphere

Reproducibility in Data-Scarce Environments

NASA Astrophysics Data System (ADS)

Darch, P. T.

2016-12-01

Among the usual requirements for reproducibility are large volumes of data and computationally intensive methods. Many fields within earth sciences, however, do not meet these requirements. Data are scarce and data-intensive methods are not well established. How can science be reproducible under these conditions? What changes, both infrastructural and cultural, are needed to advance reproducibility? This paper presents findings from a long-term social scientific case study of an emergent and data scarce field, the deep subseafloor biosphere. This field studies interactions between microbial communities living in the seafloor and the physical environments they inhabit. Factors such as these make reproducibility seem a distant goal for this community: - The relative newness of the field. Serious study began in the late 1990s; - The highly multidisciplinary nature of the field. Researchers come from a range of physical and life science backgrounds; - Data scarcity. Domain researchers produce much of these data in their own onshore laboratories by analyzing cores from international ocean drilling expeditions. Allocation of cores is negotiated between researchers from many fields. These factors interact in multiple ways to inhibit reproducibility: - Incentive structures emphasize producing new data and new knowledge rather than reanalysing extant data; - Only a few steps of laboratory analyses can be reproduced - such as analysis of DNA sequences, but not extraction of DNA from cores -, due to scarcity of cores; - Methodological heterogeneity is a consequence of multidisciplinarity, as researchers bring different techniques from diverse fields. - Few standards for data collection or analysis are available at this early stage of the field; - While datasets from multiple biological and physical phenomena can be integrated into a single workflow, curation tends to be divergent. Each type of dataset may be subject to different disparate policies and contributed to different

High-yielding continuous-flow synthesis of antimalarial drug hydroxychloroquine

PubMed Central

Telang, Nakul S; Kong, Caleb J; Verghese, Jenson; Gilliland III, Stanley E; Ahmad, Saeed; Dominey, Raymond N

2018-01-01

Numerous synthetic methods for the continuous preparation of fine chemicals and active pharmaceutical ingredients (API’s) have been reported in recent years resulting in a dramatic improvement in process efficiencies. Herein we report a highly efficient continuous synthesis of the antimalarial drug hydroxychloroquine (HCQ). Key improvements in the new process include the elimination of protecting groups with an overall yield improvement of 52% over the current commercial process. The continuous process employs a combination of packed bed reactors with continuous stirred tank reactors for the direct conversion of the starting materials to the product. This high-yielding, multigram-scale continuous synthesis provides an opportunity to achieve increase global access to hydroxychloroquine for treatment of malaria. PMID:29623120

Response to Comment on "Estimating the reproducibility of psychological science".

PubMed

Anderson, Christopher J; Bahník, Štěpán; Barnett-Cowan, Michael; Bosco, Frank A; Chandler, Jesse; Chartier, Christopher R; Cheung, Felix; Christopherson, Cody D; Cordes, Andreas; Cremata, Edward J; Della Penna, Nicolas; Estel, Vivien; Fedor, Anna; Fitneva, Stanka A; Frank, Michael C; Grange, James A; Hartshorne, Joshua K; Hasselman, Fred; Henninger, Felix; van der Hulst, Marije; Jonas, Kai J; Lai, Calvin K; Levitan, Carmel A; Miller, Jeremy K; Moore, Katherine S; Meixner, Johannes M; Munafò, Marcus R; Neijenhuijs, Koen I; Nilsonne, Gustav; Nosek, Brian A; Plessow, Franziska; Prenoveau, Jason M; Ricker, Ashley A; Schmidt, Kathleen; Spies, Jeffrey R; Stieger, Stefan; Strohminger, Nina; Sullivan, Gavin B; van Aert, Robbie C M; van Assen, Marcel A L M; Vanpaemel, Wolf; Vianello, Michelangelo; Voracek, Martin; Zuni, Kellylynn

2016-03-04

Gilbert et al. conclude that evidence from the Open Science Collaboration's Reproducibility Project: Psychology indicates high reproducibility, given the study methodology. Their very optimistic assessment is limited by statistical misconceptions and by causal inferences from selectively interpreted, correlational data. Using the Reproducibility Project: Psychology data, both optimistic and pessimistic conclusions about reproducibility are possible, and neither are yet warranted. Copyright © 2016, American Association for the Advancement of Science.

Cupping - is it reproducible? Experiments about factors determining the vacuum.

PubMed

Huber, R; Emerich, M; Braeunig, M

2011-04-01

Cupping is a traditional method for treating pain which is investigated nowadays in clinical studies. Because the methods for producing the vacuum vary considerably we tested their reproducibility. In a first set of experiments (study 1) four methods for producing the vacuum (lighter flame 2 cm (LF1), lighter flame 4 cm (LF2), alcohol flame (AF) and mechanical suction with a balloon (BA)) have been compared in 50 trials each. The cupping glass was prepared with an outlet and stop-cock, the vacuum was measured with a pressure-gauge after the cup was set to a soft rubber pad. In a second series of experiments (study 2) we investigated the stability of pressures in 20 consecutive trials in two experienced cupping practitioners and ten beginners using method AF. In study 1 all four methods yielded consistent pressures. Large differences in magnitude were, however, observed between methods (mean pressures -200±30 hPa with LF1, -310±30 hPa with LF2, -560±30 hPa with AF, and -270±16 hPa with BA). With method BA the standard deviation was reduced by a factor 2 compared to the flame methods. In study 2 beginners had considerably more difficulty obtaining a stable pressure yield than advanced cupping practitioners, showing a distinct learning curve before reaching expertise levels after about 10-20 trials. Cupping is reproducible if the exact method is described in detail. Mechanical suction with a balloon has the best reproducibility. Beginners need at least 10-20 trials to produce stable pressures. Copyright © 2010 Elsevier Ltd. All rights reserved.

Separating heat stress from moisture stress: analyzing yield response to high temperature in irrigated maize

NASA Astrophysics Data System (ADS)

Carter, Elizabeth K.; Melkonian, Jeff; Riha, Susan J.; Shaw, Stephen B.

2016-09-01

Several recent studies have indicated that high air temperatures are limiting maize (Zea mays L.) yields in the US Corn Belt and project significant yield losses with expected increases in growing season temperatures. Further work has suggested that high air temperatures are indicative of high evaporative demand, and that decreases in maize yields which correlate to high temperatures and vapor pressure deficits (VPD) likely reflect underlying soil moisture limitations. It remains unclear whether direct high temperature impacts on yields, independent of moisture stress, can be observed under current temperature regimes. Given that projected high temperature and moisture may not co-vary the same way as they have historically, quantitative analyzes of direct temperature impacts are critical for accurate yield projections and targeted mitigation strategies under shifting temperature regimes. To evaluate yield response to above optimum temperatures independent of soil moisture stress, we analyzed climate impacts on irrigated maize yields obtained from the National Corn Growers Association (NCGA) corn yield contests for Nebraska, Kansas and Missouri. In irrigated maize, we found no evidence of a direct negative impact on yield by daytime air temperature, calculated canopy temperature, or VPD when analyzed seasonally. Solar radiation was the primary yield-limiting climate variable. Our analyses suggested that elevated night temperature impacted yield by increasing rates of phenological development. High temperatures during grain-fill significantly interacted with yields, but this effect was often beneficial and included evidence of acquired thermo-tolerance. Furthermore, genetics and management—information uniquely available in the NCGA contest data—explained more yield variability than climate, and significantly modified crop response to climate. Thermo-acclimation, improved genetics and changes to management practices have the potential to partially or completely

Breeding high-yielding drought-tolerant rice: genetic variations and conventional and molecular approaches

PubMed Central

Kumar, Arvind; Dixit, Shalabh; Ram, T.; Yadaw, R. B.; Mishra, K. K.; Mandal, N. P.

2014-01-01

The increased occurrence and severity of drought stress have led to a high yield decline in rice in recent years in drought-affected areas. Drought research at the International Rice Research Institute (IRRI) over the past decade has concentrated on direct selection for grain yield under drought. This approach has led to the successful development and release of 17 high-yielding drought-tolerant rice varieties in South Asia, Southeast Asia, and Africa. In addition to this, 14 quantitative trait loci (QTLs) showing a large effect against high-yielding drought-susceptible popular varieties were identified using grain yield as a selection criterion. Six of these (qDTY 1.1, qDTY 2.2, qDTY 3.1, qDTY 3.2, qDTY 6.1, and qDTY 12.1) showed an effect against two or more high-yielding genetic backgrounds in both the lowland and upland ecosystem, indicating their usefulness in increasing the grain yield of rice under drought. The yield of popular rice varieties IR64 and Vandana has been successfully improved through a well-planned marker-assisted backcross breeding approach, and QTL introgression in several other popular varieties is in progress. The identification of large-effect QTLs for grain yield under drought and the higher yield increase under drought obtained through the use of these QTLs (which has not been reported in other cereals) indicate that rice, because of its continuous cultivation in two diverse ecosystems (upland, drought tolerant, and lowland, drought susceptible), has benefited from the existence of larger genetic variability than in other cereals. This can be successfully exploited using marker-assisted breeding. PMID:25205576

Mapping Crop Yield and Sow Date Using High Resolution Imagery

NASA Astrophysics Data System (ADS)

Royal, K.

2015-12-01

Keitasha Royal, Meha Jain, Ph.D., David Lobell, Ph.D Mapping Crop Yield and Sow Date Using High Resolution ImageryThe use of satellite imagery in agriculture is becoming increasingly more significant and valuable. Due to the emergence of new satellites, such as Skybox, these satellites provide higher resolution imagery (e.g 1m) therefore improving the ability to map smallholder agriculture. For the smallholder farm dominated area of northern India, Skybox high-resolution satellite imagery can aid in understanding how to improve farm yields. In particular, we are interested in mapping winter wheat in India, as this region produces approximately 80% of the country's wheat crop, which is important given that wheat is a staple crop that provides approximately 20% of household calories. In northeast India, the combination of increased heat stress, limited irrigation access, and the difficulty for farmers to access advanced farming technologies results in farmers only producing about 50% of their potential crop yield. The use of satellite imagery can aid in understanding wheat yields through time and help identify ways to increase crop yields in the wheat belt of India. To translate Skybox satellite data into meaningful information about wheat fields, we examine vegetation indices, such as the normalized difference vegetation index (NDVI), to measure the "greenness" of plants to help determine the health of the crops. We test our ability to predict crop characteristics, like sow date and yield, using vegetation indices of 59 fields for which we have field data in Bihar, India.

The Need for Reproducibility

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

Robey, Robert W.

2016-06-27

The purpose of this presentation is to consider issues of reproducibility, specifically it determines whether bitwise reproducible computation is possible, if computational research in DOE improves its publication process, and if reproducible results can be achieved apart from the peer review process?

Dynamics of yield-stress droplets: Morphology of impact craters

NASA Astrophysics Data System (ADS)

Neufeld, Jerome; Sohr, David; Ferrari, Leo; Dalziel, Stuart

2017-11-01

Yield strength can play an important role for the dynamics of droplets impacting on surfaces, whether at the industrial or planetary scale, and can capture a zoo of impact crater morphologies, from simple parabolic craters, to more complex forms with forms with, for example, multiple rings, central peaks. Here we show that the morphology of planetary impact craters can be reproduced in the laboratory using carbopol, a transparent yield-stress fluid, as both impactor and bulk fluid. Using high-speed video photography, we characterise the universal, transient initial excavation stage of impact and show the dependence of the subsequent relaxation to final crater morphology on impactor size, impact speed and yield stress. To further interrogate our laboratory impacts, we dye our impactor to map its final distribution and use particle tracking to determine the flow fields during impact and the maximal extent of the yield surface. We characterise the flow-fields induced during impact, and the maximal extent of the yield surface, by tracking particles within the bulk fluid and map the distribution of impactor and bulk by tracing the final distribution of dyed impactor. The results of laboratory impact droplets are used to infer the properties of planetary impactors, and aid in inter.

Low-Cost, Disposable, Flexible and Highly Reproducible Screen Printed SERS Substrates for the Detection of Various Chemicals

PubMed Central

Wu, Wei; Liu, Li; Dai, Zhigao; Liu, Juhua; Yang, Shuanglei; Zhou, Li; Xiao, Xiangheng; Jiang, Changzhong; Roy, Vellaisamy A.L.

2015-01-01

Ideal SERS substrates for sensing applications should exhibit strong signal enhancement, generate a reproducible and uniform response, and should be able to fabricate in large-scale and low-cost. Herein, we demonstrate low-cost, highly sensitive, disposable and reproducible SERS substrates by means of screen printing Ag nanoparticles (NPs) on a plastic PET (Polyethylene terephthalate) substrates. While there are many complex methods for the fabrication of SERS substrates, screen printing is suitable for large-area fabrication and overcomes the uneven radial distribution. Using as-printed Ag substrates as the SERS platform, detection of various commonly known chemicals have been done. The SERS detection limit of Rhodamine 6G (R6G) is higher than the concentration of 1 × 10−10 M. The relative standard deviation (RSD) value for 784 points on the detection of R6G and Malachite green (MG) is less than 20% revealing a homogeneous SERS distribution and high reproducibility. Moreover, melamine (MA) is detected in fresh liquid-milk without additional pretreatment, which may accelerate the application of rapid on-line detection of MA in liquid milk. Our screen printing method highlights the use of large-scale printing strategies for the fabrication of well-defined functional nanostructures with applications well beyond the field of SERS sensing. PMID:25974125

Methods for high yield production of terpenes

DOEpatents

Kutchan, Toni; Higashi, Yasuhiro; Feng, Xiaohong

2017-01-03

Provided are enhanced high yield production systems for producing terpenes in plants via the expression of fusion proteins comprising various combinations of geranyl diphosphate synthase large and small subunits and limonene synthases. Also provided are engineered oilseed plants that accumulate monoterpene and sesquiterpene hydrocarbons in their seeds, as well as methods for producing such plants, providing a system for rapidly engineering oilseed crop production platforms for terpene-based biofuels.

High yield neutron generator based on a high-current gasdynamic electron cyclotron resonance ion source

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

Skalyga, V.; Sidorov, A.; Lobachevsky State University of Nizhny Novgorod

2015-09-07

In present paper, an approach for high yield compact D-D neutron generator based on a high current gasdynamic electron cyclotron resonance ion source is suggested. Results on dense pulsed deuteron beam production with current up to 500 mA and current density up to 750 mA/cm{sup 2} are demonstrated. Neutron yield from D{sub 2}O and TiD{sub 2} targets was measured in case of its bombardment by pulsed 300 mA D{sup +} beam with 45 keV energy. Neutron yield density at target surface of 10{sup 9} s{sup −1} cm{sup −2} was detected with a system of two {sup 3}He proportional counters. Estimations based on obtained experimental resultsmore » show that neutron yield from a high quality TiD{sub 2} target bombarded by D{sup +} beam demonstrated in present work accelerated to 100 keV could reach 6 × 10{sup 10} s{sup −1} cm{sup −2}. It is discussed that compact neutron generator with such characteristics could be perspective for a number of applications like boron neutron capture therapy, security systems based on neutron scanning, and neutronography.« less

High-yield maize with large net energy yield and small global warming intensity

PubMed Central

Grassini, Patricio; Cassman, Kenneth G.

2012-01-01

Addressing concerns about future food supply and climate change requires management practices that maximize productivity per unit of arable land while reducing negative environmental impact. On-farm data were evaluated to assess energy balance and greenhouse gas (GHG) emissions of irrigated maize in Nebraska that received large nitrogen (N) fertilizer (183 kg of N⋅ha−1) and irrigation water inputs (272 mm or 2,720 m3 ha−1). Although energy inputs (30 GJ⋅ha−1) were larger than those reported for US maize systems in previous studies, irrigated maize in central Nebraska achieved higher grain and net energy yields (13.2 Mg⋅ha−1 and 159 GJ⋅ha−1, respectively) and lower GHG-emission intensity (231 kg of CO2e⋅Mg−1 of grain). Greater input-use efficiencies, especially for N fertilizer, were responsible for better performance of these irrigated systems, compared with much lower-yielding, mostly rainfed maize systems in previous studies. Large variation in energy inputs and GHG emissions across irrigated fields in the present study resulted from differences in applied irrigation water amount and imbalances between applied N inputs and crop N demand, indicating potential to further improve environmental performance through better management of these inputs. Observed variation in N-use efficiency, at any level of applied N inputs, suggests that an N-balance approach may be more appropriate for estimating soil N2O emissions than the Intergovernmental Panel on Climate Change approach based on a fixed proportion of applied N. Negative correlation between GHG-emission intensity and net energy yield supports the proposition that achieving high yields, large positive energy balance, and low GHG emissions in intensive cropping systems are not conflicting goals. PMID:22232684

High precision and high yield fabrication of dense nanoparticle arrays onto DNA origami at statistically independent binding sites

NASA Astrophysics Data System (ADS)

Takabayashi, Sadao; Klein, William P.; Onodera, Craig; Rapp, Blake; Flores-Estrada, Juan; Lindau, Elias; Snowball, Lejmarc; Sam, Joseph T.; Padilla, Jennifer E.; Lee, Jeunghoon; Knowlton, William B.; Graugnard, Elton; Yurke, Bernard; Kuang, Wan; Hughes, William L.

2014-10-01

High precision, high yield, and high density self-assembly of nanoparticles into arrays is essential for nanophotonics. Spatial deviations as small as a few nanometers can alter the properties of near-field coupled optical nanostructures. Several studies have reported assemblies of few nanoparticle structures with controlled spacing using DNA nanostructures with variable yield. Here, we report multi-tether design strategies and attachment yields for homo- and hetero-nanoparticle arrays templated by DNA origami nanotubes. Nanoparticle attachment yield via DNA hybridization is comparable with streptavidin-biotin binding. Independent of the number of binding sites, >97% site-occupation was achieved with four tethers and 99.2% site-occupation is theoretically possible with five tethers. The interparticle distance was within 2 nm of all design specifications and the nanoparticle spatial deviations decreased with interparticle spacing. Modified geometric, binomial, and trinomial distributions indicate that site-bridging, steric hindrance, and electrostatic repulsion were not dominant barriers to self-assembly and both tethers and binding sites were statistically independent at high particle densities.High precision, high yield, and high density self-assembly of nanoparticles into arrays is essential for nanophotonics. Spatial deviations as small as a few nanometers can alter the properties of near-field coupled optical nanostructures. Several studies have reported assemblies of few nanoparticle structures with controlled spacing using DNA nanostructures with variable yield. Here, we report multi-tether design strategies and attachment yields for homo- and hetero-nanoparticle arrays templated by DNA origami nanotubes. Nanoparticle attachment yield via DNA hybridization is comparable with streptavidin-biotin binding. Independent of the number of binding sites, >97% site-occupation was achieved with four tethers and 99.2% site-occupation is theoretically possible with five

High-Gum-Yielding Slash Pines Survive and Grow Well

Treesearch

S.V. Kossuth; W.J. Peters; C.R. Gansell

1982-01-01

Plantings in Georgia and Florida were established with slash pine seedlings of three genetic types: selections improved for high gum yield (IHGY), selections with improved growth and form (IGF), and commercial stock (CS). Under adverse environmental conditions in Florida, IHGY survived best at age 3, CS next best, and IGF poorest.Survival was more than twice as high in...

Reproducibility of Search Strategies Is Poor in Systematic Reviews Published in High-Impact Pediatrics, Cardiology and Surgery Journals: A Cross-Sectional Study

PubMed Central

2016-01-01

Background A high-quality search strategy is considered an essential component of systematic reviews but many do not contain reproducible search strategies. It is unclear if low reproducibility spans medical disciplines, is affected by librarian/search specialist involvement or has improved with increased awareness of reporting guidelines. Objectives To examine the reporting of search strategies in systematic reviews published in Pediatrics, Surgery or Cardiology journals in 2012 and determine rates and predictors of including a reproducible search strategy. Methods We identified all systematic reviews published in 2012 in the ten highest impact factor journals in Pediatrics, Surgery and Cardiology. Each search strategy was coded to indicate what elements were reported and whether the overall search was reproducible. Reporting and reproducibility rates were compared across disciplines and we measured the influence of librarian/search specialist involvement, discipline or endorsement of a reporting guideline on search reproducibility. Results 272 articles from 25 journals were included. Reporting of search elements ranged widely from 91% of articles naming search terms to 33% providing a full search strategy and 22% indicating the date the search was executed. Only 22% of articles provided at least one reproducible search strategy and 13% provided a reproducible strategy for all databases searched in the article. Librarians or search specialists were reported as involved in 17% of articles. There were strong disciplinary differences on the reporting of search elements. In the multivariable analysis, only discipline (Pediatrics) was a significant predictor of the inclusion of a reproducible search strategy. Conclusions Despite recommendations to report full, reproducible search strategies, many articles still do not. In addition, authors often report a single strategy as covering all databases searched, further decreasing reproducibility. Further research is needed

Automated Purification of Recombinant Proteins: Combining High-throughput with High Yield

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

Lin, Chiann Tso; Moore, Priscilla A.; Auberry, Deanna L.

2006-05-01

Protein crystallography, mapping protein interactions and other approaches of current functional genomics require not only purifying large numbers of proteins but also obtaining sufficient yield and homogeneity for downstream high-throughput applications. There is a need for the development of robust automated high-throughput protein expression and purification processes to meet these requirements. We developed and compared two alternative workflows for automated purification of recombinant proteins based on expression of bacterial genes in Escherichia coli: First - a filtration separation protocol based on expression of 800 ml E. coli cultures followed by filtration purification using Ni2+-NTATM Agarose (Qiagen). Second - a smallermore » scale magnetic separation method based on expression in 25 ml cultures of E.coli followed by 96-well purification on MagneHisTM Ni2+ Agarose (Promega). Both workflows provided comparable average yields of proteins about 8 ug of purified protein per unit of OD at 600 nm of bacterial culture. We discuss advantages and limitations of the automated workflows that can provide proteins more than 90 % pure in the range of 100 ug – 45 mg per purification run as well as strategies for optimization of these protocols.« less

Chemo-selective high yield microwave assisted reaction turns cellulose to green chemicals.

PubMed

Hassanzadeh, Salman; Aminlashgari, Nina; Hakkarainen, Minna

2014-11-04

Exceptionally high cellulose liquefaction yields, up to 87% as calculated from the amount of solid residue, were obtained under mild conditions by utilizing the synergistic effect of microwave radiation and acid catalysis. The effect of processing conditions on degradation products was fingerprinted by rapid laser desorption ionization-mass spectrometry (LDI-MS) method. The reaction was chemo-tunable, enabling production of glucose (Glc) or levulinic acid (LeA) at significantly high selectivity and yields, the relative molar yields being up to 50 and 69%, respectively. A turning point from pure depolymerization to glucose to further degradation to levulinic acid and formic acid was observed at approximately 50% liquefaction or above 140 °C. This was accompanied by the formation of small amounts of solid spherical carbonized residues. The reaction was monitored by multiple analytical techniques. The high yields were connected to the ability of the process to break the strong secondary interactions in cellulose. The developed method has great potential for future production of green platform chemicals. Copyright © 2014 Elsevier Ltd. All rights reserved.

Planar heterojunction perovskite solar cells with superior reproducibility

PubMed Central

Jeon, Ye-Jin; Lee, Sehyun; Kang, Rira; Kim, Jueng-Eun; Yeo, Jun-Seok; Lee, Seung-Hoon; Kim, Seok-Soon; Yun, Jin-Mun; Kim, Dong-Yu

2014-01-01

Perovskite solar cells (PeSCs) have been considered one of the competitive next generation power sources. To date, light-to-electric conversion efficiencies have rapidly increased to over 10%, and further improvements are expected. However, the poor device reproducibility of PeSCs ascribed to their inhomogeneously covered film morphology has hindered their practical application. Here, we demonstrate high-performance PeSCs with superior reproducibility by introducing small amounts of N-cyclohexyl-2-pyrrolidone (CHP) as a morphology controller into N,N-dimethylformamide (DMF). As a result, highly homogeneous film morphology, similar to that achieved by vacuum-deposition methods, as well as a high PCE of 10% and an extremely small performance deviation within 0.14% were achieved. This study represents a method for realizing efficient and reproducible planar heterojunction (PHJ) PeSCs through morphology control, taking a major step forward in the low-cost and rapid production of PeSCs by solving one of the biggest problems of PHJ perovskite photovoltaic technology through a facile method. PMID:25377945

Synthesis and characterization of poly (dihydroxybiphenyl borate) with high char yield for high-performance thermosetting resins

NASA Astrophysics Data System (ADS)

Wang, Shujuan; Xing, Xiaolong; Li, Jian; Jing, Xinli

2018-01-01

The objective of the current work is to synthesize novel boron-containing polymers with excellent thermal resistance, and reveal the structure and the reason for the high char yield. Thus, poly (dihydroxybiphenyl borate) (PDDB) with a more rigid molecular chain, was successfully synthesized using 4,4‧-dihydroxybiphenyl and boric acid. Structural characterizations of the prepared PDDB were performed via NMR, FTIR, XPS, and XRD analyses. The results reveal that PDDB consists of aromatic, Phsbnd Osbnd B and Bsbnd Osbnd B structures as well as a small number of boron hydroxyl and phenolic hydroxyl groups. PDDB shows good solubility in strong polar solvents, which is of great importance for the modification of thermosetting resins. TGA combined with DSC were employed to evaluate the thermal properties of PDDB, and increases in the glass transition temperature (Tg) and char yield were observed with increased boron content. Tg and char yield of PDDB (800 °C, nitrogen atmosphere) reached up to 219 °C and 66.5%, respectively. PDDB was extensively characterized during pyrolysis to reveal the high char yield of PDDB. As briefly discussed, the boron oxide and boron carbide that formed during pyrolysis play a crucial role in the high char yield of PDDB, which reduces the release of volatile carbon dioxide and carbon. This research suggests that PDDB has great potential as a novel modified agent for the improvement of the comprehensive performance of thermosetting resins to broaden their applicability in the field of advanced composites.

Reproducibility study of whole-brain 1H spectroscopic imaging with automated quantification.

PubMed

Gu, Meng; Kim, Dong-Hyun; Mayer, Dirk; Sullivan, Edith V; Pfefferbaum, Adolf; Spielman, Daniel M

2008-09-01

A reproducibility study of proton MR spectroscopic imaging ((1)H-MRSI) of the human brain was conducted to evaluate the reliability of an automated 3D in vivo spectroscopic imaging acquisition and associated quantification algorithm. A PRESS-based pulse sequence was implemented using dualband spectral-spatial RF pulses designed to fully excite the singlet resonances of choline (Cho), creatine (Cre), and N-acetyl aspartate (NAA) while simultaneously suppressing water and lipids; 1% of the water signal was left to be used as a reference signal for robust data processing, and additional lipid suppression was obtained using adiabatic inversion recovery. Spiral k-space trajectories were used for fast spectral and spatial encoding yielding high-quality spectra from 1 cc voxels throughout the brain with a 13-min acquisition time. Data were acquired with an 8-channel phased-array coil and optimal signal-to-noise ratio (SNR) for the combined signals was achieved using a weighting based on the residual water signal. Automated quantification of the spectrum of each voxel was performed using LCModel. The complete study consisted of eight healthy adult subjects to assess intersubject variations and two subjects scanned six times each to assess intrasubject variations. The results demonstrate that reproducible whole-brain (1)H-MRSI data can be robustly obtained with the proposed methods.

(re)producing Good Science Students: Girls' Participation in High School Physics

NASA Astrophysics Data System (ADS)

Carlone, Heidi B.

In this ethnographic study, the author describes the meanings of science and science student in a physics classroom in an upper-middle-class high school and the ways girls participated within these meanings. The classroom practices reproduced prototypical meanings of science (as authoritative) and science student (as "dutiful"). The results highlight girls' embrace of prototypical school science. Yet at the end of the school year, the girls did not consider themselves "science people," nor did they want to pursue physics further. The author's interpretation of these results takes seriously girls' agency in producing the meaning of the physics class (as a way to polish one's transcript) and draws attention to the promoted identities (prototypical good student identities) in the classroom. The author argues that students' agency in resisting or accepting the practices, identities, and knowledge of school science is worth understanding for the improvement of science education.

Repeatability and Reproducibility of Virtual Subjective Refraction.

PubMed

Perches, Sara; Collados, M Victoria; Ares, Jorge

2016-10-01

To establish the repeatability and reproducibility of a virtual refraction process using simulated retinal images. With simulation software, aberrated images corresponding with each step of the refraction process were calculated following the typical protocol of conventional subjective refraction. Fifty external examiners judged simulated retinal images until the best sphero-cylindrical refraction and the best visual acuity were achieved starting from the aberrometry data of three patients. Data analyses were performed to assess repeatability and reproducibility of the virtual refraction as a function of pupil size and aberrometric profile of different patients. SD values achieved in three components of refraction (M, J0, and J45) are lower than 0.25D in repeatability analysis. Regarding reproducibility, we found SD values lower than 0.25D in the most cases. When the results of virtual refraction with different pupil diameters (4 and 6 mm) were compared, the mean of differences (MoD) obtained were not clinically significant (less than 0.25D). Only one of the aberrometry profiles with high uncorrected astigmatism shows poor results for the M component in reproducibility and pupil size dependence analysis. In all cases, vision achieved was better than 0 logMAR. A comparison between the compensation obtained with virtual and conventional subjective refraction was made as an example of this application, showing good quality retinal images in both processes. The present study shows that virtual refraction has similar levels of precision as conventional subjective refraction. Moreover, virtual refraction has also shown that when high low order astigmatism is present, the refraction result is less precise and highly dependent on pupil size.

Rational design of high-yield and superior-quality rice.

PubMed

Zeng, Dali; Tian, Zhixi; Rao, Yuchun; Dong, Guojun; Yang, Yaolong; Huang, Lichao; Leng, Yujia; Xu, Jie; Sun, Chuan; Zhang, Guangheng; Hu, Jiang; Zhu, Li; Gao, Zhenyu; Hu, Xingming; Guo, Longbiao; Xiong, Guosheng; Wang, Yonghong; Li, Jiayang; Qian, Qian

2017-03-20

Rice (Oryza sativa L.) is a staple food for more than half of the world's population. To meet the ever-increasing demand for food, because of population growth and improved living standards, world rice production needs to double by 2030 1 . The development of new elite rice varieties with high yield and superior quality is challenging for traditional breeding approaches, and new strategies need to be developed. Here, we report the successful development of new elite varieties by pyramiding major genes that significantly contribute to grain quality and yield from three parents over five years. The new varieties exhibit higher yield potential and better grain quality than their parental varieties and the China's leading super-hybrid rice, Liang-you-pai-jiu (LYP9 or Pei-ai 64S/93-11). Our results demonstrate that rational design is a powerful strategy for meeting the challenges of future crop breeding, particularly in pyramiding multiple complex traits.

Highly reliable field electron emitters produced from reproducible damage-free carbon nanotube composite pastes with optimal inorganic fillers.

PubMed

Kim, Jae-Woo; Jeong, Jin-Woo; Kang, Jun-Tae; Choi, Sungyoul; Ahn, Seungjoon; Song, Yoon-Ho

2014-02-14

Highly reliable field electron emitters were developed using a formulation for reproducible damage-free carbon nanotube (CNT) composite pastes with optimal inorganic fillers and a ball-milling method. We carefully controlled the ball-milling sequence and time to avoid any damage to the CNTs, which incorporated fillers that were fully dispersed as paste constituents. The field electron emitters fabricated by printing the CNT pastes were found to exhibit almost perfect adhesion of the CNT emitters to the cathode, along with good uniformity and reproducibility. A high field enhancement factor of around 10,000 was achieved from the CNT field emitters developed. By selecting nano-sized metal alloys and oxides and using the same formulation sequence, we also developed reliable field emitters that could survive high-temperature post processing. These field emitters had high durability to post vacuum annealing at 950 °C, guaranteeing survival of the brazing process used in the sealing of field emission x-ray tubes. We evaluated the field emitters in a triode configuration in the harsh environment of a tiny vacuum-sealed vessel and observed very reliable operation for 30 h at a high current density of 350 mA cm(-2). The CNT pastes and related field emitters that were developed could be usefully applied in reliable field emission devices.

Highly reliable field electron emitters produced from reproducible damage-free carbon nanotube composite pastes with optimal inorganic fillers

NASA Astrophysics Data System (ADS)

Kim, Jae-Woo; Jeong, Jin-Woo; Kang, Jun-Tae; Choi, Sungyoul; Ahn, Seungjoon; Song, Yoon-Ho

2014-02-01

Highly reliable field electron emitters were developed using a formulation for reproducible damage-free carbon nanotube (CNT) composite pastes with optimal inorganic fillers and a ball-milling method. We carefully controlled the ball-milling sequence and time to avoid any damage to the CNTs, which incorporated fillers that were fully dispersed as paste constituents. The field electron emitters fabricated by printing the CNT pastes were found to exhibit almost perfect adhesion of the CNT emitters to the cathode, along with good uniformity and reproducibility. A high field enhancement factor of around 10 000 was achieved from the CNT field emitters developed. By selecting nano-sized metal alloys and oxides and using the same formulation sequence, we also developed reliable field emitters that could survive high-temperature post processing. These field emitters had high durability to post vacuum annealing at 950 °C, guaranteeing survival of the brazing process used in the sealing of field emission x-ray tubes. We evaluated the field emitters in a triode configuration in the harsh environment of a tiny vacuum-sealed vessel and observed very reliable operation for 30 h at a high current density of 350 mA cm-2. The CNT pastes and related field emitters that were developed could be usefully applied in reliable field emission devices.

Bremsstrahlung Dose Yield for High-Intensity Short-Pulse Laser–Solid Experiments

DOE PAGES

Liang, Taiee; Bauer, Johannes M.; Liu, James C.; ...

2016-12-01

A bremsstrahlung source term has been developed by the Radiation Protection (RP) group at SLAC National Accelerator Laboratory for high-intensity short-pulse laser–solid experiments between 10 17 and 10 22 W cm –2. This source term couples the particle-in-cell plasma code EPOCH and the radiation transport code FLUKA to estimate the bremsstrahlung dose yield from laser–solid interactions. EPOCH characterizes the energy distribution, angular distribution, and laser-to-electron conversion efficiency of the hot electrons from laser–solid interactions, and FLUKA utilizes this hot electron source term to calculate a bremsstrahlung dose yield (mSv per J of laser energy on target). The goal of thismore » paper is to provide RP guidelines and hazard analysis for high-intensity laser facilities. In conclusion, a comparison of the calculated bremsstrahlung dose yields to radiation measurement data is also made.« less

Bremsstrahlung Dose Yield for High-Intensity Short-Pulse Laser–Solid Experiments

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

Liang, Taiee; Bauer, Johannes M.; Liu, James C.

A bremsstrahlung source term has been developed by the Radiation Protection (RP) group at SLAC National Accelerator Laboratory for high-intensity short-pulse laser–solid experiments between 10 17 and 10 22 W cm –2. This source term couples the particle-in-cell plasma code EPOCH and the radiation transport code FLUKA to estimate the bremsstrahlung dose yield from laser–solid interactions. EPOCH characterizes the energy distribution, angular distribution, and laser-to-electron conversion efficiency of the hot electrons from laser–solid interactions, and FLUKA utilizes this hot electron source term to calculate a bremsstrahlung dose yield (mSv per J of laser energy on target). The goal of thismore » paper is to provide RP guidelines and hazard analysis for high-intensity laser facilities. In conclusion, a comparison of the calculated bremsstrahlung dose yields to radiation measurement data is also made.« less

Imaging of striatal dopamine transporters in rat brain with single pinhole SPECT and co-aligned MRI is highly reproducible.

PubMed

Booij, Jan; de Bruin, Kora; de Win, Maartje M L; Lavini, Cristina; den Heeten, Gerard J; Habraken, Jan B A

2003-08-01

A recently developed pinhole high-resolution SPECT system was used to measure striatal to non-specific binding ratios in rats (n = 9), after injection of the dopamine transporter ligand (123)I-FP-CIT, and to assess its test/retest reproducibility. For co-alignment purposes, the rat brain was imaged on a 1.5 Tesla clinical MRI scanner using a specially developed surface coil. The SPECT images showed clear striatal uptake. On the MR images, cerebral and extra-cerebral structures could be easily delineated. The mean striatal to non-specific [(123)I]FP-CIT binding ratios of the test/retest studies were 1.7 +/- 0.2 and 1.6 +/- 0.2, respectively. The test/retest variability was approximately 9%. We conclude that the assessment of striatal [(123)I]FP-CIT binding ratios in rats is highly reproducible.

3-D printing provides a novel approach for standardization and reproducibility of freezing devices

PubMed Central

Hu, E; Childress, William; Tiersch, Terrence R.

2017-01-01

Cryopreservation has become an important and accepted tool for long-term germplasm conservation of animals and plants. To protect genetic resources, repositories have been developed with national and international cooperation. For a repository to be effective, the genetic material submitted must be of good quality and comparable to other submissions. However, due to a variety of reasons, including constraints in knowledge and available resources, cryopreservation methods for aquatic species vary widely across user groups which reduces reproducibility and weakens quality control. Herein we describe a standardizable freezing device produced using 3-dimensional (3-D) printing and introduce the concept of network sharing to achieve aggregate high-throughput cryopreservation for aquatic species. The objectives were to: 1) adapt widely available polystyrene foam products that would be inexpensive, portable, and provide adequate work space; 2) develop a design suitable for 3-D printing that could provide multiple configurations, be inexpensive, and easy to use, and 3) evaluate various configurations to attain freezing rates suitable for various common cryopreservation containers. Through this approach, identical components can be accessed globally, and we demonstrated that 3-D printers can be used to fabricate parts for standardizable freezing devices yielding relevant and reproducible cooling rates across users. With standardized devices for freezing, methods and samples can harmonize into an aggregated high-throughput pathway not currently available for aquatic species repository development. PMID:28465185

High yield neutron generators using the DD reaction

NASA Astrophysics Data System (ADS)

Vainionpaa, J. H.; Harris, J. L.; Piestrup, M. A.; Gary, C. K.; Williams, D. L.; Apodaca, M. D.; Cremer, J. T.; Ji, Qing; Ludewigt, B. A.; Jones, G.

2013-04-01

A product line of high yield neutron generators has been developed at Adelphi technology inc. The generators use the D-D fusion reaction and are driven by an ion beam supplied by a microwave ion source. Yields of up to 5 × 109 n/s have been achieved, which are comparable to those obtained using the more efficient D-T reaction. The microwave-driven plasma uses the electron cyclotron resonance (ECR) to produce a high plasma density for high current and high atomic ion species. These generators have an actively pumped vacuum system that allows operation at reduced pressure in the target chamber, increasing the overall system reliability. Since no radioactive tritium is used, the generators can be easily serviced, and components can be easily replaced, providing essentially an unlimited lifetime. Fast neutron source size can be adjusted by selecting the aperture and target geometries according to customer specifications. Pulsed and continuous operation has been demonstrated. Minimum pulse lengths of 50 μs have been achieved. Since the generators are easily serviceable, they offer a long lifetime neutron generator for laboratories and commercial systems requiring continuous operation. Several of the generators have been enclosed in radiation shielding/moderator structures designed for customer specifications. These generators have been proven to be useful for prompt gamma neutron activation analysis (PGNAA), neutron activation analysis (NAA) and fast neutron radiography. Thus these generators make excellent fast, epithermal and thermal neutron sources for laboratories and industrial applications that require neutrons with safe operation, small footprint, low cost and small regulatory burden.

Long-term reproducibility of relative sensitivity factors obtained with CAMECA Wf

NASA Astrophysics Data System (ADS)

Gui, D.; Xing, Z. X.; Huang, Y. H.; Mo, Z. Q.; Hua, Y. N.; Zhao, S. P.; Cha, L. Z.

2008-12-01

As the wafer size continues to increase and the feature size of the integrated circuits (IC) continues to shrink, process control of IC manufacturing becomes ever more important to reduce the cost of failures caused by the drift of processes or equipments. Characterization tools with high precision and reproducibility are required to capture any abnormality of the process. Although Secondary ion mass spectrometry (SIMS) has been widely used in dopant profile control, it was reported that magnetic sector SIMS, compared to quadrupole SIMS, has lower short-term repeatability and long-term reproducibility due to the high extraction field applied between sample and extraction lens. In this paper, we demonstrate that CAMECA Wf can deliver high long-term reproducibility because of its high-level automation and improved design of immersion lens. The relative standard deviation (R.S.D.) of the relative sensitivity factors (RSF) of three typical elements, i.e., boron (B), phosphorous (P) and nitrogen (N), over 3 years are 3.7%, 5.5% and 4.1%, respectively. The high reproducibility results have a practical implication that deviation can be estimated without testing the standards.

High-resolution, regional-scale crop yield simulations for the Southwestern United States

NASA Astrophysics Data System (ADS)

Stack, D. H.; Kafatos, M.; Medvigy, D.; El-Askary, H. M.; Hatzopoulos, N.; Kim, J.; Kim, S.; Prasad, A. K.; Tremback, C.; Walko, R. L.; Asrar, G. R.

2012-12-01

Over the past few decades, there have been many process-based crop models developed with the goal of better understanding the impacts of climate, soils, and management decisions on crop yields. These models simulate the growth and development of crops in response to environmental drivers. Traditionally, process-based crop models have been run at the individual farm level for yield optimization and management scenario testing. Few previous studies have used these models over broader geographic regions, largely due to the lack of gridded high-resolution meteorological and soil datasets required as inputs for these data intensive process-based models. In particular, assessment of regional-scale yield variability due to climate change requires high-resolution, regional-scale, climate projections, and such projections have been unavailable until recently. The goal of this study was to create a framework for extending the Agricultural Production Systems sIMulator (APSIM) crop model for use at regional scales and analyze spatial and temporal yield changes in the Southwestern United States (CA, AZ, and NV). Using the scripting language Python, an automated pipeline was developed to link Regional Climate Model (RCM) output with the APSIM crop model, thus creating a one-way nested modeling framework. This framework was used to combine climate, soil, land use, and agricultural management datasets in order to better understand the relationship between climate variability and crop yield at the regional-scale. Three different RCMs were used to drive APSIM: OLAM, RAMS, and WRF. Preliminary results suggest that, depending on the model inputs, there is some variability between simulated RCM driven maize yields and historical yields obtained from the United States Department of Agriculture (USDA). Furthermore, these simulations showed strong non-linear correlations between yield and meteorological drivers, with critical threshold values for some of the inputs (e.g. minimum and

Ultra-broadband nonlinear saturable absorption of high-yield MoS2 nanosheets

NASA Astrophysics Data System (ADS)

Wei, Rongfei; Zhang, Hang; Hu, Zhongliang; Qiao, Tian; He, Xin; Guo, Qiangbing; Tian, Xiangling; Chen, Zhi; Qiu, Jianrong

2016-07-01

High-yield MoS2 nanosheets with strong nonlinear optical (NLO) responses in a broad near-infrared range were synthesized by a facile hydrothermal method. The observation of saturable absorption, which was excited by the light with photon energy smaller than the gap energy of MoS2, can be attributed to the enhancement of the hybridization between the Mo d-orbital and S p-orbital by the oxygen incorporation into MoS2. High-yield MoS2 nanosheets with high modulation depth and large saturable intensity generated a stable, passively Q-switched fiber laser pulse at 1.56 μm. The high output power of 1.08 mW can be attained under a very low pump power of 30.87 mW. Compared to recently reported passively Q-switched fiber lasers utilizing exfoliated MoS2 nanosheets, the efficiency of the laser for our passive Q-switching operation is larger and reaches 3.50%. This research may extend the understanding on the NLO properties of MoS2 and indicate the feasibility of the high-yield MoS2 nanosheets to passively Q-switched fiber laser effectively at low pump strengths.

Comment on "Estimating the reproducibility of psychological science".

PubMed

Gilbert, Daniel T; King, Gary; Pettigrew, Stephen; Wilson, Timothy D

2016-03-04

A paper from the Open Science Collaboration (Research Articles, 28 August 2015, aac4716) attempting to replicate 100 published studies suggests that the reproducibility of psychological science is surprisingly low. We show that this article contains three statistical errors and provides no support for such a conclusion. Indeed, the data are consistent with the opposite conclusion, namely, that the reproducibility of psychological science is quite high. Copyright © 2016, American Association for the Advancement of Science.

Predawn respiration rates during flowering are highly predictive of yield response in Gossypium hirsutum when yield variability is water-induced.

PubMed

Snider, John L; Chastain, Daryl R; Meeks, Calvin D; Collins, Guy D; Sorensen, Ronald B; Byrd, Seth A; Perry, Calvin D

2015-07-01

Respiratory carbon evolution by leaves under abiotic stress is implicated as a major limitation to crop productivity; however, respiration rates of fully expanded leaves are positively associated with plant growth rates. Given the substantial sensitivity of plant growth to drought, it was hypothesized that predawn respiration rates (RPD) would be (1) more sensitive to drought than photosynthetic processes and (2) highly predictive of water-induced yield variability in Gossypium hirsutum. Two studies (at Tifton and Camilla Georgia) addressed these hypotheses. At Tifton, drought was imposed beginning at the onset of flowering (first flower) and continuing for three weeks (peak bloom) followed by a recovery period, and predawn water potential (ΨPD), RPD, net photosynthesis (AN) and maximum quantum yield of photosystem II (Fv/Fm) were measured throughout the study period. At Camilla, plants were exposed to five different irrigation regimes throughout the growing season, and average ΨPD and RPD were determined between first flower and peak bloom for all treatments. For both sites, fiber yield was assessed at crop maturity. The relationships between ΨPD, RPD and yield were assessed via non-linear regression. It was concluded for field-grown G. hirsutum that (1) RPD is exceptionally sensitive to progressive drought (more so than AN or Fv/Fm) and (2) average RPD from first flower to peak bloom is highly predictive of water-induced yield variability. Copyright © 2015 Elsevier GmbH. All rights reserved.

Laser heating challenges of high yield MagLIF targets

NASA Astrophysics Data System (ADS)

Slutz, Stephen; Sefkow, Adam; Vesey, Roger

2014-10-01

The MagLIF (Magnetized Liner Inertial Fusion) concept is predicted by numerical simulation to produce fusion yields of about 100 kJ, when driven by 25 MA from the existing Z accelerator [S. A. Slutz et al. Phys. Plasmas 17, 056303 (2010)] and much higher yields with future accelerators delivering higher currents [Slutz and Vesey PRL 108, 025003 (2012)]. The fuel must be heated before compression to obtain significant fusion yields due to the relatively slow implosion velocities (~ 100 km/s) of magnetically driven liners. Lasers provide a convenient means to accomplish this pre-compressional heating of the fusion fuel, but there are challenges. The laser must penetrate a foil covering the laser entrance hole and deposit 20-30 kJ within the ~1 cm length of the liner in fuel at 6-12 mg/cc. Such high densities could result in beam scattering due to refraction and laser plasma interactions. Numerical simulations of the laser heating process are presented, which indicate that energies as high as 30 kJ could be deposited in the fuel by using two laser pulses of different wavelengths. Simulations of this process will be presented as well of results for a MagLIF design for a potential new machine delivering 50 MA of current. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under Contract DE-AC04-94AL85000.

The effects of pre-ionization using a shunt resistor on reproducibility of the x-ray emission in a dense plasma focus device

NASA Astrophysics Data System (ADS)

Piriaei, D.; Yousefi, H. R.; Mahabadi, T. D.; SalarElahi, A.; Ghoranneviss, M.

2017-08-01

In this research, the effects of pre-ionization using a shunt resistor on reproducibility of x-ray emission in a Mather type plasma focus device have been studied. This technique increased the intensities of the emitted x-rays from argon as the filling gas of the device and made the x-ray yields with similar intensities reproducible. A Mirnov coil was also used to record the variations of the plasma's magnetic field, and the wavelet spectrums of these recorded signals showed the reduced instabilities due to the application of the pre-ionization technique. Moreover, it was demonstrated that this technique was capable of reducing the number of initial runaway electrons that could increase the impurities and instabilities inside the plasma. In addition to the above-mentioned features, this technique could improve the uniform formation of the current sheath during the breakdown phase that might later lead to a high quality pinch and high intensity emitted x-rays.

Climate Based Predictability of Oil Palm Tree Yield in Malaysia.

PubMed

Oettli, Pascal; Behera, Swadhin K; Yamagata, Toshio

2018-02-02

The influence of local conditions and remote climate modes on the interannual variability of oil palm fresh fruit bunches (FFB) total yields in Malaysia and two major regions (Peninsular Malaysia and Sabah/Sarawak) is explored. On a country scale, the state of sea-surface temperatures (SST) in the tropical Pacific Ocean during the previous boreal winter is found to influence the regional climate. When El Niño occurs in the Pacific Ocean, rainfall in Malaysia reduces but air temperature increases, generating a high level of water stress for palm trees. As a result, the yearly production of FFB becomes lower than that of a normal year since the water stress during the boreal spring has an important impact on the total annual yields of FFB. Conversely, La Niña sets favorable conditions for palm trees to produce more FFB by reducing chances of water stress risk. The region of the Leeuwin current also seems to play a secondary role through the Ningaloo Niño/ Niña in the interannual variability of FFB yields. Based on these findings, a linear model is constructed and its ability to reproduce the interannual signal is assessed. This model has shown some skills in predicting the total FFB yield.

High Useful Yield and Isotopic Analysis of Uranium by Resonance Ionization Mass Spectrometry

DOE PAGES

Savina, Michael R.; Isselhardt, Brett H.; Kucher, Andrew; ...

2017-05-09

Useful yields from resonance ionization mass spectrometry can be extremely high compared to other mass spectrometry techniques, but uranium analysis shows strong matrix effects arising from the tendency of uranium to form strongly bound oxide molecules that do not dissociate appreciably on energetic ion bombardment. Here, we demonstrate a useful yield of 24% for metallic uranium. Modeling the laser ionization and ion transmission processes shows that the high useful yield is attributable to a high ion fraction achieved by resonance ionization. We quantify the reduction of uranium oxide surface layers by Ar + and Ga + sputtering. The useful yieldmore » for uranium atoms from a uranium dioxide matrix is 0.4% and rises to 2% when the surface is in sputter equilibrium with the ion beam. The lower useful yield from the oxide is almost entirely due to uranium oxide molecules reducing the neutral atom content of the sputtered flux. We also demonstrate rapid isotopic analysis of solid uranium oxide at a precision of <0.5% relative standard deviation using relatively broadband lasers to mitigate spectroscopic fractionation.« less

High Useful Yield and Isotopic Analysis of Uranium by Resonance Ionization Mass Spectrometry

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

Savina, Michael R.; Isselhardt, Brett H.; Kucher, Andrew

Useful yields from resonance ionization mass spectrometry can be extremely high compared to other mass spectrometry techniques, but uranium analysis shows strong matrix effects arising from the tendency of uranium to form strongly bound oxide molecules that do not dissociate appreciably on energetic ion bombardment. Here, we demonstrate a useful yield of 24% for metallic uranium. Modeling the laser ionization and ion transmission processes shows that the high useful yield is attributable to a high ion fraction achieved by resonance ionization. We quantify the reduction of uranium oxide surface layers by Ar + and Ga + sputtering. The useful yieldmore » for uranium atoms from a uranium dioxide matrix is 0.4% and rises to 2% when the surface is in sputter equilibrium with the ion beam. The lower useful yield from the oxide is almost entirely due to uranium oxide molecules reducing the neutral atom content of the sputtered flux. We also demonstrate rapid isotopic analysis of solid uranium oxide at a precision of <0.5% relative standard deviation using relatively broadband lasers to mitigate spectroscopic fractionation.« less

[Yield of starch extraction from plantain (Musa paradisiaca). Pilot plant study].

PubMed

Flores-Gorosquera, Emigdia; García-Suárez, Francisco J; Flores-Huicochea, Emmanuel; Núñez-Santiago, María C; González-Soto, Rosalia A; Bello-Pérez, Luis A

2004-01-01

In México, the banana (Musa paradisiaca) is cooked (boiling or deep frying) before being eaten, but the consumption is not very popular and a big quantity of the product is lost after harvesting. The unripe plantain has a high level of starch and due to this the use of banana can be diversified as raw material for starch isolation. The objective of this work was to study the starch yield at pilot plant scale. Experiments at laboratory scale were carried out using the pulp with citric acid to 0,3 % (antioxidant), in order to evaluate the different unitary operations of the process. The starch yield, based on starch presence in the pulp that can be isolated, were between 76 and 86 %, and the values at pilot plant scale were between 63 and 71 %, in different lots of banana fruit. Starch yield values were similar among the diverse lots, showing that the process is reproducible. The lower values of starch recovery at pilot plant scale are due to the loss during sieving operations; however, the amount of starch recovery is good.

High yield neutron generators using the DD reaction

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

Vainionpaa, J. H.; Harris, J. L.; Piestrup, M. A.

2013-04-19

A product line of high yield neutron generators has been developed at Adelphi technology inc. The generators use the D-D fusion reaction and are driven by an ion beam supplied by a microwave ion source. Yields of up to 5 Multiplication-Sign 10{sup 9} n/s have been achieved, which are comparable to those obtained using the more efficient D-T reaction. The microwave-driven plasma uses the electron cyclotron resonance (ECR) to produce a high plasma density for high current and high atomic ion species. These generators have an actively pumped vacuum system that allows operation at reduced pressure in the target chamber,more » increasing the overall system reliability. Since no radioactive tritium is used, the generators can be easily serviced, and components can be easily replaced, providing essentially an unlimited lifetime. Fast neutron source size can be adjusted by selecting the aperture and target geometries according to customer specifications. Pulsed and continuous operation has been demonstrated. Minimum pulse lengths of 50 {mu}s have been achieved. Since the generators are easily serviceable, they offer a long lifetime neutron generator for laboratories and commercial systems requiring continuous operation. Several of the generators have been enclosed in radiation shielding/moderator structures designed for customer specifications. These generators have been proven to be useful for prompt gamma neutron activation analysis (PGNAA), neutron activation analysis (NAA) and fast neutron radiography. Thus these generators make excellent fast, epithermal and thermal neutron sources for laboratories and industrial applications that require neutrons with safe operation, small footprint, low cost and small regulatory burden.« less

Systematic heterogenization for better reproducibility in animal experimentation.

PubMed

Richter, S Helene

2017-08-31

The scientific literature is full of articles discussing poor reproducibility of findings from animal experiments as well as failures to translate results from preclinical animal studies to clinical trials in humans. Critics even go so far as to talk about a "reproducibility crisis" in the life sciences, a novel headword that increasingly finds its way into numerous high-impact journals. Viewed from a cynical perspective, Fett's law of the lab "Never replicate a successful experiment" has thus taken on a completely new meaning. So far, poor reproducibility and translational failures in animal experimentation have mostly been attributed to biased animal data, methodological pitfalls, current publication ethics and animal welfare constraints. More recently, the concept of standardization has also been identified as a potential source of these problems. By reducing within-experiment variation, rigorous standardization regimes limit the inference to the specific experimental conditions. In this way, however, individual phenotypic plasticity is largely neglected, resulting in statistically significant but possibly irrelevant findings that are not reproducible under slightly different conditions. By contrast, systematic heterogenization has been proposed as a concept to improve representativeness of study populations, contributing to improved external validity and hence improved reproducibility. While some first heterogenization studies are indeed very promising, it is still not clear how this approach can be transferred into practice in a logistically feasible and effective way. Thus, further research is needed to explore different heterogenization strategies as well as alternative routes toward better reproducibility in animal experimentation.

Assessing the reproducibility of discriminant function analyses

PubMed Central

Andrew, Rose L.; Albert, Arianne Y.K.; Renaut, Sebastien; Rennison, Diana J.; Bock, Dan G.

2015-01-01

Data are the foundation of empirical research, yet all too often the datasets underlying published papers are unavailable, incorrect, or poorly curated. This is a serious issue, because future researchers are then unable to validate published results or reuse data to explore new ideas and hypotheses. Even if data files are securely stored and accessible, they must also be accompanied by accurate labels and identifiers. To assess how often problems with metadata or data curation affect the reproducibility of published results, we attempted to reproduce Discriminant Function Analyses (DFAs) from the field of organismal biology. DFA is a commonly used statistical analysis that has changed little since its inception almost eight decades ago, and therefore provides an opportunity to test reproducibility among datasets of varying ages. Out of 100 papers we initially surveyed, fourteen were excluded because they did not present the common types of quantitative result from their DFA or gave insufficient details of their DFA. Of the remaining 86 datasets, there were 15 cases for which we were unable to confidently relate the dataset we received to the one used in the published analysis. The reasons ranged from incomprehensible or absent variable labels, the DFA being performed on an unspecified subset of the data, or the dataset we received being incomplete. We focused on reproducing three common summary statistics from DFAs: the percent variance explained, the percentage correctly assigned and the largest discriminant function coefficient. The reproducibility of the first two was fairly high (20 of 26, and 44 of 60 datasets, respectively), whereas our success rate with the discriminant function coefficients was lower (15 of 26 datasets). When considering all three summary statistics, we were able to completely reproduce 46 (65%) of 71 datasets. While our results show that a majority of studies are reproducible, they highlight the fact that many studies still are not the

Reproducibility of dynamically represented acoustic lung images from healthy individuals

PubMed Central

Maher, T M; Gat, M; Allen, D; Devaraj, A; Wells, A U; Geddes, D M

2008-01-01

Background and aim: Acoustic lung imaging offers a unique method for visualising the lung. This study was designed to demonstrate reproducibility of acoustic lung images recorded from healthy individuals at different time points and to assess intra- and inter-rater agreement in the assessment of dynamically represented acoustic lung images. Methods: Recordings from 29 healthy volunteers were made on three separate occasions using vibration response imaging. Reproducibility was measured using quantitative, computerised assessment of vibration energy. Dynamically represented acoustic lung images were scored by six blinded raters. Results: Quantitative measurement of acoustic recordings was highly reproducible with an intraclass correlation score of 0.86 (very good agreement). Intraclass correlations for inter-rater agreement and reproducibility were 0.61 (good agreement) and 0.86 (very good agreement), respectively. There was no significant difference found between the six raters at any time point. Raters ranged from 88% to 95% in their ability to identically evaluate the different features of the same image presented to them blinded on two separate occasions. Conclusion: Acoustic lung imaging is reproducible in healthy individuals. Graphic representation of lung images can be interpreted with a high degree of accuracy by the same and by different reviewers. PMID:18024534

Electrorheological fluid with an extraordinarily high yield stress

NASA Astrophysics Data System (ADS)

Zhang, Yuling; Lu, Kunquan; Rao, Guanghui; Tian, Yu; Zhang, Shaohua; Liang, Jingkui

2002-02-01

Surface modified complex strontium titanate microparticles are synthesized by means of a modified sol-gel technique. A suspension composed of these particles immersed in a silicone oil exhibits excellent electrorheological properties attractive to industry and technology applications: a yield stress as high as 27 kPa in an applied electric field of 3 kV/mm, a low leakage current, wide dynamic ranges in temperature and shear rate, and a long-term stability against sedimentation. In addition to the high dielectric constant of strontium titanate, surfactant and water-free character of the particles may be responsible for the dramatic improvement of the electrorheological properties of the suspension.

Reproducible Crystallite Size of Mono-Dispersed and Scalable Biologically Produced Metal-Substituted Nanometer-Sized Magnetites

NASA Astrophysics Data System (ADS)

Moon, J.; Rawn, C.; Rondinone, A.; Love, L.; Roh, Y.; Lauf, R.; Phelps, T.

2008-12-01

Our previous research demonstrated that biosynthesized magnetite (biomagnetite) exhibited similar properties as chemically synthesized magnetite. To complement uses of the traditional chemically synthesized magnetite (chem-magnetite) biomagnetite must be exhibit highly reproducible sizes and be available in scalable qualities. Here we emphasize potentially advantageous properties of biomagnetite regarding size, reproducibility and scaling availability. Average crystallite size (ACS) of biomagnetites ranging from 10-100 nm was determined after varied 1) incubation times, 2) substitution of metal and lanthanide species, 3) degrees of congruent incorporation or retardation of substitution elements, 4) bacterial species with their varied ability to substitute elemental species, and 6) incubation temperature that can influence coalescence. The microbial production of biomagnetite has demonstrated capacity to make highly crystalline nanoscale particles of metal-substituted ferrites including compounds of Co, Ni, Cr, Mn, Zn and the rare earths in large quantity. Selected Zn-substituted magnetite (nominal composition of Zn0.6Fe2.4O4) has been recovered at over 1 kg (wet weight) in batches from 30 L fermentations. The massively produced extracellular magnetites were confirmed to exhibit good mono- dispersity via transmission electron microscopy (TEM). TEM also validated highly reproducible ACS of 13.1±0.8 nm size as determined through X-ray diffraction (N=7) at a 99 % confidence level. Based on the scale-up experiments performed using the 35 L reactor, the reduction in ACS variability and shorted incubation times of several days may be attributed to increases of electron donor input, and availability of divalent ions of the substitution metal with less ferrous ions in the case of doped magnetite, or a combination of the above. While costs of commercial nanometer sized magnetite (25-50 nm) may vary from 500/kg to > 1,000/kg, microbial mass production is likely capable of

Physics and Psychophysics of High-Fidelity Sound. Part III: The Components of a Sound-Reproducing System: Amplifiers and Loudspeakers.

ERIC Educational Resources Information Center

Rossing, Thomas D.

1980-01-01

Described are the components for a high-fidelity sound-reproducing system which focuses on various program sources, the amplifier, and loudspeakers. Discussed in detail are amplifier power and distortion, air suspension, loudspeaker baffles and enclosures, bass-reflex enclosure, drone cones, rear horn and acoustic labyrinth enclosures, horn…

Statistical modelling of grapevine yield in the Port Wine region under present and future climate conditions

NASA Astrophysics Data System (ADS)

Santos, João A.; Malheiro, Aureliano C.; Karremann, Melanie K.; Pinto, Joaquim G.

2011-03-01

The impact of projected climate change on wine production was analysed for the Demarcated Region of Douro, Portugal. A statistical grapevine yield model (GYM) was developed using climate parameters as predictors. Statistically significant correlations were identified between annual yield and monthly mean temperatures and monthly precipitation totals during the growing cycle. These atmospheric factors control grapevine yield in the region, with the GYM explaining 50.4% of the total variance in the yield time series in recent decades. Anomalously high March rainfall (during budburst, shoot and inflorescence development) favours yield, as well as anomalously high temperatures and low precipitation amounts in May and June (May: flowering and June: berry development). The GYM was applied to a regional climate model output, which was shown to realistically reproduce the GYM predictors. Finally, using ensemble simulations under the A1B emission scenario, projections for GYM-derived yield in the Douro Region, and for the whole of the twenty-first century, were analysed. A slight upward trend in yield is projected to occur until about 2050, followed by a steep and continuous increase until the end of the twenty-first century, when yield is projected to be about 800 kg/ha above current values. While this estimate is based on meteorological parameters alone, changes due to elevated CO2 may further enhance this effect. In spite of the associated uncertainties, it can be stated that projected climate change may significantly benefit wine yield in the Douro Valley.

Effect of Initial Conditions on Reproducibility of Scientific Research

PubMed Central

Djulbegovic, Benjamin; Hozo, Iztok

2014-01-01

Background: It is estimated that about half of currently published research cannot be reproduced. Many reasons have been offered as explanations for failure to reproduce scientific research findings- from fraud to the issues related to design, conduct, analysis, or publishing scientific research. We also postulate a sensitive dependency on initial conditions by which small changes can result in the large differences in the research findings when attempted to be reproduced at later times. Methods: We employed a simple logistic regression equation to model the effect of covariates on the initial study findings. We then fed the input from the logistic equation into a logistic map function to model stability of the results in repeated experiments over time. We illustrate the approach by modeling effects of different factors on the choice of correct treatment. Results: We found that reproducibility of the study findings depended both on the initial values of all independent variables and the rate of change in the baseline conditions, the latter being more important. When the changes in the baseline conditions vary by about 3.5 to about 4 in between experiments, no research findings could be reproduced. However, when the rate of change between the experiments is ≤2.5 the results become highly predictable between the experiments. Conclusions: Many results cannot be reproduced because of the changes in the initial conditions between the experiments. Better control of the baseline conditions in-between the experiments may help improve reproducibility of scientific findings. PMID:25132705

Effect of initial conditions on reproducibility of scientific research.

PubMed

Djulbegovic, Benjamin; Hozo, Iztok

2014-06-01

It is estimated that about half of currently published research cannot be reproduced. Many reasons have been offered as explanations for failure to reproduce scientific research findings- from fraud to the issues related to design, conduct, analysis, or publishing scientific research. We also postulate a sensitive dependency on initial conditions by which small changes can result in the large differences in the research findings when attempted to be reproduced at later times. We employed a simple logistic regression equation to model the effect of covariates on the initial study findings. We then fed the input from the logistic equation into a logistic map function to model stability of the results in repeated experiments over time. We illustrate the approach by modeling effects of different factors on the choice of correct treatment. We found that reproducibility of the study findings depended both on the initial values of all independent variables and the rate of change in the baseline conditions, the latter being more important. When the changes in the baseline conditions vary by about 3.5 to about 4 in between experiments, no research findings could be reproduced. However, when the rate of change between the experiments is ≤2.5 the results become highly predictable between the experiments. Many results cannot be reproduced because of the changes in the initial conditions between the experiments. Better control of the baseline conditions in-between the experiments may help improve reproducibility of scientific findings.

Testing high SPF sunscreens: a demonstration of the accuracy and reproducibility of the results of testing high SPF formulations by two methods and at different testing sites.

PubMed

Agin, Patricia Poh; Edmonds, Susan H

2002-08-01

The goals of this study were (i) to demonstrate that existing and widely used sun protection factor (SPF) test methodologies can produce accurate and reproducible results for high SPF formulations and (ii) to provide data on the number of test-subjects needed, the variability of the data, and the appropriate exposure increments needed for testing high SPF formulations. Three high SPF formulations were tested, according to the Food and Drug Administration's (FDA) 1993 tentative final monograph (TFM) 'very water resistant' test method and/or the 1978 proposed monograph 'waterproof' test method, within one laboratory. A fourth high SPF formulation was tested at four independent SPF testing laboratories, using the 1978 waterproof SPF test method. All laboratories utilized xenon arc solar simulators. The data illustrate that the testing conducted within one laboratory, following either the 1978 proposed or the 1993 TFM SPF test method, was able to reproducibly determine the SPFs of the formulations tested, using either the statistical analysis method in the proposed monograph or the statistical method described in the TFM. When one formulation was tested at four different laboratories, the anticipated variation in the data owing to the equipment and other operational differences was minimized through the use of the statistical method described in the 1993 monograph. The data illustrate that either the 1978 proposed monograph SPF test method or the 1993 TFM SPF test method can provide accurate and reproducible results for high SPF formulations. Further, these results can be achieved with panels of 20-25 subjects with an acceptable level of variability. Utilization of the statistical controls from the 1993 sunscreen monograph can help to minimize lab-to-lab variability for well-formulated products.

Design of high-reliability low-cost amorphous silicon modules for high energy yield

NASA Astrophysics Data System (ADS)

Jansen, Kai W.; Varvar, Anthony; Twesme, Edward; Berens, Troy; Dhere, Neelkanth G.

2008-08-01

For PV modules to fulfill their intended purpose, they must generate sufficient economic return over their lifetime to justify their initial cost. Not only must modules be manufactured at a low cost/Wp with a high energy yield (kWh/kWp), they must also be designed to withstand the significant environmental stresses experienced throughout their 25+ year lifetime. Based on field experience, the most common factors affecting the lifetime energy yield of glass-based amorphous silicon (a-Si) modules have been identified; these include: 1) light-induced degradation; 2) moisture ingress and thin film corrosion; 3) transparent conductive oxide (TCO) delamination; and 4) glass breakage. The current approaches to mitigating the effect of these degradation mechanisms are discussed and the accelerated tests designed to simulate some of the field failures are described. In some cases, novel accelerated tests have been created to facilitate the development of improved manufacturing processes, including a unique test to screen for TCO delamination. Modules using the most reliable designs are tested in high voltage arrays at customer and internal test sites, as well as at independent laboratories. Data from tests at the Florida Solar Energy Center has shown that a-Si tandem modules can demonstrate an energy yield exceeding 1200 kWh/kWp/yr in a subtropical climate. In the same study, the test arrays demonstrated low long-term power loss over two years of data collection, after initial stabilization. The absolute power produced by the test arrays varied seasonally by approximately +/-7%, as expected.

Reproducibility in a multiprocessor system

DOEpatents

Bellofatto, Ralph A; Chen, Dong; Coteus, Paul W; Eisley, Noel A; Gara, Alan; Gooding, Thomas M; Haring, Rudolf A; Heidelberger, Philip; Kopcsay, Gerard V; Liebsch, Thomas A; Ohmacht, Martin; Reed, Don D; Senger, Robert M; Steinmacher-Burow, Burkhard; Sugawara, Yutaka

2013-11-26

Fixing a problem is usually greatly aided if the problem is reproducible. To ensure reproducibility of a multiprocessor system, the following aspects are proposed; a deterministic system start state, a single system clock, phase alignment of clocks in the system, system-wide synchronization events, reproducible execution of system components, deterministic chip interfaces, zero-impact communication with the system, precise stop of the system and a scan of the system state.

Estimation of dew yield from radiative condensers by means of an energy balance model

NASA Astrophysics Data System (ADS)

Maestre-Valero, J. F.; Ragab, R.; Martínez-Alvarez, V.; Baille, A.

2012-08-01

SummaryThis paper presents an energy balance modelling approach to predict the nightly water yield and the surface temperature (Tf) of two passive radiative dew condensers (RDCs) tilted 30° from horizontal. One was fitted with a white hydrophilic polyethylene foil recommended for dew harvest and the other with a black polyethylene foil widely used in horticulture. The model was validated in south-eastern Spain by comparing the simulation outputs with field measurements of Tf and dew yield. The results indicate that the model is robust and accurate in reproducing the behaviour of the two RDCs, especially in what refers to Tf, whose estimates were very close to the observations. The results were somewhat less precise for dew yield, with a larger scatter around the 1:1 relationship. A sensitivity analysis showed that the simulated dew yield was highly sensitive to changes in relative humidity and downward longwave radiation. The proposed approach provides a useful tool to water managers for quantifying the amount of dew that could be harvested as a valuable water resource in arid, semiarid and water stressed regions.

Differential gene expression at different stages of mesocarp development in high- and low-yielding oil palm.

PubMed

Wong, Yick Ching; Teh, Huey Fang; Mebus, Katharina; Ooi, Tony Eng Keong; Kwong, Qi Bin; Koo, Ka Loo; Ong, Chuang Kee; Mayes, Sean; Chew, Fook Tim; Appleton, David R; Kulaveerasingam, Harikrishna

2017-06-21

The oil yield trait of oil palm is expected to involve multiple genes, environmental influences and interactions. Many of the underlying mechanisms that contribute to oil yield are still poorly understood. In this study, we used a microarray approach to study the gene expression profiles of mesocarp tissue at different developmental stages, comparing genetically related high- and low- oil yielding palms to identify genes that contributed to the higher oil-yielding palm and might contribute to the wider genetic improvement of oil palm breeding populations. A total of 3412 (2001 annotated) gene candidates were found to be significantly differentially expressed between high- and low-yielding palms at at least one of the different stages of mesocarp development evaluated. Gene Ontologies (GO) enrichment analysis identified 28 significantly enriched GO terms, including regulation of transcription, fatty acid biosynthesis and metabolic processes. These differentially expressed genes comprise several transcription factors, such as, bHLH, Dof zinc finger proteins and MADS box proteins. Several genes involved in glycolysis, TCA, and fatty acid biosynthesis pathways were also found up-regulated in high-yielding oil palm, among them; pyruvate dehydrogenase E1 component Subunit Beta (PDH), ATP-citrate lyase, β- ketoacyl-ACP synthases I (KAS I), β- ketoacyl-ACP synthases III (KAS III) and ketoacyl-ACP reductase (KAR). Sucrose metabolism-related genes such as Invertase, Sucrose Synthase 2 and Sucrose Phosphatase 2 were found to be down-regulated in high-yielding oil palms, compared to the lower yield palms. Our findings indicate that a higher carbon flux (channeled through down-regulation of the Sucrose Synthase 2 pathway) was being utilized by up-regulated genes involved in glycolysis, TCA and fatty acid biosynthesis leading to enhanced oil production in the high-yielding oil palm. These findings are an important stepping stone to understand the processes that lead to

Role of the N*(1535) resonance and the {pi}{sup -}p{yields}KY amplitudes in the OZI forbidden {pi}N{yields}{phi}N reaction

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

Doering, M.; Oset, E.; Zou, B. S.

2008-08-15

We study the {pi}N{yields}{phi}N reaction close to the {phi}N threshold within the chiral unitary approach, by combining the {pi}{sup -}p{yields}K{sup +}{sigma}{sup -},{pi}{sup -}p{yields}K{sup 0}{sigma}{sup 0}, and {pi}{sup -}p{yields}K{sup 0}{lambda} amplitudes with the coupling of {phi} to the K components of the final states of these reactions via quantum loops. We obtain good agreement with experiment when the dominant {pi}{sup -}p{yields}K{sup 0}{lambda} amplitude is constrained with its experimental cross section. We also evaluate the coupling of N*(1535) to {phi}N and find a moderate coupling as a consequence of partial cancellation of the large KY components of N*(1535). We also show thatmore » the N*(1535) pole approximation is too small to reproduce the measured cross section for the {pi}{sup -}N{yields}{phi}N reaction.« less

Identification of potentially high yielding irradiated cassava ‘Gajah’ genotype with different geographic coordinates

NASA Astrophysics Data System (ADS)

Subekti, I.; Khumaida, N.; Ardie, SW

2017-01-01

Cassava is one of the main and important carbohydrate producing crops in Indonesia. Thus cassava production and its tuber quality need to be improved. ‘Gajah’ genotype is a local genotypes cassava from East Kalimantan, has high potential yield (> 60 ton Ha-1). However, the harvest time of this genotype is quite long (>= 12 months). The objective of this research was to identify the high yielding cassava mutants from the gamma rays irradiated ‘Gajah’ genotype at M1V3 population and potential yield at different location. Several putative cassava mutants (12 mutants) were planted in Cikabayan Experimental Field, IPB from March 2015 to March 2016 and the yields compared with the same genotype grown at different location by seeing its coordinates to observe the potential yield. Our result showed that the fresh tuber weight per plant of some putative mutants could reach more than 8 kg (yield potential of 64 ton Ha-1). The harvested tubers also had sweet flavor, although the tubers of some putative mutants were bitter. Based on previous research study, the different geographic coordinate has resulted variability on fresh tuber yield. It seems that it needs to observe the stability of ‘Gajah’- irradiated mutants in several location in Java Island.

Contextual sensitivity in scientific reproducibility

PubMed Central

Van Bavel, Jay J.; Mende-Siedlecki, Peter; Brady, William J.; Reinero, Diego A.

2016-01-01

In recent years, scientists have paid increasing attention to reproducibility. For example, the Reproducibility Project, a large-scale replication attempt of 100 studies published in top psychology journals found that only 39% could be unambiguously reproduced. There is a growing consensus among scientists that the lack of reproducibility in psychology and other fields stems from various methodological factors, including low statistical power, researcher’s degrees of freedom, and an emphasis on publishing surprising positive results. However, there is a contentious debate about the extent to which failures to reproduce certain results might also reflect contextual differences (often termed “hidden moderators”) between the original research and the replication attempt. Although psychologists have found extensive evidence that contextual factors alter behavior, some have argued that context is unlikely to influence the results of direct replications precisely because these studies use the same methods as those used in the original research. To help resolve this debate, we recoded the 100 original studies from the Reproducibility Project on the extent to which the research topic of each study was contextually sensitive. Results suggested that the contextual sensitivity of the research topic was associated with replication success, even after statistically adjusting for several methodological characteristics (e.g., statistical power, effect size). The association between contextual sensitivity and replication success did not differ across psychological subdisciplines. These results suggest that researchers, replicators, and consumers should be mindful of contextual factors that might influence a psychological process. We offer several guidelines for dealing with contextual sensitivity in reproducibility. PMID:27217556

Contextual sensitivity in scientific reproducibility.

PubMed

Van Bavel, Jay J; Mende-Siedlecki, Peter; Brady, William J; Reinero, Diego A

2016-06-07

In recent years, scientists have paid increasing attention to reproducibility. For example, the Reproducibility Project, a large-scale replication attempt of 100 studies published in top psychology journals found that only 39% could be unambiguously reproduced. There is a growing consensus among scientists that the lack of reproducibility in psychology and other fields stems from various methodological factors, including low statistical power, researcher's degrees of freedom, and an emphasis on publishing surprising positive results. However, there is a contentious debate about the extent to which failures to reproduce certain results might also reflect contextual differences (often termed "hidden moderators") between the original research and the replication attempt. Although psychologists have found extensive evidence that contextual factors alter behavior, some have argued that context is unlikely to influence the results of direct replications precisely because these studies use the same methods as those used in the original research. To help resolve this debate, we recoded the 100 original studies from the Reproducibility Project on the extent to which the research topic of each study was contextually sensitive. Results suggested that the contextual sensitivity of the research topic was associated with replication success, even after statistically adjusting for several methodological characteristics (e.g., statistical power, effect size). The association between contextual sensitivity and replication success did not differ across psychological subdisciplines. These results suggest that researchers, replicators, and consumers should be mindful of contextual factors that might influence a psychological process. We offer several guidelines for dealing with contextual sensitivity in reproducibility.

[The reproducibility of multifocal ERG recordings].

PubMed

Meigen, T; Friedrich, A

2002-09-01

Multifocal electroretinogram recordings (mfERG) can be used to detect a local dysfunction of the retina. In this study we tested both the intrasessional and inter-sessional reproducibility of mfERG amplitudes. MfERGs from 6 eyes of 6 normal subjects were recorded on two different days using DTL electrodes. The relative coefficient of variation ( RCV) was used to quantify the amplitude reproducibility. We tested the effect of (a) session (inter- vs. intrasessional), (b) recording duration (7.3 vs. 3.6 min), (c) trace type (hexagon traces vs. ring averages), and (d) amplitude definition (peak-trough analysis vs. scalar product) on RCV. RCV was 6.5+/-0.4% (Mean+/-SEM, n=96) when averaged across all recording conditions and all subjects. The ANOVA showed a significant difference ( p=0.018) between hexagon traces and ring averages. Another significant effect ( p=0.016) occurred for the interaction of (a) and (b). MfERGs can be recorded with a high degree of reproducibility even for short recording durations and single hexagon traces. As the factor (a) did not show a significant effect, the new placement of the DTL electrode in the second session does not necessarily increase the retest variability compared to a second recording within the same session.

Recent climate variability and its impacts on soybean yields in Southern Brazil

NASA Astrophysics Data System (ADS)

Ferreira, Danielle Barros; Rao, V. Brahmananda

2011-08-01

Recent climate variability in rainfall, temperatures (maximum and minimum), and the diurnal temperature range is studied with emphasis on its influence over soybean yields in southern Brazil, during 1969 to 2002. The results showed that the soybean ( Glycine max L. Merril) yields are more affected by changes in temperature during summer, while changes in rainfall are more important during the beginning of plantation and at its peak of development. Furthermore, soybean yields in Paraná are more sensitive to rainfall variations, while soybean yields in the Rio Grande do Sul are more sensitive to variations in temperature. Effects of interannual climatic variability on soybean yields are evaluated through three agro-meteorological models: additive Stewart, multiplicative Rao, and multiplicative Jensen. The Jensen model is able to reproduce the interannual behavior of soybean yield reasonably well.

Molecular dynamics simulations with electronic stopping can reproduce experimental sputtering yields of metals impacted by large cluster ions

NASA Astrophysics Data System (ADS)

Tian, Jiting; Zhou, Wei; Feng, Qijie; Zheng, Jian

2018-03-01

An unsolved problem in research of sputtering from metals induced by energetic large cluster ions is that molecular dynamics (MD) simulations often produce sputtering yields much higher than experimental results. Different from the previous simulations considering only elastic atomic interactions (nuclear stopping), here we incorporate inelastic electrons-atoms interactions (electronic stopping, ES) into MD simulations using a friction model. In this way we have simulated continuous 45° impacts of 10-20 keV C60 on a Ag(111) surface, and found that the calculated sputtering yields can be very close to the experimental results when the model parameter is appropriately assigned. Conversely, when we ignore the effect of ES, the yields are much higher, just like the previous studies. We further expand our research to the sputtering of Au induced by continuous keV C60 or Ar100 bombardments, and obtain quite similar results. Our study indicates that the gap between the experimental and the simulated sputtering yields is probably induced by the ignorance of ES in the simulations, and that a careful treatment of this issue is important for simulations of cluster-ion-induced sputtering, especially for those aiming to compare with experiments.

Paper-based microfluidic approach for surface-enhanced raman spectroscopy and highly reproducible detection of proteins beyond picomolar concentration.

PubMed

Saha, Arindam; Jana, Nikhil R

2015-01-14

Although microfluidic approach is widely used in various point of care diagnostics, its implementation in surface enhanced Raman spectroscopy (SERS)-based detection is challenging. This is because SERS signal depends on plasmonic nanoparticle aggregation induced generation of stable electromagnetic hot spots and in currently available microfluidic platform this condition is difficult to adapt. Here we show that SERS can be adapted using simple paper based microfluidic system where both the plasmonic nanomaterials and analyte are used in mobile phase. This approach allows analyte induced controlled particle aggregation and electromagnetic hot spot generation inside the microfluidic channel with the resultant SERS signal, which is highly reproducible and sensitive. This approach has been used for reproducible detection of protein in the pico to femtomolar concentration. Presented approach is simple, rapid, and cost-effective, and requires low sample volume. Method can be extended for SERS-based detection of other biomolecules.

High Titer and Yields Achieved with Novel, Low-Severity Pretreatment Strategy

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

NREL researchers obtained high concentration sugar syrups in enzymatic hydrolysis that are fermentable to ethanol and other advanced biofuels and intermediate products at high yields. The novel DMR process is simpler and bypasses all severe pretreatment methods, thus reducing the environmental impact. The results are unprecedented. Researchers achieved a high concentration of sugars (230g/L of monomeric sugar and 270 g/L total sugar) and this low toxicity, highly fermentable syrup yielded 86 g/L ethanol (> 90 percent conversion). In addition, the lignin streams from this process can readily be converted to jet or renewable diesel blendstocks through a hydrodeoxygenation step. Themore » NREL-developed, low severity DMR process may potentially replace higher severity chemical pretreatments and associated expensive reactors constructed of exotic alloys with a simpler process, using commercial-scale equipment commonly associated with the pulp and paper industry, to produce high concentration, low toxicity sugar streams and highly reactive lignin streams from non-food renewable biomass for biological and catalytic upgrading to advanced biofuels and chemicals. The simpler DMR process with black liquor recycling could reduce environmental and life-cycle impacts, and repurpose shuttered pulp and paper mills to help revitalize rural economies.« less

SiGe epitaxial memory for neuromorphic computing with reproducible high performance based on engineered dislocations

NASA Astrophysics Data System (ADS)

Choi, Shinhyun; Tan, Scott H.; Li, Zefan; Kim, Yunjo; Choi, Chanyeol; Chen, Pai-Yu; Yeon, Hanwool; Yu, Shimeng; Kim, Jeehwan

2018-01-01

Although several types of architecture combining memory cells and transistors have been used to demonstrate artificial synaptic arrays, they usually present limited scalability and high power consumption. Transistor-free analog switching devices may overcome these limitations, yet the typical switching process they rely on—formation of filaments in an amorphous medium—is not easily controlled and hence hampers the spatial and temporal reproducibility of the performance. Here, we demonstrate analog resistive switching devices that possess desired characteristics for neuromorphic computing networks with minimal performance variations using a single-crystalline SiGe layer epitaxially grown on Si as a switching medium. Such epitaxial random access memories utilize threading dislocations in SiGe to confine metal filaments in a defined, one-dimensional channel. This confinement results in drastically enhanced switching uniformity and long retention/high endurance with a high analog on/off ratio. Simulations using the MNIST handwritten recognition data set prove that epitaxial random access memories can operate with an online learning accuracy of 95.1%.

Bright conjugated polymer nanoparticles containing a biodegradable shell produced at high yields and with tuneable optical properties by a scalable microfluidic device.

PubMed

Abelha, T F; Phillips, T W; Bannock, J H; Nightingale, A M; Dreiss, C A; Kemal, E; Urbano, L; deMello, J C; Green, M; Dailey, L A

2017-02-02

This study compares the performance of a microfluidic technique and a conventional bulk method to manufacture conjugated polymer nanoparticles (CPNs) embedded within a biodegradable poly(ethylene glycol) methyl ether-block-poly(lactide-co-glycolide) (PEG 5K -PLGA 55K ) matrix. The influence of PEG 5K -PLGA 55K and conjugated polymers cyano-substituted poly(p-phenylene vinylene) (CN-PPV) and poly(9,9-dioctylfluorene-2,1,3-benzothiadiazole) (F8BT) on the physicochemical properties of the CPNs was also evaluated. Both techniques enabled CPN production with high end product yields (∼70-95%). However, while the bulk technique (solvent displacement) under optimal conditions generated small nanoparticles (∼70-100 nm) with similar optical properties (quantum yields ∼35%), the microfluidic approach produced larger CPNs (140-260 nm) with significantly superior quantum yields (49-55%) and tailored emission spectra. CPNs containing CN-PPV showed smaller size distributions and tuneable emission spectra compared to F8BT systems prepared under the same conditions. The presence of PEG 5K -PLGA 55K did not affect the size or optical properties of the CPNs and provided a neutral net electric charge as is often required for biomedical applications. The microfluidics flow-based device was successfully used for the continuous preparation of CPNs over a 24 hour period. On the basis of the results presented here, it can be concluded that the microfluidic device used in this study can be used to optimize the production of bright CPNs with tailored properties with good reproducibility.

High-Yield Synthesis and Applications of Anisotropic Gold Nanoparticles

NASA Astrophysics Data System (ADS)

Vigderman, Leonid

This work will describe research directed towards the synthesis of anisotropic gold nanoparticles as well as their functionalization and biological applications. The thesis will begin by describing a new technique for the high-yield synthesis of gold nanorods using hydroquinone as a reducing agent. This addresses important limitations of the traditional nanorod synthesis including low yield of gold ions conversion to metallic form and inability to produce rods with longitudinal surface plasmon peak above 850 nm. The use of hydroquinone was also found to improve the synthesis of gold nanowires via the nanorod-seed mediated procedure developed in our lab. The thesis will next present the synthesis of novel starfruitshaped nanorods, mesorods, and nanowires using a modified nanorod-seed mediated procedure. The starfruit particles displayed increased activity as surfaceenhanced Raman spectroscopy (SERS) substrates as compared to smooth structures. Next, a method for the functionalization of gold nanorods using a cationic thiol, 16-mercaptohexadecyltrimethylammonium bromide (MTAB), will be described. By using this thiol, we were able to demonstrate the complete removal of toxic surfactant from the nanorods and were also able to precisely quantify the grafting density of thiol molecules on the nanorod surface through a combination of several analytical techniques. Finally, this thesis will show that MTABfunctionalized nanorods are nontoxic and can be taken up in extremely high numbers into cancer cells. The thesis will conclude by describing the surprising uptake of larger mesorods and nanowires functionalized with MTAB into cells in high quantities.

Reproducibility2020: Progress and priorities

PubMed Central

Freedman, Leonard P.; Venugopalan, Gautham; Wisman, Rosann

2017-01-01

The preclinical research process is a cycle of idea generation, experimentation, and reporting of results. The biomedical research community relies on the reproducibility of published discoveries to create new lines of research and to translate research findings into therapeutic applications. Since 2012, when scientists from Amgen reported that they were able to reproduce only 6 of 53 “landmark” preclinical studies, the biomedical research community began discussing the scale of the reproducibility problem and developing initiatives to address critical challenges. Global Biological Standards Institute (GBSI) released the “Case for Standards” in 2013, one of the first comprehensive reports to address the rising concern of irreproducible biomedical research. Further attention was drawn to issues that limit scientific self-correction, including reporting and publication bias, underpowered studies, lack of open access to methods and data, and lack of clearly defined standards and guidelines in areas such as reagent validation. To evaluate the progress made towards reproducibility since 2013, GBSI identified and examined initiatives designed to advance quality and reproducibility. Through this process, we identified key roles for funders, journals, researchers and other stakeholders and recommended actions for future progress. This paper describes our findings and conclusions. PMID:28620458

Development of high-yield influenza B virus vaccine viruses

PubMed Central

Ping, Jihui; Lopes, Tiago J. S.; Neumann, Gabriele; Kawaoka, Yoshihiro

2016-01-01

The burden of human infections with influenza A and B viruses is substantial, and the impact of influenza B virus infections can exceed that of influenza A virus infections in some seasons. Over the past few decades, viruses of two influenza B virus lineages (Victoria and Yamagata) have circulated in humans, and both lineages are now represented in influenza vaccines, as recommended by the World Health Organization. Influenza B virus vaccines for humans have been available for more than half a century, yet no systematic efforts have been undertaken to develop high-yield candidates. Therefore, we screened virus libraries possessing random mutations in the six “internal” influenza B viral RNA segments [i.e., those not encoding the major viral antigens, hemagglutinin (HA) and neuraminidase NA)] for mutants that confer efficient replication. Candidate viruses that supported high yield in cell culture were tested with the HA and NA genes of eight different viruses of the Victoria and Yamagata lineages. We identified combinations of mutations that increased the titers of candidate vaccine viruses in mammalian cells used for human influenza vaccine virus propagation and in embryonated chicken eggs, the most common propagation system for influenza viruses. These influenza B virus vaccine backbones can be used for improved vaccine virus production. PMID:27930325

Development of high-yield influenza B virus vaccine viruses.

PubMed

Ping, Jihui; Lopes, Tiago J S; Neumann, Gabriele; Kawaoka, Yoshihiro

2016-12-20

The burden of human infections with influenza A and B viruses is substantial, and the impact of influenza B virus infections can exceed that of influenza A virus infections in some seasons. Over the past few decades, viruses of two influenza B virus lineages (Victoria and Yamagata) have circulated in humans, and both lineages are now represented in influenza vaccines, as recommended by the World Health Organization. Influenza B virus vaccines for humans have been available for more than half a century, yet no systematic efforts have been undertaken to develop high-yield candidates. Therefore, we screened virus libraries possessing random mutations in the six "internal" influenza B viral RNA segments [i.e., those not encoding the major viral antigens, hemagglutinin (HA) and neuraminidase NA)] for mutants that confer efficient replication. Candidate viruses that supported high yield in cell culture were tested with the HA and NA genes of eight different viruses of the Victoria and Yamagata lineages. We identified combinations of mutations that increased the titers of candidate vaccine viruses in mammalian cells used for human influenza vaccine virus propagation and in embryonated chicken eggs, the most common propagation system for influenza viruses. These influenza B virus vaccine backbones can be used for improved vaccine virus production.

ITK: enabling reproducible research and open science

PubMed Central

McCormick, Matthew; Liu, Xiaoxiao; Jomier, Julien; Marion, Charles; Ibanez, Luis

2014-01-01

Reproducibility verification is essential to the practice of the scientific method. Researchers report their findings, which are strengthened as other independent groups in the scientific community share similar outcomes. In the many scientific fields where software has become a fundamental tool for capturing and analyzing data, this requirement of reproducibility implies that reliable and comprehensive software platforms and tools should be made available to the scientific community. The tools will empower them and the public to verify, through practice, the reproducibility of observations that are reported in the scientific literature. Medical image analysis is one of the fields in which the use of computational resources, both software and hardware, are an essential platform for performing experimental work. In this arena, the introduction of the Insight Toolkit (ITK) in 1999 has transformed the field and facilitates its progress by accelerating the rate at which algorithmic implementations are developed, tested, disseminated and improved. By building on the efficiency and quality of open source methodologies, ITK has provided the medical image community with an effective platform on which to build a daily workflow that incorporates the true scientific practices of reproducibility verification. This article describes the multiple tools, methodologies, and practices that the ITK community has adopted, refined, and followed during the past decade, in order to become one of the research communities with the most modern reproducibility verification infrastructure. For example, 207 contributors have created over 2400 unit tests that provide over 84% code line test coverage. The Insight Journal, an open publication journal associated with the toolkit, has seen over 360,000 publication downloads. The median normalized closeness centrality, a measure of knowledge flow, resulting from the distributed peer code review system was high, 0.46. PMID:24600387

ITK: enabling reproducible research and open science.

PubMed

McCormick, Matthew; Liu, Xiaoxiao; Jomier, Julien; Marion, Charles; Ibanez, Luis

2014-01-01

Reproducibility verification is essential to the practice of the scientific method. Researchers report their findings, which are strengthened as other independent groups in the scientific community share similar outcomes. In the many scientific fields where software has become a fundamental tool for capturing and analyzing data, this requirement of reproducibility implies that reliable and comprehensive software platforms and tools should be made available to the scientific community. The tools will empower them and the public to verify, through practice, the reproducibility of observations that are reported in the scientific literature. Medical image analysis is one of the fields in which the use of computational resources, both software and hardware, are an essential platform for performing experimental work. In this arena, the introduction of the Insight Toolkit (ITK) in 1999 has transformed the field and facilitates its progress by accelerating the rate at which algorithmic implementations are developed, tested, disseminated and improved. By building on the efficiency and quality of open source methodologies, ITK has provided the medical image community with an effective platform on which to build a daily workflow that incorporates the true scientific practices of reproducibility verification. This article describes the multiple tools, methodologies, and practices that the ITK community has adopted, refined, and followed during the past decade, in order to become one of the research communities with the most modern reproducibility verification infrastructure. For example, 207 contributors have created over 2400 unit tests that provide over 84% code line test coverage. The Insight Journal, an open publication journal associated with the toolkit, has seen over 360,000 publication downloads. The median normalized closeness centrality, a measure of knowledge flow, resulting from the distributed peer code review system was high, 0.46.

Exhaled breath temperature in children: reproducibility and influencing factors.

PubMed

Vermeulen, S; Barreto, M; La Penna, F; Prete, A; Martella, S; Biagiarelli, F; Villa, M P

2014-09-01

This study will investigate the reproducibility and influencing factors of exhaled breath temperature measured with the tidal breathing technique in asthmatic patients and healthy children. Exhaled breath temperature, fractional exhaled nitric oxide, and spirometry were assessed in 124 children (63 healthy and 61 asthmatic), aged 11.2 ± 2.5 year, M/F 73/51. A modified version of the American Thoracic Society questionnaire on the child's present and past respiratory history was obtained from parents. Parents were also asked to provide detailed information on their child's medication use during the previous 4 weeks. Ear temperature, ambient temperature, and relative-ambient humidity were also recorded. Exhaled breath temperature measurements were highly reproducible; the second measurement was higher than the first measurement, consistent with a test-retest situation. In 13 subjects, between-session within-day reproducibility of exhaled breath temperature was still high. Exhaled breath temperature increased with age and relative-ambient humidity. Exhaled breath temperature was comparable in healthy and asthmatic children; when adjusted for potential confounders (i.e. ambient conditions and subject characteristics), thermal values of asthmatic patients exceeded those of the healthy children by 1.1 °C. Normalized exhaled breath temperature, by subtracting ambient temperature, was lower in asthmatic patients treated with inhaled corticosteroids than in those who were corticosteroid-naive. Measurements of exhaled breath temperature are highly reproducible, yet influenced by several factors. Corrected values, i.e. normalized exhaled breath temperature, could help us to assess the effect of therapy with inhaled corticosteroids. More studies are needed to improve the usefulness of the exhaled breath temperature measured with the tidal breathing technique in children.

High Photoluminescence Quantum Yield in Band Gap Tunable Bromide Containing Mixed Halide Perovskites.

PubMed

Sutter-Fella, Carolin M; Li, Yanbo; Amani, Matin; Ager, Joel W; Toma, Francesca M; Yablonovitch, Eli; Sharp, Ian D; Javey, Ali

2016-01-13

Hybrid organic-inorganic halide perovskite based semiconductor materials are attractive for use in a wide range of optoelectronic devices because they combine the advantages of suitable optoelectronic attributes and simultaneously low-cost solution processability. Here, we present a two-step low-pressure vapor-assisted solution process to grow high quality homogeneous CH3NH3PbI3-xBrx perovskite films over the full band gap range of 1.6-2.3 eV. Photoluminescence light-in versus light-out characterization techniques are used to provide new insights into the optoelectronic properties of Br-containing hybrid organic-inorganic perovskites as a function of optical carrier injection by employing pump-powers over a 6 orders of magnitude dynamic range. The internal luminescence quantum yield of wide band gap perovskites reaches impressive values up to 30%. This high quantum yield translates into substantial quasi-Fermi level splitting and high "luminescence or optically implied" open-circuit voltage. Most importantly, both attributes, high internal quantum yield and high optically implied open-circuit voltage, are demonstrated over the entire band gap range (1.6 eV ≤ Eg ≤ 2.3 eV). These results establish the versatility of Br-containing perovskite semiconductors for a variety of applications and especially for the use as high-quality top cell in tandem photovoltaic devices in combination with industry dominant Si bottom cells.

PCR amplification of up to 35-kb DNA with high fidelity and high yield from lambda bacteriophage templates.

PubMed Central

Barnes, W M

1994-01-01

A target length limitation to PCR amplification of DNA has been identified and addressed. Concomitantly, the base-pair fidelity, the ability to use PCR products as primers, and the maximum yield of target fragment were increased. These improvements were achieved by the combination of a high level of an exonuclease-free, N-terminal deletion mutant of Taq DNA polymerase, Klentaq1, with a very low level of a thermostable DNA polymerase exhibiting a 3'-exonuclease activity (Pfu, Vent, or Deep Vent). At least 35 kb can be amplified to high yields from 1 ng of lambda DNA template. Images PMID:8134376

A highly reproducible quantitative viral outgrowth assay for the measurement of the replication-competent latent HIV-1 reservoir.

PubMed

Fun, Axel; Mok, Hoi Ping; Wills, Mark R; Lever, Andrew M

2017-02-24

Cure of Human Immunodeficiency Virus (HIV) infection remains elusive due to the persistence of HIV in a latent reservoir. Strategies to eradicate latent infection can only be evaluated with robust, sensitive and specific assays to quantitate reactivatable latent virus. We have taken the standard peripheral blood mononuclear cell (PBMC) based viral outgrowth methodology and from it created a logistically simpler and more highly reproducible assay to quantify replication-competent latent HIV in resting CD4 + T cells, both increasing accuracy and decreasing cost and labour. Purification of resting CD4 + T cells from whole PBMC is expedited and achieved in 3 hours, less than half the time of conventional protocols. Our indicator cell line, SupT1-CCR5 cells (a clonal cell line expressing CD4, CXCR4 and CCR5) provides a readily available standardised readout. Reproducibility compares favourably to other published assays but with reduced cost, labour and assay heterogeneity without compromising sensitivity.

A novel highly reproducible and lethal nonhuman primate model for orthopox virus infection.

PubMed

Kramski, Marit; Mätz-Rensing, Kerstin; Stahl-Hennig, Christiane; Kaup, Franz-Josef; Nitsche, Andreas; Pauli, Georg; Ellerbrok, Heinz

2010-04-29

The intentional re-introduction of Variola virus (VARV), the agent of smallpox, into the human population is of great concern due its bio-terroristic potential. Moreover, zoonotic infections with Cowpox (CPXV) and Monkeypox virus (MPXV) cause severe diseases in humans. Smallpox vaccines presently available can have severe adverse effects that are no longer acceptable. The efficacy and safety of new vaccines and antiviral drugs for use in humans can only be demonstrated in animal models. The existing nonhuman primate models, using VARV and MPXV, need very high viral doses that have to be applied intravenously or intratracheally to induce a lethal infection in macaques. To overcome these drawbacks, the infectivity and pathogenicity of a particular CPXV was evaluated in the common marmoset (Callithrix jacchus).A CPXV named calpox virus was isolated from a lethal orthopox virus (OPV) outbreak in New World monkeys. We demonstrated that marmosets infected with calpox virus, not only via the intravenous but also the intranasal route, reproducibly develop symptoms resembling smallpox in humans. Infected animals died within 1-3 days after onset of symptoms, even when very low infectious viral doses of 5x10(2) pfu were applied intranasally. Infectious virus was demonstrated in blood, saliva and all organs analyzed.We present the first characterization of a new OPV infection model inducing a disease in common marmosets comparable to smallpox in humans. Intranasal virus inoculation mimicking the natural route of smallpox infection led to reproducible infection. In vivo titration resulted in an MID(50) (minimal monkey infectious dose 50%) of 8.3x10(2) pfu of calpox virus which is approximately 10,000-fold lower than MPXV and VARV doses applied in the macaque models. Therefore, the calpox virus/marmoset model is a suitable nonhuman primate model for the validation of vaccines and antiviral drugs. Furthermore, this model can help study mechanisms of OPV pathogenesis.

Secondary electron emission yield from high aspect ratio carbon velvet surfaces

NASA Astrophysics Data System (ADS)

Jin, Chenggang; Ottaviano, Angelica; Raitses, Yevgeny

2017-11-01

The plasma electrons bombarding a plasma-facing wall surface can induce secondary electron emission (SEE) from the wall. A strong SEE can enhance the power losses by reducing the wall sheath potential and thereby increasing the electron flux from the plasma to the wall. The use of the materials with surface roughness and the engineered materials with surface architecture is known to reduce the effective SEE by trapping the secondary electrons. In this work, we demonstrate a 65% reduction of SEE yield using a velvet material consisting of high aspect ratio carbon fibers. The measurements of SEE yield for different velvet samples using the electron beam in vacuum demonstrate the dependence of the SEE yield on the fiber length and the packing density, which is strongly affected by the alignment of long velvet fibers with respect to the electron beam impinging on the velvet sample. The results of SEE measurements support the previous observations of the reduced SEE measured in Hall thrusters.

Enriched reproducing kernel particle method for fractional advection-diffusion equation

NASA Astrophysics Data System (ADS)

Ying, Yuping; Lian, Yanping; Tang, Shaoqiang; Liu, Wing Kam

2018-06-01

The reproducing kernel particle method (RKPM) has been efficiently applied to problems with large deformations, high gradients and high modal density. In this paper, it is extended to solve a nonlocal problem modeled by a fractional advection-diffusion equation (FADE), which exhibits a boundary layer with low regularity. We formulate this method on a moving least-square approach. Via the enrichment of fractional-order power functions to the traditional integer-order basis for RKPM, leading terms of the solution to the FADE can be exactly reproduced, which guarantees a good approximation to the boundary layer. Numerical tests are performed to verify the proposed approach.

Associated strangeness production in the pp{yields}pK{sup +}K{sup -}p and pp{yields}pK{sup +{pi}0{Sigma}0} reactions

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

Xie Jujun; Department of Physics, Zhengzhou University, Zhengzhou, Henan 450001; Wilkin, Colin

2010-08-15

The total and differential cross sections for associated strangeness production in the pp{yields}pK{sup +}K{sup -}p and pp{yields}pK{sup +{pi}0{Sigma}0} reactions have been studied in a unified approach using an effective Lagrangian model. It is assumed that both the K{sup -}p and {pi}{sup 0{Sigma}0} final states originate from the decay of the {Lambda}(1405) that was formed in the production chain pp{yields}p(N*(1535){yields}K{sup +{Lambda}}(1405)). The available experimental data are well reproduced, especially the ratio of the two total cross sections, which is much less sensitive to the particular model of the entrance channel. The significant coupling of the N*(1535) to {Lambda}(1405)K is further evidencemore » for large ss-bar components in the quark wave function of the N*(1535).« less

Development of High Yield Feedstocks and Biomass Conversion Technology for Renewable Energy

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

Hashimoto, Andrew G.; Crow, Susan; DeBeryshe, Barbara

2015-04-09

This project had two main goals. The first goal was to evaluate several high yielding tropical perennial grasses as feedstock for biofuel production, and to characterize the feedstock for compatible biofuel production systems. The second goal was to assess the integration of renewable energy systems for Hawaii. The project focused on high-yield grasses (napiergrass, energycane, sweet sorghum, and sugarcane). Field plots were established to evaluate the effects of elevation (30, 300 and 900 meters above sea level) and irrigation (50%, 75% and 100% of sugarcane plantation practice) on energy crop yields and input. The test plots were extensive monitored including:more » hydrologic studies to measure crop water use and losses through seepage and evapotranspiration; changes in soil carbon stock; greenhouse gas flux (CO 2, CH 4, and N 2O) from the soil surface; and root morphology, biomass, and turnover. Results showed significant effects of environment on crop yields. In general, crop yields decrease as the elevation increased, being more pronounced for sweet sorghum and energycane than napiergrass. Also energy crop yields were higher with increased irrigation levels, being most pronounced with energycane and less so with sweet sorghum. Daylight length greatly affected sweet sorghum growth and yields. One of the energy crops (napiergrass) was harvested at different ages (2, 4, 6, and 8 months) to assess the changes in feedstock characteristics with age and potential to generate co-products. Although there was greater potential for co-products from younger feedstock, the increased production was not sufficient to offset the additional cost of harvesting multiple times per year. The feedstocks were also characterized to assess their compatibility with biochemical and thermochemical conversion processes. The project objectives are being continued through additional support from the Office of Naval Research, and the Biomass Research and Development Initiative. Renewable

High Photoluminescence Quantum Yield in Band Gap Tunable Bromide Containing Mixed Halide Perovskites

DOE PAGES

Sutter-Fella, Carolin M.; Li, Yanbo; Amani, Matin; ...

2015-12-21

Hybrid organic-inorganic halide perovskite based semiconductor materials are attractive for use in a wide range of optoelectronic devices because they combine the advantages of suitable optoelectronic attributes and simultaneously low-cost solution processability. Here, we present a two-step low-pressure vapor-assisted solution process to grow high quality homogeneous CH 3NH 3PbI 3-xBr x perovskite films over the full band gap range of 1.6-2.3 eV. Photoluminescence light-in versus light-out characterization techniques are used to provide new insights into the optoelectronic properties of Br-containing hybrid organic-inorganic perovskites as a function of optical carrier injection by employing pump-powers over a 6 orders of magnitude dynamicmore » range. The internal luminescence quantum yield of wide band gap perovskites reaches impressive values up to 30%. This high quantum yield translates into substantial quasi-Fermi level splitting and high "luminescence or optically implied" open-circuit voltage. Most importantly, both attributes, high internal quantum yield and high optically implied open-circuit voltage, are demonstrated over the entire band gap range (1.6 eV ≤ E g ≤ 2.3 eV). These results establish the versatility of Br-containing perovskite semiconductors for a variety of applications and especially for the use as high-quality top cell in tandem photovoltaic devices in combination with industry dominant Si bottom cells. (Figure Presented).« less

The Road to Reproducibility in Animal Research.

PubMed

Jilka, Robert L

2016-07-01

Reproducibility of research findings is the hallmark of scientific advance. However, the recently noted lack of reproducibility and transparency of published research using animal models of human biology and disease has alarmed funders, scientists, and the public. Improved reporting of methodology and better use of statistical tools are needed to enhance the quality and utility of published research. Reporting guidelines like Animal Research: Reporting In Vivo Experiments (ARRIVE) have been devised to achieve these goals, but most biomedical research journals, including the JBMR, have not been able to obtain high compliance. Cooperative efforts among authors, reviewers and editors-empowered by increased awareness of their responsibilities, and enabled by user-friendly guidelines-are needed to solve this problem. © 2016 American Society for Bone and Mineral Research. © 2016 American Society for Bone and Mineral Research.

Trade-offs between high yields and greenhouse gas emissions in irrigation wheat cropland in China

NASA Astrophysics Data System (ADS)

Cui, Z. L.; Wu, L.; Ye, Y. L.; Ma, W. Q.; Chen, X. P.; Zhang, F. S.

2014-04-01

Although the concept of producing higher yields with reduced greenhouse gas (GHG) emissions is a goal that attracts increasing public and scientific attention, the trade-off between high yields and GHG emissions in intensive agricultural production is not well understood. Here, we hypothesize that there exists a mechanistic relationship between wheat grain yield and GHG emission, and that could be transformed into better agronomic management. A total 33 sites of on-farm experiments were investigated to evaluate the relationship between grain yield and GHG emissions using two systems (conventional practice, CP; high-yielding systems, HY) of intensive winter wheat (Triticum aestivum L.) in China. Furthermore, we discussed the potential to produce higher yields with lower GHG emissions based on a survey of 2938 farmers. Compared to the CP system, grain yield was 39% (2352 kg ha-1) higher in the HY system, while GHG emissions increased by only 10%, and GHG emission intensity was reduced by 21%. The current intensive winter wheat system with farmers' practice had a median yield and maximum GHG emission rate of 6050 kg ha-1 and 4783 kg CO2 eq ha-1, respectively; however, this system can be transformed to maintain yields while reducing GHG emissions by 26% (6077 kg ha-1, and 3555 kg CO2 eq ha-1). Further, the HY system was found to increase grain yield by 39% with a simultaneous reduction in GHG emissions by 18% (8429 kg ha-1, and 3905 kg CO2 eq ha-1, respectively). In the future, we suggest moving the trade-off relationships and calculations from grain yield and GHG emissions to new measures of productivity and environmental protection using innovative management technologies.

Variable sensitivity of US maize yield to high temperatures across developmental stages

NASA Astrophysics Data System (ADS)

Butler, E. E.; Huybers, P. J.

2013-12-01

The sensitivity of maize to high temperatures has been widely demonstrated. Furthermore, field work has indicated that reproductive development stages are particularly sensitive to stress, but this relationship has not been quantified across a wide geographic region. Here, the relationship between maize yield and temperature variations is examined as a function of developmental stage. US state-level data from the National Agriculture Statistics Service provide dates for six growing stages: planting, silking, doughing, dented, mature, and harvested. Temperatures that correspond to each developmental stage are then inferred from a network of weather station observations interpolated to the county level, and a multiple linear regression technique is employed to estimate the sensitivity of county yield outcomes to variations in growing-degree days and an analogous measure of high temperatures referred to as killing-degree days. Uncertainties in the transition times between county-level growth stages are accounted for. Results indicate that the silking and dented stages are generally the most sensitive to killing degree days, with silking the most sensitive stage in the US South and dented the most sensitive in the US North. These variable patterns of sensitivity aid in interpreting which weather events are of greatest significance to maize yields and provide some insight into how shifts in planting time or changes in developmental timing would influence the risks associated with exposure to high temperatures.

Role of the N*(1535) in pp{yields}pp{phi} and {pi}{sup -}p{yields}n{phi} reactions

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

Xie Jujun; Graduate University of Chinese Academy of Sciences, Beijing 100049; Zou Bingsong

2008-01-15

The near-threshold {phi}-meson production in proton-proton and {pi}{sup -}p collisions is studied with the assumption that the production mechanism is due to the sub-N{phi}-threshold N*(1535) resonance. The {pi}{sup 0}-,{eta}-, and {rho}{sup 0}-meson exchanges for proton-proton collisions are considered. It is shown that the contribution to the pp{yields}pp{phi} reaction from the t-channel {pi}{sup 0}-meson exchange is dominant. With a significant N*(1535)N{phi} coupling [g{sub N*(1535)N{phi}}{sup 2}/4{pi}=0.13], both pp{yields}pp{phi} and {pi}{sup -}p{yields}n{phi} data are very well reproduced. The significant coupling of the N*(1535) resonance to N{phi} is compatible with previous indications of a large ss component in the quark wave function of themore » N*(1535) resonance and may be the real origin of the significant enhancement of the {phi} production over the naive OZI-rule predictions.« less

Extractive Fermentation of Sugarcane Juice to Produce High Yield and Productivity of Bioethanol

NASA Astrophysics Data System (ADS)

Rofiqah, U.; Widjaja, T.; Altway, A.; Bramantyo, A.

2017-04-01

Ethanol production by batch fermentation requires a simple process and it is widely used. Batch fermentation produces ethanol with low yield and productivity due to the accumulation of ethanol in which poisons microorganisms in the fermenter. Extractive fermentation technique is applied to solve the microorganism inhibition problem by ethanol. Extractive fermentation technique can produce ethanol with high yield and productivity. In this process raffinate still, contains much sugar because conversion in the fermentation process is not perfect. Thus, to enhance ethanol yield and productivity, recycle system is applied by returning the raffinate from the extraction process to the fermentation process. This raffinate also contains ethanol which would inhibit the performance of microorganisms in producing ethanol during the fermentation process. Therefore, this study aims to find the optimum condition for the amount of solvent to broth ratio (S: B) and recycle to fresh feed ratio (R: F) which enter the fermenter to produce high yield and productivity. This research was carried out by experiment. In the experiment, sugarcane juice was fermented using Zymomonasmobilis mutant. The fermentation broth was extracted using amyl alcohol. The process was integrated with the recycle system by varying the recycle ratio. The highest yield and productivity is 22.3901% and 103.115 g / L.h respectively, obtained in a process that uses recycle to fresh feed ratio (R: F) of 50:50 and solvents to both ratio of 1.

Facile high-yield synthesis of polyaniline nanosticks with intrinsic stability and electrical conductivity.

PubMed

Li, Xin-Gui; Li, Ang; Huang, Mei-Rong

2008-01-01

Chemical oxidative polymerization at 15 degrees C was used for the simple and productive synthesis of polyaniline (PAN) nanosticks. The effect of polymerization media on the yield, size, stability, and electrical conductivity of the PAN nanosticks was studied by changing the concentration and nature of the acid medium and oxidant and by introducing organic solvent. Molecular and supramolecular structure, size, and size distribution of the PAN nanosticks were characterized by UV/Vis and IR spectroscopy, X-ray diffraction, laser particle-size analysis, and transmission electron microscopy. Introduction of organic solvent is advantageous for enhancing the yield of PAN nanosticks but disadvantageous for formation of PAN nanosticks with small size and high conductivity. The concentration and nature of the acid medium have a major influence on the polymerization yield and conductivity of the nanosized PAN. The average diameter and length of PAN nanosticks produced with 2 M HNO(3) and 0.5 M H(2)SO(4) as acid media are about 40 and 300 nm, respectively. The PAN nanosticks obtained in an optimal medium (i.e., 2 M HNO(3)) exhibit the highest conductivity of 2.23 S cm(-1) and the highest yield of 80.7 %. A mechanism of formation of nanosticks instead of nanoparticles is proposed. Nanocomposite films of the PAN nanosticks with poly(vinyl alcohol) show a low percolation threshold of 0.2 wt %, at which the film retains almost the same transparency and strength as pure poly(vinyl alcohol) but 262 000 times the conductivity of pure poly(vinyl alcohol) film. The present synthesis of PAN nanosticks requires no external stabilizer and provides a facile and direct route for fabrication of PAN nanosticks with high yield, controllable size, intrinsic self-stability, strong redispersibility, high purity, and optimizable conductivity.

Usability and reproducibility of tear meniscus values generated via swept-source optical coherence tomography and the slit lamp with a graticule method.

PubMed

Imamura, Hitoshi; Tabuchi, Hitoshi; Nakakura, Shunsuke; Nagasato, Daisuke; Baba, Hiroaki; Kiuchi, Yoshiaki

2018-04-01

To investigate the usability and the reproducibility of the tear meniscus values via swept-source optical coherence tomography (SS-OCT) and the conventional slit lamp microscope method with a graticule. The right eye was examined in 90 healthy adult subjects who were grouped according to age (group 1: 20-39 years; group 2: 40-59 years; group 3: ≥60 years). The tear meniscus height (TMH) and tear meniscus area were measured using SS-OCT and TMH by the slit lamp microscope method. The reproducibility of each method was calculated using intraclass correlation coefficients (ICCs) in additionally enrolled 30 healthy young subjects. We also evaluated TMH at 3 mm from the corneal center in both temporal and nasal directions using SS-OCT. The mean of the TMH values measured by SS-OCT was significantly higher than those measured by the slit lamp method (328 vs. 212 μm, P < 0.001, respectively). High reproducibility was observed for each method (ICC > 0.75 for both). No statistically significant differences were found in TMH among the age groups using both SS-OCT and slit lamp methods (P = 0.985, 0.380, respectively). TMH values at both sides of the corneal center were significantly smaller than those at the corneal center (P < 0.0001). TMH values obtained by the slit lamp method were lower than those obtained by SS-OCT. However, both methods yielded highly reproducible TMH measurements, suggesting that they are clinically useful. Tear meniscus values did not vary by age but by measurement points in our cohort.

High-Yield Production of Levulinic Acid from Pretreated Cow Dung in Dilute Acid Aqueous Solution.

PubMed

Su, Jialei; Shen, Feng; Qiu, Mo; Qi, Xinhua

2017-02-14

Agricultural waste cow dung was used as feedstock for the production of a high value-added chemical levulinic acid (LA) in dilute acid aqueous solutions. A high LA yield of 338.9 g/kg was obtained from the pretreated cow dung, which was much higher than that obtained from the crude cow dung (135 g/kg), mainly attributed to the breakage of the lignin fraction in the lignocellulose structure of the cow dung by potassium hydroxide (KOH) pretreatment, and thus enhanced the accessibility of cow dung to the acid sites in the catalytic reaction. Meanwhile, another value-added chemical formic acid could be obtained with a yield of ca. 160 g/kg in the process, implying a total production of ca. 500 g/kg yield for LA and formic acid from the pretreated cow dung with the proposed process. The developed process was shown to be tolerant to high initial substrate loading with a satisfied LA yield. This work provides a promising strategy for the value-increment utilization of liglocellulosic agricultural residues.

Wafer scale fabrication of carbon nanotube thin film transistors with high yield

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

Tian, Boyuan; Liang, Xuelei, E-mail: liangxl@pku.edu.cn, E-mail: ssxie@iphy.ac.cn; Yan, Qiuping

Carbon nanotube thin film transistors (CNT-TFTs) are promising candidates for future high performance and low cost macro-electronics. However, most of the reported CNT-TFTs are fabricated in small quantities on a relatively small size substrate. The yield of large scale fabrication and the performance uniformity of devices on large size substrates should be improved before the CNT-TFTs reach real products. In this paper, 25 200 devices, with various geometries (channel width and channel length), were fabricated on 4-in. size ridged and flexible substrates. Almost 100% device yield were obtained on a rigid substrate with high out-put current (>8 μA/μm), high on/off current ratiomore » (>10{sup 5}), and high mobility (>30 cm{sup 2}/V·s). More importantly, uniform performance in 4-in. area was achieved, and the fabrication process can be scaled up. The results give us more confidence for the real application of the CNT-TFT technology in the near future.« less

Reproducible fabrication of stable small nano Pt with high activity for sensor applications.

PubMed

Ye, Pingping; Guo, Xiaoyu; Liu, Guiting; Chen, Huifen; Pan, Yuxia; Wen, Ying; Yang, Haifeng

2013-07-26

Pt nanoparticles with an average size of 2-3 nm in diameter were reproducibly synthesized by reduction of H₂PtCl₆ solution containing inositol hexaphosphate (IP₆) as the stabilizing agent. Single crystals with Pt(111) faces of the resulting cubic nanoparticles were revealed by the electron diffraction pattern. The PtNPs-IP₆ nanoparticles were used to modify an electrode as a nonenzymatic sensor for H₂O₂ detection, exhibiting a fast response and high sensitivity. A low detection limit of 2.0 × 10⁻⁷ M (S/N = 3) with two linear ranges between 2.4 × 10⁻⁷ and 1.3 × 10⁻³ M (R² = 0.9987) and between 1.3 × 10⁻³ and 1.3 × 10⁻² M (R² = 0.9980) was achieved. The attractive electrochemical performance of PtNPs-IP₆ enables it to be employed as a promising material for the development of Pt-based analytical systems and other applications.

Central Corneal Thickness Reproducibility among Ten Different Instruments.

PubMed

Pierro, Luisa; Iuliano, Lorenzo; Gagliardi, Marco; Ambrosi, Alessandro; Rama, Paolo; Bandello, Francesco

2016-11-01

To assess agreement between one ultrasonic (US) and nine optical instruments for the measurement of central corneal thickness (CCT), and to evaluate intra- and inter-operator reproducibility. In this observational cross-sectional study, two masked operators measured CCT thickness twice in 28 healthy eyes. We used seven spectral-domain optical coherence tomography (SD-OCT) devices, one time-domain OCT, one Scheimpflug camera, and one US-based instrument. Inter- and intra-operator reproducibility was evaluated by intraclass correlation coefficient (ICC), coefficient of variation (CV), and Bland-Altman test analysis. Instrument-to-instrument reproducibility was determined by ANOVA for repeated measurements. We also tested how the devices disagreed regarding systemic bias and random error using a structural equation model. Mean CCT of all instruments ranged from 536 ± 42 μm to 577 ± 40 μm. An instrument-to-instrument correlation test showed high values among the 10 investigated devices (correlation coefficient range 0.852-0.995; p values <0.0001 in all cases). The highest correlation coefficient values were registered between 3D OCT-2000 Topcon-Spectral OCT/SLO Opko (0.995) and Cirrus HD-OCT Zeiss-RS-3000 Nidek (0.995), whereas the lowest were seen between SS-1000 CASIA and Spectral OCT/SLO Opko (0.852). ICC and CV showed excellent inter- and intra-operator reproducibility for all optic-based devices, except for the US-based device. Bland-Altman analysis demonstrated low mean biases between operators. Despite highlighting good intra- and inter-operator reproducibility, we found that a scale bias between instruments might interfere with thorough CCT monitoring. We suggest that optimal monitoring is achieved with the same operator and the same device.

Testing Reproducibility in Earth Sciences

NASA Astrophysics Data System (ADS)

Church, M. A.; Dudill, A. R.; Frey, P.; Venditti, J. G.

2017-12-01

Reproducibility represents how closely the results of independent tests agree when undertaken using the same materials but different conditions of measurement, such as operator, equipment or laboratory. The concept of reproducibility is fundamental to the scientific method as it prevents the persistence of incorrect or biased results. Yet currently the production of scientific knowledge emphasizes rapid publication of previously unreported findings, a culture that has emerged from pressures related to hiring, publication criteria and funding requirements. Awareness and critique of the disconnect between how scientific research should be undertaken, and how it actually is conducted, has been prominent in biomedicine for over a decade, with the fields of economics and psychology more recently joining the conversation. The purpose of this presentation is to stimulate the conversation in earth sciences where, despite implicit evidence in widely accepted classifications, formal testing of reproducibility is rare.As a formal test of reproducibility, two sets of experiments were undertaken with the same experimental procedure, at the same scale, but in different laboratories. Using narrow, steep flumes and spherical glass beads, grain size sorting was examined by introducing fine sediment of varying size and quantity into a mobile coarse bed. The general setup was identical, including flume width and slope; however, there were some variations in the materials, construction and lab environment. Comparison of the results includes examination of the infiltration profiles, sediment mobility and transport characteristics. The physical phenomena were qualitatively reproduced but not quantitatively replicated. Reproduction of results encourages more robust research and reporting, and facilitates exploration of possible variations in data in various specific contexts. Following the lead of other fields, testing of reproducibility can be incentivized through changes to journal

Highly reproducible and reliable metal/graphene contact by ultraviolet-ozone treatment

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

Li, Wei; Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899; Hacker, Christina A.

2014-03-21

Resist residue from the device fabrication process is a significant source of contamination at the metal/graphene contact interface. Ultraviolet Ozone (UVO) treatment is proven here, by X-ray photoelectron spectroscopy and Raman measurement, to be an effective way of cleaning the metal/graphene interface. Electrical measurements of devices that were fabricated by using UVO treatment of the metal/graphene contact region show that stable and reproducible low resistance metal/graphene contacts are obtained and the electrical properties of the graphene channel remain unaffected.

Effect of high oleic acid soybean on seed oil, protein concentration, and yield

USDA-ARS?s Scientific Manuscript database

Soybeans with high oleic acid content are desired by oil processors because of their improved oxidative stability for broader use in food, fuel and other products. However, non-GMO high-oleic soybeans have tended to have low seed yield. The objective of this study was to test non-GMO, high-oleic s...

High-yield production of herbicidal thaxtomins and analogs in a nonpathogenic Streptomyces strain.

PubMed

Jiang, Guangde; Zhang, Yucheng; Powell, Magan M; Zhang, Peilan; Zuo, Ran; Zhang, Yi; Kallifidas, Dimitrios; Tieu, Albert M; Luesch, Hendrik; Loria, Rosemary; Ding, Yousong

2018-03-30

Thaxtomins are virulence factors of most plant pathogenic Streptomyces strains. Due to their potent herbicidal activity, attractive environmental compatibility and inherent biodegradability, thaxtomins are key active ingredients of bioherbicides approved by the United States Environmental Protection Agency. However, the low yield of thaxtomins in native Streptomyces producers limits their wide agricultural applications. Here, we describe the high-yield production of thaxtomins in a heterologous host. The thaxtomin gene cluster from S. scabiei 87.22 was cloned and expressed in S. albus J1074 after chromosomal integration. The production of thaxtomins and nitro-tryptophan analogs were observed using LC-MS analysis. When culturing the engineered S. albus J1074 in the minimal medium TMDc, the yield of the most abundant and herbicidal analog, thaxtomin A, was 10 times higher than S. scabiei 87.22, and optimization of the medium resulted in the highest yield of thaxtomin analogs at about 222 mg/L. Further engineering of the thaxtomin biosynthetic gene cluster through gene deletion led to the production of multiple biosynthetic intermediates important to the chemical synthesis of new analogs. Additionally, the versatility of the thaxtomin biosynthetic system in S. albus J1074 was capitalized to produce one unnatural fluorinated analog 5-F-thaxtomin A, whose structure was elucidated by a combination of MS and 1D and 2D NMR analyses. Natural and unnatural thaxtomins demonstrated potent herbicidal activity in radish seedling assays. These results indicated that S. albus J1074 has the potential to produce thaxtomins and thereof with high yield, fostering their agricultural applications. IMPORTANCE Thaxtomins are agriculturally valuable herbicidal natural products but the productivity of native producers is limiting. Heterologous expression of thaxtomin gene cluster in S. albus J1074 resulted in the highest yield of thaxtomins ever reported, representing a significant leap

Reproducibility of HTS-SQUID magnetocardiography in an unshielded clinical environment.

PubMed

Leder, U; Schrey, F; Haueisen, J; Dörrer, L; Schreiber, J; Liehr, M; Schwarz, G; Solbrig, O; Figulla, H R; Seidel, P

2001-07-01

A new technology has been developed which measures the magnetic field of the human heart (magnetocardiogram, MCG) by using high temperature superconducting (HTS) sensors. These sensors can be operated at the temperature of liquid nitrogen without electromagnetic shielding. We tested the reproducibility of HTS-MCG measurements in healthy volunteers. Unshielded HTS-MCG measurements were performed in 18 healthy volunteers in left precordial position in two separate sessions in a clinical environment. The heart cycles of 10 min were averaged, smoothed, the baselines were adjusted, and the data were standardized to the respective areas under the curves (AUC) of the absolute values of the QRST amplitudes. The QRS complexes and the ST-T intervals were used to assess the reproducibility of the two measurements. Ratios (R(QRS), R(STT)) were calculated by dividing the AUC of the first measurement by the ones of the second measurement. The linear correlation coefficients (CORR(QRS), CORR(STT)) of the time intervals of the two measurements were calculated, too. The HTS-MCG signal was completely concealed by the high noise level in the raw data. The averaging and smoothing algorithms unmasked the QRS complex and the ST segment. A high reproducibility was found for the QRS complex (R(QRS)=1.2+/-0.3, CORR(QRS)=0.96+/-0.06). Similarly to the shape of the ECG it was characterized by three bends, the Q, R, and S waves. In the ST-T interval, the reproducibility was considerably lower (R(STT)=0.9+/-0.2, CORR(STT)=0.66+/-0.28). In contrast to the shape of the ECG, a baseline deflection after the T wave which may belong to U wave activity was found in a number of volunteers. HTS-MCG devices can be operated in a clinical environment without shielding. Whereas the reproducibility was found to be high for the depolarization interval, it was considerably lower for the ST segment and for the T wave. Therefore, before clinically applying HTS-MCG systems to the detection of repolarization

Using prediction markets to estimate the reproducibility of scientific research.

PubMed

Dreber, Anna; Pfeiffer, Thomas; Almenberg, Johan; Isaksson, Siri; Wilson, Brad; Chen, Yiling; Nosek, Brian A; Johannesson, Magnus

2015-12-15

Concerns about a lack of reproducibility of statistically significant results have recently been raised in many fields, and it has been argued that this lack comes at substantial economic costs. We here report the results from prediction markets set up to quantify the reproducibility of 44 studies published in prominent psychology journals and replicated in the Reproducibility Project: Psychology. The prediction markets predict the outcomes of the replications well and outperform a survey of market participants' individual forecasts. This shows that prediction markets are a promising tool for assessing the reproducibility of published scientific results. The prediction markets also allow us to estimate probabilities for the hypotheses being true at different testing stages, which provides valuable information regarding the temporal dynamics of scientific discovery. We find that the hypotheses being tested in psychology typically have low prior probabilities of being true (median, 9%) and that a "statistically significant" finding needs to be confirmed in a well-powered replication to have a high probability of being true. We argue that prediction markets could be used to obtain speedy information about reproducibility at low cost and could potentially even be used to determine which studies to replicate to optimally allocate limited resources into replications.

Using prediction markets to estimate the reproducibility of scientific research

PubMed Central

Dreber, Anna; Pfeiffer, Thomas; Almenberg, Johan; Isaksson, Siri; Wilson, Brad; Chen, Yiling; Nosek, Brian A.; Johannesson, Magnus

2015-01-01

Concerns about a lack of reproducibility of statistically significant results have recently been raised in many fields, and it has been argued that this lack comes at substantial economic costs. We here report the results from prediction markets set up to quantify the reproducibility of 44 studies published in prominent psychology journals and replicated in the Reproducibility Project: Psychology. The prediction markets predict the outcomes of the replications well and outperform a survey of market participants’ individual forecasts. This shows that prediction markets are a promising tool for assessing the reproducibility of published scientific results. The prediction markets also allow us to estimate probabilities for the hypotheses being true at different testing stages, which provides valuable information regarding the temporal dynamics of scientific discovery. We find that the hypotheses being tested in psychology typically have low prior probabilities of being true (median, 9%) and that a “statistically significant” finding needs to be confirmed in a well-powered replication to have a high probability of being true. We argue that prediction markets could be used to obtain speedy information about reproducibility at low cost and could potentially even be used to determine which studies to replicate to optimally allocate limited resources into replications. PMID:26553988

Characterization of Novel Materials with Very Low Secondary Electron Emission Yield for Use in High-Power Microwave Devices

NASA Astrophysics Data System (ADS)

Svimonishvili, Tengiz; Zameroski, Nathan; Gilmore, Mark; Schamiloglu, Edl; Gaudet, John; Yan, Lincan

2004-11-01

Secondary Electron Emission (SEE) results from bombarding materials with electrons, atoms, or ions. The amount of secondary emission depends on factors such as bulk and surface properties of materials, energy of incident particles, and their angle of incidence. Total secondary electron emission yield, defined as the number of secondary electrons ejected per primary electron, is an important material parameter. Materials with high yield find use, for instance, in photomultiplier tubes, whereas materials with low yield, such as graphite, are used for SEE suppression in high-power microwave devices. The lower the SEE yield, the better the performance of high-power microwave devices (for example, gyrotrons). Employing a low-energy electron gun (energy range from 5 eV to 2000 eV), our work aims at characterizing and eventually identifying novel materials (with the lowest possible SEE yield) that will enhance operation and efficiency of high-power microwave devices.

Microbial electrolysis cells for high yield hydrogen gas production from organic matter.

PubMed

Logan, Bruce E; Call, Douglas; Cheng, Shaoan; Hamelers, Hubertus V M; Sleutels, Tom H J A; Jeremiasse, Adriaan W; Rozendal, René A

2008-12-01

The use of electrochemically active bacteria to break down organic matter, combined with the addition of a small voltage (> 0.2 V in practice) in specially designed microbial electrolysis cells (MECs), can result in a high yield of hydrogen gas. While microbial electrolysis was invented only a few years ago, rapid developments have led to hydrogen yields approaching 100%, energy yields based on electrical energy input many times greater than that possible by water electrolysis, and increased gas production rates. MECs used to make hydrogen gas are similar in design to microbial fuel cells (MFCs) that produce electricity, but there are important differences in architecture and analytical methods used to evaluate performance. We review here the materials, architectures, performance, and energy efficiencies of these MEC systems that show promise as a method for renewable and sustainable energy production, and wastewater treatment.

Reproducibility of clinical research in critical care: a scoping review.

PubMed

Niven, Daniel J; McCormick, T Jared; Straus, Sharon E; Hemmelgarn, Brenda R; Jeffs, Lianne; Barnes, Tavish R M; Stelfox, Henry T

2018-02-21

The ability to reproduce experiments is a defining principle of science. Reproducibility of clinical research has received relatively little scientific attention. However, it is important as it may inform clinical practice, research agendas, and the design of future studies. We used scoping review methods to examine reproducibility within a cohort of randomized trials examining clinical critical care research and published in the top general medical and critical care journals. To identify relevant clinical practices, we searched the New England Journal of Medicine, The Lancet, and JAMA for randomized trials published up to April 2016. To identify a comprehensive set of studies for these practices, included articles informed secondary searches within other high-impact medical and specialty journals. We included late-phase randomized controlled trials examining therapeutic clinical practices in adults admitted to general medical-surgical or specialty intensive care units (ICUs). Included articles were classified using a reproducibility framework. An original study was the first to evaluate a clinical practice. A reproduction attempt re-evaluated that practice in a new set of participants. Overall, 158 practices were examined in 275 included articles. A reproduction attempt was identified for 66 practices (42%, 95% CI 33-50%). Original studies reported larger effects than reproduction attempts (primary endpoint, risk difference 16.0%, 95% CI 11.6-20.5% vs. 8.4%, 95% CI 6.0-10.8%, P = 0.003). More than half of clinical practices with a reproduction attempt demonstrated effects that were inconsistent with the original study (56%, 95% CI 42-68%), among which a large number were reported to be efficacious in the original study and to lack efficacy in the reproduction attempt (34%, 95% CI 19-52%). Two practices reported to be efficacious in the original study were found to be harmful in the reproduction attempt. A minority of critical care practices with research published

Sputtering yields of carbon based materials under high particle flux with low energy

NASA Astrophysics Data System (ADS)

Nakamura, K.; Nagase, A.; Dairaku, M.; Akiba, M.; Araki, M.; Okumura, Y.

1995-04-01

A new ion source which can produce high particle flux beams at low energies has been developed. This paper presents preliminary results on the sputtering yield of the carbon fiber reinforced composites (CFCs) measured with the new ion source. The sputtering yields of 1D and 2D CFCs, which are candidate materials for the divertor armour tiles, have been measured by the weight loss method under the hydrogen and deuterium particle fluxes of 2 ˜ 7 × 10 20/m 2 s at 50 ˜ 150 eV. Preferential sputtering of the matrix was observed on CFCs which included the matrix of 40 ˜ 60 w%. The energy dependence of the sputtering yields was weak. The sputtering yields of CFCs normally irradiated with deuterium beam were from 0.073 to 0.095, and were around three times larger than those with hydrogen beam.

Secondary electron emission yield from high aspect ratio carbon velvet surfaces

DOE PAGES

Jin, Chenggang; Ottaviano, Angelica; Raitses, Yevgeny

2017-11-01

The plasma electrons bombarding a plasma-facing wall surface can induce secondary electron emission (SEE) from the wall. A strong SEE can enhance the power losses by reducing the wall sheath potential and thereby increasing the electron flux from the plasma to the wall. The use of the materials with surface roughness and the engineered materials with surface architecture is known to reduce the effective SEE by trapping the secondary electrons. In this work, we demonstrate a 65% reduction of SEE yield using a velvet material consisting of high aspect ratio carbon fibers. The measurements of SEE yield for different velvetmore » samples using the electron beam in vacuum demonstrate the dependence of the SEE yield on the fiber length and the packing density, which is strongly affected by the alignment of long velvet fibers with respect to the electron beam impinging on the velvet sample. Furthermore, the results of SEE measurements support the previous observations of the reduced SEE measured in Hall thrusters.« less

Introduction to the special issue on recentering science: Replication, robustness, and reproducibility in psychophysiology.

PubMed

Kappenman, Emily S; Keil, Andreas

2017-01-01

In recent years, the psychological and behavioral sciences have increased efforts to strengthen methodological practices and publication standards, with the ultimate goal of enhancing the value and reproducibility of published reports. These issues are especially important in the multidisciplinary field of psychophysiology, which yields rich and complex data sets with a large number of observations. In addition, the technological tools and analysis methods available in the field of psychophysiology are continually evolving, widening the array of techniques and approaches available to researchers. This special issue presents articles detailing rigorous and systematic evaluations of tasks, measures, materials, analysis approaches, and statistical practices in a variety of subdisciplines of psychophysiology. These articles highlight challenges in conducting and interpreting psychophysiological research and provide data-driven, evidence-based recommendations for overcoming those challenges to produce robust, reproducible results in the field of psychophysiology. © 2016 Society for Psychophysiological Research.

Construction high-yield candidate influenza vaccine viruses in Vero cells by reassortment.

PubMed

Yu, Wei; Yang, Fan; Yang, Jinghui; Ma, Lei; Cun, Yina; Song, Shaohui; Liao, Guoyang

2016-11-01

Usage of influenza vaccine is the best choice measure for preventing and conclusion of influenza virus infection. Although it has been used of chicken embryo to produce influenza vaccine, following with WHO recommended vaccine strain, there were uncontrollable factors and its deficiencies, specially, during an influenza pandemic in the world. The Vero cells are used for vaccine production of a few strains including influenza virus, because of its homology with human, recommended by WHO. However, as known most of the influenza viruses strains could not culture by Vero cells. It was used two high-yield influenza viruses adapted in Vero cells as donor viruses, such as A/Yunnan/1/2005Va (H3N2) and B/Yunnan/2/2005Va (B), to construct high-yield wild influenza virus in Vero cells under antibody selection pressure. After reassortment and passages, it obtained the new Vaccine strains with A/Tianjin/15/2009Va (H1N1), A/Fujian/196/2009Va (H3N2) and B/Chongqing/1384/2010Va (B), which was not only completely keeping their original antigenic (HA and NA), but also grown well in Vero cells with high-yield. All results of gene analysis and HA, HI shown that this reassortment method could be used to find new direction to product the influenza vaccine. J. Med. Virol. 88:1914-1921, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Apparently low reproducibility of true differential expression discoveries in microarray studies.

PubMed

Zhang, Min; Yao, Chen; Guo, Zheng; Zou, Jinfeng; Zhang, Lin; Xiao, Hui; Wang, Dong; Yang, Da; Gong, Xue; Zhu, Jing; Li, Yanhui; Li, Xia

2008-09-15

Differentially expressed gene (DEG) lists detected from different microarray studies for a same disease are often highly inconsistent. Even in technical replicate tests using identical samples, DEG detection still shows very low reproducibility. It is often believed that current small microarray studies will largely introduce false discoveries. Based on a statistical model, we show that even in technical replicate tests using identical samples, it is highly likely that the selected DEG lists will be very inconsistent in the presence of small measurement variations. Therefore, the apparently low reproducibility of DEG detection from current technical replicate tests does not indicate low quality of microarray technology. We also demonstrate that heterogeneous biological variations existing in real cancer data will further reduce the overall reproducibility of DEG detection. Nevertheless, in small subsamples from both simulated and real data, the actual false discovery rate (FDR) for each DEG list tends to be low, suggesting that each separately determined list may comprise mostly true DEGs. Rather than simply counting the overlaps of the discovery lists from different studies for a complex disease, novel metrics are needed for evaluating the reproducibility of discoveries characterized with correlated molecular changes. Supplementaty information: Supplementary data are available at Bioinformatics online.

Uncertainties in Predicting Rice Yield by Current Crop Models Under a Wide Range of Climatic Conditions

NASA Technical Reports Server (NTRS)

Li, Tao; Hasegawa, Toshihiro; Yin, Xinyou; Zhu, Yan; Boote, Kenneth; Adam, Myriam; Bregaglio, Simone; Buis, Samuel; Confalonieri, Roberto; Fumoto, Tamon;

Limitations to photosynthesis under light and heat stress in three high-yielding wheat genotypes.

PubMed

Monneveux, Philippe; Pastenes, Claudio; Reynolds, Matthew P

2003-06-01

Three high-yielding wheat genotypes (T. aestivum L., c.v. Siete Cerros, Seri and Bacanora, released in 1966, 1982 and 1988, respectively) were grown under irrigation in two high radiation, low relative humidity environments (Tlaltizapan and Ciudad Obregon CIMMYT experimental stations, Mexico). Gas exchange and fluorescence parameters were assessed on the flag leaf during the day. Carbon isotope discrimination (delta) was analysed in flag leaf at anthesis and in grain at maturity. In both environments, gas exchange and fluorescence parameters varied markedly with irradiance and temperature. Analysis of their respective variation indicated the occurrence of photo-respiration and photo-inhibition, particularly in Tlaltizapan, the warmest environment, and in Siete Cerros. In Ciudad Obregon (high-yielding environment) lower Ci (internal CO2 concentration) and delta La (carbon isotope discrimination of the leaf) suggested a higher intrinsic photosynthetic capacity in the variety Bacanora. Higher yield of this genotype was also associated with higher Fv'/Fo' (ratio of photochemical and non photochemical rate constants in the light) and Fm'/Fm (ratio of the non photochemical rate constants in the dark and light adapted state).

Simulations of super-ellipse hohlraum targets as a path to high neutron yields

NASA Astrophysics Data System (ADS)

Milovich, Jose; Amendt, Peter; Storm, Erik; Robey, Harry; Haan, Steve; Landen, Otto; Meezan, Nathan; Lindl, John

2017-10-01

Recently neutron yields in excess of 1016 have been achieved at the National Ignition Facility (NIF) using a low-density gas fill hohlraum and a subscale high-density-carbon capsule. The laser power used was near the current maximum level allowed on the inner cones of the NIF laser. While more energy can be extracted from the laser to provide additional improvement on the neutron yield, a more efficient design is desired. A new effort has begun to investigate alternatives to the current cylinder-shaped hohlraum for driving larger capsules (1.1 mm outer radius). If these new hohlraums can preserve the implosion symmetry, the additional absorbed energy is expected to provide a path to high neutron yield and potential ignition. Super-ellipse hohlraums, a generalization of an earlier rugby hohlraum design, have the advantage of a larger waist diameter and reduced parasitic energy losses from the corners of cylindrical hohlraums while still being able to produce the required capsule drive at the current energy and power limits available at the NIF. We will present plausible designs of these hohlraums based on the Lamé mathematical construction, and discuss their prospects to reach high neutron gains. Prepared by LLNL under Contract DE-AC52-07NA27344.

Equivalence and test-retest reproducibility of conventional and extended-high-frequency audiometric thresholds obtained using pure-tone and narrow-band-noise stimuli.

PubMed

John, Andrew B; Kreisman, Brian M

2017-09-01

Extended high-frequency (EHF) audiometry is useful for evaluating ototoxic exposures and may relate to speech recognition, localisation and hearing aid benefit. There is a need to determine whether common clinical practice for EHF audiometry using tone and noise stimuli is reliable. We evaluated equivalence and compared test-retest (TRT) reproducibility for audiometric thresholds obtained using pure tones and narrowband noise (NBN) from 0.25 to 16 kHz. Thresholds and test-retest reproducibility for stimuli in the conventional (0.25-6 kHz) and EHF (8-16 kHz) frequency ranges were compared in a repeated-measures design. A total of 70 ears of adults with normal hearing. Thresholds obtained using NBN were significantly lower than thresholds obtained using pure tones from 0.5 to 16 kHz, but not 0.25 kHz. Good TRT reproducibility (within 2 dB) was observed for both stimuli at all frequencies. Responses at the lower limit of the presentation range for NBN centred at 14 and 16 kHz suggest unreliability for NBN as a threshold stimulus at these frequencies. Thresholds in the conventional and EHF ranges showed good test-retest reproducibility, but differed between stimulus types. Care should be taken when comparing pure-tone thresholds with NBN thresholds especially at these frequencies.

Panel-based Genetic Diagnostic Testing for Inherited Eye Diseases is Highly Accurate and Reproducible and More Sensitive for Variant Detection Than Exome Sequencing

PubMed Central

Bujakowska, Kinga M.; Sousa, Maria E.; Fonseca-Kelly, Zoë D.; Taub, Daniel G.; Janessian, Maria; Wang, Dan Yi; Au, Elizabeth D.; Sims, Katherine B.; Sweetser, David A.; Fulton, Anne B.; Liu, Qin; Wiggs, Janey L.; Gai, Xiaowu; Pierce, Eric A.

2015-01-01

Purpose Next-generation sequencing (NGS) based methods are being adopted broadly for genetic diagnostic testing, but the performance characteristics of these techniques have not been fully defined with regard to test accuracy and reproducibility. Methods We developed a targeted enrichment and NGS approach for genetic diagnostic testing of patients with inherited eye disorders, including inherited retinal degenerations, optic atrophy and glaucoma. In preparation for providing this Genetic Eye Disease (GEDi) test on a CLIA-certified basis, we performed experiments to measure the sensitivity, specificity, reproducibility as well as the clinical sensitivity of the test. Results The GEDi test is highly reproducible and accurate, with sensitivity and specificity for single nucleotide variant detection of 97.9% and 100%, respectively. The sensitivity for variant detection was notably better than the 88.3% achieved by whole exome sequencing (WES) using the same metrics, due to better coverage of targeted genes in the GEDi test compared to commercially available exome capture sets. Prospective testing of 192 patients with IRDs indicated that the clinical sensitivity of the GEDi test is high, with a diagnostic rate of 51%. Conclusion The data suggest that based on quantified performance metrics, selective targeted enrichment is preferable to WES for genetic diagnostic testing. PMID:25412400

An International Ki67 Reproducibility Study

PubMed Central

2013-01-01

Background In breast cancer, immunohistochemical assessment of proliferation using the marker Ki67 has potential use in both research and clinical management. However, lack of consistency across laboratories has limited Ki67’s value. A working group was assembled to devise a strategy to harmonize Ki67 analysis and increase scoring concordance. Toward that goal, we conducted a Ki67 reproducibility study. Methods Eight laboratories received 100 breast cancer cases arranged into 1-mm core tissue microarrays—one set stained by the participating laboratory and one set stained by the central laboratory, both using antibody MIB-1. Each laboratory scored Ki67 as percentage of positively stained invasive tumor cells using its own method. Six laboratories repeated scoring of 50 locally stained cases on 3 different days. Sources of variation were analyzed using random effects models with log2-transformed measurements. Reproducibility was quantified by intraclass correlation coefficient (ICC), and the approximate two-sided 95% confidence intervals (CIs) for the true intraclass correlation coefficients in these experiments were provided. Results Intralaboratory reproducibility was high (ICC = 0.94; 95% CI = 0.93 to 0.97). Interlaboratory reproducibility was only moderate (central staining: ICC = 0.71, 95% CI = 0.47 to 0.78; local staining: ICC = 0.59, 95% CI = 0.37 to 0.68). Geometric mean of Ki67 values for each laboratory across the 100 cases ranged 7.1% to 23.9% with central staining and 6.1% to 30.1% with local staining. Factors contributing to interlaboratory discordance included tumor region selection, counting method, and subjective assessment of staining positivity. Formal counting methods gave more consistent results than visual estimation. Conclusions Substantial variability in Ki67 scoring was observed among some of the world’s most experienced laboratories. Ki67 values and cutoffs for clinical decision-making cannot be transferred between laboratories without

[Reproducibility of subjective refraction measurement].

PubMed

Grein, H-J; Schmidt, O; Ritsche, A

2014-11-01

Reproducibility of subjective refraction measurement is limited by various factors. The main factors affecting reproducibility include the characteristics of the measurement method and of the subject and the examiner. This article presents the results of a study on this topic, focusing on the reproducibility of subjective refraction measurement in healthy eyes. The results of previous studies are not all presented in the same way by the respective authors and cannot be fully standardized without consulting the original scientific data. To the extent that they are comparable, the results of our study largely correspond largely with those of previous investigations: During repeated subjective refraction measurement, 95% of the deviation from the mean value was approximately ±0.2 D to ±0.65 D for the spherical equivalent and cylindrical power. The reproducibility of subjective refraction measurement in healthy eyes is limited, even under ideal conditions. Correct assessment of refraction results is only feasible after identifying individual variability. Several measurements are required. Refraction cannot be measured without a tolerance range. The English full-text version of this article is available at SpringerLink (under supplemental).

Reproducing Epidemiologic Research and Ensuring Transparency.

PubMed

Coughlin, Steven S

2017-08-15

Measures for ensuring that epidemiologic studies are reproducible include making data sets and software available to other researchers so they can verify published findings, conduct alternative analyses of the data, and check for statistical errors or programming errors. Recent developments related to the reproducibility and transparency of epidemiologic studies include the creation of a global platform for sharing data from clinical trials and the anticipated future extension of the global platform to non-clinical trial data. Government agencies and departments such as the US Department of Veterans Affairs Cooperative Studies Program have also enhanced their data repositories and data sharing resources. The Institute of Medicine and the International Committee of Medical Journal Editors released guidance on sharing clinical trial data. The US National Institutes of Health has updated their data-sharing policies. In this issue of the Journal, Shepherd et al. (Am J Epidemiol. 2017;186:387-392) outline a pragmatic approach for reproducible research with sensitive data for studies for which data cannot be shared because of legal or ethical restrictions. Their proposed quasi-reproducible approach facilitates the dissemination of statistical methods and codes to independent researchers. Both reproducibility and quasi-reproducibility can increase transparency for critical evaluation, further dissemination of study methods, and expedite the exchange of ideas among researchers. © The Author(s) 2017. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A Novel Highly Reproducible and Lethal Nonhuman Primate Model for Orthopox Virus Infection

PubMed Central

Kramski, Marit; Mätz-Rensing, Kerstin; Stahl-Hennig, Christiane; Kaup, Franz-Josef; Nitsche, Andreas; Pauli, Georg; Ellerbrok, Heinz

2010-01-01

The intentional re-introduction of Variola virus (VARV), the agent of smallpox, into the human population is of great concern due its bio-terroristic potential. Moreover, zoonotic infections with Cowpox (CPXV) and Monkeypox virus (MPXV) cause severe diseases in humans. Smallpox vaccines presently available can have severe adverse effects that are no longer acceptable. The efficacy and safety of new vaccines and antiviral drugs for use in humans can only be demonstrated in animal models. The existing nonhuman primate models, using VARV and MPXV, need very high viral doses that have to be applied intravenously or intratracheally to induce a lethal infection in macaques. To overcome these drawbacks, the infectivity and pathogenicity of a particular CPXV was evaluated in the common marmoset (Callithrix jacchus). A CPXV named calpox virus was isolated from a lethal orthopox virus (OPV) outbreak in New World monkeys. We demonstrated that marmosets infected with calpox virus, not only via the intravenous but also the intranasal route, reproducibly develop symptoms resembling smallpox in humans. Infected animals died within 1–3 days after onset of symptoms, even when very low infectious viral doses of 5×102 pfu were applied intranasally. Infectious virus was demonstrated in blood, saliva and all organs analyzed. We present the first characterization of a new OPV infection model inducing a disease in common marmosets comparable to smallpox in humans. Intranasal virus inoculation mimicking the natural route of smallpox infection led to reproducible infection. In vivo titration resulted in an MID50 (minimal monkey infectious dose 50%) of 8.3×102 pfu of calpox virus which is approximately 10,000-fold lower than MPXV and VARV doses applied in the macaque models. Therefore, the calpox virus/marmoset model is a suitable nonhuman primate model for the validation of vaccines and antiviral drugs. Furthermore, this model can help study mechanisms of OPV pathogenesis. PMID

Hippocampal volume change measurement: quantitative assessment of the reproducibility of expert manual outlining and the automated methods FreeSurfer and FIRST.

PubMed

Mulder, Emma R; de Jong, Remko A; Knol, Dirk L; van Schijndel, Ronald A; Cover, Keith S; Visser, Pieter J; Barkhof, Frederik; Vrenken, Hugo

2014-05-15

To measure hippocampal volume change in Alzheimer's disease (AD) or mild cognitive impairment (MCI), expert manual delineation is often used because of its supposed accuracy. It has been suggested that expert outlining yields poorer reproducibility as compared to automated methods, but this has not been investigated. To determine the reproducibilities of expert manual outlining and two common automated methods for measuring hippocampal atrophy rates in healthy aging, MCI and AD. From the Alzheimer's Disease Neuroimaging Initiative (ADNI), 80 subjects were selected: 20 patients with AD, 40 patients with mild cognitive impairment (MCI) and 20 healthy controls (HCs). Left and right hippocampal volume change between baseline and month-12 visit was assessed by using expert manual delineation, and by the automated software packages FreeSurfer (longitudinal processing stream) and FIRST. To assess reproducibility of the measured hippocampal volume change, both back-to-back (BTB) MPRAGE scans available for each visit were analyzed. Hippocampal volume change was expressed in μL, and as a percentage of baseline volume. Reproducibility of the 1-year hippocampal volume change was estimated from the BTB measurements by using linear mixed model to calculate the limits of agreement (LoA) of each method, reflecting its measurement uncertainty. Using the delta method, approximate p-values were calculated for the pairwise comparisons between methods. Statistical analyses were performed both with inclusion and exclusion of visibly incorrect segmentations. Visibly incorrect automated segmentation in either one or both scans of a longitudinal scan pair occurred in 7.5% of the hippocampi for FreeSurfer and in 6.9% of the hippocampi for FIRST. After excluding these failed cases, reproducibility analysis for 1-year percentage volume change yielded LoA of ±7.2% for FreeSurfer, ±9.7% for expert manual delineation, and ±10.0% for FIRST. Methods ranked the same for reproducibility of 1

Electrical Detection of C-Reactive Protein Using a Single Free-Standing, Thermally Controlled Piezoresistive Microcantilever for Highly Reproducible and Accurate Measurements

PubMed Central

Yen, Yi-Kuang; Lai, Yu-Cheng; Hong, Wei-Ting; Pheanpanitporn, Yotsapoom; Chen, Chuin-Shan; Huang, Long-Sun

2013-01-01

This study demonstrates a novel method for electrical detection of C-reactive protein (CRP) as a means of identifying an infection in the body, or as a cardiovascular disease risk assay. The method uses a single free-standing, thermally controlled piezoresistive microcantilever biosensor. In a commonly used sensing arrangement of conventional dual cantilevers in the Wheatstone bridge circuit, reference and gold-coated sensing cantilevers that inherently have heterogeneous surface materials and different multilayer structures may yield independent responses to the liquid environmental changes of chemical substances, flow field and temperature, leading to unwanted signal disturbance for biosensing targets. In this study, the single free-standing microcantilever for biosensing applications is employed to resolve the dual-beam problem of individual responses in chemical solutions and, in a thermally controlled system, to maintain its sensor performance due to the sensitive temperature effect. With this type of single temperature-controlled microcantilever sensor, the electrical detection of various CRP concentrations from 1 μg/mL to 200 μg/mL was performed, which covers the clinically relevant range. Induced surface stresses were measured at between 0.25 N/m and 3.4 N/m with high reproducibility. Moreover, the binding affinity (KD) of CRP and anti-CRP interaction was found to be 18.83 ± 2.99 μg/mL, which agreed with results in previous reported studies. This biosensing technique thus proves valuable in detecting inflammation, and in cardiovascular disease risk assays. PMID:23899933

Very high CO2 reduces photosynthesis, dark respiration and yield in wheat

NASA Technical Reports Server (NTRS)

Reuveni, J.; Bugbee, B.

1997-01-01

Although terrestrial CO2 concentrations, [CO2] are not expected to reach 1000 micromoles mol-1 for many decades, CO2 levels in closed systems such as growth chambers and glasshouses, can easily exceed this concentration. CO2 levels in life support systems in space can exceed 10000 micromoles mol-1 (1%). Here we studied the effect of six CO2 concentrations, from ambient up to 10000 micromoles mol-1, on seed yield, growth and gas exchange of two wheat cultivars (USU-Apogee and Veery-l0). Elevating [CO2] from 350 to 1000 micromoles mol-1 increased seed yield (by 33%), vegetative biomass (by 25%) and number of heads m-2 (by 34%) of wheat plants. Elevation of [CO2] from 1000 to 10000 micromoles mol-1 decreased seed yield (by 37%), harvest index (by 14%), mass per seed (by 9%) and number of seeds per head (by 29%). This very high [CO2] had a negligible, non-significant effect on vegetative biomass, number of heads m-2 and seed mass per head. A sharp decrease in seed yield, harvest index and seeds per head occurred by elevating [CO2] from 1000 to 2600 micromoles mol-1. Further elevation of [CO2] from 2600 to 10000 micromoles mol-1 caused a further but smaller decrease. The effect of CO2 on both wheat cultivars was similar for all growth parameters. Similarly there were no differences in the response to high [CO2] between wheat grown hydroponically in growth chambers under fluorescent lights and those grown in soilless media in a glasshouse under sunlight and high pressure sodium lamps. There was no correlation between high [CO2] and ethylene production by flag leaves or by wheat heads. Therefore, the reduction in seed set in wheat plants is not mediated by ethylene. The photosynthetic rate of whole wheat plants was 8% lower and dark respiration of the wheat heads 25% lower when exposed to 2600 micromoles mol-1 CO2 compared to ambient [CO2]. It is concluded that the reduction in the seed set can be mainly explained by the reduction in the dark respiration in wheat heads

Repeatability and Reproducibility in Proteomic Identifications by Liquid Chromatography—Tandem Mass Spectrometry

PubMed Central

Tabb, David L.; Vega-Montoto, Lorenzo; Rudnick, Paul A.; Variyath, Asokan Mulayath; Ham, Amy-Joan L.; Bunk, David M.; Kilpatrick, Lisa E.; Billheimer, Dean D.; Blackman, Ronald K.; Cardasis, Helene L.; Carr, Steven A.; Clauser, Karl R.; Jaffe, Jacob D.; Kowalski, Kevin A.; Neubert, Thomas A.; Regnier, Fred E.; Schilling, Birgit; Tegeler, Tony J.; Wang, Mu; Wang, Pei; Whiteaker, Jeffrey R.; Zimmerman, Lisa J.; Fisher, Susan J.; Gibson, Bradford W.; Kinsinger, Christopher R.; Mesri, Mehdi; Rodriguez, Henry; Stein, Steven E.; Tempst, Paul; Paulovich, Amanda G.; Liebler, Daniel C.; Spiegelman, Cliff

2009-01-01

The complexity of proteomic instrumentation for LC-MS/MS introduces many possible sources of variability. Data-dependent sampling of peptides constitutes a stochastic element at the heart of discovery proteomics. Although this variation impacts the identification of peptides, proteomic identifications are far from completely random. In this study, we analyzed interlaboratory data sets from the NCI Clinical Proteomic Technology Assessment for Cancer to examine repeatability and reproducibility in peptide and protein identifications. Included data spanned 144 LC-MS/MS experiments on four Thermo LTQ and four Orbitrap instruments. Samples included yeast lysate, the NCI-20 defined dynamic range protein mix, and the Sigma UPS 1 defined equimolar protein mix. Some of our findings reinforced conventional wisdom, such as repeatability and reproducibility being higher for proteins than for peptides. Most lessons from the data, however, were more subtle. Orbitraps proved capable of higher repeatability and reproducibility, but aberrant performance occasionally erased these gains. Even the simplest protein digestions yielded more peptide ions than LC-MS/MS could identify during a single experiment. We observed that peptide lists from pairs of technical replicates overlapped by 35–60%, giving a range for peptide-level repeatability in these experiments. Sample complexity did not appear to affect peptide identification repeatability, even as numbers of identified spectra changed by an order of magnitude. Statistical analysis of protein spectral counts revealed greater stability across technical replicates for Orbitraps, making them superior to LTQ instruments for biomarker candidate discovery. The most repeatable peptides were those corresponding to conventional tryptic cleavage sites, those that produced intense MS signals, and those that resulted from proteins generating many distinct peptides. Reproducibility among different instruments of the same type lagged behind

Supportability of a High-Yield-Stress Slurry in a New Stereolithography-Based Ceramic Fabrication Process

NASA Astrophysics Data System (ADS)

He, Li; Song, Xuan

2018-03-01

In recent years, ceramic fabrication using stereolithography (SLA) has gained in popularity because of its high accuracy and density that can be achieved in the final part of production. One of the key challenges in ceramic SLA is that support structures are required for building overhanging features, whereas removing these support structures without damaging the components is difficult. In this research, a suspension-enclosing projection-stereolithography process is developed to overcome this challenge. This process uses a high-yield-stress ceramic slurry as the feedstock material and exploits the elastic force of the material to support overhanging features without the need for building additional support structures. Ceramic slurries with different solid loadings are studied to identify the rheological properties most suitable for supporting overhanging features. An analytical model of a double doctor-blade module is established to obtain uniform and thin recoating layers from a high-yield-stress slurry. Several test cases highlight the feasibility of using a high-yield-stress slurry to support overhanging features in SLA.

Crop Yield Predictions - High Resolution Statistical Model for Intra-season Forecasts Applied to Corn in the US

NASA Astrophysics Data System (ADS)

Cai, Y.

2017-12-01

Accurately forecasting crop yields has broad implications for economic trading, food production monitoring, and global food security. However, the variation of environmental variables presents challenges to model yields accurately, especially when the lack of highly accurate measurements creates difficulties in creating models that can succeed across space and time. In 2016, we developed a sequence of machine-learning based models forecasting end-of-season corn yields for the US at both the county and national levels. We combined machine learning algorithms in a hierarchical way, and used an understanding of physiological processes in temporal feature selection, to achieve high precision in our intra-season forecasts, including in very anomalous seasons. During the live run, we predicted the national corn yield within 1.40% of the final USDA number as early as August. In the backtesting of the 2000-2015 period, our model predicts national yield within 2.69% of the actual yield on average already by mid-August. At the county level, our model predicts 77% of the variation in final yield using data through the beginning of August and improves to 80% by the beginning of October, with the percentage of counties predicted within 10% of the average yield increasing from 68% to 73%. Further, the lowest errors are in the most significant producing regions, resulting in very high precision national-level forecasts. In addition, we identify the changes of important variables throughout the season, specifically early-season land surface temperature, and mid-season land surface temperature and vegetation index. For the 2017 season, we feed 2016 data to the training set, together with additional geospatial data sources, aiming to make the current model even more precise. We will show how our 2017 US corn yield forecasts converges in time, which factors affect the yield the most, as well as present our plans for 2018 model adjustments.

High yield production of extracellular recombinant levansucrase by Bacillus megaterium.

PubMed

Korneli, Claudia; Biedendieck, Rebekka; David, Florian; Jahn, Dieter; Wittmann, Christoph

2013-04-01

In this study, a high yield production bioprocess with recombinant Bacillus megaterium for the production of the extracellular enzyme levansucrase (SacB) was developed. For basic optimization of culture parameters and nutrients, a recombinant B. megaterium reporter strain that produced green fluorescent protein under control of a vector-based xylose-inducible promoter was used. It enabled efficient microtiter plate-based screening via fluorescence analysis. A pH value of pH 6, 20 % of dissolved oxygen, 37 °C, and elevated levels of biotin (100 μg L(-1)) were found optimal with regard to high protein yield and reduced overflow metabolism. Among the different compounds tested, fructose and glycerol were identified as the preferred source of carbon. Subsequently, the settings were transferred to a B. megaterium strain recombinantly producing levansucrase SacB based on the plasmid-located xylose-inducible expression system. In shake flask culture under the optimized conditions, the novel strain already secreted the target enzyme in high amounts (14 U mL(-1) on fructose and 17.2 U mL(-1) on glycerol). This was further increased in high cell density fed-batch processes up to 55 U mL(-1), reflecting a levansucrase concentration of 0.52 g L(-1). This is 100-fold more than previous efforts for this enzyme in B. megaterium and more than 10-fold higher than reported values of other extracellular protein produced in this microorganism so far. The recombinant strain could also handle raw glycerol from biodiesel industry which provided the same amount and quality of the recombinant protein and suggests future implementation into existing biorefinery concepts.

High-yield production of a stable Vero cell-based vaccine candidate against the highly pathogenic avian influenza virus H5N1

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

Zhou, Fangye; Zhou, Jian; Ma, Lei

Highlights: Black-Right-Pointing-Pointer Vero cell-based HPAI H5N1 vaccine with stable high yield. Black-Right-Pointing-Pointer Stable high yield derived from the YNVa H3N2 backbone. Black-Right-Pointing-Pointer H5N1/YNVa has a similar safety and immunogenicity to H5N1delta. -- Abstract: Highly pathogenic avian influenza (HPAI) viruses pose a global pandemic threat, for which rapid large-scale vaccine production technology is critical for prevention and control. Because chickens are highly susceptible to HPAI viruses, the supply of chicken embryos for vaccine production might be depleted during a virus outbreak. Therefore, developing HPAI virus vaccines using other technologies is critical. Meeting vaccine demand using the Vero cell-based fermentation process hasmore » been hindered by low stability and yield. In this study, a Vero cell-based HPAI H5N1 vaccine candidate (H5N1/YNVa) with stable high yield was achieved by reassortment of the Vero-adapted (Va) high growth A/Yunnan/1/2005(H3N2) (YNVa) virus with the A/Anhui/1/2005(H5N1) attenuated influenza vaccine strain (H5N1delta) using the 6/2 method. The reassorted H5N1/YNVa vaccine maintained a high hemagglutination (HA) titer of 1024. Furthermore, H5N1/YNVa displayed low pathogenicity and uniform immunogenicity compared to that of the parent virus.« less

Processable high-carbon-yielding polymer for micro- and nanofabrication

NASA Astrophysics Data System (ADS)

Perpall, Mark W.; Zengin, Huseyin; Perera, K. Prasanna U.; Zhou, Wensheng; Shah, Hiren; Wu, Xinyu; Creager, Stephen E.; Smith, Dennis W., Jr.; Foulger, Stephen H.; Ballato, John M.

2003-01-01

Bis-ortho-Diynyl Arene (BODA) monomers polymerize to network polynapthalene by the thermally-driven Bergman cyclization and subsequent radical polymerization via oligomeric intermediates that can be melt or solution processed. Further heating of the network to 1000 °C affords a high-yield glassy carbon structure that retains the approximate size and dimensions of the polymer precursor. The higher carbon-yield for BODA networks (75- 80 % by mass) is significantly greater than that of traditional phenol-formaldehyde resins and other carbon precursor polymers leading to its greater dimensional stability. Phenyl terminated BODA derived polymers were fabricated using microprocessing such as the micromolding in capillaries (MIMIC) technique, direct microtransfer molding, and molding in quartz capillary tubes. Nano-scale fabrication using closed packed silica spheres as templates was demonstrated with an hydroxy-terminated monomer which exhibits greatly enhanced compatibility for silica surfaces. After pyrolysis to glassy carbon, the silica is chemically etched leaving an inverse carbon opal photonic crystal which is electrically conductive. The wavelength of light diffracted is a function of the average refractive index of the carbon/ filler composite, which can be modified for use as sensitive detector elements.

High-Yield Synthesis and Optical Properties of Carbon Nanotube Porins

DOE PAGES

Tunuguntla, Ramya H.; Chen, Xi; Belliveau, Allison; ...

2017-01-18

Carbon nanotube porins (CNTPs) are a convenient membrane-based model system for studying nanofluidic transport that replicates a number of key structural features of biological membrane channels. We present a generalized approach for CNTP synthesis using sonochemistry-assisted segmenting of carbon nanotubes. Prolonged tip sonication in the presence of lipid molecules debundles and fragments long carbon nanotube aggregates into stable and water-soluble individual CNTPs with lengths in the range 5–20 nm. We discuss the main parameters that determine the efficiency and the yield of this process, describe the optimized conditions for high-yield CNTP synthesis, and demonstrate that this methodology can be adaptedmore » for synthesis of CNTPs of different diameters. We also present the optical properties of CNTPs and show that a combination of Raman and UV–vis–NIR spectroscopy can be used to monitor the quality of the CNTP synthesis. Altogether, CNTPs represent a versatile nanopore building block for creating higher-order functional biomimetic materials.« less

High-wafer-yield, high-performance vertical cavity surface-emitting lasers

NASA Astrophysics Data System (ADS)

Li, Gabriel S.; Yuen, Wupen; Lim, Sui F.; Chang-Hasnain, Constance J.

1996-04-01

Vertical cavity surface emitting lasers (VCSELs) with very low threshold current and voltage of 340 (mu) A and 1.5 V is achieved. The molecular beam epitaxially grown wafers are grown with a highly accurate, low cost and versatile pre-growth calibration technique. One- hundred percent VCSEL wafer yield is obtained. Low threshold current is achieved with a native oxide confined structure with excellent current confinement. Single transverse mode with stable, predetermined polarization direction up to 18 times threshold is also achieved, due to stable index guiding provided by the structure. This is the highest value reported to data for VCSELs. We have established that p-contact annealing in these devices is crucial for low voltage operation, contrary to the general belief. Uniform doping in the mirrors also appears not to be inferior to complicated doping engineering. With these design rules, very low threshold voltage VCSELs are achieved with very simple growth and fabrication steps.

Creating high yield water soluble luminescent graphene quantum dots via exfoliating and disintegrating carbon nanotubes and graphite flakes.

PubMed

Lin, Liangxu; Zhang, Shaowei

2012-10-21

We have developed an effective method to exfoliate and disintegrate multi-walled carbon nanotubes and graphite flakes. With this technique, high yield production of luminescent graphene quantum dots with high quantum yield and low oxidization can be achieved.

Optimizing multi-dimensional high throughput screening using zebrafish

PubMed Central

Truong, Lisa; Bugel, Sean M.; Chlebowski, Anna; Usenko, Crystal Y.; Simonich, Michael T.; Massey Simonich, Staci L.; Tanguay, Robert L.

2016-01-01

The use of zebrafish for high throughput screening (HTS) for chemical bioactivity assessments is becoming routine in the fields of drug discovery and toxicology. Here we report current recommendations from our experiences in zebrafish HTS. We compared the effects of different high throughput chemical delivery methods on nominal water concentration, chemical sorption to multi-well polystyrene plates, transcription responses, and resulting whole animal responses. We demonstrate that digital dispensing consistently yields higher data quality and reproducibility compared to standard plastic tip-based liquid handling. Additionally, we illustrate the challenges in using this sensitive model for chemical assessment when test chemicals have trace impurities. Adaptation of these better practices for zebrafish HTS should increase reproducibility across laboratories. PMID:27453428

Cervical vertebrae maturation method morphologic criteria: poor reproducibility.

PubMed

Nestman, Trenton S; Marshall, Steven D; Qian, Fang; Holton, Nathan; Franciscus, Robert G; Southard, Thomas E

2011-08-01

The cervical vertebrae maturation (CVM) method has been advocated as a predictor of peak mandibular growth. A careful review of the literature showed potential methodologic errors that might influence the high reported reproducibility of the CVM method, and we recently established that the reproducibility of the CVM method was poor when these potential errors were eliminated. The purpose of this study was to further investigate the reproducibility of the individual vertebral patterns. In other words, the purpose was to determine which of the individual CVM vertebral patterns could be classified reliably and which could not. Ten practicing orthodontists, trained in the CVM method, evaluated the morphology of cervical vertebrae C2 through C4 from 30 cephalometric radiographs using questions based on the CVM method. The Fleiss kappa statistic was used to assess interobserver agreement when evaluating each cervical vertebrae morphology question for each subject. The Kendall coefficient of concordance was used to assess the level of interobserver agreement when determining a "derived CVM stage" for each subject. Interobserver agreement was high for assessment of the lower borders of C2, C3, and C4 that were either flat or curved in the CVM method, but interobserver agreement was low for assessment of the vertebral bodies of C3 and C4 when they were either trapezoidal, rectangular horizontal, square, or rectangular vertical; this led to the overall poor reproducibility of the CVM method. These findings were reflected in the Fleiss kappa statistic. Furthermore, nearly 30% of the time, individual morphologic criteria could not be combined to generate a final CVM stage because of incompatible responses to the 5 questions. Intraobserver agreement in this study was only 62%, on average, when the inconclusive stagings were excluded as disagreements. Intraobserver agreement was worse (44%) when the inconclusive stagings were included as disagreements. For the group of subjects

Multiyear high-resolution carbon exchange over European croplands from the integration of observed crop yields into CarbonTracker Europe

NASA Astrophysics Data System (ADS)

Combe, Marie; Vilà-Guerau de Arellano, Jordi; de Wit, Allard; Peters, Wouter

2016-04-01

Carbon exchange over croplands plays an important role in the European carbon cycle over daily-to-seasonal time scales. Not only do crops occupy one fourth of the European land area, but their photosynthesis and respiration are large and affect CO2 mole fractions at nearly every atmospheric CO2 monitoring site. A better description of this crop carbon exchange in our CarbonTracker Europe data assimilation system - which currently treats crops as unmanaged grasslands - could strongly improve its ability to constrain terrestrial carbon fluxes. Available long-term observations of crop yield, harvest, and cultivated area allow such improvements, when combined with the new crop-modeling framework we present. This framework can model the carbon fluxes of 10 major European crops at high spatial and temporal resolution, on a 12x12 km grid and 3-hourly time-step. The development of this framework is threefold: firstly, we optimize crop growth using the process-based WOrld FOod STudies (WOFOST) agricultural crop growth model. Simulated yields are downscaled to match regional crop yield observations from the Statistical Office of the European Union (EUROSTAT) by estimating a yearly regional parameter for each crop species: the yield gap factor. This step allows us to better represent crop phenology, to reproduce the observed multiannual European crop yields, and to construct realistic time series of the crop carbon fluxes (gross primary production, GPP, and autotrophic respiration, Raut) on a fine spatial and temporal resolution. Secondly, we combine these GPP and Raut fluxes with a simple soil respiration model to obtain the total ecosystem respiration (TER) and net ecosystem exchange (NEE). And thirdly, we represent the horizontal transport of carbon that follows crop harvest and its back-respiration into the atmosphere during harvest consumption. We distribute this carbon using observations of the density of human and ruminant populations from EUROSTAT. We assess the model

Reproducibility of abdominal fat assessment by ultrasound and computed tomography.

PubMed

Mauad, Fernando Marum; Chagas-Neto, Francisco Abaeté; Benedeti, Augusto César Garcia Saab; Nogueira-Barbosa, Marcello Henrique; Muglia, Valdair Francisco; Carneiro, Antonio Adilton Oliveira; Muller, Enrico Mattana; Elias Junior, Jorge

2017-01-01

To test the accuracy and reproducibility of ultrasound and computed tomography (CT) for the quantification of abdominal fat in correlation with the anthropometric, clinical, and biochemical assessments. Using ultrasound and CT, we determined the thickness of subcutaneous and intra-abdominal fat in 101 subjects-of whom 39 (38.6%) were men and 62 (61.4%) were women-with a mean age of 66.3 years (60-80 years). The ultrasound data were correlated with the anthropometric, clinical, and biochemical parameters, as well as with the areas measured by abdominal CT. Intra-abdominal thickness was the variable for which the correlation with the areas of abdominal fat was strongest (i.e., the correlation coefficient was highest). We also tested the reproducibility of ultrasound and CT for the assessment of abdominal fat and found that CT measurements of abdominal fat showed greater reproducibility, having higher intraobserver and interobserver reliability than had the ultrasound measurements. There was a significant correlation between ultrasound and CT, with a correlation coefficient of 0.71. In the assessment of abdominal fat, the intraobserver and interobserver reliability were greater for CT than for ultrasound, although both methods showed high accuracy and good reproducibility.

Sandwich ELISA Microarrays: Generating Reliable and Reproducible Assays for High-Throughput Screens

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

Gonzalez, Rachel M.; Varnum, Susan M.; Zangar, Richard C.

The sandwich ELISA microarray is a powerful screening tool in biomarker discovery and validation due to its ability to simultaneously probe for multiple proteins in a miniaturized assay. The technical challenges of generating and processing the arrays are numerous. However, careful attention to possible pitfalls in the development of your antibody microarray assay can overcome these challenges. In this chapter, we describe in detail the steps that are involved in generating a reliable and reproducible sandwich ELISA microarray assay.

31 CFR 356.21 - How are awards at the high yield or discount rate calculated?

Code of Federal Regulations, 2010 CFR

2010-07-01

... discount rate calculated? 356.21 Section 356.21 Money and Finance: Treasury Regulations Relating to Money... high yield or discount rate calculated? (a) Awards to submitters. We generally prorate bids at the highest accepted yield or discount rate under § 356.20(a)(2) of this part. For example, if 80.15% is the...

An attempt to reproduce high burn-up structure by ion irradiation of SIMFUEL

NASA Astrophysics Data System (ADS)

Baranov, V. G.; Lunev, A. V.; Reutov, V. F.; Tenishev, A. V.; Isaenkova, M. G.; Khlunov, A. V.

2014-09-01

Experiments in IC-100 and U-400 cyclotrons were conducted with SIMFUEL pellets (11.47 wt.% of fission products simulators) to reproduce some aspects of the long-term irradiation conditions in epithermal reactors. Pellets were irradiated with Xe16+, Xe24+ and He+ at energies ranging from 20 keV (He+) to 320 keV (Xe16+) and 1-90 MeV (Xe24+). Some samples were subsequently annealed to obtain larger grain sizes and to study defects recovery. The major microstructural changes consisted in grain sub-division observed on SEM and AFM images and change in composition registered by EPMA (pellets irradiated with 1-90 MeV Xe24+ ions at fluence of 5 × 1015 cm-2). Lattice distortion and increase in dislocation density is also noted according to X-ray data. At low energies and high fluences formation of bubbles (20 keV He+ at 5.5 × 1017 cm-2) was observed. Grain sub-division exhibits full coverage of the grain body and preservation of former grain boundaries. The size of sub-grains depends on local dislocation density and changes from 200 nm to 400 nm along the irradiated surface. Beneath it the size ranges from 150 to 600 nm. Sub-grains are not observed in samples irradiated by low-energy ions even at high dislocation densities.

Fabrication of reproducible, integration-compatible hybrid molecular/si electronics.

PubMed

Yu, Xi; Lovrinčić, Robert; Kraynis, Olga; Man, Gabriel; Ely, Tal; Zohar, Arava; Toledano, Tal; Cahen, David; Vilan, Ayelet

2014-12-29

Reproducible molecular junctions can be integrated within standard CMOS technology. Metal-molecule-semiconductor junctions are fabricated by direct Si-C binding of hexadecane or methyl-styrene onto oxide-free H-Si(111) surfaces, with the lateral size of the junctions defined by an etched SiO2 well and with evaporated Pb as the top contact. The current density, J, is highly reproducible with a standard deviation in log(J) of 0.2 over a junction diameter change from 3 to 100 μm. Reproducibility over such a large range indicates that transport is truly across the molecules and does not result from artifacts like edge effects or defects in the molecular monolayer. Device fabrication is tested for two n-Si doping levels. With highly doped Si, transport is dominated by tunneling and reveals sharp conductance onsets at room temperature. Using the temperature dependence of current across medium-doped n-Si, the molecular tunneling barrier can be separated from the Si-Schottky one, which is a 0.47 eV, in agreement with the molecular-modified surface dipole and quite different from the bare Si-H junction. This indicates that Pb evaporation does not cause significant chemical changes to the molecules. The ability to manufacture reliable devices constitutes important progress toward possible future hybrid Si-based molecular electronics. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Enhanced electron yield from laser-driven wakefield acceleration in high-Z gas jets.

PubMed

Mirzaie, Mohammad; Hafz, Nasr A M; Li, Song; Liu, Feng; He, Fei; Cheng, Ya; Zhang, Jie

2015-10-01

An investigation of the electron beam yield (charge) form helium, nitrogen, and neon gas jet plasmas in a typical laser-plasma wakefield acceleration experiment is carried out. The charge measurement is made by imaging the electron beam intensity profile on a fluorescent screen into a charge coupled device which was cross-calibrated with an integrated current transformer. The dependence of electron beam charge on the laser and plasma conditions for the aforementioned gases are studied. We found that laser-driven wakefield acceleration in low Z-gas jet targets usually generates high-quality and well-collimated electron beams with modest yields at the level of 10-100 pC. On the other hand, filamentary electron beams which are observed from high-Z gases at higher densities reached much higher yields. Evidences for cluster formation were clearly observed in the nitrogen gas jet target, where we received the highest electron beam charge of ∼1.7 nC. Those intense electron beams will be beneficial for the applications on the generation of bright X-rays, gamma rays radiations, and energetic positrons via the bremsstrahlung or inverse-scattering processes.

High quantum-yield phosphors via quantum splitting and upconversion

NASA Astrophysics Data System (ADS)

Jeong, Joayoung

The Gd3+ ion has been used to induce quantum splitting in luminescent materials by using cross-relaxation energy transfer (CRET). In Nd:LiGdF4, quantum splitting results from a two-step CRET between Gd3+ and Nd3+, first involving a transition 6G→6I on Gd3+ and an excitation within the 4f3 configuration of Nd3+ followed by a second CRET that brings Gd3+ to 6P7/2. The excited Nd3+ ion rapidly relaxes nonradiatively to the emitting 4F3/2. The excited Gd3+ ion then transfers its energy back to Nd3+, which gives rise to the second photon. The result is a quantum yield of 1.05 +/- 0.35 with emission in the NIR following excitation at 175 nm. GdF3:Pr3+, Eu 3+ also exhibits quantum splitting, but only at very low concentration of Pr3+ (0.3%) and Eu3+ (0.2%), resulting in a quantum yield of approximately 20% under 160-nm excitation. Host intrinsic emission via a self-trapped exciton (STE) was also examined as a means to sensitize Gd3+ emission. The material ScPO4:Gd 3+ exhibits a high absolute quantum yield of 0.9 +/- 0.2 under 170-nm excitation, demonstrating a potentially new and efficient pathway for exciting quantum splitting phosphors. Single crystals of the material GdZrF7 were grown, and its structure was established via single-crystal X-ray diffraction methods. Doped samples of GdZrF7:Yb3+, Er3+ exhibit bright up-conversion luminescence with light output that is up to twice that of a commercial material based on the host Gd2O2S. When doped with Eu3+, the fluoride also emits a nearly white color under vacuum ultraviolet excitation with an absolute quantum yield near 0.9. The new compound Gd4.67(SiO4)3S was synthesized and studied. The structure was established via single-crystal X-ray methods, and the luminescence of Tb3+ samples was investigated.

Flow “Fine” Synthesis: High Yielding and Selective Organic Synthesis by Flow Methods

PubMed Central

2015-01-01

Abstract The concept of flow “fine” synthesis, that is, high yielding and selective organic synthesis by flow methods, is described. Some examples of flow “fine” synthesis of natural products and APIs are discussed. Flow methods have several advantages over batch methods in terms of environmental compatibility, efficiency, and safety. However, synthesis by flow methods is more difficult than synthesis by batch methods. Indeed, it has been considered that synthesis by flow methods can be applicable for the production of simple gasses but that it is difficult to apply to the synthesis of complex molecules such as natural products and APIs. Therefore, organic synthesis of such complex molecules has been conducted by batch methods. On the other hand, syntheses and reactions that attain high yields and high selectivities by flow methods are increasingly reported. Flow methods are leading candidates for the next generation of manufacturing methods that can mitigate environmental concerns toward sustainable society. PMID:26337828

Label-free protein quantification using LC-coupled ion trap or FT mass spectrometry: Reproducibility, linearity, and application with complex proteomes.

PubMed

Wang, Guanghui; Wu, Wells W; Zeng, Weihua; Chou, Chung-Lin; Shen, Rong-Fong

2006-05-01

A critical step in protein biomarker discovery is the ability to contrast proteomes, a process referred generally as quantitative proteomics. While stable-isotope labeling (e.g., ICAT, 18O- or 15N-labeling, or AQUA) remains the core technology used in mass spectrometry-based proteomic quantification, increasing efforts have been directed to the label-free approach that relies on direct comparison of peptide peak areas between LC-MS runs. This latter approach is attractive to investigators for its simplicity as well as cost effectiveness. In the present study, the reproducibility and linearity of using a label-free approach to highly complex proteomes were evaluated. Various amounts of proteins from different proteomes were subjected to repeated LC-MS analyses using an ion trap or Fourier transform mass spectrometer. Highly reproducible data were obtained between replicated runs, as evidenced by nearly ideal Pearson's correlation coefficients (for ion's peak areas or retention time) and average peak area ratios. In general, more than 50% and nearly 90% of the peptide ion ratios deviated less than 10% and 20%, respectively, from the average in duplicate runs. In addition, the multiplicity ratios of the amounts of proteins used correlated nicely with the observed averaged ratios of peak areas calculated from detected peptides. Furthermore, the removal of abundant proteins from the samples led to an improvement in reproducibility and linearity. A computer program has been written to automate the processing of data sets from experiments with groups of multiple samples for statistical analysis. Algorithms for outlier-resistant mean estimation and for adjusting statistical significance threshold in multiplicity of testing were incorporated to minimize the rate of false positives. The program was applied to quantify changes in proteomes of parental and p53-deficient HCT-116 human cells and found to yield reproducible results. Overall, this study demonstrates an alternative

Extracting DNA from 'jaws': high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material.

PubMed

Nielsen, E E; Morgan, J A T; Maher, S L; Edson, J; Gauthier, M; Pepperell, J; Holmes, B J; Bennett, M B; Ovenden, J R

2017-05-01

Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here, we assessed and optimized the usefulness of abundant archived skeletal material from sharks as a source of DNA for temporal genomic studies. Six different methods for DNA extraction, encompassing two different commercial kits and three different protocols, were applied to material, so-called bio-swarf, from contemporary and archived jaws and vertebrae of tiger sharks (Galeocerdo cuvier). Protocols were compared for DNA yield and quality using a qPCR approach. For jaw swarf, all methods provided relatively high DNA yield and quality, while large differences in yield between protocols were observed for vertebrae. Similar results were obtained from samples of white shark (Carcharodon carcharias). Application of the optimized methods to 38 museum and private angler trophy specimens dating back to 1912 yielded sufficient DNA for downstream genomic analysis for 68% of the samples. No clear relationships between age of samples, DNA quality and quantity were observed, likely reflecting different preparation and storage methods for the trophies. Trial sequencing of DNA capture genomic libraries using 20 000 baits revealed that a significant proportion of captured sequences were derived from tiger sharks. This study demonstrates that archived shark jaws and vertebrae are potential high-yield sources of DNA for genomic-scale analysis. It also highlights that even for similar tissue types, a careful evaluation of extraction protocols can vastly improve DNA yield. © 2016 John Wiley & Sons Ltd.

High-resolution 3D coronary vessel wall imaging with near 100% respiratory efficiency using epicardial fat tracking: reproducibility and comparison with standard methods.

PubMed

Scott, Andrew D; Keegan, Jennifer; Firmin, David N

2011-01-01

To quantitatively assess the performance and reproducibility of 3D spiral coronary artery wall imaging with beat-to-beat respiratory-motion-correction (B2B-RMC) compared to navigator gated 2D spiral and turbo-spin-echo (TSE) acquisitions. High-resolution (0.7 × 0.7 mm) cross-sectional right coronary wall acquisitions were performed in 10 subjects using four techniques (B2B-RMC 3D spiral with alternate (2RR) and single (1RR) R-wave gating, navigator-gated 2D spiral (2RR) and navigator-gated 2D TSE (2RR)) on two occasions. Wall thickness measurements were compared with repeated measures analysis of variance (ANOVA). Reproducibility was assessed with the intraclass correlation coefficient (ICC). In all, 91% (73/80) of acquisitions were successful (failures: four TSE, two 3D spiral (1RR) and one 3D spiral (2RR)). Respiratory efficiency of the B2B-RMC was less variable and substantially higher than for navigator gating (99.6 ± 1.2% vs. 39.0 ± 7.5%, P < 0.0001). Coronary wall thicknesses (± standard deviation [SD]) were not significantly different: 1.10 ± 0.14 mm (3D spiral (2RR)), 1.20 ± 0.16 mm (3D spiral (1RR)), 1.14 ± 0.15 mm (2D spiral), and 1.21 ± 0.17 mm (TSE). Wall thickness reproducibility ranged from good (ICC = 0.65, 3D spiral (1RR)) to excellent (ICC = 0.87, 3D spiral (2RR)). High-resolution 3D spiral imaging with B2B-RMC permits coronary vessel wall assessment over multiple thin contiguous slices in a clinically feasible duration. Excellent reproducibility of the technique potentially enables studies of disease progression/regression. Copyright © 2010 Wiley-Liss, Inc.

Thou Shalt Be Reproducible! A Technology Perspective

PubMed Central

Mair, Patrick

2016-01-01

This article elaborates on reproducibility in psychology from a technological viewpoint. Modern open source computational environments are shown and explained that foster reproducibility throughout the whole research life cycle, and to which emerging psychology researchers should be sensitized, are shown and explained. First, data archiving platforms that make datasets publicly available are presented. Second, R is advocated as the data-analytic lingua franca in psychology for achieving reproducible statistical analysis. Third, dynamic report generation environments for writing reproducible manuscripts that integrate text, data analysis, and statistical outputs such as figures and tables in a single document are described. Supplementary materials are provided in order to get the reader started with these technologies. PMID:27471486

10 CFR 95.43 - Authority to reproduce.

Code of Federal Regulations, 2013 CFR

2013-01-01

... CSA, Secret and Confidential documents may be reproduced. Reproduced copies of classified documents... material must be conspicuously marked with the same classification markings as the material being...

10 CFR 95.43 - Authority to reproduce.

Code of Federal Regulations, 2011 CFR

2011-01-01

... CSA, Secret and Confidential documents may be reproduced. Reproduced copies of classified documents... material must be conspicuously marked with the same classification markings as the material being...

10 CFR 95.43 - Authority to reproduce.

Code of Federal Regulations, 2010 CFR

2010-01-01

... CSA, Secret and Confidential documents may be reproduced. Reproduced copies of classified documents... material must be conspicuously marked with the same classification markings as the material being...

10 CFR 95.43 - Authority to reproduce.

Code of Federal Regulations, 2014 CFR

2014-01-01

... CSA, Secret and Confidential documents may be reproduced. Reproduced copies of classified documents... material must be conspicuously marked with the same classification markings as the material being...

10 CFR 95.43 - Authority to reproduce.

Code of Federal Regulations, 2012 CFR

2012-01-01

... CSA, Secret and Confidential documents may be reproduced. Reproduced copies of classified documents... material must be conspicuously marked with the same classification markings as the material being...

High-yield production of pure tagatose from fructose by a three-step enzymatic cascade reaction.

PubMed

Lee, Seon-Hwa; Hong, Seung-Hye; Kim, Kyoung-Rok; Oh, Deok-Kun

2017-08-01

To produce tagatose from fructose with a high conversion rate and to establish a high-yield purification method of tagatose from the reaction mixture. Fructose at 1 M (180 g l -1 ) was converted to 0.8 M (144 g l -1 ) tagatose by a three-step enzymatic cascade reaction, involving hexokinase, plus ATP, fructose-1,6-biphosphate aldolase, phytase, over 16 h with a productivity of 9 g l -1 h -1 . No byproducts were detected. Tagatose was recrystallized from ethanol to a purity of 99.9% and a yield of 96.3%. Overall, tagatose at 99.9% purity was obtained from fructose with a yield of 77%. This is the first biotechnological production of tagatose from fructose and the first application of solvent recrystallization for the purification of rare sugars.

Creation of High-Yield Polyhydroxyalkanoates Engineered Strains by Low Energy Ion Implantation

NASA Astrophysics Data System (ADS)

Qian, Shiquan; Cheng, Ying; Zhu, Suwen; Cheng, Beijiu

2008-12-01

Polyhydroxyalkanoates (PHAs), as a candidate for biodegradable plastic materials, can be synthesized by numerous microorganisms. However, as its production cost is high in comparison with those of chemically synthesized plastics, a lot of research has been focused on the efficient production of PHAs using different methods. In the present study, the mutation effects of PHAs production in strain pCB4 were investigated with implantation of low energy ions. It was found that under the implantation conditions of 7.8 × 1014 N+/cm2 at 10 keV, a high-yield PHAs strain with high genetic stability was generated from many mutants. After optimizing its fermentation conditions, the biomass, PHAs concentration and PHAs content of pCBH4 reached 2.26 g/L, 1.81 g/L, and 80.08% respectively, whereas its wild type controls were about 1.24 g/L, 0.61 g/L, and 49.20%. Moreover, the main constituent of PHAs was identified as poly-3-hydroxybutyrates (PHB) in the mutant stain and the yield of this compound was increased up to 41.33% in contrast to that of 27.78% in the wild type strain.

Neutron temporal diagnostic for high-yield deuterium-tritium cryogenic implosions on OMEGA

DOE PAGES

Stoeckl, C.; Boni, R.; Ehrne, F.; ...

2016-05-10

A next-generation neutron temporal diagnostic (NTD) capable of recording high-quality data for the highest anticipated yield cryogenic DT implosion experiments was recently installed at the Omega Laser Facility. A high-quality measurement of the neutron production width is required to determine the hot-spot pressure achieved in inertial confinement fusion experiments—a key metric in assessing the quality of these implosions. The design of this NTD is based on a fast-rise-time plastic scintillator, which converts the neutron kinetic energy to 350- to 450-nm-wavelength light. The light from the scintillator inside the nose-cone assembly is relayed ~16 m to a streak camera in amore » well-shielded location. An ~200× reduction in neutron background was observed during the first high-yield DT cryogenic implosions compared to the current NTD installation on OMEGA. An impulse response of ~40±10 ps was measured in a dedicated experiment using hard x rays from a planar target irradiated with a 10-ps short pulse from the OMEGA EP laser. Furthermore, the measured instrument response includes contributions from the scintillator rise time, optical relay, and streak camera.« less

Neutron temporal diagnostic for high-yield deuterium–tritium cryogenic implosions on OMEGA

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

Stoeckl, C.; Boni, R.; Ehrne, F.

A next-generation neutron temporal diagnostic (NTD) capable of recording high-quality data for the highest anticipated yield cryogenic deuterium–tritium (DT) implosion experiments was recently installed at the Omega Laser Facility. A high-quality measurement of the neutron production width is required to determine the hot-spot pressure achieved in inertial confinement fusion experiments—a key metric in assessing the quality of these implosions. The design of this NTD is based on a fast-rise-time plastic scintillator, which converts the neutron kinetic energy to 350- to 450-nm-wavelength light. The light from the scintillator inside the nose-cone assembly is relayed ∼16 m to a streak camera inmore » a well-shielded location. An ∼200× reduction in neutron background was observed during the first high-yield DT cryogenic implosions compared to the current NTD installation on OMEGA. An impulse response of ∼40 ± 10 ps was measured in a dedicated experiment using hard x-rays from a planar target irradiated with a 10-ps short pulse from the OMEGA EP laser. The measured instrument response includes contributions from the scintillator rise time, optical relay, and streak camera.« less

Neutron temporal diagnostic for high-yield deuterium-tritium cryogenic implosions on OMEGA

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

Stoeckl, C.; Boni, R.; Ehrne, F.

A next-generation neutron temporal diagnostic (NTD) capable of recording high-quality data for the highest anticipated yield cryogenic DT implosion experiments was recently installed at the Omega Laser Facility. A high-quality measurement of the neutron production width is required to determine the hot-spot pressure achieved in inertial confinement fusion experiments—a key metric in assessing the quality of these implosions. The design of this NTD is based on a fast-rise-time plastic scintillator, which converts the neutron kinetic energy to 350- to 450-nm-wavelength light. The light from the scintillator inside the nose-cone assembly is relayed ~16 m to a streak camera in amore » well-shielded location. An ~200× reduction in neutron background was observed during the first high-yield DT cryogenic implosions compared to the current NTD installation on OMEGA. An impulse response of ~40±10 ps was measured in a dedicated experiment using hard x rays from a planar target irradiated with a 10-ps short pulse from the OMEGA EP laser. Furthermore, the measured instrument response includes contributions from the scintillator rise time, optical relay, and streak camera.« less

Reproducibility of the spectral components of the electroencephalogram during driver fatigue.

PubMed

Lal, Saroj K L; Craig, Ashley

2005-02-01

To date, no study has tested the reproducibility of EEG changes that occur during driver fatigue. For the EEG changes to be useful in the development of a fatigue countermeasure device the EEG response during each onset period of fatigue in individuals needs to be reproducible. It should be noted that fatigue during driving is not a continuous process but consists of successive episodes of 'microsleeps' where the subject may go in and out of a fatigue state. The aim of the present study was to investigate the reproducibility of fatigue during driving in both professional and non-professional drivers. Thirty five non-professional drivers and twenty professional drivers were tested during two separate sessions of a driver simulator task. EEG, EOG and behavioural measurements of fatigue were obtained during the driving task. The results showed high reproducibility for the delta and theta bands (r>0.95) in both groups of drivers. The results are discussed in light of implications for future studies and for the development of an EEG based fatigue countermeasure device.

Field-based high throughput phenotyping rapidly identifies genomic regions controlling yield components in rice

PubMed Central

Tanger, Paul; Klassen, Stephen; Mojica, Julius P.; Lovell, John T.; Moyers, Brook T.; Baraoidan, Marietta; Naredo, Maria Elizabeth B.; McNally, Kenneth L.; Poland, Jesse; Bush, Daniel R.; Leung, Hei; Leach, Jan E.; McKay, John K.

2017-01-01

To ensure food security in the face of population growth, decreasing water and land for agriculture, and increasing climate variability, crop yields must increase faster than the current rates. Increased yields will require implementing novel approaches in genetic discovery and breeding. Here we demonstrate the potential of field-based high throughput phenotyping (HTP) on a large recombinant population of rice to identify genetic variation underlying important traits. We find that detecting quantitative trait loci (QTL) with HTP phenotyping is as accurate and effective as traditional labor-intensive measures of flowering time, height, biomass, grain yield, and harvest index. Genetic mapping in this population, derived from a cross of an modern cultivar (IR64) with a landrace (Aswina), identified four alleles with negative effect on grain yield that are fixed in IR64, demonstrating the potential for HTP of large populations as a strategy for the second green revolution. PMID:28220807

One-step synthesis of high-yield biodiesel from waste cooking oils by a novel and highly methanol-tolerant immobilized lipase.

PubMed

Wang, Xiumei; Qin, Xiaoli; Li, Daoming; Yang, Bo; Wang, Yonghua

2017-07-01

This study reported a novel immobilized MAS1 lipase from marine Streptomyces sp. strain W007 for synthesizing high-yield biodiesel from waste cooking oils (WCO) with one-step addition of methanol in a solvent-free system. Immobilized MAS1 lipase was selected for the transesterification reactions with one-step addition of methanol due to its much more higher biodiesel yield (89.50%) when compared with the other three commercial immobilized lipases (<10%). The highest biodiesel yield (95.45%) was acquired with one-step addition of methanol under the optimized conditions. Moreover, it was observed that immobilized MAS1 lipase retained approximately 70% of its initial activity after being used for four batch cycles. Finally, the obtained biodiesel was further characterized using FT-IR, 1 H and 13 C NMR spectroscopy. These findings indicated that immobilized MAS1 lipase is a promising catalyst for biodiesel production from WCO with one-step addition of methanol under high methanol concentration. Copyright © 2017 Elsevier Ltd. All rights reserved.

Measurement of gas yields and flow rates using a custom flowmeter

USGS Publications Warehouse

Circone, S.; Kirby, S.H.; Pinkston, J.C.; Stern, L.A.

2001-01-01

A simple gas collection apparatus based on the principles of a Torricelli tube has been designed and built to measure gas volume yields and flow rates. This instrument is routinely used to monitor and collect methane gas released during methane hydrate dissociation experiments. It is easily and inexpensively built, operates at ambient pressures and temperatures, and measures gas volumes of up to 7 L to a precision of about 15 ml (about 0.0025 mol). It is capable of measuring gas flow rates varying from more than 103 to less than 10-1 ml/min during gas evolution events that span minutes to several days. We have obtained a highly reproducible hydrate number of n=5.891 with a propagated uncertainty of ??0.020 for synthetic methane hydrate. ?? 2001 American Institute of Physics.

Maximizing the quantitative accuracy and reproducibility of Förster resonance energy transfer measurement for screening by high throughput widefield microscopy

PubMed Central

Schaufele, Fred

2013-01-01

Förster resonance energy transfer (FRET) between fluorescent proteins (FPs) provides insights into the proximities and orientations of FPs as surrogates of the biochemical interactions and structures of the factors to which the FPs are genetically fused. As powerful as FRET methods are, technical issues have impeded their broad adoption in the biologic sciences. One hurdle to accurate and reproducible FRET microscopy measurement stems from variable fluorescence backgrounds both within a field and between different fields. Those variations introduce errors into the precise quantification of fluorescence levels on which the quantitative accuracy of FRET measurement is highly dependent. This measurement error is particularly problematic for screening campaigns since minimal well-to-well variation is necessary to faithfully identify wells with altered values. High content screening depends also upon maximizing the numbers of cells imaged, which is best achieved by low magnification high throughput microscopy. But, low magnification introduces flat-field correction issues that degrade the accuracy of background correction to cause poor reproducibility in FRET measurement. For live cell imaging, fluorescence of cell culture media in the fluorescence collection channels for the FPs commonly used for FRET analysis is a high source of background error. These signal-to-noise problems are compounded by the desire to express proteins at biologically meaningful levels that may only be marginally above the strong fluorescence background. Here, techniques are presented that correct for background fluctuations. Accurate calculation of FRET is realized even from images in which a non-flat background is 10-fold higher than the signal. PMID:23927839

Reproducibility of airway luminal size in asthma measured by HRCT.

PubMed

Brown, Robert H; Henderson, Robert J; Sugar, Elizabeth A; Holbrook, Janet T; Wise, Robert A

2017-10-01

Brown RH, Henderson RJ, Sugar EA, Holbrook JT, Wise RA, on behalf of the American Lung Association Airways Clinical Research Centers. Reproducibility of airway luminal size in asthma measured by HRCT. J Appl Physiol 123: 876-883, 2017. First published July 13, 2017; doi:10.1152/japplphysiol.00307.2017.-High-resolution CT (HRCT) is a well-established imaging technology used to measure lung and airway morphology in vivo. However, there is a surprising lack of studies examining HRCT reproducibility. The CPAP Trial was a multicenter, randomized, three-parallel-arm, sham-controlled 12-wk clinical trial to assess the use of a nocturnal continuous positive airway pressure (CPAP) device on airway reactivity to methacholine. The lack of a treatment effect of CPAP on clinical or HRCT measures provided an opportunity for the current analysis. We assessed the reproducibility of HRCT imaging over 12 wk. Intraclass correlation coefficients (ICCs) were calculated for individual airway segments, individual lung lobes, both lungs, and air trapping. The ICC [95% confidence interval (CI)] for airway luminal size at total lung capacity ranged from 0.95 (0.91, 0.97) to 0.47 (0.27, 0.69). The ICC (95% CI) for airway luminal size at functional residual capacity ranged from 0.91 (0.85, 0.95) to 0.32 (0.11, 0.65). The ICC measurements for airway distensibility index and wall thickness were lower, ranging from poor (0.08) to moderate (0.63) agreement. The ICC for air trapping at functional residual capacity was 0.89 (0.81, 0.94) and varied only modestly by lobe from 0.76 (0.61, 0.87) to 0.95 (0.92, 0.97). In stable well-controlled asthmatic subjects, it is possible to reproducibly image unstimulated airway luminal areas over time, by region, and by size at total lung capacity throughout the lungs. Therefore, any changes in luminal size on repeat CT imaging are more likely due to changes in disease state and less likely due to normal variability. NEW & NOTEWORTHY There is a surprising lack

High char yield epoxy curing agents

NASA Technical Reports Server (NTRS)

Delvigs, P.; Serafini, T. T.; Vanucci, R. D.

1981-01-01

Class of imide-amine curing agents preserves structural integrity, prevents fiber release, and is fully compatible with conventional epoxy resins; agents do not detract from composite properties while greatly reducing char yield. Materials utilizing curing are used in aerospace, automotive, and other structural components where deterioration must be minimized and fiber release avoided in event of fire.

Climate Change Impacts on Sediment Yield in Headwaters of a High-latitude Region in China

NASA Astrophysics Data System (ADS)

Zhou, Y.; Xu, Y. J.; Wang, J., , Dr; Weihua, X.; Huang, Y.

2017-12-01

Climate change is expected to have strongest effects in higher latitude regions. Despite intensive research on possible hydrological responses to global warming in these regions, our knowledge of climate change on surface erosion and sediment yield in high-latitude headwaters is limited. In this study, we used the Soil and Water Assessment Tool (SWAT) to predict future runoff and sediment yield from the headwaters of a high-latitude river basin in China's far northeast. The SWAT model was first calibrated with historical discharge records and the model parameterization achieved satisfactory validation. The calibrated model was then applied to two greenhouse gas concentration trajectories, RCP4.5 and RCP8.5, for the period from 2020 to 2050 to estimate future runoff. Sediment yields for this period were predicted using a discharge-sediment load rating curve developed from field measurements in the past nine years. Our preliminary results show an increasing trend of sediment yield under both climate change scenarios, and that the increase is more pronounced in the summer and autumn months. Changes in precipitation and temperature seem to exert variable impacts on runoff and sediment yield at interannual and seasonal scales in these headwaters. These findings imply that the current river basin management in the region needs to be reviewed and improved in order to be effective under a changing climate.

Creating a High-Touch Recruitment Event: Utilizing Faculty to Recruit and Yield Students

ERIC Educational Resources Information Center

Freed, Lindsey R.; Howell, Leanne L.

2018-01-01

The following article describes the planning and implementation of a university student recruitment event that produced a high (new) student yield. Detailed descriptions of how staff and faculty worked together to plan and implement this event are described.

Studies of fission fragment yields via high-resolution γ-ray spectroscopy

NASA Astrophysics Data System (ADS)

Wilson, J. N.; Lebois, M.; Qi, L.; Amador-Celdran, P.; Bleuel, D.; Briz, J. A.; Carroll, R.; Catford, W.; Witte, H. De; Doherty, D. T.; Eloirdi, R.; Georgiev, G.; Gottardo, A.; Goasduff, A.; Hadyñska-Klek, K.; Hauschild, K.; Hess, H.; Ingeberg, V.; Konstantinopoulos, T.; Ljungvall, J.; Lopez-Martens, A.; Lorusso, G.; Lozeva, R.; Lutter, R.; Marini, P.; Matea, I.; Materna, T.; Mathieu, L.; Oberstedt, A.; Oberstedt, S.; Panebianco, S.; Podolyak, Zs.; Porta, A.; Regan, P. H.; Reiter, P.; Rezynkina, K.; Rose, S. J.; Sahin, E.; Seidlitz, M.; Serot, O.; Shearman, R.; Siebeck, B.; Siem, S.; Smith, A. G.; Tveten, G. M.; Verney, D.; Warr, N.; Zeiser, F.; Zielinska, M.

2018-03-01

Precise spectroscopic information on the fast neutron induced fission of the 238U(n,f) reaction was recently gained using a new technique which involved coupling of the Miniball high resolution y-ray spectrometer and the LICORNE directional neutron source. The experiment allowed measurement of the isotopic fission yields for around 40 even-even nuclei at an incident neutron energy of around 2 MeV where yield data are very sparse. In addition spectroscopic information on very neutron-rich fission products was obtained. Results were compared to models, both the JEFF-3.1.1 data base and the GEF code, and large discrepancies for the S1 fission mode in the Sn/Mo isotope pair were discovered. This suggests that current models are overestimating the role played by spherical shell effects in fast neutron induced fission. In late 2017 and 2018 the nu-ball hybrid spectrometer will be constructed at the IPN Orsay to perform further experimental investigations with directional neutrons coupled to a powerful hybrid Ge/LaBr3 detector array. This will open up new possibilities for measurements of fission yields for fast-neutron-induced fission using the spectroscopic technique and will be complimentary to other methods being developed.

New approach to increasing rice lodging resistance and biomass yield through the use of high gibberellin producing varieties.

PubMed

Okuno, Ayako; Hirano, Ko; Asano, Kenji; Takase, Wakana; Masuda, Reiko; Morinaka, Yoichi; Ueguchi-Tanaka, Miyako; Kitano, Hidemi; Matsuoka, Makoto

2014-01-01

Traditional breeding for high-yielding rice has been dependent on the widespread use of fertilizers and the cultivation of gibberellin (GA)-deficient semi-dwarf varieties. The use of semi-dwarf plants facilitates high grain yield since these varieties possess high levels of lodging resistance, and thus could support the high grain weight. Although this approach has been successful in increasing grain yield, it is desirable to further improve grain production and also to breed for high biomass. In this study, we re-examined the effect of GA on rice lodging resistance and biomass yield using several GA-deficient mutants (e.g. having defects in the biosynthesis or perception of GA), and high-GA producing line or mutant. GA-deficient mutants displayed improved bending-type lodging resistance due to their short stature; however they showed reduced breaking-type lodging resistance and reduced total biomass. In plants producing high amounts of GA, the bending-type lodging resistance was inferior to the original cultivars. The breaking-type lodging resistance was improved due to increased lignin accumulation and/or larger culm diameters. Further, these lines had an increase in total biomass weight. These results show that the use of rice cultivars producing high levels of GA would be a novel approach to create higher lodging resistance and biomass.

Highly reproducible laser beam scanning device for an internal source laser desorption microprobe Fourier transform mass spectrometer

NASA Astrophysics Data System (ADS)

Scott, Jill R.; Tremblay, Paul L.

2002-03-01

Traditionally, mass spectrometry has relied on manipulating the sample target to provide scanning capabilities for laser desorption microprobes. This has been problematic for an internal source laser desorption Fourier transform mass spectrometer (LD-FTMS) because of the high magnetic field (7 Tesla) and geometric constraints of the superconducting magnet bore. To overcome these limitations, we have implemented a unique external laser scanning mechanism for an internal source LD-FTMS. This mechanism provides adjustable resolution enhancement so that the spatial resolution at the target is not limited to that of the stepper motors at the light source (˜5 μm/step). The spatial resolution is now limited by the practical optical diffraction limit of the final focusing lens. The scanning mechanism employs a virtual source that is wavelength independent up to the final focusing lens, which can be controlled remotely to account for focal length dependence on wavelength. A binary index provides an automatic alignment feature. The virtual source is located ˜9 ft from the sample; therefore, it is completely outside of the vacuum system and beyond the 50 G line of the fringing magnetic field. To eliminate reproducibility problems associated with vacuum pump vibrations, we have taken advantage of the magnetic field inherent to the FTMS to utilize Lenz's law for vibrational dampening. The LD-FTMS microprobe has exceptional reproducibility, which enables successive mapping sequences for depth-profiling studies.

Reproducibility of peripapillary retinal nerve fiber layer thickness with spectral domain cirrus high-definition optical coherence tomography in normal eyes.

PubMed

Hong, Samin; Kim, Chan Yun; Lee, Won Seok; Seong, Gong Je

2010-01-01

To assess the reproducibility of the new spectral domain Cirrus high-definition optical coherence tomography (HD-OCT; Carl Zeiss Meditec, Dublin, CA, USA) for analysis of peripapillary retinal nerve fiber layer (RNFL) thickness in healthy eyes. Thirty healthy Korean volunteers were enrolled. Three optic disc cube 200 x 200 Cirrus HD-OCT scans were taken on the same day in discontinuous sessions by the same operator without using the repeat scan function. The reproducibility of the calculated RNFL thickness and probability code were determined by the intraclass correlation coefficient (ICC), coefficient of variation (CV), test-retest variability, and Fleiss' generalized kappa (kappa). Thirty-six eyes were analyzed. For average RNFL thickness, the ICC was 0.970, CV was 2.38%, and test-retest variability was 4.5 microm. For all quadrants except the nasal, ICCs were 0.972 or higher and CVs were 4.26% or less. Overall test-retest variability ranged from 5.8 to 8.1 microm. The kappa value of probability codes for average RNFL thickness was 0.690. The kappa values of quadrants and clock-hour sectors were lower in the nasal areas than in other areas. The reproducibility of Cirrus HD-OCT to analyze peripapillary RNFL thickness in healthy eyes was excellent compared with the previous reports for time domain Stratus OCT. For the calculated RNFL thickness and probability code, variability was relatively higher in the nasal area, and more careful analyses are needed.

Reproducibility of abdominal fat assessment by ultrasound and computed tomography

PubMed Central

Mauad, Fernando Marum; Chagas-Neto, Francisco Abaeté; Benedeti, Augusto César Garcia Saab; Nogueira-Barbosa, Marcello Henrique; Muglia, Valdair Francisco; Carneiro, Antonio Adilton Oliveira; Muller, Enrico Mattana; Elias Junior, Jorge

2017-01-01

Objective: To test the accuracy and reproducibility of ultrasound and computed tomography (CT) for the quantification of abdominal fat in correlation with the anthropometric, clinical, and biochemical assessments. Materials and Methods: Using ultrasound and CT, we determined the thickness of subcutaneous and intra-abdominal fat in 101 subjects-of whom 39 (38.6%) were men and 62 (61.4%) were women-with a mean age of 66.3 years (60-80 years). The ultrasound data were correlated with the anthropometric, clinical, and biochemical parameters, as well as with the areas measured by abdominal CT. Results: Intra-abdominal thickness was the variable for which the correlation with the areas of abdominal fat was strongest (i.e., the correlation coefficient was highest). We also tested the reproducibility of ultrasound and CT for the assessment of abdominal fat and found that CT measurements of abdominal fat showed greater reproducibility, having higher intraobserver and interobserver reliability than had the ultrasound measurements. There was a significant correlation between ultrasound and CT, with a correlation coefficient of 0.71. Conclusion: In the assessment of abdominal fat, the intraobserver and interobserver reliability were greater for CT than for ultrasound, although both methods showed high accuracy and good reproducibility. PMID:28670024

High-Yield Secretion of Multiple Client Proteins in Aspergillus

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

Segato, F.; Damasio, A. R. L.; Goncalves, T. A.

2012-07-15

Production of pure and high-yield client proteins is an important technology that addresses the need for industrial applications of enzymes as well as scientific experiments in protein chemistry and crystallization. Fungi are utilized in industrial protein production because of their ability to secrete large quantities of proteins. In this study, we engineered a high-expression-secretion vector, pEXPYR that directs proteins towards the extracellular medium in two Aspergillii host strains, examine the effect of maltose-induced over-expression and protein secretion as well as time and pH-dependent protein stability in the medium. We describe five client proteins representing a core set of hemicellulose degradingmore » enzymes that accumulated up to 50-100 mg/L of protein. Using a recyclable genetic marker that allows serial insertion of multiple genes, simultaneous hyper-secretion of three client proteins in a single host strain was accomplished.« less

Field-based high throughput phenotyping rapidly identifies genomic regions controlling yield components in rice

DOE PAGES

Tanger, Paul; Klassen, Stephen; Mojica, Julius P.; ...

2017-02-21

In order to ensure food security in the face of population growth, decreasing water and land for agriculture, and increasing climate variability, crop yields must increase faster than the current rates. Increased yields will require implementing novel approaches in genetic discovery and breeding. We demonstrate the potential of field-based high throughput phenotyping (HTP) on a large recombinant population of rice to identify genetic variation underlying important traits. We find that detecting quantitative trait loci (QTL) with HTP phenotyping is as accurate and effective as traditional labor- intensive measures of flowering time, height, biomass, grain yield, and harvest index. Furthermore, geneticmore » mapping in this population, derived from a cross of an modern cultivar (IR64) with a landrace (Aswina), identified four alleles with negative effect on grain yield that are fixed in IR64, demonstrating the potential for HTP of large populations as a strategy for the second green revolution.« less

Field-based high throughput phenotyping rapidly identifies genomic regions controlling yield components in rice

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

Tanger, Paul; Klassen, Stephen; Mojica, Julius P.

In order to ensure food security in the face of population growth, decreasing water and land for agriculture, and increasing climate variability, crop yields must increase faster than the current rates. Increased yields will require implementing novel approaches in genetic discovery and breeding. We demonstrate the potential of field-based high throughput phenotyping (HTP) on a large recombinant population of rice to identify genetic variation underlying important traits. We find that detecting quantitative trait loci (QTL) with HTP phenotyping is as accurate and effective as traditional labor- intensive measures of flowering time, height, biomass, grain yield, and harvest index. Furthermore, geneticmore » mapping in this population, derived from a cross of an modern cultivar (IR64) with a landrace (Aswina), identified four alleles with negative effect on grain yield that are fixed in IR64, demonstrating the potential for HTP of large populations as a strategy for the second green revolution.« less

Research Reproducibility in Geosciences: Current Landscape, Practices and Perspectives

NASA Astrophysics Data System (ADS)

Yan, An

2016-04-01

Reproducibility of research can gauge the validity of its findings. Yet currently we lack understanding of how much of a problem research reproducibility is in geosciences. We developed an online survey on faculty and graduate students in geosciences, and received 136 responses from research institutions and universities in Americas, Asia, Europe and other parts of the world. This survey examined (1) the current state of research reproducibility in geosciences by asking researchers' experiences with unsuccessful replication work, and what obstacles that lead to their replication failures; (2) the current reproducibility practices in community by asking what efforts researchers made to try to reproduce other's work and make their own work reproducible, and what the underlying factors that contribute to irreproducibility are; (3) the perspectives on reproducibility by collecting researcher's thoughts and opinions on this issue. The survey result indicated that nearly 80% of respondents who had ever reproduced a published study had failed at least one time in reproducing. Only one third of the respondents received helpful feedbacks when they contacted the authors of a published study for data, code, or other information. The primary factors that lead to unsuccessful replication attempts are insufficient details of instructions in published literature, and inaccessibility of data, code and tools needed in the study. Our findings suggest a remarkable lack of research reproducibility in geoscience. Changing the incentive mechanism in academia, as well as developing policies and tools that facilitate open data and code sharing are the promising ways for geosciences community to alleviate this reproducibility problem.

Exogenously Applied Plant Growth Regulators Enhance the Morpho-Physiological Growth and Yield of Rice under High Temperature.

PubMed

Fahad, Shah; Hussain, Saddam; Saud, Shah; Hassan, Shah; Ihsan, Zahid; Shah, Adnan N; Wu, Chao; Yousaf, Muhammad; Nasim, Wajid; Alharby, Hesham; Alghabari, Fahad; Huang, Jianliang

2016-01-01

A 2-year experiment was conducted to ascertain the effects of exogenously applied plant growth regulators (PGR) on rice growth and yield attributes under high day (HDT) and high night temperature (HNT). Two rice cultivars (IR-64 and Huanghuazhan) were subjected to temperature treatments in controlled growth chambers and four different combinations of ascorbic acid (Vc), alpha-tocopherol (Ve), brassinosteroids (Br), methyl jasmonates (MeJA), and triazoles (Tr) were applied. High temperature severely affected rice morphology, and also reduced leaf area, above-, and below-ground biomass, photosynthesis, and water use efficiency, while increased the leaf water potential of both rice cultivars. Grain yield and its related attributes except number of panicles, were reduced under high temperature. The HDT posed more negative effects on rice physiological attributes, while HNT was more detrimental for grain formation and yield. The Huanghuazhan performed better than IR-64 under high temperature stress with better growth and higher grain yield. Exogenous application of PGRs was helpful in alleviating the adverse effects of high temperature. Among PGR combinations, the Vc+Ve+MejA+Br was the most effective treatment for both cultivars under high temperature stress. The highest grain production by Vc+Ve+MejA+Br treated plants was due to enhanced photosynthesis, spikelet fertility and grain filling, which compensated the adversities of high temperature stress. Taken together, these results will be of worth for further understanding the adaptation and survival mechanisms of rice to high temperature and will assist in developing heat-resistant rice germplasm in future.

Optimizing multi-dimensional high throughput screening using zebrafish.

PubMed

Truong, Lisa; Bugel, Sean M; Chlebowski, Anna; Usenko, Crystal Y; Simonich, Michael T; Simonich, Staci L Massey; Tanguay, Robert L

2016-10-01

The use of zebrafish for high throughput screening (HTS) for chemical bioactivity assessments is becoming routine in the fields of drug discovery and toxicology. Here we report current recommendations from our experiences in zebrafish HTS. We compared the effects of different high throughput chemical delivery methods on nominal water concentration, chemical sorption to multi-well polystyrene plates, transcription responses, and resulting whole animal responses. We demonstrate that digital dispensing consistently yields higher data quality and reproducibility compared to standard plastic tip-based liquid handling. Additionally, we illustrate the challenges in using this sensitive model for chemical assessment when test chemicals have trace impurities. Adaptation of these better practices for zebrafish HTS should increase reproducibility across laboratories. Copyright © 2016 Elsevier Inc. All rights reserved.

Metabolic engineering of biomass for high energy density: oilseed-like triacylglycerol yields from plant leaves

PubMed Central

Vanhercke, Thomas; El Tahchy, Anna; Liu, Qing; Zhou, Xue-Rong; Shrestha, Pushkar; Divi, Uday K; Ral, Jean-Philippe; Mansour, Maged P; Nichols, Peter D; James, Christopher N; Horn, Patrick J; Chapman, Kent D; Beaudoin, Frederic; Ruiz-López, Noemi; Larkin, Philip J; de Feyter, Robert C; Singh, Surinder P; Petrie, James R

2014-01-01

High biomass crops have recently attracted significant attention as an alternative platform for the renewable production of high energy storage lipids such as triacylglycerol (TAG). While TAG typically accumulates in seeds as storage compounds fuelling subsequent germination, levels in vegetative tissues are generally low. Here, we report the accumulation of more than 15% TAG (17.7% total lipids) by dry weight in Nicotiana tabacum (tobacco) leaves by the co-expression of three genes involved in different aspects of TAG production without severely impacting plant development. These yields far exceed the levels found in wild-type leaf tissue as well as previously reported engineered TAG yields in vegetative tissues of Arabidopsis thaliana and N. tabacum. When translated to a high biomass crop, the current levels would translate to an oil yield per hectare that exceeds those of most cultivated oilseed crops. Confocal fluorescence microscopy and mass spectrometry imaging confirmed the accumulation of TAG within leaf mesophyll cells. In addition, we explored the applicability of several existing oil-processing methods using fresh leaf tissue. Our results demonstrate the technical feasibility of a vegetative plant oil production platform and provide for a step change in the bioenergy landscape, opening new prospects for sustainable food, high energy forage, biofuel and biomaterial applications. PMID:24151938

Determining the Critical Dose Threshold of Electron-Induced Electron Yield for Minimally Charged Highly Insulating Materials

NASA Astrophysics Data System (ADS)

Hoffmann, Ryan; Dennison, J. R.; Abbott, Jonathan

2006-03-01

When incident energetic electrons interact with a material, they excite electrons within the material to escape energies. The electron emission is quantified as the ratio of emitted electrons to incident particle flux, termed electron yield. Measuring the electron yield of insulators is difficult due to dynamic surface charge accumulation which directly affects landing energies and the potential barrier that emitted electrons must overcome. Our recent measurements of highly insulating materials have demonstrated significant changes in total yield curves and yield decay curves for very small electron doses equivalent to a trapped charge density of <10^10 electrons /cm^3. The Chung-Everhart theory provides a basic model for the behavior of the electron emission spectra which we relate to yield decay curves as charge is allowed to accumulate. Yield measurements as a function of dose for polyimide (Kapton^TM) and microcrystalline SiO2 will be presented. We use our data and model to address the question of whether there is a minimal dose threshold at which the accumulated charge no longer affects the yield.

Can the Λ CDM model reproduce MOND-like behavior?

NASA Astrophysics Data System (ADS)

Dai, De-Chang; Lu, Chunyu

2017-12-01

It is usually believed that MOND can describe the galactic rotational curves with only baryonic matter and without any dark matter very well, while the Λ CDM model is expected to have difficulty in reproducing MOND-like behavior. Here, we use EAGLE's data to learn whether the Λ CDM model can reproduce MOND-like behavior. EAGLE's simulation result clearly reproduces the MOND-like behavior for ab⪆10-12 m/s 2 at z =0 , although the acceleration constant, a0, is a little larger than the observational data indicate. We find that a0 increases with the redshift in a way different from what Milgrom proposed (a0∝H ). Therefore, while galaxy rotation curves can be fitted by MOND's empirical function in the Λ CDM model, there is no clear connection between a0 and the Hubble constant. We also find that a0 at z ⪆1 is well separated from a0 at z =0 . Once we have enough galaxies observed at high redshifts, we will be able to rule out the modified gravity model based on MOND-like empirical function with a z -independent a0.

Repeatability and reproducibility of corneal thickness using SOCT Copernicus HR.

PubMed

Vidal, Silvia; Viqueira, Valentín; Mas, David; Domenech, Begoña

2013-05-01

The aim of this study is to determine the reliability of corneal thickness measurements derived from SOCT Copernicus HR (Fourier domain OCT). Thirty healthy eyes of 30 subjects were evaluated. One eye of each patient was chosen randomly. Images were obtained of the central (up to 2.0 mm from the corneal apex) and paracentral (2.0 to 4.0 mm) cornea. We assessed corneal thickness (central and paracentral) and epithelium thickness. The intra-observer repeatability data were analysed using the intra-class correlation coefficient (ICC) for a range of 95 per cent within-subject standard deviation (S(W)) and the within-subject coefficient of variation (C(W)). The level of agreement by Bland-Altman analysis was also represented for the study of the reproducibility between observers and agreement between methods of measurement (automatic versus manual). The mean value of the central corneal thickness (CCT) was 542.4 ± 30.1 μm (SD). There was a high intra-observer agreement, finding the best result in the central sector with an intra-class correlation coefficient of 0.99, 95 per cent CI (0.989 to 0.997) and the worst, in the minimum corneal thickness, with an intra-class correlation coefficient of 0.672, 95 per cent CI (0.417 to 0.829). Reproducibility between observers was very high. The best result was found in the central sector thickness obtained both manually and automatically with an intra-class correlation coefficient of 0.990 in both cases and the worst result in the maximum corneal thickness with an intra-class correlation coefficient of 0.827. The agreement between measurement methods was also very high with intra-class correlation coefficient greater than 0.91. On the other hand the repeatability and reproducibility for epithelial measurements was poor. Pachymetric mapping with SOCT Copernicus HR was found to be highly repeatable and reproducible. We found that the device lacks an appropriate ergonomic design as proper focusing of the laser beam onto the

High-yield exfoliation of tungsten disulphide nanosheets by rational mixing of low-boiling-point solvents

NASA Astrophysics Data System (ADS)

Sajedi-Moghaddam, Ali; Saievar-Iranizad, Esmaiel

2018-01-01

Developing high-throughput, reliable, and facile approaches for producing atomically thin sheets of transition metal dichalcogenides is of great importance to pave the way for their use in real applications. Here, we report a highly promising route for exfoliating two-dimensional tungsten disulphide sheets by using binary combination of low-boiling-point solvents. Experimental results show significant dependence of exfoliation yield on the type of solvents as well as relative volume fraction of each solvent. The highest yield was found for appropriate combination of isopropanol/water (20 vol% isopropanol and 80 vol% water) which is approximately 7 times higher than that in pure isopropanol and 4 times higher than that in pure water. The dramatic increase in exfoliation yield can be attributed to perfect match between the surface tension of tungsten disulphide and binary solvent system. Furthermore, solvent molecular size also has a profound impact on the exfoliation efficiency, due to the steric repulsion.

Power law behavior of the isotope yield distributions in the multifragmentation regime of heavy ion reactions

NASA Astrophysics Data System (ADS)

Huang, M.; Wada, R.; Chen, Z.; Keutgen, T.; Kowalski, S.; Hagel, K.; Barbui, M.; Bonasera, A.; Bottosso, C.; Materna, T.; Natowitz, J. B.; Qin, L.; Rodrigues, M. R. D.; Sahu, P. K.; Schmidt, K. J.; Wang, J.

2010-11-01

Isotope yield distributions in the multifragmentation regime were studied with high-quality isotope identification, focusing on the intermediate mass fragments (IMFs) produced in semiviolent collisions. The yields were analyzed within the framework of a modified Fisher model. Using the ratio of the mass-dependent symmetry energy coefficient relative to the temperature, asym/T, extracted in previous work and that of the pairing term, ap/T, extracted from this work, and assuming that both reflect secondary decay processes, the experimentally observed isotope yields were corrected for these effects. For a given I=N-Z value, the corrected yields of isotopes relative to the yield of C12 show a power law distribution Y(N,Z)/Y(12C)~A-τ in the mass range 1⩽A⩽30, and the distributions are almost identical for the different reactions studied. The observed power law distributions change systematically when I of the isotopes changes and the extracted τ value decreases from 3.9 to 1.0 as I increases from -1 to 3. These observations are well reproduced by a simple deexcitation model, with which the power law distribution of the primary isotopes is determined to be τprim=2.4±0.2, suggesting that the disassembling system at the time of the fragment formation is indeed at, or very near, the critical point.

Electron-induced electron yields of uncharged insulating materials

NASA Astrophysics Data System (ADS)

Hoffmann, Ryan Carl

Presented here are electron-induced electron yield measurements from high-resistivity, high-yield materials to support a model for the yield of uncharged insulators. These measurements are made using a low-fluence, pulsed electron beam and charge neutralization to minimize charge accumulation. They show charging induced changes in the total yield, as much as 75%, even for incident electron fluences of <3 fC/mm2, when compared to an uncharged yield. The evolution of the yield as charge accumulates in the material is described in terms of electron recapture, based on the extended Chung and Everhart model of the electron emission spectrum and the dual dynamic layer model for internal charge distribution. This model is used to explain charge-induced total yield modification measured in high-yield ceramics, and to provide a method for determining electron yield of uncharged, highly insulating, high-yield materials. A sequence of materials with progressively greater charge susceptibility is presented. This series starts with low-yield Kapton derivative called CP1, then considers a moderate-yield material, Kapton HN, and ends with a high-yield ceramic, polycrystalline aluminum oxide. Applicability of conductivity (both radiation induced conductivity (RIC) and dark current conductivity) to the yield is addressed. Relevance of these results to spacecraft charging is also discussed.

Epidemiology and impact of Fasciola hepatica exposure in high-yielding dairy herds

PubMed Central

Howell, Alison; Baylis, Matthew; Smith, Rob; Pinchbeck, Gina; Williams, Diana

2015-01-01

The liver fluke Fasciola hepatica is a trematode parasite with a worldwide distribution and is the cause of important production losses in the dairy industry. The aim of this observational study was to assess the prevalence of exposure to F. hepatica in a group of high yielding dairy herds, to determine the risk factors and investigate their associations with production and fertility parameters. Bulk milk tank samples from 606 herds that supply a single retailer with liquid milk were tested with an antibody ELISA for F. hepatica. Multivariable linear regression was used to investigate the effect of farm management and environmental risk factors on F. hepatica exposure. Higher rainfall, grazing boggy pasture, presence of beef cattle on farm, access to a stream or pond and smaller herd size were associated with an increased risk of exposure. Univariable regression was used to look for associations between fluke exposure and production-related variables including milk yield, composition, somatic cell count and calving index. Although causation cannot be assumed, a significant (p < 0.001) negative association was seen between F. hepatica exposure and estimated milk yield at the herd level, representing a 15% decrease in yield for an increase in F. hepatica exposure from the 25th to the 75th percentile. This remained significant when fertility, farm management and environmental factors were controlled for. No associations were found between F. hepatica exposure and any of the other production, disease or fertility variables. PMID:26093971

Simple, high-yield purification of xanthine oxidase from bovine milk.

PubMed

Ozer, N; Müftüoglu, M; Ataman, D; Ercan, A; Ogüs, I H

1999-05-13

Xanthine oxidase, a commercially important enzyme with a wide area of application, was extracted from fresh milk, without added preservatives, using toluene and heat. The short purification procedure, with high yield, consisted of extraction, ammonium sulfate fractionation, and DEAE-Sepharose (fast flow) column chromatography. Xanthine oxidase was eluted as a single activity peak from the column using a buffer gradient. The purification fold, specific activity and yield for the purified xanthine oxidase were 328, 10.161 U/mg and 69%, respectively. The enzyme was concentrated by ultrafiltration, although 31% of the activity was lost during concentration, no change in specific activity was observed. Activity and protein gave coincident staining bands on native polyacrylamide gels. The intensity and the number of bands were dependent on the oxidative state(s) of the enzyme; reduction by 2-mercaptoethanol decreased the intensity of the slow-moving bands and increased the intensity of the fastest-moving band. Following sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), two major bands (molecular masses of 152 and 131 kDa) were observed, accounting for > or = 95% of xanthine oxidase. Native- and SDS-PAGE showed that the purified xanthine oxidase becomes a heterodimer due to endogenous proteases.

The flux qubit revisited to enhance coherence and reproducibility

PubMed Central

Yan, Fei; Gustavsson, Simon; Kamal, Archana; Birenbaum, Jeffrey; Sears, Adam P; Hover, David; Gudmundsen, Ted J.; Rosenberg, Danna; Samach, Gabriel; Weber, S; Yoder, Jonilyn L.; Orlando, Terry P.; Clarke, John; Kerman, Andrew J.; Oliver, William D.

2016-01-01

The scalable application of quantum information science will stand on reproducible and controllable high-coherence quantum bits (qubits). Here, we revisit the design and fabrication of the superconducting flux qubit, achieving a planar device with broad-frequency tunability, strong anharmonicity, high reproducibility and relaxation times in excess of 40 μs at its flux-insensitive point. Qubit relaxation times T1 across 22 qubits are consistently matched with a single model involving resonator loss, ohmic charge noise and 1/f-flux noise, a noise source previously considered primarily in the context of dephasing. We furthermore demonstrate that qubit dephasing at the flux-insensitive point is dominated by residual thermal-photons in the readout resonator. The resulting photon shot noise is mitigated using a dynamical decoupling protocol, resulting in T2≈85 μs, approximately the 2T1 limit. In addition to realizing an improved flux qubit, our results uniquely identify photon shot noise as limiting T2 in contemporary qubits based on transverse qubit–resonator interaction. PMID:27808092

Three Dimensions of Reproducibility in Natural Language Processing.

PubMed

Cohen, K Bretonnel; Xia, Jingbo; Zweigenbaum, Pierre; Callahan, Tiffany J; Hargraves, Orin; Goss, Foster; Ide, Nancy; Névéol, Aurélie; Grouin, Cyril; Hunter, Lawrence E

2018-05-01

Despite considerable recent attention to problems with reproducibility of scientific research, there is a striking lack of agreement about the definition of the term. That is a problem, because the lack of a consensus definition makes it difficult to compare studies of reproducibility, and thus to have even a broad overview of the state of the issue in natural language processing. This paper proposes an ontology of reproducibility in that field. Its goal is to enhance both future research and communication about the topic, and retrospective meta-analyses. We show that three dimensions of reproducibility, corresponding to three kinds of claims in natural language processing papers, can account for a variety of types of research reports. These dimensions are reproducibility of a conclusion , of a finding , and of a value. Three biomedical natural language processing papers by the authors of this paper are analyzed with respect to these dimensions.

High yield cell-free production of integral membrane proteins without refolding or detergents.

PubMed

Wuu, Jessica J; Swartz, James R

2008-05-01

Integral membrane proteins act as critical cellular components and are important drug targets. However, difficulties in producing membrane proteins have hampered investigations of structure and function. In vivo production systems are often limited by cell toxicity, and previous in vitro approaches have required unnatural folding pathways using detergents or lipid solutions. To overcome these limitations, we present an improved cell-free expression system which produces high yields of integral membrane proteins without the use of detergents or refolding steps. Our cell-free reaction activates an Escherichia coli-derived cell extract for transcription and translation. Purified E. coli inner membrane vesicles supply membrane-bound components and the lipid environment required for insertion and folding. Using this system, we demonstrated successful synthesis of two complex integral membrane transporters, the tetracycline pump (TetA) and mannitol permease (MtlA), in yields of 570+/-50 microg/mL and 130+/-30 microg/mL of vesicle-associated protein, respectively. These yields are up to 400 times typical in vivo concentrations. Insertion and folding of these proteins are verified by sucrose flotation, protease digestion, and activity assays. Whereas TetA incorporates efficiently into vesicle membranes with over two-thirds of the synthesized protein being inserted, MtlA yields appear to be limited by insufficient concentrations of a membrane-associated chaperone.

Rotary head type reproducing apparatus

DOEpatents

Takayama, Nobutoshi; Edakubo, Hiroo; Kozuki, Susumu; Takei, Masahiro; Nagasawa, Kenichi

1986-01-01

In an apparatus of the kind arranged to reproduce, with a plurality of rotary heads, an information signal from a record bearing medium having many recording tracks which are parallel to each other with the information signal recorded therein and with a plurality of different pilot signals of different frequencies also recorded one by one, one in each of the recording tracks, a plurality of different reference signals of different frequencies are simultaneously generated. A tracking error is detected by using the different reference signals together with the pilot signals which are included in signals reproduced from the plurality of rotary heads.

Reproducibility of gastrocnemius medialis muscle architecture during treadmill running.

PubMed

Giannakou, Erasmia; Aggeloussis, Nickos; Arampatzis, Adamantios

2011-12-01

The purpose of this study was to assess the reproducibility of fascicle length (FL) and pennation angle (PA) of gastrocnemius medialis (GM) muscle during running in vivo. Twelve male recreational long distance runners (mean±SD; age: 24±3 years, mass: 76±7kg) ran on a treadmill at a speed of 3.0m/s, wearing their own running shoes, for two different 10min sessions that were at least 2 days apart. For each test day 10 acceptable trials were recorded. Ankle and knee joint angle data were recorded by a Vicon 624 system with three cameras operating at 120Hz. B-mode ultrasonography was used to examine fascicle length and pennation angle of gastrocnemius medialis muscle. The ultrasound probe was firmly secured on the muscle belly using a lightweight foam fixation. The results indicated that fascicle length and pennation angle demonstrated high reproducibility values during treadmill running both for within and between test days. The root mean square scores between the repeated waveforms of pennation angle and fascicle length were small (∼2° and ∼3.5mm, respectively). However, ∼14 trials for pennation angle and ∼9 trials for fascicle length may be required in order to record accurate data from muscle architecture parameters. In conclusion, ultrasound measurements may be highly reproducible during dynamic movements such as treadmill running, provided that a proper fixation is used in order to assure the constant location and orientation of the ultrasound probe throughout the movement. Copyright © 2011 Elsevier Ltd. All rights reserved.

Genotypic variability enhances the reproducibility of an ecological study.

PubMed

Milcu, Alexandru; Puga-Freitas, Ruben; Ellison, Aaron M; Blouin, Manuel; Scheu, Stefan; Freschet, Grégoire T; Rose, Laura; Barot, Sebastien; Cesarz, Simone; Eisenhauer, Nico; Girin, Thomas; Assandri, Davide; Bonkowski, Michael; Buchmann, Nina; Butenschoen, Olaf; Devidal, Sebastien; Gleixner, Gerd; Gessler, Arthur; Gigon, Agnès; Greiner, Anna; Grignani, Carlo; Hansart, Amandine; Kayler, Zachary; Lange, Markus; Lata, Jean-Christophe; Le Galliard, Jean-François; Lukac, Martin; Mannerheim, Neringa; Müller, Marina E H; Pando, Anne; Rotter, Paula; Scherer-Lorenzen, Michael; Seyhun, Rahme; Urban-Mead, Katherine; Weigelt, Alexandra; Zavattaro, Laura; Roy, Jacques

2018-02-01

Many scientific disciplines are currently experiencing a 'reproducibility crisis' because numerous scientific findings cannot be repeated consistently. A novel but controversial hypothesis postulates that stringent levels of environmental and biotic standardization in experimental studies reduce reproducibility by amplifying the impacts of laboratory-specific environmental factors not accounted for in study designs. A corollary to this hypothesis is that a deliberate introduction of controlled systematic variability (CSV) in experimental designs may lead to increased reproducibility. To test this hypothesis, we had 14 European laboratories run a simple microcosm experiment using grass (Brachypodium distachyon L.) monocultures and grass and legume (Medicago truncatula Gaertn.) mixtures. Each laboratory introduced environmental and genotypic CSV within and among replicated microcosms established in either growth chambers (with stringent control of environmental conditions) or glasshouses (with more variable environmental conditions). The introduction of genotypic CSV led to 18% lower among-laboratory variability in growth chambers, indicating increased reproducibility, but had no significant effect in glasshouses where reproducibility was generally lower. Environmental CSV had little effect on reproducibility. Although there are multiple causes for the 'reproducibility crisis', deliberately including genetic variability may be a simple solution for increasing the reproducibility of ecological studies performed under stringently controlled environmental conditions.

Reproducibility of a silicone-based test food to masticatory performance evaluation by different sieve methods.

PubMed

Sánchez-Ayala, Alfonso; Vilanova, Larissa Soares Reis; Costa, Marina Abrantes; Farias-Neto, Arcelino

2014-01-01

The aim of this study was to evaluate the reproducibility of the condensation silicone Optosil Comfort® as an artificial test food for masticatory performance evaluation. Twenty dentate subjects with mean age of 23.3±0.7 years were selected. Masticatory performance was evaluated using the simple (MPI), the double (IME) and the multiple sieve methods. Trials were carried out five times by three examiners: three times by the first, and once by the second and third examiners. Friedman's test was used to find the differences among time trials. Reproducibility was determined by the intra-class correlation (ICC) test (α=0.05). No differences among time trials were found, except for MPI-4 mm (p=0.022) from the first examiner results. The intra-examiner reproducibility (ICC) of almost all data was high (ICC≥0.92, p<0.001), being moderate only for MPI-0.50 mm (ICC=0.89, p<0.001). The inter-examiner reproducibility was high (ICC>0.93, p<0.001) for all results. For the multiple sieve method, the average mean of absolute difference from repeated measurements were lower than 1 mm. This trend was observed only from MPI-0.50 to MPI-1.4 for the single sieve method, and from IME-0.71/0.50 to IME-1.40/1.00 for the double sieve method. The results suggest that regardless of the method used, the reproducibility of Optosil Comfort® is high.

Optimizing rice yields while minimizing yield-scaled global warming potential.

PubMed

Pittelkow, Cameron M; Adviento-Borbe, Maria A; van Kessel, Chris; Hill, James E; Linquist, Bruce A

2014-05-01

To meet growing global food demand with limited land and reduced environmental impact, agricultural greenhouse gas (GHG) emissions are increasingly evaluated with respect to crop productivity, i.e., on a yield-scaled as opposed to area basis. Here, we compiled available field data on CH4 and N2 O emissions from rice production systems to test the hypothesis that in response to fertilizer nitrogen (N) addition, yield-scaled global warming potential (GWP) will be minimized at N rates that maximize yields. Within each study, yield N surplus was calculated to estimate deficit or excess N application rates with respect to the optimal N rate (defined as the N rate at which maximum yield was achieved). Relationships between yield N surplus and GHG emissions were assessed using linear and nonlinear mixed-effects models. Results indicate that yields increased in response to increasing N surplus when moving from deficit to optimal N rates. At N rates contributing to a yield N surplus, N2 O and yield-scaled N2 O emissions increased exponentially. In contrast, CH4 emissions were not impacted by N inputs. Accordingly, yield-scaled CH4 emissions decreased with N addition. Overall, yield-scaled GWP was minimized at optimal N rates, decreasing by 21% compared to treatments without N addition. These results are unique compared to aerobic cropping systems in which N2 O emissions are the primary contributor to GWP, meaning yield-scaled GWP may not necessarily decrease for aerobic crops when yields are optimized by N fertilizer addition. Balancing gains in agricultural productivity with climate change concerns, this work supports the concept that high rice yields can be achieved with minimal yield-scaled GWP through optimal N application rates. Moreover, additional improvements in N use efficiency may further reduce yield-scaled GWP, thereby strengthening the economic and environmental sustainability of rice systems. © 2013 John Wiley & Sons Ltd.

Metabolic engineering of biomass for high energy density: oilseed-like triacylglycerol yields from plant leaves.

PubMed

Vanhercke, Thomas; El Tahchy, Anna; Liu, Qing; Zhou, Xue-Rong; Shrestha, Pushkar; Divi, Uday K; Ral, Jean-Philippe; Mansour, Maged P; Nichols, Peter D; James, Christopher N; Horn, Patrick J; Chapman, Kent D; Beaudoin, Frederic; Ruiz-López, Noemi; Larkin, Philip J; de Feyter, Robert C; Singh, Surinder P; Petrie, James R

2014-02-01

High biomass crops have recently attracted significant attention as an alternative platform for the renewable production of high energy storage lipids such as triacylglycerol (TAG). While TAG typically accumulates in seeds as storage compounds fuelling subsequent germination, levels in vegetative tissues are generally low. Here, we report the accumulation of more than 15% TAG (17.7% total lipids) by dry weight in Nicotiana tabacum (tobacco) leaves by the co-expression of three genes involved in different aspects of TAG production without severely impacting plant development. These yields far exceed the levels found in wild-type leaf tissue as well as previously reported engineered TAG yields in vegetative tissues of Arabidopsis thaliana and N. tabacum. When translated to a high biomass crop, the current levels would translate to an oil yield per hectare that exceeds those of most cultivated oilseed crops. Confocal fluorescence microscopy and mass spectrometry imaging confirmed the accumulation of TAG within leaf mesophyll cells. In addition, we explored the applicability of several existing oil-processing methods using fresh leaf tissue. Our results demonstrate the technical feasibility of a vegetative plant oil production platform and provide for a step change in the bioenergy landscape, opening new prospects for sustainable food, high energy forage, biofuel and biomaterial applications. © 2013 CSIRO. Plant Biotechnology Journal published by Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Empirical evaluation of cross-site reproducibility in radiomic features for characterizing prostate MRI

NASA Astrophysics Data System (ADS)

Chirra, Prathyush; Leo, Patrick; Yim, Michael; Bloch, B. Nicolas; Rastinehad, Ardeshir R.; Purysko, Andrei; Rosen, Mark; Madabhushi, Anant; Viswanath, Satish

2018-02-01

The recent advent of radiomics has enabled the development of prognostic and predictive tools which use routine imaging, but a key question that still remains is how reproducible these features may be across multiple sites and scanners. This is especially relevant in the context of MRI data, where signal intensity values lack tissue specific, quantitative meaning, as well as being dependent on acquisition parameters (magnetic field strength, image resolution, type of receiver coil). In this paper we present the first empirical study of the reproducibility of 5 different radiomic feature families in a multi-site setting; specifically, for characterizing prostate MRI appearance. Our cohort comprised 147 patient T2w MRI datasets from 4 different sites, all of which were first pre-processed to correct acquisition-related for artifacts such as bias field, differing voxel resolutions, as well as intensity drift (non-standardness). 406 3D voxel wise radiomic features were extracted and evaluated in a cross-site setting to determine how reproducible they were within a relatively homogeneous non-tumor tissue region; using 2 different measures of reproducibility: Multivariate Coefficient of Variation and Instability Score. Our results demonstrated that Haralick features were most reproducible between all 4 sites. By comparison, Laws features were among the least reproducible between sites, as well as performing highly variably across their entire parameter space. Similarly, the Gabor feature family demonstrated good cross-site reproducibility, but for certain parameter combinations alone. These trends indicate that despite extensive pre-processing, only a subset of radiomic features and associated parameters may be reproducible enough for use within radiomics-based machine learning classifier schemes.

[Effects of nitrogen application level on soil nitrate accumulation and ammonia volatilization in high-yielding wheat field].

PubMed

Wang, Dong; Yu, Zhenwen; Yu, Wenming; Shi, Yu; Zhou, Zhongxin

2006-09-01

The study showed that during the period from sowing to pre-wintering, the soil nitrate in high-yielding wheat field moved down to deeper layers, and accumulated in the layers below 140 cm. An application rate of 96-168 kg N x hm(-2) increased the nitrate content in 0-60 cm soil layer and the wheat grain yield and its protein content, and decreased the proportion of apparent N loss to applied N and the ammonia volatilization loss from basal nitrogen. Applying 240 kg N x hm(-2) promoted the downward movement of soil nitrate and its accumulation in deeper layers, increased the proportion of apparent N loss to applied N and the ammonia volatilization loss from basal nitrogen, had no significant effect on the protein content of wheat grain, but decreased the grain yield. The appropriate application rate of nitrogen on high-yielding wheat field was 132-204 kg N x hm(-2).

A reproducible and scalable procedure for preparing bacterial extracts for cell-free protein synthesis.

PubMed

Katsura, Kazushige; Matsuda, Takayoshi; Tomabechi, Yuri; Yonemochi, Mayumi; Hanada, Kazuharu; Ohsawa, Noboru; Sakamoto, Kensaku; Takemoto, Chie; Shirouzu, Mikako

2017-11-01

Cell-free protein synthesis is a useful method for preparing proteins for functional or structural analyses. However, batch-to-batch variability with regard to protein synthesis activity remains a problem for large-scale production of cell extract in the laboratory. To address this issue, we have developed a novel procedure for large-scale preparation of bacterial cell extract with high protein synthesis activity. The developed procedure comprises cell cultivation using a fermentor, harvesting and washing of cells by tangential flow filtration, cell disruption with high-pressure homogenizer and continuous diafiltration. By optimizing and combining these methods, ∼100 ml of the cell extract was prepared from 150 g of Escherichia coli cells. The protein synthesis activities, defined as the yield of protein per unit of absorbance at 260 nm of the cell extract, were shown to be reproducible, and the average activity of several batches was twice that obtained using a previously reported method. In addition, combinatorial use of the high-pressure homogenizer and diafiltration increased the scalability, indicating that the cell concentration at disruption varies from 0.04 to 1 g/ml. Furthermore, addition of Gam protein and examinations of the N-terminal sequence rendered the extract prepared here useful for rapid screening with linear DNA templates. © The Authors 2017. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

High-throughput and high-yield fabrication of uniaxially-aligned chitosan-based nanofibers by centrifugal electrospinning

PubMed Central

Erickson, Ariane E.; Edmondson, Dennis; Chang, Fei-Chien; Wood, Dave; Gong, Alex; Levengood, Sheeny Lan; Zhang, Miqin

2016-01-01

The inability to produce large quantities of nanofibers has been a primary obstacle in advancement and commercialization of electrospinning technologies, especially when aligned nanofibers are desired. Here, we present a high-throughput centrifugal electrospinning (HTP-CES) system capable of producing a large number of highly-aligned nanofiber samples with high-yield and tunable diameters. The versatility of the design was revealed when bead-less nanofibers were produced from copolymer chitosan/polycaprolactone (C-PCL) solutions despite variations in polymer blend composition or spinneret needle gauge. Compared to conventional electrospinning techniques, fibers spun with the HTP-CES not only exhibited superior alignment, but also better diameter uniformity. Nanofiber alignment was quantified using Fast Fourier Transform (FFT) analysis. In addition, a concave correlation between the needle diameter and resultant fiber diameter was identified. This system can be easily scaled up for industrial production of highly-aligned nanofibers with tunable diameters that can potentially meet the requirements for various engineering and biomedical applications. PMID:26428148

Inflow, Outflow, Yields, and Stellar Population Mixing in Chemical Evolution Models

NASA Astrophysics Data System (ADS)

Andrews, Brett H.; Weinberg, David H.; Schönrich, Ralph; Johnson, Jennifer A.

2017-02-01

Chemical evolution models are powerful tools for interpreting stellar abundance surveys and understanding galaxy evolution. However, their predictions depend heavily on the treatment of inflow, outflow, star formation efficiency (SFE), the stellar initial mass function, the SN Ia delay time distribution, stellar yields, and stellar population mixing. Using flexCE, a flexible one-zone chemical evolution code, we investigate the effects of and trade-offs between parameters. Two critical parameters are SFE and the outflow mass-loading parameter, which shift the knee in [O/Fe]-[Fe/H] and the equilibrium abundances that the simulations asymptotically approach, respectively. One-zone models with simple star formation histories follow narrow tracks in [O/Fe]-[Fe/H] unlike the observed bimodality (separate high-α and low-α sequences) in this plane. A mix of one-zone models with inflow timescale and outflow mass-loading parameter variations, motivated by the inside-out galaxy formation scenario with radial mixing, reproduces the two sequences better than a one-zone model with two infall epochs. We present [X/Fe]-[Fe/H] tracks for 20 elements assuming three different supernova yield models and find some significant discrepancies with solar neighborhood observations, especially for elements with strongly metallicity-dependent yields. We apply principal component abundance analysis to the simulations and existing data to reveal the main correlations among abundances and quantify their contributions to variation in abundance space. For the stellar population mixing scenario, the abundances of α-elements and elements with metallicity-dependent yields dominate the first and second principal components, respectively, and collectively explain 99% of the variance in the model. flexCE is a python package available at https://github.com/bretthandrews/flexCE.

Reproducibility and validity of the Shanghai Men's Health Study physical activity questionnaire.

PubMed

Jurj, Adriana L; Wen, Wanqing; Xiang, Yong-Bing; Matthews, Charles E; Liu, Dake; Zheng, Wei; Shu, Xiao-Ou

2007-05-15

Reproducibility and validity of the physical activity questionnaire (PAQ) used in the Shanghai Men's Health Study (2003-2006, People's Republic of China) was evaluated in a random sample of 196 participants aged 40-74 years. Participants completed a PAQ at baseline and again 1 year later, 12 monthly 7-day physical activity recalls, and four quarterly 1-week physical activity logs. Reproducibility was evaluated by using the two PAQs and validity by comparing the PAQs with 1-year averages of the two criterion measures: 7-day physical activity recall and physical activity log. The PAQ had moderate to high reproducibility for measuring adult exercise participation (kappa = 0.60) and energy expenditure (r(s) = 0.68), nonexercise activities (correlation coefficients = 0.42-0.68), and total daily energy expenditure (r(s) = 0.68, kappa(quartiles) = 0.47). Correlations between the PAQ and criterion measures of adult exercise were 0.45 (7-day physical activity recall) and 0.51 (physical activity log) for the first PAQ and 0.62 (7-day physical activity recall) and 0.71 (physical activity log) for the second PAQ. Correlations between PAQ nonexercise activities and the physical activity log and 7-day physical activity recall were 0.31-0.86. Correlations for total energy expenditure were high (0.62-0.77). Results indicate that the Shanghai Men's Health Study PAQ has reasonable reproducibility and validity for classifying men by their level of exercise and nonexercise activities in this cohort.

Where next for the reproducibility agenda in computational biology?

PubMed

Lewis, Joanna; Breeze, Charles E; Charlesworth, Jane; Maclaren, Oliver J; Cooper, Jonathan

2016-07-15

The concept of reproducibility is a foundation of the scientific method. With the arrival of fast and powerful computers over the last few decades, there has been an explosion of results based on complex computational analyses and simulations. The reproducibility of these results has been addressed mainly in terms of exact replicability or numerical equivalence, ignoring the wider issue of the reproducibility of conclusions through equivalent, extended or alternative methods. We use case studies from our own research experience to illustrate how concepts of reproducibility might be applied in computational biology. Several fields have developed 'minimum information' checklists to support the full reporting of computational simulations, analyses and results, and standardised data formats and model description languages can facilitate the use of multiple systems to address the same research question. We note the importance of defining the key features of a result to be reproduced, and the expected agreement between original and subsequent results. Dynamic, updatable tools for publishing methods and results are becoming increasingly common, but sometimes come at the cost of clear communication. In general, the reproducibility of computational research is improving but would benefit from additional resources and incentives. We conclude with a series of linked recommendations for improving reproducibility in computational biology through communication, policy, education and research practice. More reproducible research will lead to higher quality conclusions, deeper understanding and more valuable knowledge.

Breeding cassava for higher yield

USDA-ARS?s Scientific Manuscript database

Cassava is a root crop grown for food and for starch production. Breeding progress is slowed by asexual production and high levels of heterozygosity. Germplasm resources are rich and accessible to breeders through genebanks worldwide. Breeding objectives include high root yield, yield stability, dis...

Yield: it's now an entitlement

NASA Astrophysics Data System (ADS)

George, Bill

1994-09-01

Only a few years ago, the primary method of cost reduction and productivity improvement in the semiconductor industry was increasing manufacturing yields throughout the process. Many of the remarkable reliability improvements realized over the past decade have come about as a result of actions that were originally taken primarily to improve device yields. Obviously, the practice of productivity improvement through yield enhancement is limited to the attainment of 100% yield, at which point some other mechanism must be employed. Traditionally, new products have been introduced to manufacturing at a point of relative immaturity, and semiconductor producers have relied on the traditional `learning curve' method of yield improvement to attain profitable levels of manufacturing yield. Recently, results of a survey of several fabs by a group of University of California at Berkeley researchers in the Competitive Semiconductor Manufacturing Program indicate that most factories learn at about the same rate after startup, in terms of both line yield and defectivity. If this is indeed generally true, then the most competitive factor is the one that starts with the highest yield, and it is difficult to displace a leader once his lead has been established. The two observations made above carry enormous implications for the semiconductor development or manufacturing professional. First, one must achieve very high yields in order to even play the game. Second, the achievement of competitive yields over time in the life of a factory is determined even before the factory is opened, in the planning and development phase. Third, and perhaps most uncomfortable for those of us who have relied on yield improvement as a cost driver, the winners of the nineties will find new levers to drive costs down, having already gotten the benefit of very high yield. This paper looks at the question of how the winners will achieve the critical measures of success, high initial yield and utilization

Simplified and reproducible radiochemical separations for the production of high specific activity 61Cu, 64Cu, 86Y and 55Co

NASA Astrophysics Data System (ADS)

Valdovinos, Hector F.; Graves, Stephen; Barnhart, Todd; Nickles, Robert J.

2017-05-01

Four positron-emitting radiometals 61Cu, 64Cu, 86Y and 55Co are increasingly being employed as labels for positron emission tomography (PET) imaging due to their favorable half-lives that match the pharmacokinetics of targeting moeities such as peptides, antibodies and antibody fragments and due to their use in internal dosimetry and treatment planning of targeted radionuclide therapy when they are substituted by their therapeutic analogues 67Cu, 90Y and 58mCo. The main disadvantage of the production methods reported in the literature for these radionuclides is that the final separated radioactive product is diluted in a large volume (> 5 mL), which obligates a lengthy evaporation step in a large vessel that is difficult to automate in-line after the chromatographic steps and that results in a highly variable amount of radioactivity lost in the vessel's surface. In this work we present simplified radiochemical separation methods for the production of 61Cu, 64Cu, 86Y and 55Co that result in: 1) a final eluate volume ≤ 600 µL; 2) reproducible separation yields of 84±4%, 82±6%, 94±5% and 93±6%, respectively; and 3) effective specific activities of 64.0±45.0 GBq/μmol NOTA, 114.9±40.1 GBq/μmol NOTA, 1.4±0.5 GBq/μmol DTPA and 10.1±5.7 GBq/μmol NOTA, respectively; without compromising the recycling efficiencies of the respective isotopically-enriched target materials 60Ni, 64Ni, 86SrCO3 and 58Ni, which accounted for 98±1%, 96±3%, 90±3% and 94±1%, respectively.

Fourier modeling of the BOLD response to a breath-hold task: Optimization and reproducibility.

PubMed

Pinto, Joana; Jorge, João; Sousa, Inês; Vilela, Pedro; Figueiredo, Patrícia

2016-07-15

Cerebrovascular reactivity (CVR) reflects the capacity of blood vessels to adjust their caliber in order to maintain a steady supply of brain perfusion, and it may provide a sensitive disease biomarker. Measurement of the blood oxygen level dependent (BOLD) response to a hypercapnia-inducing breath-hold (BH) task has been frequently used to map CVR noninvasively using functional magnetic resonance imaging (fMRI). However, the best modeling approach for the accurate quantification of CVR maps remains an open issue. Here, we compare and optimize Fourier models of the BOLD response to a BH task with a preparatory inspiration, and assess the test-retest reproducibility of the associated CVR measurements, in a group of 10 healthy volunteers studied over two fMRI sessions. Linear combinations of sine-cosine pairs at the BH task frequency and its successive harmonics were added sequentially in a nested models approach, and were compared in terms of the adjusted coefficient of determination and corresponding variance explained (VE) of the BOLD signal, as well as the number of voxels exhibiting significant BOLD responses, the estimated CVR values, and their test-retest reproducibility. The brain average VE increased significantly with the Fourier model order, up to the 3rd order. However, the number of responsive voxels increased significantly only up to the 2nd order, and started to decrease from the 3rd order onwards. Moreover, no significant relative underestimation of CVR values was observed beyond the 2nd order. Hence, the 2nd order model was concluded to be the optimal choice for the studied paradigm. This model also yielded the best test-retest reproducibility results, with intra-subject coefficients of variation of 12 and 16% and an intra-class correlation coefficient of 0.74. In conclusion, our results indicate that a Fourier series set consisting of a sine-cosine pair at the BH task frequency and its two harmonics is a suitable model for BOLD-fMRI CVR measurements

Peripapillary nerve fiber layer thickness measurement reproducibility using optical coherence tomography.

PubMed

Villain, Max A; Greenfield, David S

2003-01-01

To assess reproducibility of quadrantic and clock hour sectors of retinal nerve fiber layer thickness in normal eyes using optical coherence tomography. Normal eyes of healthy volunteers meeting eligibility criteria were imaged by two inexperienced operators. Six 360 degrees circular scans with a diameter of 3.4 mm centered on the optic disc were obtained during each scanning session, and a baseline image was formed using 3 high-quality images defined by the software. Images were obtained on three different days within a 4-week period. Variance and coefficient of variation (CV) were calculated for quadrantic and retinal nerve fiber layer clock hour sectors obtained from the baseline image. Five normal eyes were scanned. Intraoperator reproducibility was high. The mean (+/- SD) CV for total retinal nerve fiber layer thickness was 5.3 +/- 3.82% and 4.33 +/- 3.7% for operators 1 and 2, respectively. Interoperator reproducibility was good with statistically similar variance for all quadrantic and clock hour retinal nerve fiber layer parameters (P = .42 to .99). The nasal retinal nerve fiber layer was the most variable sector for both operators (mean CV: 10.42% and 7.83% for operators 1 and 2, respectively). Differences in mean total, nasal, temporal, and superior retinal nerve fiber layer thickness were not statistically significant between operators for all eyes; however, for inferior retinal nerve fiber layer thickness, there was a significant (P = .0007) difference between operators in one eye. Peripapillary retinal nerve fiber layer thickness assessments using optical coherence tomography have good intraoperator and interoperator reproducibility. Inexperienced operators can generate useful measurement data with acceptable levels of variance.

Future consequences of decreasing marginal production efficiency in the high-yielding dairy cow.

PubMed

Moallem, U

2016-04-01

The objectives were to examine the gross and marginal production efficiencies in high-yielding dairy cows and the future consequences on dairy industry profitability. Data from 2 experiments were used in across-treatments analysis (n=82 mid-lactation multiparous Israeli-Holstein dairy cows). Milk yields, body weights (BW), and dry matter intakes (DMI) were recorded daily. In both experiments, cows were fed a diet containing 16.5 to 16.6% crude protein and net energy for lactation (NEL) at 1.61 Mcal/kg of dry matter (DM). The means of milk yield, BW, DMI, NEL intake, and energy required for maintenance were calculated individually over the whole study, and used to calculate gross and marginal efficiencies. Data were analyzed in 2 ways: (1) simple correlation between variables; and (2) cows were divided into 3 subgroups, designated low, moderate, and high DMI (LDMI, MDMI, and HDMI), according to actual DMI per day: ≤ 26 kg (n=27); >26 through 28.2 kg (n=28); and >28.2 kg (n=27). The phenotypic Pearson correlations among variables were analyzed, and the GLM procedure was used to test differences between subgroups. The relationships between milk and fat-corrected milk yields and the corresponding gross efficiencies were positive, whereas BW and gross production efficiency were negatively correlated. The marginal production efficiency from DM and energy consumed decreased with increasing DMI. The difference between BW gain as predicted by the National Research Council model (2001) and the present measurements increased with increasing DMI (r=0.68). The average calculated energy balances were 1.38, 2.28, and 4.20 Mcal/d (standard error of the mean=0.64) in the LDMI, MDMI, and HDMI groups, respectively. The marginal efficiency for milk yields from DMI or energy consumed was highest in LDMI, intermediate in MDMI, and lowest in HDMI. The predicted BW gains for the whole study period were 22.9, 37.9, and 75.8 kg for the LDMI, MDMI, and HDMI groups, respectively. The

10 CFR 1016.35 - Authority to reproduce Restricted Data.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 4 2010-01-01 2010-01-01 false Authority to reproduce Restricted Data. 1016.35 Section 1016.35 Energy DEPARTMENT OF ENERGY (GENERAL PROVISIONS) SAFEGUARDING OF RESTRICTED DATA Control of Information § 1016.35 Authority to reproduce Restricted Data. Secret Restricted Data will not be reproduced...

10 CFR 1016.35 - Authority to reproduce Restricted Data.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 4 2011-01-01 2011-01-01 false Authority to reproduce Restricted Data. 1016.35 Section 1016.35 Energy DEPARTMENT OF ENERGY (GENERAL PROVISIONS) SAFEGUARDING OF RESTRICTED DATA Control of Information § 1016.35 Authority to reproduce Restricted Data. Secret Restricted Data will not be reproduced...

High-Yield Hydrogen Production from Starch and Water by a Synthetic Enzymatic Pathway

PubMed Central

Zhang, Y.-H. Percival; Evans, Barbara R.; Mielenz, Jonathan R.; Hopkins, Robert C.; Adams, Michael W.W.

2007-01-01

Background The future hydrogen economy offers a compelling energy vision, but there are four main obstacles: hydrogen production, storage, and distribution, as well as fuel cells. Hydrogen production from inexpensive abundant renewable biomass can produce cheaper hydrogen, decrease reliance on fossil fuels, and achieve zero net greenhouse gas emissions, but current chemical and biological means suffer from low hydrogen yields and/or severe reaction conditions. Methodology/Principal Findings Here we demonstrate a synthetic enzymatic pathway consisting of 13 enzymes for producing hydrogen from starch and water. The stoichiometric reaction is C6H10O5 (l)+7 H2O (l)→12 H2 (g)+6 CO2 (g). The overall process is spontaneous and unidirectional because of a negative Gibbs free energy and separation of the gaseous products with the aqueous reactants. Conclusions Enzymatic hydrogen production from starch and water mediated by 13 enzymes occurred at 30°C as expected, and the hydrogen yields were much higher than the theoretical limit (4 H2/glucose) of anaerobic fermentations. Significance The unique features, such as mild reaction conditions (30°C and atmospheric pressure), high hydrogen yields, likely low production costs ($∼2/kg H2), and a high energy-density carrier starch (14.8 H2-based mass%), provide great potential for mobile applications. With technology improvements and integration with fuel cells, this technology also solves the challenges associated with hydrogen storage, distribution, and infrastructure in the hydrogen economy. PMID:17520015

The Titan haze revisted: Magnetospheric energy sorces quantitative tholin yields

NASA Technical Reports Server (NTRS)

Thompson, W. Reid; Mcdonald, Gene D.; Sagan, Carl

1994-01-01

We present laboratory measurements of the radiation yields of complex organic solids produced from N2/CH4 gas mixtures containing 10 or 0.1% CH4. These tholins are thought to resemble organic aerosols produced in the atmospheres of Titan, Pluto, and Triton. The tholin yields are large compared to the total yield of gaseous products: nominally, 13 (C + N)/100 eV for Titan tholin and 2.1 (C + N)/100 eV for Triton tholin. High-energy magnetospheric electrons responsible for tholin production represents a class distinct from the plasma electrons considered in models of Titan's aiglow. Electrons with E greater than 20 keV provide an energy flux approximately 1 x 10(exp -2) erg/cm/sec, implying from our measured tholin yields a mass flux of 0.5 to 4.0 x 10(exp -14) g/sq cm/sec of tholin. (The corresponding thickness of the tholin sedimentary column accumulated over 4 Gyr on Titan's surface is 4 to 30 m). This figure is in agreement with required mass fluxes computed from recent radiative transfer and sedimentation models. If, however, theses results, derived from experiments at approximately 2 mb, are applied to lower pressure levels toward peak auroral electron energy deposition and scaled with pressure as the gas-phase organic yields, the derived tholin mass flux is at least an order of magnitude less. We attrribute this difference to the fact that tholin synthesis occurs well below the level of maximum electron energy depositon and to possible contributions to tholis from UV-derived C2-hydrocarbons. We conclude that Tita tholin, produced by magnetospheric electrons, is alone sufficient to supply at least a significant fraction of Titan's haze-a result consistent with the fact that the optical properties of Titan tholin, among all proposed material, are best at reproducing Titan's geometric albedo spectrum from near UV to mid-IR in light-scattering models.

Reproducible research in palaeomagnetism

NASA Astrophysics Data System (ADS)

Lurcock, Pontus; Florindo, Fabio

2015-04-01

The reproducibility of research findings is attracting increasing attention across all scientific disciplines. In palaeomagnetism as elsewhere, computer-based analysis techniques are becoming more commonplace, complex, and diverse. Analyses can often be difficult to reproduce from scratch, both for the original researchers and for others seeking to build on the work. We present a palaeomagnetic plotting and analysis program designed to make reproducibility easier. Part of the problem is the divide between interactive and scripted (batch) analysis programs. An interactive desktop program with a graphical interface is a powerful tool for exploring data and iteratively refining analyses, but usually cannot operate without human interaction. This makes it impossible to re-run an analysis automatically, or to integrate it into a larger automated scientific workflow - for example, a script to generate figures and tables for a paper. In some cases the parameters of the analysis process itself are not saved explicitly, making it hard to repeat or improve the analysis even with human interaction. Conversely, non-interactive batch tools can be controlled by pre-written scripts and configuration files, allowing an analysis to be 'replayed' automatically from the raw data. However, this advantage comes at the expense of exploratory capability: iteratively improving an analysis entails a time-consuming cycle of editing scripts, running them, and viewing the output. Batch tools also tend to require more computer expertise from their users. PuffinPlot is a palaeomagnetic plotting and analysis program which aims to bridge this gap. First released in 2012, it offers both an interactive, user-friendly desktop interface and a batch scripting interface, both making use of the same core library of palaeomagnetic functions. We present new improvements to the program that help to integrate the interactive and batch approaches, allowing an analysis to be interactively explored and refined

Physiological Mechanisms Underlying the High-Grain Yield and High-Nitrogen Use Efficiency of Elite Rice Varieties under a Low Rate of Nitrogen Application in China.

PubMed

Wu, Lilian; Yuan, Shen; Huang, Liying; Sun, Fan; Zhu, Guanglong; Li, Guohui; Fahad, Shah; Peng, Shaobing; Wang, Fei

2016-01-01

Selecting rice varieties with a high nitrogen (N) use efficiency (NUE) is the best approach to reduce N fertilizer application in rice production and is one of the objectives of the Green Super Rice (GSR) Project in China. However, the performance of elite candidate GSR varieties under low N supply remains unclear. In the present study, differences in the grain yield and NUE of 13 and 14 candidate varieties with two controls were determined at a N rate of 100 kg ha(-1) in field experiments in 2014 and 2015, respectively. The grain yield for all of the rice varieties ranged from 8.67 to 11.09 t ha(-1), except for a japonica rice variety YG29, which had a grain yield of 6.42 t ha(-1). HY549 and YY4949 produced the highest grain yield, reflecting a higher biomass production and harvest index in 2014 and 2015, respectively. Total N uptake at maturity (TNPM) ranged from 144 to 210 kg ha(-1), while the nitrogen use efficiency for grain production (NUEg) ranged from 35.2 to 62.0 kg kg(-1). Both TNPM and NUEg showed a significant quadratic correlation with grain yield, indicating that it is possible to obtain high grain yield and NUEg with the reduction of TNPM. The correlation between N-related parameters and yield-related traits suggests that promoting pre-heading growth could increase TNPM, while high biomass accumulation during the grain filling period and large panicles are important for a higher NUEg. In addition, there were significant and negative correlations between the NUEg and N concentrations in leaf, stem, and grain tissues at maturity. Further improvements in NUEg require a reduction in the stem N concentration but not the leaf N concentration. The daily grain yield was the only parameter that significantly and positively correlated with both TNPMand NUEg. This study determined variations in the grain yield and NUE of elite candidate GSR rice varieties and provided plant traits that could be used as selection criteria in breeding N-efficient rice varieties.

Reproducibility of Regional Pulse Wave Velocity in Healthy Subjects

PubMed Central

Lee, Nak Bum

2009-01-01

Background/Aims Despite the clinical importance and widespread use of pulse wave velocity (PWV), there are no standards for pulse sensors or for system requirements to ensure accurate pulse wave measurement. We assessed the reproducibility of PWV values using a newly developed PWV measurement system. Methods The system used in this study was the PP-1000, which simultaneously provides regional PWV values from arteries at four different sites (carotid, femoral, radial, and dorsalis pedis). Seventeen healthy male subjects without any cardiovascular disease participated in this study. Two observers performed two consecutive measurements in the same subject in random order. To evaluate the reproducibility of the system, two sets of analyses (within-observer and between-observer) were performed. Results The means±SD of PWV for the aorta, arm, and leg were 7.0±1.48, 8.43±1.14, and 8.09±0.98 m/s as measured by observer A and 6.76±1.00, 7.97±0.80, and 7.97±0.72 m/s by observer B, respectively. Between-observer differences for the aorta, arm, and leg were 0.14±0.62, 0.18±0.84, and 0.07±0.86 m/s, respectively, and the correlation coefficients were high, especially for aortic PWV (r=0.93). All the measurements showed significant correlation coefficients, ranging from 0.94 to 0.99. Conclusions The PWV measurement system used in this study provides accurate analysis results with high reproducibility. It is necessary to provide an accurate algorithm for the detection of additional features such as flow wave, reflection wave, and dicrotic notch from a pulse waveform. PMID:19270477

The Measurement of Strong-Interaction Effects in High-Z Sigma Hyperonic Atoms.

NASA Astrophysics Data System (ADS)

Phillips, William Clarke

Strong-interaction effects have been observed in the X-ray spectra of atoms formed with Sigma ^- in lead and tungsten. In the experiment, performed at the Alternating Gradient Synchrotron of Brookhaven National Laboratory, negative kaons were brought to rest in a novel laminar target consisting of thin sheets of high-Z material in a liquid hydrogen bath. The geometry of the target was designed to optimize the production of high-Z Sigma^- atoms and the detection of their subsequent de-excitation X rays. A method of identifying the energetic pi^+ from the production reaction K^-+ p toSigma^- +pi^+ resulted in a factor of 15 improvement in the signal-to -noise ratio of the Sigma^- atom X-rays over that of previous experiments. The X-ray spectra were recorded by three high-resolution intrinsic Ge detectors and analyzed for shifts, broadenings, and yield reductions of the final X-ray transitions before absorption of the Sigma^- into the nucleus. A lineshape function which reflected the non-Gaussian response of the X-ray spectroscopy system was developed for this analysis. The results are(UNFORMATTED TABLE OR EQUATION FOLLOWS)eqalign {Sigma^- - W (10to9): varepsilon = 650 +/- 30 eV,&quadGamma = 380 +/- 70 eV,quad %Y = .98 +/- .04cr Sigma^- - Pb (10to9): varepsilon = 510 +/- 50 eV,&quadGamma = 290 +/- 140 eV, quad %Y = .53 +/- .04cr} (TABLE/EQUATION ENDS)where varepsilon = E_{rm meds} - E_{rm calc }, Gamma is the Lorentzian FWHM, and %Y is the ratio (measured yield)/(yield calculated with no strong interaction). Optical model calculations with a = (0.928 + i0.022) fm are able to reproduce all observed effects in the Sigma^--W spectra. Such calculations with a = (0.247 + i0.039) fm reproduce the observed shift and width of the (10to9) transition in Sigma^--Pb, but fail to reproduce the observed yield reduction. It is doubtful if the current status of the theory of Sigma ^--N interactions can explain this discrepancy.

The Z {yields} cc-bar {yields} {gamma}{gamma}*, Z {yields} bb-bar {yields} {gamma}{gamma}* triangle diagrams and the Z {yields} {gamma}{psi}, Z {yields} {gamma}Y decays

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

Achasov, N. N., E-mail: achasov@math.nsc.ru

2011-03-15

The approach to the Z {yields} {gamma}{psi} and Z {yields} {gamma}Y decay study is presented in detail, based on the sum rules for the Z {yields} cc-bar {yields} {gamma}{gamma}* and Z {yields} bb-bar {yields} {gamma}{gamma}* amplitudes and their derivatives. The branching ratios of the Z {yields} {gamma}{psi} and Z {yields} {gamma}Y decays are calculated for different hypotheses on saturation of the sum rules. The lower bounds of {Sigma}{sub {psi}} BR(Z {yields} {gamma}{psi}) = 1.95 Multiplication-Sign 10{sup -7} and {Sigma}{sub {upsilon}} BR(Z {yields} {gamma}Y) = 7.23 Multiplication-Sign 10{sup -7} are found. Deviations from the lower bounds are discussed, including the possibilitymore » of BR(Z {yields} {gamma}J/{psi}(1S)) {approx} BR(Z {yields} {gamma}Y(1S)) {approx} 10{sup -6}, that could be probably measured in LHC. The angular distributions in the Z {yields} {gamma}{psi} and Z {yields} {gamma}Y decays are also calculated.« less

Capsule symmetry sensitivity and hohlraum symmetry calculations for the z-pinch driven hohlraum high-yield concept

NASA Astrophysics Data System (ADS)

Vesey, Roger; Cuneo, M. E.; Hanson Porter, D. L., Jr.; Mehlhorn, T. A.; Ruggles, L. E.; Simpson, W. W.; Hammer, J. H.; Landen, O.

2000-10-01

Capsule radiation symmetry is a crucial issue in the design of the z-pinch driven hohlraum approach to high-yield inertial confinement fusion [1]. Capsule symmetry may be influenced by power imbalance of the two z-pinch x-ray sources, and by hohlraum effects (geometry, time-dependent albedo, wall motion). We have conducted two-dimensional radiation-hydrodynamics calculations to estimate the symmetry sensitivity of the 220 eV beryllium ablator capsule that nominally yields 400 MJ in this concept. These estimates then determine the symmetry requirements to be met by the hohlraum design (for even Legendre modes) and by the top-bottom pinch imbalance and mistiming (for odd Legendre modes). We have used a combination of 2- and 3-D radiosity ("viewfactor"), and 2-D radiation-hydrodynamics calculations to identify hohlraum geometries that meet these symmetry requirements for high-yield, and are testing these models against ongoing Z foam ball symmetry experiments. 1. J. H. Hammer et al., Phys. Plas. 6, 2129 (1999).

Hexamethylenetetramine-mediated growth of grain-boundary-passivation CH3NH3PbI3 for highly reproducible and stable perovskite solar cells

NASA Astrophysics Data System (ADS)

Zheng, Yan-Zhen; Li, Xi-Tao; Zhao, Er-Fei; Lv, Xin-Ding; Meng, Fan-Li; Peng, Chao; Lai, Xue-Sen; Huang, Meilan; Cao, Guozhong; Tao, Xia; Chen, Jian-Feng

2018-02-01

Simultaneously achieving the long-term device stability and reproducibility has proven challenging in perovskite solar cells because solution-processing produced perovskite film with grain boundary is sensitive to moisture. Herein, we develop a hexamethylenetetramine (HMTA)-mediated one-step solution-processing deposition strategy that leads to the formation of high-purity and grain-boundary-passivation CH3NH3PbI3 film and thereby advances cell optoelectronic performance. Through morphological and structural characterizations and theoretical calculations, we demonstrate that HMTA fully occupies the moisture-exposed surface to build a bridge across grain boundary and coordinates with Pb ions to inhibit the formation of detrimental PbI2. Such HMTA-mediated grown CH3NH3PbI3 films achieves a decent augmentation of power conversion efficiency (PCE) from 12.70% to 17.87%. A full coverage of PbI2-free CH3NH3PbI3 surface on ZnO also boosts the device's stability and reproducibility.

Fast and inexpensive synthesis of pentacene with high yield using 6,13-pentacenequinone as precursor

NASA Astrophysics Data System (ADS)

Mota, María L.; Rodriguez, Bibiana; Carrillo, Amanda; Ambrosio, Roberto C.; Luque, Priscy A.; Mireles, Marcela; Vivaldo, Israel; Quevedo, Manuel A.

2018-02-01

Pentacene is an important semiconductor in the field of organic electronics. In this work is presented an alternative synthesis procedure to obtain pentacene from 6,13-pentacenequinone as a precursor. Synthesis of pentacene was performed in two reactions, Diels-Adler cycloaddition of 6,13-pentacenequinone followed by 6,13-pentacenequinone reduction to pentacene, employing LiAlH4 as reducing agent. The products were characterized by Fourier Transform Infrared Spectroscopy (FTIR), 1H-Nuclear Magnetic Resonance Spectroscopy (1H-NMR), X-Ray Diffraction (XRD), Thermogravimetric Analysis (TGA) and Ultraviolet-Visible Spectroscopy (UV-VIS). In this work, 6,13-pentacenequinone was synthetized with a high yield (55%) using an alternative method. The optimization process resulted in an overall reduction of reaction time while exhibiting high yield. The method presented here provides an affordable pentacene synthesis route with high purity, which can be further applied for research and development of organic electronic applications.

Simulating large-scale crop yield by using perturbed-parameter ensemble method

NASA Astrophysics Data System (ADS)

Iizumi, T.; Yokozawa, M.; Sakurai, G.; Nishimori, M.

2010-12-01

is still high in most grids regardless of the countries. However, the model showed comparatively low reproducibility in the slope areas, such as around the Rocky Mountains in South Dakota, around the Great Xing'anling Mountains in Heilongjiang, and around the Brazilian Plateau. As there is a wide-ranging local climate conditions in the complex terrain, such as the slope of mountain, the GCM grid-scale weather inputs is likely one of major sources of error. The results of this study highlight the benefits of the perturbed-parameter ensemble method in simulating crop yield on a GCM grid scale: (1) the posterior PDF of parameter could quantify the uncertainty of parameter value of the crop model associated with the local crop production aspects; (2) the method can explicitly account for the uncertainty of parameter value in the crop model simulations; (3) the method achieve a Monte Carlo approximation of probability of sub-grid scale yield, accounting for the nonlinear response of crop yield to weather and management; (4) the method is therefore appropriate to aggregate the simulated sub-grid scale yields to a grid-scale yield and it may be a reason for high performance of the model in capturing inter-annual variation of yield.

Analysis of polymorphisms in milk proteins from cloned and sexually reproduced goats.

PubMed

Xing, H; Shao, B; Gu, Y Y; Yuan, Y G; Zhang, T; Zang, J; Cheng, Y

2015-12-08

This study evaluates the relationship between the genotype and milk protein components in goats. Milk samples were collected from cloned goats and normal white goats during different postpartum (or abortion) phases. Two cloned goats, originated from the same somatic line of goat mammary gland epithelial cells, and three sexually reproduced normal white goats with no genetic relationships were used as the control. The goats were phylogenetically analyzed by polymerase chain reaction-restriction fragment length polymorphism. The milk protein components were identified by sodium dodecyl sulfate polyacrylamide gel electrophoresis. The results indicated that despite the genetic fingerprints being identical, the milk protein composition differed between the two cloned goats. The casein content of cloned goat C-50 was significantly higher than that of cloned goat C-4. Conversely, although the genetic fingerprints of the normal white goats N-1, N-2, and N-3 were not identical, the milk protein profiles did not differ significantly in their milk samples (obtained on postpartum day 15, 20, 25, 30, and 150). These results indicated an association between milk protein phenotypes and genetic polymorphisms, epigenetic regulation, and/or non-chromosomal factors. This study extends the knowledge of goat milk protein polymorphisms, and provides new strategies for the breeding of high milk-yielding goats.

Undefined cellulase formulations hinder scientific reproducibility

DOE PAGES

Himmel, Michael E.; Abbas, Charles A.; Baker, John O.; ...

2017-11-28

In the shadow of a burgeoning biomass-to-fuels industry, biological conversion of lignocellulose to fermentable sugars in a cost-effective manner is key to the success of second-generation and advanced biofuel production. For the effective comparison of one cellulase preparation to another, cellulase assays are typically carried out with one or more engineered cellulase formulations or natural exoproteomes of known performance serving as positive controls. When these formulations have unknown composition, as is the case with several widely used commercial products, it becomes impossible to compare or reproduce work done today to work done in the future, where, for example, such preparationsmore » may not be available. Therefore, being a critical tenet of science publishing, experimental reproducibility is endangered by the continued use of these undisclosed products. We propose the introduction of standard procedures and materials to produce specific and reproducible cellulase formulations. These formulations are to serve as yardsticks to measure improvements and performance of new cellulase formulations.« less

Undefined cellulase formulations hinder scientific reproducibility

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

Himmel, Michael E.; Abbas, Charles A.; Baker, John O.

In the shadow of a burgeoning biomass-to-fuels industry, biological conversion of lignocellulose to fermentable sugars in a cost-effective manner is key to the success of second-generation and advanced biofuel production. For the effective comparison of one cellulase preparation to another, cellulase assays are typically carried out with one or more engineered cellulase formulations or natural exoproteomes of known performance serving as positive controls. When these formulations have unknown composition, as is the case with several widely used commercial products, it becomes impossible to compare or reproduce work done today to work done in the future, where, for example, such preparationsmore » may not be available. Therefore, being a critical tenet of science publishing, experimental reproducibility is endangered by the continued use of these undisclosed products. We propose the introduction of standard procedures and materials to produce specific and reproducible cellulase formulations. These formulations are to serve as yardsticks to measure improvements and performance of new cellulase formulations.« less

On the origin of reproducible sequential activity in neural circuits

NASA Astrophysics Data System (ADS)

Afraimovich, V. S.; Zhigulin, V. P.; Rabinovich, M. I.

2004-12-01

Robustness and reproducibility of sequential spatio-temporal responses is an essential feature of many neural circuits in sensory and motor systems of animals. The most common mathematical images of dynamical regimes in neural systems are fixed points, limit cycles, chaotic attractors, and continuous attractors (attractive manifolds of neutrally stable fixed points). These are not suitable for the description of reproducible transient sequential neural dynamics. In this paper we present the concept of a stable heteroclinic sequence (SHS), which is not an attractor. SHS opens the way for understanding and modeling of transient sequential activity in neural circuits. We show that this new mathematical object can be used to describe robust and reproducible sequential neural dynamics. Using the framework of a generalized high-dimensional Lotka-Volterra model, that describes the dynamics of firing rates in an inhibitory network, we present analytical results on the existence of the SHS in the phase space of the network. With the help of numerical simulations we confirm its robustness in presence of noise in spite of the transient nature of the corresponding trajectories. Finally, by referring to several recent neurobiological experiments, we discuss possible applications of this new concept to several problems in neuroscience.

On the origin of reproducible sequential activity in neural circuits.

PubMed

Afraimovich, V S; Zhigulin, V P; Rabinovich, M I

2004-12-01

Robustness and reproducibility of sequential spatio-temporal responses is an essential feature of many neural circuits in sensory and motor systems of animals. The most common mathematical images of dynamical regimes in neural systems are fixed points, limit cycles, chaotic attractors, and continuous attractors (attractive manifolds of neutrally stable fixed points). These are not suitable for the description of reproducible transient sequential neural dynamics. In this paper we present the concept of a stable heteroclinic sequence (SHS), which is not an attractor. SHS opens the way for understanding and modeling of transient sequential activity in neural circuits. We show that this new mathematical object can be used to describe robust and reproducible sequential neural dynamics. Using the framework of a generalized high-dimensional Lotka-Volterra model, that describes the dynamics of firing rates in an inhibitory network, we present analytical results on the existence of the SHS in the phase space of the network. With the help of numerical simulations we confirm its robustness in presence of noise in spite of the transient nature of the corresponding trajectories. Finally, by referring to several recent neurobiological experiments, we discuss possible applications of this new concept to several problems in neuroscience.

A Permanent-Magnet Microwave Ion Source For A Compact High-Yield Neutron Generator

NASA Astrophysics Data System (ADS)

Waldmann, O.; Ludewigt, B.

2011-06-01

We present recent work on the development of a microwave ion source that will be used in a high-yield compact neutron generator for active interrogation applications. The sealed tube generator will be capable of producing high neutron yields, 5×1011 n/s for D-T and ˜1×1010 n/s for D-D reactions, while remaining transportable. We constructed a microwave ion source (2.45 GHz) with permanent magnets to provide the magnetic field strength of 87.5 mT necessary for satisfying the electron cyclotron resonance (ECR) condition. Microwave ion sources can produce high extracted beam currents at the low gas pressures required for sealed tube operation and at lower power levels than previously used RF-driven ion sources. A 100 mA deuterium/tritium beam will be extracted through a large slit (60×6 mm2) to spread the beam power over a larger target area. This paper describes the design of the permanent-magnet microwave ion source and discusses the impact of the magnetic field design on the source performance. The required equivalent proton beam current density of 40 mA/cm2 was extracted at a moderate microwave power of 400 W with an optimized magnetic field.

Reproducibility in Natural Language Processing: A Case Study of Two R Libraries for Mining PubMed/MEDLINE.

PubMed

Cohen, K Bretonnel; Xia, Jingbo; Roeder, Christophe; Hunter, Lawrence E

2016-05-01

There is currently a crisis in science related to highly publicized failures to reproduce large numbers of published studies. The current work proposes, by way of case studies, a methodology for moving the study of reproducibility in computational work to a full stage beyond that of earlier work. Specifically, it presents a case study in attempting to reproduce the reports of two R libraries for doing text mining of the PubMed/MEDLINE repository of scientific publications. The main findings are that a rational paradigm for reproduction of natural language processing papers can be established; the advertised functionality was difficult, but not impossible, to reproduce; and reproducibility studies can produce additional insights into the functioning of the published system. Additionally, the work on reproducibility lead to the production of novel user-centered documentation that has been accessed 260 times since its publication-an average of once a day per library.

Establishing a high yielding streptomyces-based cell-free protein synthesis system.

PubMed

Li, Jian; Wang, He; Kwon, Yong-Chan; Jewett, Michael C

2017-06-01

Cell-free protein synthesis (CFPS) has emerged as a powerful platform for applied biotechnology and synthetic biology, with a range of applications in synthesizing proteins, evolving proteins, and prototyping genetic circuits. To expand the current CFPS repertoire, we report here the development and optimization of a Streptomyces-based CFPS system for the expression of GC-rich genes. By developing a streamlined crude extract preparation protocol and optimizing reaction conditions, we were able to achieve active enhanced green fluorescent protein (EGFP) yields of greater than 50 μg/mL with batch reactions lasting up to 3 h. By adopting a semi-continuous reaction format, the EGFP yield could be increased to 282 ± 8 μg/mL and the reaction time was extended to 48 h. Notably, our extract preparation procedures were robust to multiple Streptomyces lividans and Streptomyces coelicolor strains, although expression yields varied. We show that our optimized Streptomyces lividans system provides benefits when compared to an Escherichia coli-based CFPS system for increasing percent soluble protein expression for four Streptomyces-originated high GC-content genes that are involved in biosynthesis of the nonribosomal peptides tambromycin and valinomycin. Looking forward, we believe that our Streptomyces-based CFPS system will contribute significantly towards efforts to express complex natural product gene clusters (e.g., nonribosomal peptides and polyketides), providing a new avenue for obtaining and studying natural product biosynthesis pathways. Biotechnol. Bioeng. 2017;114: 1343-1353. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Acid soil infertility effects on peanut yields and yield components

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

Blamey, F.P.C.

1983-01-01

The interpretation of soil amelioration experiments with peanuts is made difficult by the unpredictibility of the crop and by the many factors altered when ameliorating acid soils. The present study was conducted to investigate the effects of lime and gypsum applications on peanut kernel yield via the three first order yield components, pods per ha, kernels per pod, and kernel mass. On an acid medium sandy loam soil (typic Plinthustult), liming resulted in a highly significant kernel yield increase of 117% whereas gypsum applications were of no significant benefit. As indicated by path coefficient analysis, an increase in the numbermore » of pods per ha was markedly more important in increasing yield than an increase in either the number of kernels per pod or kernel mass. Furthermore, exch. Al was found to be particularly detrimental to pod number. It was postulated that poor peanut yields resulting from acid soil infertility were mainly due to the depressive effect of exch. Al on pod number. Exch. Ca appeared to play a secondary role by ameliorating the adverse effects of exch. Al.« less

Reproducibility of African giant pouched rats detecting Mycobacterium tuberculosis.

PubMed

Ellis, Haylee; Mulder, Christiaan; Valverde, Emilio; Poling, Alan; Edwards, Timothy

2017-04-24

African pouched rats sniffing sputum samples provided by local clinics have significantly increased tuberculosis case findings in Tanzania and Mozambique. The objective of this study was to determine the reproducibility of rat results. Over an 18-month period 11,869 samples were examined by the rats. Intra-rater reliability was assessed through Yule's Q. Inter-rater reliability was assessed with Krippendorff's alpha. Intra-rater reliability was high, with a mean Yule's Q of 0.9. Inter-rater agreement was fair, with Krippendorf's alpha ranging from 0.15 to 0.45. Both Intra- and Inter-rater reliability was independent of the sex of the animals, but they were positively correlated with age. Both intra- and inter-rater agreement was lowest for samples designated as smear-negative by the clinics. Overall, the reproducibility of tuberculosis detection rat results was fair and diagnostic results were therefore independent of the rats used.

Towards Reproducibility in Computational Hydrology

NASA Astrophysics Data System (ADS)

Hutton, Christopher; Wagener, Thorsten; Freer, Jim; Han, Dawei; Duffy, Chris; Arheimer, Berit

2017-04-01

Reproducibility is a foundational principle in scientific research. The ability to independently re-run an experiment helps to verify the legitimacy of individual findings, and evolve (or reject) hypotheses and models of how environmental systems function, and move them from specific circumstances to more general theory. Yet in computational hydrology (and in environmental science more widely) the code and data that produces published results are not regularly made available, and even if they are made available, there remains a multitude of generally unreported choices that an individual scientist may have made that impact the study result. This situation strongly inhibits the ability of our community to reproduce and verify previous findings, as all the information and boundary conditions required to set up a computational experiment simply cannot be reported in an article's text alone. In Hutton et al 2016 [1], we argue that a cultural change is required in the computational hydrological community, in order to advance and make more robust the process of knowledge creation and hypothesis testing. We need to adopt common standards and infrastructures to: (1) make code readable and re-useable; (2) create well-documented workflows that combine re-useable code together with data to enable published scientific findings to be reproduced; (3) make code and workflows available, easy to find, and easy to interpret, using code and code metadata repositories. To create change we argue for improved graduate training in these areas. In this talk we reflect on our progress in achieving reproducible, open science in computational hydrology, which are relevant to the broader computational geoscience community. In particular, we draw on our experience in the Switch-On (EU funded) virtual water science laboratory (http://www.switch-on-vwsl.eu/participate/), which is an open platform for collaboration in hydrological experiments (e.g. [2]). While we use computational hydrology as

OpenMS - A platform for reproducible analysis of mass spectrometry data.

PubMed

Pfeuffer, Julianus; Sachsenberg, Timo; Alka, Oliver; Walzer, Mathias; Fillbrunn, Alexander; Nilse, Lars; Schilling, Oliver; Reinert, Knut; Kohlbacher, Oliver

2017-11-10

In recent years, several mass spectrometry-based omics technologies emerged to investigate qualitative and quantitative changes within thousands of biologically active components such as proteins, lipids and metabolites. The research enabled through these methods potentially contributes to the diagnosis and pathophysiology of human diseases as well as to the clarification of structures and interactions between biomolecules. Simultaneously, technological advances in the field of mass spectrometry leading to an ever increasing amount of data, demand high standards in efficiency, accuracy and reproducibility of potential analysis software. This article presents the current state and ongoing developments in OpenMS, a versatile open-source framework aimed at enabling reproducible analyses of high-throughput mass spectrometry data. It provides implementations of frequently occurring processing operations on MS data through a clean application programming interface in C++ and Python. A collection of 185 tools and ready-made workflows for typical MS-based experiments enable convenient analyses for non-developers and facilitate reproducible research without losing flexibility. OpenMS will continue to increase its ease of use for developers as well as users with improved continuous integration/deployment strategies, regular trainings with updated training materials and multiple sources of support. The active developer community ensures the incorporation of new features to support state of the art research. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Engineering of Corynebacterium glutamicum for high-yield L-valine production under oxygen deprivation conditions.

PubMed

Hasegawa, Satoshi; Suda, Masako; Uematsu, Kimio; Natsuma, Yumi; Hiraga, Kazumi; Jojima, Toru; Inui, Masayuki; Yukawa, Hideaki

2013-02-01

We previously demonstrated efficient L-valine production by metabolically engineered Corynebacterium glutamicum under oxygen deprivation. To achieve the high productivity, a NADH/NADPH cofactor imbalance during the synthesis of l-valine was overcome by engineering NAD-preferring mutant acetohydroxy acid isomeroreductase (AHAIR) and using NAD-specific leucine dehydrogenase from Lysinibacillus sphaericus. Lactate as a by-product was largely eliminated by disrupting the lactate dehydrogenase gene ldhA. Nonetheless, a few other by-products, particularly succinate, were still produced and acted to suppress the L-valine yield. Eliminating these by-products therefore was deemed key to improving theL-valine yield. By additionally disrupting the phosphoenolpyruvate carboxylase gene ppc, succinate production was effectively suppressed, but both glucose consumption and L-valine production dropped considerably due to the severely elevated intracellular NADH/NAD(+) ratio. In contrast, this perturbed intracellular redox state was more than compensated for by deletion of three genes associated with NADH-producing acetate synthesis and overexpression of five glycolytic genes, including gapA, encoding NADH-inhibited glyceraldehyde-3-phosphate dehydrogenase. Inserting feedback-resistant mutant acetohydroxy acid synthase and NAD-preferring mutant AHAIR in the chromosome resulted in higher L-valine yield and productivity. Deleting the alanine transaminase gene avtA suppressed alanine production. The resultant strain produced 1,280 mM L-valine at a yield of 88% mol mol of glucose(-1) after 24 h under oxygen deprivation, a vastly improved yield over our previous best.

Engineering of Corynebacterium glutamicum for High-Yield l-Valine Production under Oxygen Deprivation Conditions

PubMed Central

Hasegawa, Satoshi; Suda, Masako; Uematsu, Kimio; Natsuma, Yumi; Hiraga, Kazumi; Jojima, Toru; Inui, Masayuki

2013-01-01

We previously demonstrated efficient l-valine production by metabolically engineered Corynebacterium glutamicum under oxygen deprivation. To achieve the high productivity, a NADH/NADPH cofactor imbalance during the synthesis of l-valine was overcome by engineering NAD-preferring mutant acetohydroxy acid isomeroreductase (AHAIR) and using NAD-specific leucine dehydrogenase from Lysinibacillus sphaericus. Lactate as a by-product was largely eliminated by disrupting the lactate dehydrogenase gene ldhA. Nonetheless, a few other by-products, particularly succinate, were still produced and acted to suppress the l-valine yield. Eliminating these by-products therefore was deemed key to improving the l-valine yield. By additionally disrupting the phosphoenolpyruvate carboxylase gene ppc, succinate production was effectively suppressed, but both glucose consumption and l-valine production dropped considerably due to the severely elevated intracellular NADH/NAD+ ratio. In contrast, this perturbed intracellular redox state was more than compensated for by deletion of three genes associated with NADH-producing acetate synthesis and overexpression of five glycolytic genes, including gapA, encoding NADH-inhibited glyceraldehyde-3-phosphate dehydrogenase. Inserting feedback-resistant mutant acetohydroxy acid synthase and NAD-preferring mutant AHAIR in the chromosome resulted in higher l-valine yield and productivity. Deleting the alanine transaminase gene avtA suppressed alanine production. The resultant strain produced 1,280 mM l-valine at a yield of 88% mol mol of glucose−1 after 24 h under oxygen deprivation, a vastly improved yield over our previous best. PMID:23241971

Quantifying reproducibility in computational biology: the case of the tuberculosis drugome.

PubMed

Garijo, Daniel; Kinnings, Sarah; Xie, Li; Xie, Lei; Zhang, Yinliang; Bourne, Philip E; Gil, Yolanda

2013-01-01

How easy is it to reproduce the results found in a typical computational biology paper? Either through experience or intuition the reader will already know that the answer is with difficulty or not at all. In this paper we attempt to quantify this difficulty by reproducing a previously published paper for different classes of users (ranging from users with little expertise to domain experts) and suggest ways in which the situation might be improved. Quantification is achieved by estimating the time required to reproduce each of the steps in the method described in the original paper and make them part of an explicit workflow that reproduces the original results. Reproducing the method took several months of effort, and required using new versions and new software that posed challenges to reconstructing and validating the results. The quantification leads to "reproducibility maps" that reveal that novice researchers would only be able to reproduce a few of the steps in the method, and that only expert researchers with advance knowledge of the domain would be able to reproduce the method in its entirety. The workflow itself is published as an online resource together with supporting software and data. The paper concludes with a brief discussion of the complexities of requiring reproducibility in terms of cost versus benefit, and a desiderata with our observations and guidelines for improving reproducibility. This has implications not only in reproducing the work of others from published papers, but reproducing work from one's own laboratory.

Slope Controls Grain Yield and Climatic Yield in Mountainous Yunnan province, China

NASA Astrophysics Data System (ADS)

Duan, X.; Rong, L.; Gu, Z.; Feng, D.

2017-12-01

Mountainous regions are increasingly vulnerable to food insecurity because of limited arable land, growing population pressure, and climate change. Development of sustainable mountain agriculture will require an increased understanding of the effects of environmental factors on grain and climatic yields. The objective of this study was to explore the relationships between actual grain yield, climatic yield, and environmental factors in a mountainous region in China. We collected data on the average grain yield per unit area in 119 counties in Yunnan province from 1985 to 2012, and chose 17 environmental factors for the same period. Our results showed that actual grain yield ranged from 1.43 to 6.92 t·ha-1, and the climatic yield ranged from -0.15 to -0.01 t·ha-1. Lower climatic yield but higher grain yield was generally found in central areas and at lower slopes and elevations in the western and southwestern counties of Yunnan province. Higher climatic yield but lower grain yield were found in northwestern parts of Yunnan province on steep slopes. Annual precipation and temperature had a weak influence on the climatic yield. Slope explained 44.62 and 26.29% of the variation in grain yield and climatic yield. The effects of topography on grain and climatic yields were greater than climatic factors. Slope was the most important environmental variable for the variability in climatic and grain yields in the mountainous Yunnan province due to the highly heterogeneous topographic conditions. Conversion of slopes to terraces in areas with higher climatic yields is an effective way to maintain grain production in response to climate variability. Additionally, soil amendments and soil and water conservation measures should be considered to maintain soil fertility and aid in sustainable development in central areas, and in counties at lower slopes and elevations in western and southwestern Yunnan province.

Experimental Techniques Verified for Determining Yield and Flow Surfaces

NASA Technical Reports Server (NTRS)

Lerch, Brad A.; Ellis, Rod; Lissenden, Cliff J.

1998-01-01

Structural components in aircraft engines are subjected to multiaxial loads when in service. For such components, life prediction methodologies are dependent on the accuracy of the constitutive models that determine the elastic and inelastic portions of a loading cycle. A threshold surface (such as a yield surface) is customarily used to differentiate between reversible and irreversible flow. For elastoplastic materials, a yield surface can be used to delimit the elastic region in a given stress space. The concept of a yield surface is central to the mathematical formulation of a classical plasticity theory, but at elevated temperatures, material response can be highly time dependent. Thus, viscoplastic theories have been developed to account for this time dependency. Since the key to many of these theories is experimental validation, the objective of this work (refs. 1 and 2) at the NASA Lewis Research Center was to verify that current laboratory techniques and equipment are sufficient to determine flow surfaces at elevated temperatures. By probing many times in the axial-torsional stress space, we could define the yield and flow surfaces. A small offset definition of yield (10 me) was used to delineate the boundary between reversible and irreversible behavior so that the material state remained essentially unchanged and multiple probes could be done on the same specimen. The strain was measured with an off-the-shelf multiaxial extensometer that could measure the axial and torsional strains over a wide range of temperatures. The accuracy and resolution of this extensometer was verified by comparing its data with strain gauge data at room temperature. The extensometer was found to have sufficient resolution for these experiments. In addition, the amount of crosstalk (i.e., the accumulation of apparent strain in one direction when strain in the other direction is applied) was found to be negligible. Tubular specimens were induction heated to determine the flow

Inflow, Outflow, Yields, and Stellar Population Mixing in Chemical Evolution Models

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

Andrews, Brett H.; Weinberg, David H.; Schönrich, Ralph

Chemical evolution models are powerful tools for interpreting stellar abundance surveys and understanding galaxy evolution. However, their predictions depend heavily on the treatment of inflow, outflow, star formation efficiency (SFE), the stellar initial mass function, the SN Ia delay time distribution, stellar yields, and stellar population mixing. Using flexCE, a flexible one-zone chemical evolution code, we investigate the effects of and trade-offs between parameters. Two critical parameters are SFE and the outflow mass-loading parameter, which shift the knee in [O/Fe]–[Fe/H] and the equilibrium abundances that the simulations asymptotically approach, respectively. One-zone models with simple star formation histories follow narrow tracksmore » in [O/Fe]–[Fe/H] unlike the observed bimodality (separate high- α and low- α sequences) in this plane. A mix of one-zone models with inflow timescale and outflow mass-loading parameter variations, motivated by the inside-out galaxy formation scenario with radial mixing, reproduces the two sequences better than a one-zone model with two infall epochs. We present [X/Fe]–[Fe/H] tracks for 20 elements assuming three different supernova yield models and find some significant discrepancies with solar neighborhood observations, especially for elements with strongly metallicity-dependent yields. We apply principal component abundance analysis to the simulations and existing data to reveal the main correlations among abundances and quantify their contributions to variation in abundance space. For the stellar population mixing scenario, the abundances of α -elements and elements with metallicity-dependent yields dominate the first and second principal components, respectively, and collectively explain 99% of the variance in the model. flexCE is a python package available at https://github.com/bretthandrews/flexCE.« less

Simple and Reproducible Two-Stage Agitation Speed Control Strategy for Enhanced Triterpene Production by Lingzhi or Reishi Medicinal Mushrooms, Ganoderma lucidum ACCC G0119 (Higher Basidiomycetes) Based on Submerged Liquid Fermentation.

PubMed

Feng, Jie; Feng, Na; Yang, Yan; Liu, Fang; Zhang, Jingsong; Jia, Wei; Lin, Chi-Chung

2015-01-01

Triterpenes are important anticancer agents produced by batch submerged liquid fermentation, with the medicinal mushroom Ganoderma lucidum ACCC G0119, which was investigated under various dissolved oxygen levels by varying agitation speeds. Three kinetic parameters were analyzed: specific mycelial growth rate (μsmg), specific glucose consumption rate (qsgc), and specific triterpene production rate (qstp). High concentration, yield, and productivity of triterpenes were achieved by developing a simple and reproducible two-stage agitation speed control strategy. At the first 40 h, agitation speed was controlled at 150 rpm to obtain the quickest peak qstp for triterpene production, subsequently agitation speed was controlled at 100 rpm to maintain high qstp for high triterpene accumulation. The maximum concentration of triterpenes reached 0.086 g/l with the yield of 6.072 g/kg and the productivity of 6.532 × 10-4 g/(l·h), which were 39.61%, 36.48%, and 49.22%, respectively, better than the best results controlled by fixed agitation speeds. Conceivably, such a triterpene fermentation production strategy would be useful for industrial large-scale production of triterpenes with G. lucidum.

Opening Reproducible Research

NASA Astrophysics Data System (ADS)

Nüst, Daniel; Konkol, Markus; Pebesma, Edzer; Kray, Christian; Klötgen, Stephanie; Schutzeichel, Marc; Lorenz, Jörg; Przibytzin, Holger; Kussmann, Dirk

2016-04-01

Open access is not only a form of publishing such that research papers become available to the large public free of charge, it also refers to a trend in science that the act of doing research becomes more open and transparent. When science transforms to open access we not only mean access to papers, research data being collected, or data being generated, but also access to the data used and the procedures carried out in the research paper. Increasingly, scientific results are generated by numerical manipulation of data that were already collected, and may involve simulation experiments that are completely carried out computationally. Reproducibility of research findings, the ability to repeat experimental procedures and confirm previously found results, is at the heart of the scientific method (Pebesma, Nüst and Bivand, 2012). As opposed to the collection of experimental data in labs or nature, computational experiments lend themselves very well for reproduction. Some of the reasons why scientists do not publish data and computational procedures that allow reproduction will be hard to change, e.g. privacy concerns in the data, fear for embarrassment or of losing a competitive advantage. Others reasons however involve technical aspects, and include the lack of standard procedures to publish such information and the lack of benefits after publishing them. We aim to resolve these two technical aspects. We propose a system that supports the evolution of scientific publications from static papers into dynamic, executable research documents. The DFG-funded experimental project Opening Reproducible Research (ORR) aims for the main aspects of open access, by improving the exchange of, by facilitating productive access to, and by simplifying reuse of research results that are published over the Internet. Central to the project is a new form for creating and providing research results, the executable research compendium (ERC), which not only enables third parties to

Thermic conversion of benzene into 6-phenylfulvene with high yield mediated by GaP nanocrystals.

PubMed

Gao, Shanmin; Lu, Jun; Zhao, Yan; Chen, Nan; Xie, Yi

2002-12-07

With GaP nanocrystals being used in a close reaction system, 6-phenylfulvene is successfully obtained via a high yield thermic conversion from benzene, which provides the possibility of applying nanocrystals to mediate organic reactions.

Low LET radiolysis escape yields for reducing radicals and H2 in pressurized high temperature water

NASA Astrophysics Data System (ADS)

Sterniczuk, Marcin; Yakabuskie, Pamela A.; Wren, J. Clara; Jacob, Jasmine A.; Bartels, David M.

2016-04-01

Low Linear Energy Transfer (LET) radiolysis escape yields (G values) are reported for the sum (G(radH)+G(e-)aq) and for G(H2) in subcritical water up to 350 °C. The scavenger system 1-10 mM acetate/0.001 M hydroxide/0.00048 M N2O was used with simultaneous mass spectroscopic detection of H2 and N2 product. Temperature-dependent measurements were carried out with 2.5 MeV electrons from a van de Graaff accelerator, while room temperature calibration measurements were done with a 60Co gamma source. The concentrations and dose range were carefully chosen so that initial spur chemistry is not perturbed and the N2 product yield corresponds to those reducing radicals that escape recombination in pure water. In comparison with a recent review recommendation of Elliot and Bartels (AECL report 153-127160-450-001, 2009), the measured reducing radical yield is seven percent smaller at room temperature but in fairly good agreement above 150 °C. The H2 escape yield is in good agreement throughout the temperature range with several previous studies that used much larger radical scavenging rates. Previous analysis of earlier high temperature measurements of Gesc(radOH) is shown to be flawed, although the actual G values may be nearly correct. The methodology used in the present report greatly reduces the range of possible error and puts the high temperature escape yields for low-LET radiation on a much firmer quantitative foundation than was previously available.

Evaluation of the reproducibility of lung motion probability distribution function (PDF) using dynamic MRI.

PubMed

Cai, Jing; Read, Paul W; Altes, Talissa A; Molloy, Janelle A; Brookeman, James R; Sheng, Ke

2007-01-21

Treatment planning based on probability distribution function (PDF) of patient geometries has been shown a potential off-line strategy to incorporate organ motion, but the application of such approach highly depends upon the reproducibility of the PDF. In this paper, we investigated the dependences of the PDF reproducibility on the imaging acquisition parameters, specifically the scan time and the frame rate. Three healthy subjects underwent a continuous 5 min magnetic resonance (MR) scan in the sagittal plane with a frame rate of approximately 10 f s-1, and the experiments were repeated with an interval of 2 to 3 weeks. A total of nine pulmonary vessels from different lung regions (upper, middle and lower) were tracked and the dependences of their displacement PDF reproducibility were evaluated as a function of scan time and frame rate. As results, the PDF reproducibility error decreased with prolonged scans and appeared to approach equilibrium state in subjects 2 and 3 within the 5 min scan. The PDF accuracy increased in the power function with the increase of frame rate; however, the PDF reproducibility showed less sensitivity to frame rate presumably due to the randomness of breathing which dominates the effects. As the key component of the PDF-based treatment planning, the reproducibility of the PDF affects the dosimetric accuracy substantially. This study provides a reference for acquiring MR-based PDF of structures in the lung.

Reproducibility in Natural Language Processing: A Case Study of Two R Libraries for Mining PubMed/MEDLINE

PubMed Central

Cohen, K. Bretonnel; Xia, Jingbo; Roeder, Christophe; Hunter, Lawrence E.

2018-01-01

There is currently a crisis in science related to highly publicized failures to reproduce large numbers of published studies. The current work proposes, by way of case studies, a methodology for moving the study of reproducibility in computational work to a full stage beyond that of earlier work. Specifically, it presents a case study in attempting to reproduce the reports of two R libraries for doing text mining of the PubMed/MEDLINE repository of scientific publications. The main findings are that a rational paradigm for reproduction of natural language processing papers can be established; the advertised functionality was difficult, but not impossible, to reproduce; and reproducibility studies can produce additional insights into the functioning of the published system. Additionally, the work on reproducibility lead to the production of novel user-centered documentation that has been accessed 260 times since its publication—an average of once a day per library. PMID:29568821

State-of-the-art exposure chamber for highly controlled and reproducible THz biological effects studies

NASA Astrophysics Data System (ADS)

Cerna, Cesario Z.; Elam, David P.; Echchgadda, Ibtissam; Sloan, Mark A.; Wilmink, Gerald J.

2014-03-01

Terahertz (THz) imaging and sensing technologies are increasingly being used at international airports for security screening purposes and at major medical centers for cancer and burn diagnosis. The emergence of new THz applications has directly resulted in an increased interest regarding the biological effects associated with this frequency range. Knowledge of THz biological effects is also desired for the safe use of THz systems, identification of health hazards, and development of empirically-based safety standards. In this study, we developed a state-of-the-art exposure chamber that allowed for highly controlled and reproducible studies of THz biological effects. This innovative system incorporated an industry grade cell incubator system that permitted a highly controlled exposure environment, where temperatures could be maintained at 37 °C +/- 0.1 °C, carbon dioxide (CO2) levels at 5% +/- 0.1%, and relative humidity (RH) levels at 95% +/- 1%. To maximize the THz power transmitted to the cell culture region inside the humid incubator, a secondary custom micro-chamber was fabricated and incorporated into the system. This micro-chamber shields the THz beam from the incubator environment and could be nitrogen-purged to eliminate water absorption effects. Additionally, a microscope that allowed for real-time visualization of the live cells before, during, and after THz exposure was integrated into the exposure system.

A high yield neutron target for cancer therapy

NASA Technical Reports Server (NTRS)

Alger, D. L.; Steinberg, R.

1972-01-01

A rotating target was developed that has the potential for providing an initial yield of 10 to the 13th power neutrons per second by the T(d,n)He-4 reaction, and a useable lifetime in excess of 600 hours. This yield and lifetime are indicated for a 300 Kv and 30 mA deuteron accelerator and a 30 microns thick titanium tritide film formed of the stoichiometric compound TiT2. The potential for extended lifetime is made possible by incorporating a sputtering electrode that permits use of titanium tritide thicknesses much greater than the deuteron range. The electrode is used to remove in situ depleted titanium layers to expose fresh tritide beneath. The utilization of the rotating target as a source of fast neutrons for cancer therapy is discussed.

High-Yield Synthesis of Stoichiometric Boron Nitride Nanostructures

DOE PAGES

Nocua, José E.; Piazza, Fabrice; Weiner, Brad R.; ...

2009-01-01

Boron nimore » tride (BN) nanostructures are structural analogues of carbon nanostructures but have completely different bonding character and structural defects. They are chemically inert, electrically insulating, and potentially important in mechanical applications that include the strengthening of light structural materials. These applications require the reliable production of bulk amounts of pure BN nanostructures in order to be able to reinforce large quantities of structural materials, hence the need for the development of high-yield synthesis methods of pure BN nanostructures. Using borazine ( B 3 N 3 H 6 ) as chemical precursor and the hot-filament chemical vapor deposition (HFCVD) technique, pure BN nanostructures with cross-sectional sizes ranging between 20 and 50 nm were obtained, including nanoparticles and nanofibers. Their crystalline structure was characterized by (XRD), their morphology and nanostructure was examined by (SEM) and (TEM), while their chemical composition was studied by (EDS), (FTIR), (EELS), and (XPS). Taken altogether, the results indicate that all the material obtained is stoichiometric nanostructured BN with hexagonal and rhombohedral crystalline structure.« less

Parametric studies on droplet generation reproducibility for applications with biological relevant fluids

PubMed Central

Eichler, Marko; Römer, Robert; Grodrian, Andreas; Lemke, Karen; Nagel, Krees; Klages, Claus‐Peter; Gastrock, Gunter

2017-01-01

Abstract Although the great potential of droplet based microfluidic technologies for routine applications in industry and academia has been successfully demonstrated over the past years, its inherent potential is not fully exploited till now. Especially regarding to the droplet generation reproducibility and stability, two pivotally important parameters for successful applications, there is still a need for improvement. This is even more considerable when droplets are created to investigate tissue fragments or cell cultures (e.g. suspended cells or 3D cell cultures) over days or even weeks. In this study we present microfluidic chips composed of a plasma coated polymer, which allow surfactants‐free, highly reproducible and stable droplet generation from fluids like cell culture media. We demonstrate how different microfluidic designs and different flow rates (and flow rate ratios) affect the reproducibility of the droplet generation process and display the applicability for a wide variety of bio(techno)logically relevant media. PMID:29399017

SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer.

PubMed

Beccuti, Marco; Cordero, Francesca; Arigoni, Maddalena; Panero, Riccardo; Amparore, Elvio G; Donatelli, Susanna; Calogero, Raffaele A

2018-03-01

Short reads sequencing technology has been used for more than a decade now. However, the analysis of RNAseq and ChIPseq data is still computational demanding and the simple access to raw data does not guarantee results reproducibility between laboratories. To address these two aspects, we developed SeqBox, a cheap, efficient and reproducible RNAseq/ChIPseq hardware/software solution based on NUC6I7KYK mini-PC (an Intel consumer game computer with a fast processor and a high performance SSD disk), and Docker container platform. In SeqBox the analysis of RNAseq and ChIPseq data is supported by a friendly GUI. This allows access to fast and reproducible analysis also to scientists with/without scripting experience. Docker container images, docker4seq package and the GUI are available at http://www.bioinformatica.unito.it/reproducibile.bioinformatics.html. beccuti@di.unito.it. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Language-Agnostic Reproducible Data Analysis Using Literate Programming.

PubMed

Vassilev, Boris; Louhimo, Riku; Ikonen, Elina; Hautaniemi, Sampsa

2016-01-01

A modern biomedical research project can easily contain hundreds of analysis steps and lack of reproducibility of the analyses has been recognized as a severe issue. While thorough documentation enables reproducibility, the number of analysis programs used can be so large that in reality reproducibility cannot be easily achieved. Literate programming is an approach to present computer programs to human readers. The code is rearranged to follow the logic of the program, and to explain that logic in a natural language. The code executed by the computer is extracted from the literate source code. As such, literate programming is an ideal formalism for systematizing analysis steps in biomedical research. We have developed the reproducible computing tool Lir (literate, reproducible computing) that allows a tool-agnostic approach to biomedical data analysis. We demonstrate the utility of Lir by applying it to a case study. Our aim was to investigate the role of endosomal trafficking regulators to the progression of breast cancer. In this analysis, a variety of tools were combined to interpret the available data: a relational database, standard command-line tools, and a statistical computing environment. The analysis revealed that the lipid transport related genes LAPTM4B and NDRG1 are coamplified in breast cancer patients, and identified genes potentially cooperating with LAPTM4B in breast cancer progression. Our case study demonstrates that with Lir, an array of tools can be combined in the same data analysis to improve efficiency, reproducibility, and ease of understanding. Lir is an open-source software available at github.com/borisvassilev/lir.

Language-Agnostic Reproducible Data Analysis Using Literate Programming

PubMed Central

Vassilev, Boris; Louhimo, Riku; Ikonen, Elina; Hautaniemi, Sampsa

2016-01-01

A modern biomedical research project can easily contain hundreds of analysis steps and lack of reproducibility of the analyses has been recognized as a severe issue. While thorough documentation enables reproducibility, the number of analysis programs used can be so large that in reality reproducibility cannot be easily achieved. Literate programming is an approach to present computer programs to human readers. The code is rearranged to follow the logic of the program, and to explain that logic in a natural language. The code executed by the computer is extracted from the literate source code. As such, literate programming is an ideal formalism for systematizing analysis steps in biomedical research. We have developed the reproducible computing tool Lir (literate, reproducible computing) that allows a tool-agnostic approach to biomedical data analysis. We demonstrate the utility of Lir by applying it to a case study. Our aim was to investigate the role of endosomal trafficking regulators to the progression of breast cancer. In this analysis, a variety of tools were combined to interpret the available data: a relational database, standard command-line tools, and a statistical computing environment. The analysis revealed that the lipid transport related genes LAPTM4B and NDRG1 are coamplified in breast cancer patients, and identified genes potentially cooperating with LAPTM4B in breast cancer progression. Our case study demonstrates that with Lir, an array of tools can be combined in the same data analysis to improve efficiency, reproducibility, and ease of understanding. Lir is an open-source software available at github.com/borisvassilev/lir. PMID:27711123

Reproducibility of Ultrasound-Guided High Intensity Focused Ultrasound (HIFU) Thermal Lesions in Minimally-Invasive Brain Surgery

NASA Astrophysics Data System (ADS)

Zahedi, Sulmaz

This study aims to prove the feasibility of using Ultrasound-Guided High Intensity Focused Ultrasound (USg-HIFU) to create thermal lesions in neurosurgical applications, allowing for precise ablation of brain tissue, while simultaneously providing real time imaging. To test the feasibility of the system, an optically transparent HIFU compatible tissue-mimicking phantom model was produced. USg-HIFU was then used for ablation of the phantom, with and without targets. Finally, ex vivo lamb brain tissue was imaged and ablated using the USg-HIFU system. Real-time ultrasound images and videos obtained throughout the ablation process showing clear lesion formation at the focal point of the HIFU transducer. Post-ablation gross and histopathology examinations were conducted to verify thermal and mechanical damage in the ex vivo lamb brain tissue. Finally, thermocouple readings were obtained, and HIFU field computer simulations were conducted to verify findings. Results of the study concluded reproducibility of USg-HIFU thermal lesions for neurosurgical applications.

Identification and reproducibility of dietary patterns in a Danish cohort: the Inter99 study.

PubMed

Lau, Cathrine; Glümer, Charlotte; Toft, Ulla; Tetens, Inge; Carstensen, Bendix; Jørgensen, Torben; Borch-Johnsen, Knut

2008-05-01

We aimed to identify dietary patterns in a Danish adult population and assess the reproducibility of the dietary patterns identified. Baseline data of 3,372 women and 3,191 men (30-60 years old) from the population-based survey Inter99 was used. Food intake, assessed by a FFQ, was aggregated into thirty-four separate food groups. Dietary patterns were identified by principal component analysis. Confirmatory factor analysis and Bland Altman plots were used to assess the reproducibility of the dietary patterns identified. The Bland Altman plots were used as an alternative and new method. Two factors were retained for both women and men, which accounted for 15.1-17.4 % of the total variation. The 'Traditional' pattern was characterised by high loadings ( > or = 0.40) on paté or high-fat meat for sandwiches, mayonnaise salads, red meat, potatoes, butter and lard, low-fat fish, low-fat meat for sandwiches, and sauces. The 'Modern' pattern was characterised by high loadings on vegetables, fruit, mixed vegetable dishes, vegetable oil and vinegar dressing, poultry, and pasta, rice and wheat kernels. Small differences were observed between patterns identified for women and men. The root mean square error approximation from the confirmatory factor analysis was 0.08. The variation observed from the Bland Altman plots of factors from explorative v. confirmative analyses and explorative analyses from two sub-samples was between 18.8 and 47.7 %. Pearson's correlation was >0.89 (P < 0.0001). The reproducibility was better for women than for men. We conclude that the 'Traditional' and 'Modern' dietary patterns identified were reproducible.

Simultaneous achievement of high ethanol yield and titer in Clostridium thermocellum.

PubMed

Tian, Liang; Papanek, Beth; Olson, Daniel G; Rydzak, Thomas; Holwerda, Evert K; Zheng, Tianyong; Zhou, Jilai; Maloney, Marybeth; Jiang, Nannan; Giannone, Richard J; Hettich, Robert L; Guss, Adam M; Lynd, Lee R

2016-01-01

Biofuel production from plant cell walls offers the potential for sustainable and economically attractive alternatives to petroleum-based products. Fuels from cellulosic biomass are particularly promising, but would benefit from lower processing costs. Clostridium thermocellum can rapidly solubilize and ferment cellulosic biomass, making it a promising candidate microorganism for consolidated bioprocessing for biofuel production, but increases in product yield and titer are still needed. Here, we started with an engineered C. thermocellum strain where the central metabolic pathways to products other than ethanol had been deleted. After two stages of adaptive evolution, an evolved strain was selected with improved yield and titer. On chemically defined medium with crystalline cellulose as substrate, the evolved strain produced 22.4 ± 1.4 g/L ethanol from 60 g/L cellulose. The resulting yield was about 0.39 gETOH/gGluc eq, which is 75 % of the maximum theoretical yield. Genome resequencing, proteomics, and biochemical analysis were used to examine differences between the original and evolved strains. A two step selection method successfully improved the ethanol yield and the titer. This evolved strain has the highest ethanol yield and titer reported to date for C. thermocellum, and is an important step in the development of this microbe for industrial applications.

High-yield production of mannitol by Leuconostoc pseudomesenteroides CTCC G123 from chicory-derived inulin hydrolysate.

PubMed

Zhang, Min; Gu, Lei; Cheng, Chao; Zhu, Junru; Wu, Hao; Ma, Jiangfeng; Dong, Weiliang; Kong, Xiangping; Jiang, Min; Ouyang, Pingkai

2017-08-01

Chicory is an agricultural plant with considerable potential as a carbohydrate substrate for low-cost production of biochemicals. In this work, the production of mannitol by Leuconostoc pseudomesenteroides CTCC G123 from chicory-derived inulin hydrolysate was investigated. The bioconversion process initially suffered from the leakage of fructose to the phosphoketolase pathway, resulting in a low mannitol yield. When inulin hydrolysate was supplemented with glucose as a substrate for mannitol production in combination with aeration induction and nicotinic acid induced redox modulation strategies, the mannitol yield greatly improved. Under these conditions, significant improvement in the glucose consumption rate, intracellular NADH levels and mannitol dehydrogenase specific activity were observed, with mannitol production increasing from 64.6 to 88.1 g/L and overall yield increase from 0.69 to 0.94 g/g. This work demonstrated an efficient method for the production of mannitol from inulin hydrolysate with a high overall yield.

Find_tfSBP: find thermodynamics-feasible and smallest balanced pathways with high yield from large-scale metabolic networks.

PubMed

Xu, Zixiang; Sun, Jibin; Wu, Qiaqing; Zhu, Dunming

2017-12-11

Biologically meaningful metabolic pathways are important references in the design of industrial bacterium. At present, constraint-based method is the only way to model and simulate a genome-scale metabolic network under steady-state criteria. Due to the inadequate assumption of the relationship in gene-enzyme-reaction as one-to-one unique association, computational difficulty or ignoring the yield from substrate to product, previous pathway finding approaches can't be effectively applied to find out the high yield pathways that are mass balanced in stoichiometry. In addition, the shortest pathways may not be the pathways with high yield. At the same time, a pathway, which exists in stoichiometry, may not be feasible in thermodynamics. By using mixed integer programming strategy, we put forward an algorithm to identify all the smallest balanced pathways which convert the source compound to the target compound in large-scale metabolic networks. The resulting pathways by our method can finely satisfy the stoichiometric constraints and non-decomposability condition. Especially, the functions of high yield and thermodynamics feasibility have been considered in our approach. This tool is tailored to direct the metabolic engineering practice to enlarge the metabolic potentials of industrial strains by integrating the extensive metabolic network information built from systems biology dataset.

Unexpected high yields of carbonyl and peroxide products of aqueous isoprene ozonolysis and implications

NASA Astrophysics Data System (ADS)

Wang, H. L.; Huang, D.; Zhang, X.; Zhao, Y.; Chen, Z. M.

2012-03-01

The aqueous phase reaction of volatile organic compounds (VOCs) has not been considered in most analyses of atmospheric chemical processes. However, some experimental evidence has shown that, compared to the corresponding gas phase reaction, the aqueous chemical processes of VOCs in the bulk solutions and surfaces of ambient wet particles (cloud, fog, and wet aerosols) may potentially contribute to the products and formation of secondary organic aerosol (SOA). In the present study, we performed a laboratory experiment of the aqueous ozonolysis of isoprene at different pHs (3-7) and temperatures (4-25 °C). We detected three important kinds of products, including carbonyl compounds, peroxide compounds, and organic acids. Our results showed that the molar yields of these products were nearly independent of the investigated pHs and temperatures. These products included (1) carbonyls: 56.7 ± 6.7% formaldehyde, 42.8 ± 2.5% methacrolein (MAC), and 57.7 ± 3.4% methyl vinyl ketone (MVK); (2) peroxides: 53.4 ± 4.1% hydrogen peroxide (H2O2) and 15.1 ± 3.1% hydroxylmethyl hydroperoxide (HMHP); and (3) organic acids: undetectable (< 1% estimated by the detection limit). Based on the amounts of products formed and the isoprene consumed, the total carbon yield was estimated to be 95 ± 4%. This implied that most of the products in the reaction system were detected. Of note, the combined yields of both MAC + MVK and H2O2 + HMHP in the aqueous isoprene ozonolysis were much higher than those observed in the corresponding gas phase reaction. We suggested that these unexpected high yields of carbonyls and peroxides were related to the greater capability of condensed water, compared to water vapor, to stabilize energy-rich Criegee radicals. This aqueous ozonolysis of isoprene (and possibly other biogenic VOCs) could potentially occur on the surfaces of ambient wet particles and plants. Moreover, the high-yield carbonyl and peroxide products might provide a considerable source of

Reproducibility in Computational Neuroscience Models and Simulations

PubMed Central

McDougal, Robert A.; Bulanova, Anna S.; Lytton, William W.

2016-01-01

Objective Like all scientific research, computational neuroscience research must be reproducible. Big data science, including simulation research, cannot depend exclusively on journal articles as the method to provide the sharing and transparency required for reproducibility. Methods Ensuring model reproducibility requires the use of multiple standard software practices and tools, including version control, strong commenting and documentation, and code modularity. Results Building on these standard practices, model sharing sites and tools have been developed that fit into several categories: 1. standardized neural simulators, 2. shared computational resources, 3. declarative model descriptors, ontologies and standardized annotations; 4. model sharing repositories and sharing standards. Conclusion A number of complementary innovations have been proposed to enhance sharing, transparency and reproducibility. The individual user can be encouraged to make use of version control, commenting, documentation and modularity in development of models. The community can help by requiring model sharing as a condition of publication and funding. Significance Model management will become increasingly important as multiscale models become larger, more detailed and correspondingly more difficult to manage by any single investigator or single laboratory. Additional big data management complexity will come as the models become more useful in interpreting experiments, thus increasing the need to ensure clear alignment between modeling data, both parameters and results, and experiment. PMID:27046845

Reproducibility of the retinal vascular response to flicker light in Asians.

PubMed

Nguyen, Thanh T; Kreis, Andreas J; Kawasaki, Ryo; Wang, Jie Jin; Seifert, Bernd-U; Vilser, Walthard; Nagel, Edgar; Wong, Tien Y

2009-12-01

Dilation of retinal vessels in response to diffuse luminance flicker may reflect endothelial function. Although this has previously been shown to be reproducible in whites, there have been no similar data in Asians. We assess the reproducibility of repeated measurements of this response in Asians. Healthy Asians (n = 33) with normal vision and no history of glaucoma, age-related macular degeneration, cataract, or retinal arterial/venous occlusion participated in this study. Repeated measures from the same subjects were taken 30-60 min apart using the Dynamic Vessel Analyser (DVA, IMEDOS, Jena, Germany). Modification was made to the shape of the light source for Asian participants. Correlations of the first and second measures were assessed using Pearson correlation (R(2)), and agreement between the two measures was shown using Bland-Altman plots. After modification to the shape of the light source, almost perfect correlation was found between the 1st and 2nd measurements of baseline arteriolar (R(2) = 0.95) and venular diameters (R(2) = 0.98) of arteriolar maximum dilation (R(2) = 0.85). Substantially high correlation between the 1st and 2nd measurements of venular maximum dilation was found (R(2) = 0.80). Measurements of the dilation response of retinal vessels to diffuse luminance flicker an Asian sample using the DVA show high reproducibility for repeated measures over a short period of time. Such measurements may allow non-invasive quantification of endothelial function to study its association with systemic and ocular diseases.

Reproducibility of myelin content-based human habenula segmentation at 3 Tesla.

PubMed

Kim, Joo-Won; Naidich, Thomas P; Joseph, Joshmi; Nair, Divya; Glasser, Matthew F; O'halloran, Rafael; Doucet, Gaelle E; Lee, Won Hee; Krinsky, Hannah; Paulino, Alejandro; Glahn, David C; Anticevic, Alan; Frangou, Sophia; Xu, Junqian

2018-03-26

In vivo morphological study of the human habenula, a pair of small epithalamic nuclei adjacent to the dorsomedial thalamus, has recently gained significant interest for its role in reward and aversion processing. However, segmenting the habenula from in vivo magnetic resonance imaging (MRI) is challenging due to the habenula's small size and low anatomical contrast. Although manual and semi-automated habenula segmentation methods have been reported, the test-retest reproducibility of the segmented habenula volume and the consistency of the boundaries of habenula segmentation have not been investigated. In this study, we evaluated the intra- and inter-site reproducibility of in vivo human habenula segmentation from 3T MRI (0.7-0.8 mm isotropic resolution) using our previously proposed semi-automated myelin contrast-based method and its fully-automated version, as well as a previously published manual geometry-based method. The habenula segmentation using our semi-automated method showed consistent boundary definition (high Dice coefficient, low mean distance, and moderate Hausdorff distance) and reproducible volume measurement (low coefficient of variation). Furthermore, the habenula boundary in our semi-automated segmentation from 3T MRI agreed well with that in the manual segmentation from 7T MRI (0.5 mm isotropic resolution) of the same subjects. Overall, our proposed semi-automated habenula segmentation showed reliable and reproducible habenula localization, while its fully-automated version offers an efficient way for large sample analysis. © 2018 Wiley Periodicals, Inc.

Development of a New Class of Scintillating Fibres with Very Short Decay Time and High Light Yield

NASA Astrophysics Data System (ADS)

Borshchev, O.; Cavalcante, A. B. R.; Gavardi, L.; Gruber, L.; Joram, C.; Ponomarenko, S.; Shinji, O.; Surin, N.

2017-05-01

We present first studies of a new class of scintillating fibres which are characterised by very short decay times and high light yield. The fibres are based on a novel type of luminophores admixed to a polystyrene core matrix. These so-called Nanostructured Organosilicon Luminophores (NOL) have high photoluminescense quantum yield and decay times just above 1 ns. A blue and a green emitting prototype fibre with 250 μm diameter were produced and characterised in terms of attenuation length, ionisation light yield, decay time and tolerance to x-ray irradiation. The well-established Kuraray SCSF-78 and SCSF-3HF fibres were taken as references. Even though the two prototype fibres mark just an intermediate step in an ongoing development, their performance is already on a competitive level. In particular, their decay time constants are about a factor of two shorter than the fastest known fibres, which makes them promising candidates for time critical applications.

Reproducing oil paint gloss in print for the purpose of creating reproductions of Old Masters

NASA Astrophysics Data System (ADS)

Elkhuizen, Willemijn S.; Lenseigne, Boris A. J.; Baar, Teun; Verhofstad, Wim; Tempelman, Erik; Geraedts, Jo M. P.; Dik, Joris

2015-03-01

In the field of Fine Art reproduction, 3D scanning plus 3D printing, combined with dedicated software, now allows to capture and reproduce the color and texture of oil paintings. However, for life-like reproduction of the material appearance of such paintings, the typical gloss and translucency must also be included, which is currently not the case. The aim of this paper is to elaborate on the challenges and results of capturing and reproducing oil paint gloss (next to texture and color) using a scanning and printing system. A sample was hand-made using oil paint and acrylic varnish, and its gloss was then reproduced. A gloss map of the painted sample was acquired using a high end DLSR camera and a simple acquisition protocol. Next, Océ High Resolution 3D printing technology was used to create samples with spatially varying gloss. For this, two different strategies were combined: (1) multilevel half-toning of the colors was used to reproduce matte color layers, and (2) varnish was half-toned on top in increasing coverage to recreate increasing gloss levels. This paper presents an overview of the state-of-the-art literature in gloss reproduction and perception, our process of reproduction as well as the visual evaluation of the quality of the created reproduction.

High-throughput miniaturized bioreactors for cell culture process development: reproducibility, scalability, and control.

PubMed

Rameez, Shahid; Mostafa, Sigma S; Miller, Christopher; Shukla, Abhinav A

2014-01-01

Decreasing the timeframe for cell culture process development has been a key goal toward accelerating biopharmaceutical development. Advanced Microscale Bioreactors (ambr™) is an automated micro-bioreactor system with miniature single-use bioreactors with a 10-15 mL working volume controlled by an automated workstation. This system was compared to conventional bioreactor systems in terms of its performance for the production of a monoclonal antibody in a recombinant Chinese Hamster Ovary cell line. The miniaturized bioreactor system was found to produce cell culture profiles that matched across scales to 3 L, 15 L, and 200 L stirred tank bioreactors. The processes used in this article involve complex feed formulations, perturbations, and strict process control within the design space, which are in-line with processes used for commercial scale manufacturing of biopharmaceuticals. Changes to important process parameters in ambr™ resulted in predictable cell growth, viability and titer changes, which were in good agreement to data from the conventional larger scale bioreactors. ambr™ was found to successfully reproduce variations in temperature, dissolved oxygen (DO), and pH conditions similar to the larger bioreactor systems. Additionally, the miniature bioreactors were found to react well to perturbations in pH and DO through adjustments to the Proportional and Integral control loop. The data presented here demonstrates the utility of the ambr™ system as a high throughput system for cell culture process development. © 2014 American Institute of Chemical Engineers.

Milk yield and composition, nutrition, body conformation traits, body condition scores, fertility and diseases in high-yielding dairy cows--Part 1.

PubMed

Aeberhard, K; Bruckmaier, R M; Kuepfer, U; Blum, J W

2001-03-01

Twenty-nine pairs of high-yielding dairy cows (HC; > or = 45 kg/day reached at least once during lactation) and corresponding control cows (CC; with milk yields representing the average yield of the herds) were examined on 29 Swiss farms from March 1995 to September 1996. The hypotheses were tested that there are differences in feed intake, body-conformation traits, body weight (BW), body condition score (BCS), fertility status and disease incidence between HC and CC cows. Cows were studied 2 weeks before and at 5, 9, 13, 17 and 40 weeks post-partum. HC cows produced more energy-corrected milk (ECM) than CC cows (10,670 +/- 321 kg in 293 +/- 5 days and 8385 +/- 283 kg in 294 +/- 4 days, respectively; P < or = 0.001) and yields in the first 100 days of lactation were greater in HC than in CC cows (46.2 +/- 1.1 and 36.2 +/- 1.0 kg ECM/day, respectively; P < or = 0.001). Concentrate intake was greater (P < or = 0.05) in HC than in CC cows (7.6 +/- 0.5 and 5.7 +/- 0.5 kg/day, respectively) and dry matter intakes (measured in week 5 of lactation over 3 days on six farms) were greater in HC than in CC cows (24.0 +/- 1.1 and 20.3 +/- 1.1 kg/day, respectively; P < or = 0.001). HC cows were taller than CC cows (wither heights 143.3 +/- 0.8 and 140.1 +/- 0.8 cm, respectively; P < or = 0.01). Although BW in HC cows was greater than in CC cows throughout the study, differences and decreases of BW during lactation were not significant. BCS at the end of pregnancy and decrements during lactation were similar in HC and CC cows. Fertility parameters were similar in HC and CC cows. Incidences of mastitis, claw and feet problems, hypocalcemia/downer cow syndrome, ovarian cysts and abortions were similar in HC and CC cows, but there were more indigestion problems in HC than in CC cows.

Reproducible Tissue Homogenization and Protein Extraction for Quantitative Proteomics Using MicroPestle-Assisted Pressure-Cycling Technology.

PubMed

Shao, Shiying; Guo, Tiannan; Gross, Vera; Lazarev, Alexander; Koh, Ching Chiek; Gillessen, Silke; Joerger, Markus; Jochum, Wolfram; Aebersold, Ruedi

2016-06-03

The reproducible and efficient extraction of proteins from biopsy samples for quantitative analysis is a critical step in biomarker and translational research. Recently, we described a method consisting of pressure-cycling technology (PCT) and sequential windowed acquisition of all theoretical fragment ions-mass spectrometry (SWATH-MS) for the rapid quantification of thousands of proteins from biopsy-size tissue samples. As an improvement of the method, we have incorporated the PCT-MicroPestle into the PCT-SWATH workflow. The PCT-MicroPestle is a novel, miniaturized, disposable mechanical tissue homogenizer that fits directly into the microTube sample container. We optimized the pressure-cycling conditions for tissue lysis with the PCT-MicroPestle and benchmarked the performance of the system against the conventional PCT-MicroCap method using mouse liver, heart, brain, and human kidney tissues as test samples. The data indicate that the digestion of the PCT-MicroPestle-extracted proteins yielded 20-40% more MS-ready peptide mass from all tissues tested with a comparable reproducibility when compared to the conventional PCT method. Subsequent SWATH-MS analysis identified a higher number of biologically informative proteins from a given sample. In conclusion, we have developed a new device that can be seamlessly integrated into the PCT-SWATH workflow, leading to increased sample throughput and improved reproducibility at both the protein extraction and proteomic analysis levels when applied to the quantitative proteomic analysis of biopsy-level samples.

How to Write a Reproducible Paper

NASA Astrophysics Data System (ADS)

Irving, D. B.

2016-12-01

The geosciences have undergone a computational revolution in recent decades, to the point where almost all modern research relies heavily on software and code. Despite this profound change in the research methods employed by geoscientists, the reporting of computational results has changed very little in academic journals. This lag has led to something of a reproducibility crisis, whereby it is impossible to replicate and verify most of today's published computational results. While it is tempting to decry the slow response of journals and funding agencies in the face of this crisis, there are very few examples of reproducible research upon which to base new communication standards. In an attempt to address this deficiency, this presentation will describe a procedure for reporting computational results that was employed in a recent Journal of Climate paper. The procedure was developed to be consistent with recommended computational best practices and seeks to minimize the time burden on authors, which has been identified as the most important barrier to publishing code. It should provide a starting point for geoscientists looking to publish reproducible research, and could be adopted by journals as a formal minimum communication standard.

Tools and techniques for computational reproducibility.

PubMed

Piccolo, Stephen R; Frampton, Michael B

2016-07-11

When reporting research findings, scientists document the steps they followed so that others can verify and build upon the research. When those steps have been described in sufficient detail that others can retrace the steps and obtain similar results, the research is said to be reproducible. Computers play a vital role in many research disciplines and present both opportunities and challenges for reproducibility. Computers can be programmed to execute analysis tasks, and those programs can be repeated and shared with others. The deterministic nature of most computer programs means that the same analysis tasks, applied to the same data, will often produce the same outputs. However, in practice, computational findings often cannot be reproduced because of complexities in how software is packaged, installed, and executed-and because of limitations associated with how scientists document analysis steps. Many tools and techniques are available to help overcome these challenges; here we describe seven such strategies. With a broad scientific audience in mind, we describe the strengths and limitations of each approach, as well as the circumstances under which each might be applied. No single strategy is sufficient for every scenario; thus we emphasize that it is often useful to combine approaches.

Growth and yield models for central hardwoods

Treesearch

Martin E. Dale; Donald E. Hilt

1989-01-01

Over the last 20 years computers have become an efficient tool to estimate growth and yield. Computerized yield estimates vary from simple approximation or interpolation of traditional normal yield tables to highly sophisticated programs that simulate the growth and yield of each individual tree.

Hot spots of wheat yield decline with rising temperatures.

PubMed

Asseng, Senthold; Cammarano, Davide; Basso, Bruno; Chung, Uran; Alderman, Phillip D; Sonder, Kai; Reynolds, Matthew; Lobell, David B

2017-06-01

Many of the irrigated spring wheat regions in the world are also regions with high poverty. The impacts of temperature increase on wheat yield in regions of high poverty are uncertain. A grain yield-temperature response function combined with a quantification of model uncertainty was constructed using a multimodel ensemble from two key irrigated spring wheat areas (India and Sudan) and applied to all irrigated spring wheat regions in the world. Southern Indian and southern Pakistani wheat-growing regions with large yield reductions from increasing temperatures coincided with high poverty headcounts, indicating these areas as future food security 'hot spots'. The multimodel simulations produced a linear absolute decline of yields with increasing temperature, with uncertainty varying with reference temperature at a location. As a consequence of the linear absolute yield decline, the relative yield reductions are larger in low-yielding environments (e.g., high reference temperature areas in southern India, southern Pakistan and all Sudan wheat-growing regions) and farmers in these regions will be hit hardest by increasing temperatures. However, as absolute yield declines are about the same in low- and high-yielding regions, the contributed deficit to national production caused by increasing temperatures is higher in high-yielding environments (e.g., northern India) because these environments contribute more to national wheat production. Although Sudan could potentially grow more wheat if irrigation is available, grain yields would be low due to high reference temperatures, with future increases in temperature further limiting production. © 2016 John Wiley & Sons Ltd.

Cerebrovascular reactivity measurement in cerebral small vessel disease: Rationale and reproducibility of a protocol for MRI acquisition and image processing.

PubMed

Thrippleton, Michael J; Shi, Yulu; Blair, Gordon; Hamilton, Iona; Waiter, Gordon; Schwarzbauer, Christian; Pernet, Cyril; Andrews, Peter Jd; Marshall, Ian; Doubal, Fergus; Wardlaw, Joanna M

2018-02-01

Background Impaired autoregulation may contribute to the pathogenesis of cerebral small vessel disease. Reliable protocols for measuring microvascular reactivity are required to test this hypothesis and for providing secondary endpoints in clinical trials. Aims To develop and assess a protocol for acquisition and processing of cerebrovascular reactivity by MRI, in subcortical tissue of patients with small vessel disease and minor stroke. Methods We recruited 15 healthy volunteers, testing paradigms using 1- and 3-min 6% CO 2 challenges with repeat scanning, and 15 patients with history of minor stroke. We developed a protocol to measure cerebrovascular reactivity and delay times, assessing tolerability and reproducibility in grey and white matter areas. Results The 3-min paradigm yielded more reproducible data than the 1-min paradigm (CV respectively: 7.9-15.4% and 11.7-70.2% for cerebrovascular reactivity in grey matter), and was less reproducible in white matter (16.1-24.4% and 27.5-141.0%). Tolerability was similar for the two paradigms, but mean cerebrovascular reactivity and cerebrovascular reactivity delay were significantly higher for the 3-min paradigm in most regions. Patient tolerability was high with no evidence of greater failure rate (1/15 patients vs. 2/15 volunteers withdrew at the first visit). Grey matter cerebrovascular reactivity was lower in patients than in volunteers (0.110-0.234 vs. 0.172-0.313%/mmHg; p < 0.05 in 6/8 regions), as was the white matter cerebrovascular reactivity delay (16.2-43.9 vs. 31.1-47.9 s; p < 0.05 in 4/8 regions). Conclusions An effective and well-tolerated protocol for measurement of cerebrovascular reactivity was developed for use in ongoing and future trials to investigate small vessel disease pathophysiology and to measure treatment effects.

Sensitivity of simulated maize crop yields to regional climate in the Southwestern United States

NASA Astrophysics Data System (ADS)

Kim, S.; Myoung, B.; Stack, D.; Kim, J.; Hatzopoulos, N.; Kafatos, M.

2013-12-01

The sensitivity of maize yield to the regional climate in the Southwestern United States (SW US) has been investigated by using a crop-yield simulation model (APSIM) in conjunction with meteorological forcings (daily minimum and maximum temperature, precipitation, and radiation) from the North American Regional Reanalysis (NARR) dataset. The primary focus of this study is to look at the effects of interannual variations of atmospheric components on the crop productivity in the SW US over the 21-year period (1991 to 2011). First of all, characteristics and performance of APSIM was examined by comparing simulated maize yields with observed yields from United States Department of Agriculture (USDA) and the leaf-area index (LAI) from MODIS satellite data. Comparisons of the simulated maize yield with the available observations show that the crop model can reasonably reproduce observed maize yields. Sensitivity tests were performed to assess the relative contribution of each climate driver to regional crop yield. Sensitivity experiments show that potential crop production responds nonlinearly to climate drivers and the yield sensitivity varied among geographical locations depending on their mean climates. Lastly, a detailed analysis of both the spatial and temporal variations of each climate driver in the regions where maize is actually grown in three states (CA, AZ, and NV) in the SW US was performed.

Selected wild strains of Agaricus bisporus produce high yields of mushrooms at 25°C.

PubMed

Navarro, Pilar; Savoie, Jean-Michel

2015-01-01

To cultivate the button mushroom Agaricus bisporus in warm countries or during summer in temperate countries, while saving energy, is a challenge that could be addressed by using the biological diversity of the species. The objective was to evaluate the yield potential of eight wild strains previously selected in small scale experiments for their ability to produce mature fruiting bodies at 25°C and above. Culture units of 8 kg of compost were used. The yield expressed as weight or number per surface unit and earliness of fruiting were recorded during cultivation in climatic rooms at 17, 25 or 30°C. Only strains of A. bisporus var. burnettii were able to fruit at 30°C. At 25°C they produced the highest yields (27 kg m(-2)) and had best earliness. The yields at 25°C for the strains of A. bisporus var. bisporus ranged from 12 to 16 kg m(-2). The yield ratios 25°C/17°C ranged from 0.8 to 1.2. The variety burnettii originated in the Sonoran Desert in California showed adaptation for quickly producing fruiting bodies at high temperature when humidity conditions were favorable. Strains of the variety bisporus showed interesting potentials for their ability to produce mature fruiting bodies at higher temperature than present cultivars and might be used in breeding programs. Copyright © 2012 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

Fast co-pyrolysis of waste newspaper with high-density polyethylene for high yields of alcohols and hydrocarbons.

PubMed

Chen, Weimin; Shi, Shukai; Chen, Minzhi; Zhou, Xiaoyan

2017-09-01

Waste newspaper (WP) was first co-pyrolyzed with high-density polyethylene (HDPE) using pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) to enhance the yields of alcohols and hydrocarbons. The effects of WP: HDPE feed ratio (100:0, 75:25, 50:50, 25:75, 0:100) and temperature (500-800°C) on products distribution were investigated and the interaction mechanism during co-pyrolysis was also proposed. Maximum yields of alcohols and hydrocarbons reached 85.88% (feed ratio 50:50wt.%, 600°C). Hydrogen supplements and deoxidation by HDPE and subsequently fragments recombination result in the conversion of aldehydes and ketones into branched hydrocarbons. Radicals from WP degradation favor the secondary crack for HDPE products resulting in the formation of linear hydrocarbons with low carbon number. Hydrocarbons with activated radical site from HDPE degradation were interacted with hydroxyl from WP degradation promoting the formation of linear long chain alcohols. Moreover, co-pyrolysis significantly enhanced condensable oil qualities, which were close to commercial diesel No. 0. Copyright © 2017 Elsevier Ltd. All rights reserved.

Diversity, Stability, and Reproducibility in Stochastically Assembled Microbial Ecosystems

NASA Astrophysics Data System (ADS)

Goyal, Akshit; Maslov, Sergei

2018-04-01

Microbial ecosystems are remarkably diverse, stable, and usually consist of a mixture of core and peripheral species. Here we propose a conceptual model exhibiting all these emergent properties in quantitative agreement with real ecosystem data, specifically species abundance and prevalence distributions. Resource competition and metabolic commensalism drive the stochastic ecosystem assembly in our model. We demonstrate that even when supplied with just one resource, ecosystems can exhibit high diversity, increasing stability, and partial reproducibility between samples.

Towards interoperable and reproducible QSAR analyses: Exchange of datasets.

PubMed

Spjuth, Ola; Willighagen, Egon L; Guha, Rajarshi; Eklund, Martin; Wikberg, Jarl Es

2010-06-30

QSAR is a widely used method to relate chemical structures to responses or properties based on experimental observations. Much effort has been made to evaluate and validate the statistical modeling in QSAR, but these analyses treat the dataset as fixed. An overlooked but highly important issue is the validation of the setup of the dataset, which comprises addition of chemical structures as well as selection of descriptors and software implementations prior to calculations. This process is hampered by the lack of standards and exchange formats in the field, making it virtually impossible to reproduce and validate analyses and drastically constrain collaborations and re-use of data. We present a step towards standardizing QSAR analyses by defining interoperable and reproducible QSAR datasets, consisting of an open XML format (QSAR-ML) which builds on an open and extensible descriptor ontology. The ontology provides an extensible way of uniquely defining descriptors for use in QSAR experiments, and the exchange format supports multiple versioned implementations of these descriptors. Hence, a dataset described by QSAR-ML makes its setup completely reproducible. We also provide a reference implementation as a set of plugins for Bioclipse which simplifies setup of QSAR datasets, and allows for exporting in QSAR-ML as well as old-fashioned CSV formats. The implementation facilitates addition of new descriptor implementations from locally installed software and remote Web services; the latter is demonstrated with REST and XMPP Web services. Standardized QSAR datasets open up new ways to store, query, and exchange data for subsequent analyses. QSAR-ML supports completely reproducible creation of datasets, solving the problems of defining which software components were used and their versions, and the descriptor ontology eliminates confusions regarding descriptors by defining them crisply. This makes is easy to join, extend, combine datasets and hence work collectively, but

Towards interoperable and reproducible QSAR analyses: Exchange of datasets

PubMed Central

2010-01-01

Background QSAR is a widely used method to relate chemical structures to responses or properties based on experimental observations. Much effort has been made to evaluate and validate the statistical modeling in QSAR, but these analyses treat the dataset as fixed. An overlooked but highly important issue is the validation of the setup of the dataset, which comprises addition of chemical structures as well as selection of descriptors and software implementations prior to calculations. This process is hampered by the lack of standards and exchange formats in the field, making it virtually impossible to reproduce and validate analyses and drastically constrain collaborations and re-use of data. Results We present a step towards standardizing QSAR analyses by defining interoperable and reproducible QSAR datasets, consisting of an open XML format (QSAR-ML) which builds on an open and extensible descriptor ontology. The ontology provides an extensible way of uniquely defining descriptors for use in QSAR experiments, and the exchange format supports multiple versioned implementations of these descriptors. Hence, a dataset described by QSAR-ML makes its setup completely reproducible. We also provide a reference implementation as a set of plugins for Bioclipse which simplifies setup of QSAR datasets, and allows for exporting in QSAR-ML as well as old-fashioned CSV formats. The implementation facilitates addition of new descriptor implementations from locally installed software and remote Web services; the latter is demonstrated with REST and XMPP Web services. Conclusions Standardized QSAR datasets open up new ways to store, query, and exchange data for subsequent analyses. QSAR-ML supports completely reproducible creation of datasets, solving the problems of defining which software components were used and their versions, and the descriptor ontology eliminates confusions regarding descriptors by defining them crisply. This makes is easy to join, extend, combine datasets

Yield determination and water-use effenciency of wheat under water-limited conditions in the U.S. southern high plains

USDA-ARS?s Scientific Manuscript database

Drought is the most important stress for reducing wheat (Triticum aestivum L.) yield and water-use efficiency (WUE) on the U.S. Southern High Plains. Adoption of cultivars with higher yield and WUE under drought conditions is critical in the area. The objective of this study was to investigate the p...

Yield determination and water use efficiency of wheat under water-limited conditions in the U.S. Southern High Plains.

USDA-ARS?s Scientific Manuscript database

Drought is the most important stress for reducing wheat (Triticum aestivum L.) yield and water use efficiency (WUE) in the U.S. Southern High Plains (SHP). Adoption of cultivars with higher yield and WUE under drought conditions in critical in the area. The objective of this study was to investiga...

Boron application improves yield of rice cultivars under high temperature stress during vegetative and reproductive stages.

PubMed

Shahid, Mohammad; Nayak, Amaresh Kumar; Tripathi, Rahul; Katara, Jawahar Lal; Bihari, Priyanka; Lal, Banwari; Gautam, Priyanka

2018-04-12

It is reported that high temperatures (HT) would cause a marked decrease in world rice production. In tropical regions, high temperatures are a constraint to rice production and the most damaging effect is on spikelet sterility. Boron (B) plays a very important role in the cell wall formation, sugar translocation, and reproduction of the rice crop and could play an important role in alleviating high temperature stress. A pot culture experiment was conducted to study the effect of B application on high temperature tolerance of rice cultivars in B-deficient soil. The treatments comprised of four boron application treatments viz. control (B0), soil application of 1 kg B ha -1 (B1), soil application of 2 kg B ha -1 (B2), and foliar spray of 0.2% B (Bfs); three rice cultivars viz. Annapurna (HT stress tolerant), Naveen, and Shatabdi (both HT stress susceptible); and three temperature regimes viz. ambient (AT), HT at vegetative stage (HTV), and HT at reproductive stage (HTR). The results revealed that high temperature stress during vegetative or flowering stage reduced grain yield of rice cultivars mainly because of low pollen viability and spikelet fertility. The effects of high temperature on the spikelet fertility and grain filling varied among cultivars and the growth stages of plant when exposed to the high temperature stress. Under high temperature stress, the tolerant cultivar displays higher cell membrane stability, less accumulation of osmolytes, more antioxidant enzyme activities, and higher pollen viability and spikelet fertility than the susceptible cultivars. In the present work, soil application of boron was effective in reducing the negative effects of high temperature both at vegetative and reproductive stages. Application of B results into higher grain yield under both ambient and high temperature condition over control for all the three cultivars; however, more increase was observed for the susceptible cultivar over the tolerant one. The results

Boron application improves yield of rice cultivars under high temperature stress during vegetative and reproductive stages

NASA Astrophysics Data System (ADS)

Shahid, Mohammad; Nayak, Amaresh Kumar; Tripathi, Rahul; Katara, Jawahar Lal; Bihari, Priyanka; Lal, Banwari; Gautam, Priyanka

2018-04-01

It is reported that high temperatures (HT) would cause a marked decrease in world rice production. In tropical regions, high temperatures are a constraint to rice production and the most damaging effect is on spikelet sterility. Boron (B) plays a very important role in the cell wall formation, sugar translocation, and reproduction of the rice crop and could play an important role in alleviating high temperature stress. A pot culture experiment was conducted to study the effect of B application on high temperature tolerance of rice cultivars in B-deficient soil. The treatments comprised of four boron application treatments viz. control (B0), soil application of 1 kg B ha-1 (B1), soil application of 2 kg B ha-1 (B2), and foliar spray of 0.2% B (Bfs); three rice cultivars viz. Annapurna (HT stress tolerant), Naveen, and Shatabdi (both HT stress susceptible); and three temperature regimes viz. ambient (AT), HT at vegetative stage (HTV), and HT at reproductive stage (HTR). The results revealed that high temperature stress during vegetative or flowering stage reduced grain yield of rice cultivars mainly because of low pollen viability and spikelet fertility. The effects of high temperature on the spikelet fertility and grain filling varied among cultivars and the growth stages of plant when exposed to the high temperature stress. Under high temperature stress, the tolerant cultivar displays higher cell membrane stability, less accumulation of osmolytes, more antioxidant enzyme activities, and higher pollen viability and spikelet fertility than the susceptible cultivars. In the present work, soil application of boron was effective in reducing the negative effects of high temperature both at vegetative and reproductive stages. Application of B results into higher grain yield under both ambient and high temperature condition over control for all the three cultivars; however, more increase was observed for the susceptible cultivar over the tolerant one. The results suggest

Development of high-sensitive, reproducible colloidal surface-enhanced Raman spectroscopy active substrate using silver nanocubes for potential biosensing applications

NASA Astrophysics Data System (ADS)

Hasna, Kudilatt; Lakshmi, Kiran; Ezhuthachan Jayaraj, Madambi Kunjukuttan; Kumar, Kumaran Rajeev; Matham, Murukeshan Vadakke

2016-04-01

Surface-enhanced Raman spectroscopy (SERS) has emerged as one of the thrust research areas that could find potential applications in bio and chemical sensing. We developed colloidal SERS active substrate with excellent sensitivity and high reproducibility using silver nanocube (AgNC) synthesized via the solvothermal method. Finite-difference time-domain simulation was carried out in detail to visualize dipole generation in the nanocube during localized surface plasmon resonance and to locate the respective hot spots in AgNC responsible for the huge Raman enhancement. The prediction is verified by the SERS analysis of the synthesized nanocubes using Rhodamine 6G molecule. An excellent sensitivity with a detection limit of 10-17 M and a very high enhancement factor of 1.2×108 confirms the "hot spots" in the nanocube. SERS activity is also carried out for crystal violet and for food adulterant Sudan I molecule. Finally, label-free DNA detection is performed to demonstrate the versatility of SERS as a potential biosensor.

Reproducible Bioinformatics Research for Biologists

USDA-ARS?s Scientific Manuscript database

This book chapter describes the current Big Data problem in Bioinformatics and the resulting issues with performing reproducible computational research. The core of the chapter provides guidelines and summaries of current tools/techniques that a noncomputational researcher would need to learn to pe...

A High-Yield Synthesis of Chalcopyrite CuIn S 2 Nanoparticles with Exceptional Size Control

DOE PAGES

Sun, Chivin; Gardner, Joseph S.; Shurdha, Endrit; ...

2009-01-01

We repormore » t high-yield and efficient size-controlled syntheses of Chalcopyrite CuIn S 2 nanoparticles by decomposing molecular single source precursors (SSPs) via microwave irradiation in the presence of 1,2-ethanedithiol at reaction temperatures as low as 100 ° C and times as short as 30 minutes. The nanoparticles sizes were 1.8 nm to 10.8 nm as reaction temperatures were varied from 100 ° C to 200 ° C with the bandgaps from 2.71 eV to 1.28 eV with good size control and high yields (64%–95%). The resulting nanoparticles were analyzed by XRD, UV-Vis, ICP-OES, XPS, SEM, EDS, and HRTEM. Titration studies by 1 H NMR using SSP 1 with 1,2-ethanedithiol and benzyl mercaptan were conducted to elucidate the formation of Chalcopyrite CuIn S 2 nanoparticles.« less

Crystal growth and characterization of europium doped KCaI3, a high light yield scintillator

NASA Astrophysics Data System (ADS)

Lindsey, Adam C.; Zhuravleva, Mariya; Stand, Luis; Wu, Yuntao; Melcher, Charles L.

2015-10-01

The presented study reports on the spectroscopic characteristics of a new high performance scintillation material KCaI3:Eu. The growth of ∅ 17 mm boules using the Bridgman-Stockbarger method in fused silica ampoules is demonstrated to produce yellow tinted, yet transparent single crystals suitable for use in spectroscopic applications due to very promising performance. Scintillation light yield of 72,000 ± 3000 ph/MeV and energy resolution of 3% (FWHM) at 662 keV and 6.1% at 122 keV was obtained from small single crystals of approximately 15 mm3. For a much larger 3.8 cm3 detector, 4.4% and 7.3% for the same energy. Proportionality of the scintillation response to the energy of ionizing radiation is within 96% of the ideal response over an energy range of 14-662 keV. The high light yield and energy resolution of KCaI3:Eu make it suitable for potential use in domestic security applications requiring radionuclide identification.

Automated Generation of Technical Documentation and Provenance for Reproducible Research

NASA Astrophysics Data System (ADS)

Jolly, B.; Medyckyj-Scott, D.; Spiekermann, R.; Ausseil, A. G.

2017-12-01

Data provenance and detailed technical documentation are essential components of high-quality reproducible research, however are often only partially addressed during a research project. Recording and maintaining this information during the course of a project can be a difficult task to get right as it is a time consuming and often boring process for the researchers involved. As a result, provenance records and technical documentation provided alongside research results can be incomplete or may not be completely consistent with the actual processes followed. While providing access to the data and code used by the original researchers goes some way toward enabling reproducibility, this does not count as, or replace, data provenance. Additionally, this can be a poor substitute for good technical documentation and is often more difficult for a third-party to understand - particularly if they do not understand the programming language(s) used. We present and discuss a tool built from the ground up for the production of well-documented and reproducible spatial datasets that are created by applying a series of classification rules to a number of input layers. The internal model of the classification rules required by the tool to process the input data is exploited to also produce technical documentation and provenance records with minimal additional user input. Available provenance records that accompany input datasets are incorporated into those that describe the current process. As a result, each time a new iteration of the analysis is performed the documentation and provenance records are re-generated to provide an accurate description of the exact process followed. The generic nature of this tool, and the lessons learned during its creation, have wider application to other fields where the production of derivative datasets must be done in an open, defensible, and reproducible way.

Light-mediated self-organization of sunflower stands increases oil yield in the field

PubMed Central

López Pereira, Mónica; Sadras, Victor O.; Batista, William; Casal, Jorge J.; Hall, Antonio J.

2017-01-01

Here, we show a unique crop response to intraspecific interference, whereby neighboring sunflower plants in a row avoid each other by growing toward a more favorable light environment and collectively increase production per unit land area. In high-density stands, a given plant inclined toward one side of the interrow space, and the immediate neighbors inclined in the opposite direction. This process started early as an incipient inclination of pioneer plants, and the arrangement propagated gradually as a “wave” of alternate inclination that persisted until maturity. Measurements and experimental manipulation of light spectral composition indicate that these responses are mediated by changes in the red/far-red ratio of the light, which is perceived by phytochrome. Cellular automata simulations reproduced the patterns of stem inclination in field experiments, supporting the proposition of self-organization of stand structure. Under high crop population densities (10 and 14 plants per m2), as yet unachievable in commercial farms with current hybrids due to lodging and diseases, self-organized crops yielded between 19 and 47% more oil than crops forced to remain erect. PMID:28696316

Light-mediated self-organization of sunflower stands increases oil yield in the field.

PubMed

López Pereira, Mónica; Sadras, Victor O; Batista, William; Casal, Jorge J; Hall, Antonio J

2017-07-25

Here, we show a unique crop response to intraspecific interference, whereby neighboring sunflower plants in a row avoid each other by growing toward a more favorable light environment and collectively increase production per unit land area. In high-density stands, a given plant inclined toward one side of the interrow space, and the immediate neighbors inclined in the opposite direction. This process started early as an incipient inclination of pioneer plants, and the arrangement propagated gradually as a "wave" of alternate inclination that persisted until maturity. Measurements and experimental manipulation of light spectral composition indicate that these responses are mediated by changes in the red/far-red ratio of the light, which is perceived by phytochrome. Cellular automata simulations reproduced the patterns of stem inclination in field experiments, supporting the proposition of self-organization of stand structure. Under high crop population densities (10 and 14 plants per m 2 ), as yet unachievable in commercial farms with current hybrids due to lodging and diseases, self-organized crops yielded between 19 and 47% more oil than crops forced to remain erect.

A natural variant of NAL1, selected in high-yield rice breeding programs, pleiotropically increases photosynthesis rate.

PubMed

Takai, Toshiyuki; Adachi, Shunsuke; Taguchi-Shiobara, Fumio; Sanoh-Arai, Yumiko; Iwasawa, Norio; Yoshinaga, Satoshi; Hirose, Sakiko; Taniguchi, Yojiro; Yamanouchi, Utako; Wu, Jianzhong; Matsumoto, Takashi; Sugimoto, Kazuhiko; Kondo, Katsuhiko; Ikka, Takashi; Ando, Tsuyu; Kono, Izumi; Ito, Sachie; Shomura, Ayahiko; Ookawa, Taiichiro; Hirasawa, Tadashi; Yano, Masahiro; Kondo, Motohiko; Yamamoto, Toshio

2013-01-01

Improvement of leaf photosynthesis is an important strategy for greater crop productivity. Here we show that the quantitative trait locus GPS (GREEN FOR PHOTOSYNTHESIS) in rice (Oryza sativa L.) controls photosynthesis rate by regulating carboxylation efficiency. Map-based cloning revealed that GPS is identical to NAL1 (NARROW LEAF1), a gene previously reported to control lateral leaf growth. The high-photosynthesis allele of GPS was found to be a partial loss-of-function allele of NAL1. This allele increased mesophyll cell number between vascular bundles, which led to thickened leaves, and it pleiotropically enhanced photosynthesis rate without the detrimental side effects observed in previously identified nal1 mutants, such as dwarf plant stature. Furthermore, pedigree analysis suggested that rice breeders have repeatedly selected the high-photosynthesis allele in high-yield breeding programs. The identification and utilization of NAL1 (GPS) can enhance future high-yield breeding and provides a new strategy for increasing rice productivity.

A natural variant of NAL1, selected in high-yield rice breeding programs, pleiotropically increases photosynthesis rate

PubMed Central

Takai, Toshiyuki; Adachi, Shunsuke; Taguchi-Shiobara, Fumio; Sanoh-Arai, Yumiko; Iwasawa, Norio; Yoshinaga, Satoshi; Hirose, Sakiko; Taniguchi, Yojiro; Yamanouchi, Utako; Wu, Jianzhong; Matsumoto, Takashi; Sugimoto, Kazuhiko; Kondo, Katsuhiko; Ikka, Takashi; Ando, Tsuyu; Kono, Izumi; Ito, Sachie; Shomura, Ayahiko; Ookawa, Taiichiro; Hirasawa, Tadashi; Yano, Masahiro; Kondo, Motohiko; Yamamoto, Toshio

2013-01-01

Improvement of leaf photosynthesis is an important strategy for greater crop productivity. Here we show that the quantitative trait locus GPS (GREEN FOR PHOTOSYNTHESIS) in rice (Oryza sativa L.) controls photosynthesis rate by regulating carboxylation efficiency. Map-based cloning revealed that GPS is identical to NAL1 (NARROW LEAF1), a gene previously reported to control lateral leaf growth. The high-photosynthesis allele of GPS was found to be a partial loss-of-function allele of NAL1. This allele increased mesophyll cell number between vascular bundles, which led to thickened leaves, and it pleiotropically enhanced photosynthesis rate without the detrimental side effects observed in previously identified nal1 mutants, such as dwarf plant stature. Furthermore, pedigree analysis suggested that rice breeders have repeatedly selected the high-photosynthesis allele in high-yield breeding programs. The identification and utilization of NAL1 (GPS) can enhance future high-yield breeding and provides a new strategy for increasing rice productivity. PMID:23985993

Reproducibility and quantitation of amplicon sequencing-based detection

PubMed Central

Zhou, Jizhong; Wu, Liyou; Deng, Ye; Zhi, Xiaoyang; Jiang, Yi-Huei; Tu, Qichao; Xie, Jianping; Van Nostrand, Joy D; He, Zhili; Yang, Yunfeng

2011-01-01

To determine the reproducibility and quantitation of the amplicon sequencing-based detection approach for analyzing microbial community structure, a total of 24 microbial communities from a long-term global change experimental site were examined. Genomic DNA obtained from each community was used to amplify 16S rRNA genes with two or three barcode tags as technical replicates in the presence of a small quantity (0.1% wt/wt) of genomic DNA from Shewanella oneidensis MR-1 as the control. The technical reproducibility of the amplicon sequencing-based detection approach is quite low, with an average operational taxonomic unit (OTU) overlap of 17.2%±2.3% between two technical replicates, and 8.2%±2.3% among three technical replicates, which is most likely due to problems associated with random sampling processes. Such variations in technical replicates could have substantial effects on estimating β-diversity but less on α-diversity. A high variation was also observed in the control across different samples (for example, 66.7-fold for the forward primer), suggesting that the amplicon sequencing-based detection approach could not be quantitative. In addition, various strategies were examined to improve the comparability of amplicon sequencing data, such as increasing biological replicates, and removing singleton sequences and less-representative OTUs across biological replicates. Finally, as expected, various statistical analyses with preprocessed experimental data revealed clear differences in the composition and structure of microbial communities between warming and non-warming, or between clipping and non-clipping. Taken together, these results suggest that amplicon sequencing-based detection is useful in analyzing microbial community structure even though it is not reproducible and quantitative. However, great caution should be taken in experimental design and data interpretation when the amplicon sequencing-based detection approach is used for quantitative

Reproducibility of studies on text mining for citation screening in systematic reviews: Evaluation and checklist.

PubMed

Olorisade, Babatunde Kazeem; Brereton, Pearl; Andras, Peter

2017-09-01

Independent validation of published scientific results through study replication is a pre-condition for accepting the validity of such results. In computation research, full replication is often unrealistic for independent results validation, therefore, study reproduction has been justified as the minimum acceptable standard to evaluate the validity of scientific claims. The application of text mining techniques to citation screening in the context of systematic literature reviews is a relatively young and growing computational field with high relevance for software engineering, medical research and other fields. However, there is little work so far on reproduction studies in the field. In this paper, we investigate the reproducibility of studies in this area based on information contained in published articles and we propose reporting guidelines that could improve reproducibility. The study was approached in two ways. Initially we attempted to reproduce results from six studies, which were based on the same raw dataset. Then, based on this experience, we identified steps considered essential to successful reproduction of text mining experiments and characterized them to measure how reproducible is a study given the information provided on these steps. 33 articles were systematically assessed for reproducibility using this approach. Our work revealed that it is currently difficult if not impossible to independently reproduce the results published in any of the studies investigated. The lack of information about the datasets used limits reproducibility of about 80% of the studies assessed. Also, information about the machine learning algorithms is inadequate in about 27% of the papers. On the plus side, the third party software tools used are mostly free and available. The reproducibility potential of most of the studies can be significantly improved if more attention is paid to information provided on the datasets used, how they were partitioned and utilized, and

Repeatability and Reproducibility of Decisions by Latent Fingerprint Examiners

PubMed Central

Ulery, Bradford T.; Hicklin, R. Austin; Buscaglia, JoAnn; Roberts, Maria Antonia

2012-01-01

The interpretation of forensic fingerprint evidence relies on the expertise of latent print examiners. We tested latent print examiners on the extent to which they reached consistent decisions. This study assessed intra-examiner repeatability by retesting 72 examiners on comparisons of latent and exemplar fingerprints, after an interval of approximately seven months; each examiner was reassigned 25 image pairs for comparison, out of total pool of 744 image pairs. We compare these repeatability results with reproducibility (inter-examiner) results derived from our previous study. Examiners repeated 89.1% of their individualization decisions, and 90.1% of their exclusion decisions; most of the changed decisions resulted in inconclusive decisions. Repeatability of comparison decisions (individualization, exclusion, inconclusive) was 90.0% for mated pairs, and 85.9% for nonmated pairs. Repeatability and reproducibility were notably lower for comparisons assessed by the examiners as “difficult” than for “easy” or “moderate” comparisons, indicating that examiners' assessments of difficulty may be useful for quality assurance. No false positive errors were repeated (n = 4); 30% of false negative errors were repeated. One percent of latent value decisions were completely reversed (no value even for exclusion vs. of value for individualization). Most of the inter- and intra-examiner variability concerned whether the examiners considered the information available to be sufficient to reach a conclusion; this variability was concentrated on specific image pairs such that repeatability and reproducibility were very high on some comparisons and very low on others. Much of the variability appears to be due to making categorical decisions in borderline cases. PMID:22427888

Gold@silver bimetal nanoparticles/pyramidal silicon 3D substrate with high reproducibility for high-performance SERS

NASA Astrophysics Data System (ADS)

Zhang, Chao; Jiang, Shou Zhen; Yang, Cheng; Li, Chong Hui; Huo, Yan Yan; Liu, Xiao Yun; Liu, Ai Hua; Wei, Qin; Gao, Sai Sai; Gao, Xing Guo; Man, Bao Yuan

2016-05-01

A novel and efficient surface enhanced Raman scattering (SERS) substrate has been presented based on Gold@silver/pyramidal silicon 3D substrate (Au@Ag/3D-Si). By combining the SERS activity of Ag, the chemical stability of Au and the large field enhancement of 3D-Si, the Au@Ag/3D-Si substrate possesses perfect sensitivity, homogeneity, reproducibility and chemical stability. Using R6G as probe molecule, the SERS results imply that the Au@Ag/3D-Si substrate is superior to the 3D-Si, Ag/3D-Si and Au/3D-Si substrate. We also confirmed these excellent behaviors in theory via a commercial COMSOL software. The corresponding experimental and theoretical results indicate that our proposed Au@Ag/3D-Si substrate is expected to develop new opportunities for label-free SERS detections in biological sensors, biomedical diagnostics and food safety.

A decade of precision agriculture impacts on grain yield and yield variation

USDA-ARS?s Scientific Manuscript database

Targeting management practices and inputs with precision agriculture has high potential to meet some of the grand challenges of sustainability in the coming century, including simultaneously improving crop yields and reducing environmental impacts. Although the potential is high, few studies have do...

High pressure thermal hydrolysis as pre-treatment to increase the methane yield during anaerobic digestion of microalgae.

PubMed

Keymer, Philip; Ruffell, Ian; Pratt, Steven; Lant, Paul

2013-03-01

Anaerobic digestion of algal biomass will be an essential component of algal biofuel production systems, yet the methane yield from digestion of algae is typically much lower than the theoretical potential. In this work, high pressure thermal hydrolysis (HPTH) is shown to enhance methane yield during algae digestion. HPTH pre-treatment was applied to both raw algae and algal residue resulting from lipid extraction. HPTH and even the lipid extraction process itself increased methane yield, by 81% and 33% respectively; in combination they increased yield by 110% over that of the raw algae (18L CH4 gVS(-1) substrate). HPTH had little effect on the rate of anaerobic digestion, however lipid extraction enhanced it by 33% over that for raw algae (0.21day(-1)). Digestion resulted in solubilisation of nitrogen (and phosphorous to a lesser degree) in all cases, showing that there is potential for nutrient recycling for algal growth. Copyright © 2013 Elsevier Ltd. All rights reserved.

Interlaboratory Reproducibility of Droplet Digital Polymerase Chain Reaction Using a New DNA Reference Material Format.

PubMed

Pinheiro, Leonardo B; O'Brien, Helen; Druce, Julian; Do, Hongdo; Kay, Pippa; Daniels, Marissa; You, Jingjing; Burke, Daniel; Griffiths, Kate; Emslie, Kerry R

2017-11-07

Use of droplet digital PCR technology (ddPCR) is expanding rapidly in the diversity of applications and number of users around the world. Access to relatively simple and affordable commercial ddPCR technology has attracted wide interest in use of this technology as a molecular diagnostic tool. For ddPCR to effectively transition to a molecular diagnostic setting requires processes for method validation and verification and demonstration of reproducible instrument performance. In this study, we describe the development and characterization of a DNA reference material (NMI NA008 High GC reference material) comprising a challenging methylated GC-rich DNA template under a novel 96-well microplate format. A scalable process using high precision acoustic dispensing technology was validated to produce the DNA reference material with a certified reference value expressed in amount of DNA molecules per well. An interlaboratory study, conducted using blinded NA008 High GC reference material to assess reproducibility among seven independent laboratories demonstrated less than 4.5% reproducibility relative standard deviation. With the exclusion of one laboratory, laboratories had appropriate technical competency, fully functional instrumentation, and suitable reagents to perform accurate ddPCR based DNA quantification measurements at the time of the study. The study results confirmed that NA008 High GC reference material is fit for the purpose of being used for quality control of ddPCR systems, consumables, instrumentation, and workflow.

Reproducibility of CMRO2 determination using dynamic 17 O MRI.

PubMed

Niesporek, Sebastian C; Umathum, Reiner; Lommen, Jonathan M; Behl, Nicolas G R; Paech, Daniel; Bachert, Peter; Ladd, Mark E; Nagel, Armin M

2018-06-01

To assess the reproducibility of 17 O MRI-based determination of the cerebral metabolic rate of oxygen consumption (CMRO 2 ) in healthy volunteers. To assess the influence of image acquisition and reconstruction parameters on dynamic quantification of functional parameters such as CMRO 2 . Dynamic 17 O MRI data were simulated and used to investigate influences of temporal resolution (Δt) and partial volume correction (PVC) on the determination of CMRO 2 . Three healthy volunteers were examined in two separate examinations. In vivo 17 O MRI measurements were conducted with a nominal spatial resolution of (7.5 mm) 3 using a density-adapted radial sequence with golden angle acquisition scheme. In each measurement, 4.0 ± 0.1 L of 70%-enriched 17 O gas were administered using a rebreathing system. Data were corrected with a PVC algorithm, and CMRO 2 was determined in gray matter (GM) and white matter (WM) compartments using a three-phase metabolic model (baseline, 17 O inhalation, decay phase). Comparison with the ground truth of simulations revealed improved CMRO 2 determination after application of PVC and with Δt ≤ 2:00 min. Evaluation of in vivo data yields to CMRO 2,GM  = 2.31 ± 0.1 μmol/g/min and to CMRO 2,WM  = 0.69 ± 0.04 μmol/g/min with coefficients of variation (CoV) of 0.3-5.5% and 4.3-5.0% for intra-volunteer and inter-volunteer data, respectively. This in vivo 17 O inhalation study demonstrated that the proposed experimental setup enables reproducible determination of CMRO 2 in healthy volunteers. Magn Reson Med 79:2923-2934, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Reproducible nucleation sites for flux dendrites in MgB 2

NASA Astrophysics Data System (ADS)

Johansen, T. H.; Shantsev, D. V.; Olsen, Å. A. F.; Roussel, M.; Pan, A. V.; Dou, S. X.

2007-12-01

Magneto-optical imaging was used to study dendritic flux penetration in films of MgB 2. By repeating experiments under the same external conditions, reproducible features were seen in the pattern formation; dendrites tend to nucleate from fixed locations along the edge. However, their detailed structure deeper inside the film is never reproduced. The reproducibility in nucleation sites is explained as a result of edge roughness causing field hot spots.

Genotypic Variation in Yield, Yield Components, Root Morphology and Architecture, in Soybean in Relation to Water and Phosphorus Supply

PubMed Central

He, Jin; Jin, Yi; Du, Yan-Lei; Wang, Tao; Turner, Neil C.; Yang, Ru-Ping; Siddique, Kadambot H. M.; Li, Feng-Min

2017-01-01

Water shortage and low phosphorus (P) availability limit yields in soybean. Roots play important roles in water-limited and P-deficient environment, but the underlying mechanisms are largely unknown. In this study we determined the responses of four soybean [Glycine max (L.) Merr.] genotypes [Huandsedadou (HD), Bailudou (BLD), Jindou 21 (J21), and Zhonghuang 30 (ZH)] to three P levels [applied 0 (P0), 60 (P60), and 120 (P120) mg P kg-1 dry soil to the upper 0.4 m of the soil profile] and two water treatment [well-watered (WW) and water-stressed (WS)] with special reference to root morphology and architecture, we compared yield and its components, root morphology and root architecture to find out which variety and/or what kind of root architecture had high grain yield under P and drought stress. The results showed that water stress and low P, respectively, significantly reduced grain yield by 60 and 40%, daily water use by 66 and 31%, P accumulation by 40 and 80%, and N accumulation by 39 and 65%. The cultivar ZH with the lowest daily water use had the highest grain yield at P60 and P120 under drought. Increased root length was positively associated with N and P accumulation in both the WW and WS treatments, but not with grain yield under water and P deficits. However, in the WS treatment, high adventitious and lateral root densities were associated with high N and P uptake per unit root length which in turn was significantly and positively associated with grain yield. Our results suggest that (1) genetic variation of grain yield, daily water use, P and N accumulation, and root morphology and architecture were observed among the soybean cultivars and ZH had the best yield performance under P and water limited conditions; (2) water has a major influence on nutrient uptake and grain yield, while additional P supply can modestly increase yields under drought in some soybean genotypes; (3) while conserved water use plays an important role in grain yield under drought

Genotypic Variation in Yield, Yield Components, Root Morphology and Architecture, in Soybean in Relation to Water and Phosphorus Supply.

PubMed

He, Jin; Jin, Yi; Du, Yan-Lei; Wang, Tao; Turner, Neil C; Yang, Ru-Ping; Siddique, Kadambot H M; Li, Feng-Min

2017-01-01

Water shortage and low phosphorus (P) availability limit yields in soybean. Roots play important roles in water-limited and P-deficient environment, but the underlying mechanisms are largely unknown. In this study we determined the responses of four soybean [ Glycine max (L.) Merr.] genotypes [Huandsedadou (HD), Bailudou (BLD), Jindou 21 (J21), and Zhonghuang 30 (ZH)] to three P levels [applied 0 (P0), 60 (P60), and 120 (P120) mg P kg -1 dry soil to the upper 0.4 m of the soil profile] and two water treatment [well-watered (WW) and water-stressed (WS)] with special reference to root morphology and architecture, we compared yield and its components, root morphology and root architecture to find out which variety and/or what kind of root architecture had high grain yield under P and drought stress. The results showed that water stress and low P, respectively, significantly reduced grain yield by 60 and 40%, daily water use by 66 and 31%, P accumulation by 40 and 80%, and N accumulation by 39 and 65%. The cultivar ZH with the lowest daily water use had the highest grain yield at P60 and P120 under drought. Increased root length was positively associated with N and P accumulation in both the WW and WS treatments, but not with grain yield under water and P deficits. However, in the WS treatment, high adventitious and lateral root densities were associated with high N and P uptake per unit root length which in turn was significantly and positively associated with grain yield. Our results suggest that (1) genetic variation of grain yield, daily water use, P and N accumulation, and root morphology and architecture were observed among the soybean cultivars and ZH had the best yield performance under P and water limited conditions; (2) water has a major influence on nutrient uptake and grain yield, while additional P supply can modestly increase yields under drought in some soybean genotypes; (3) while conserved water use plays an important role in grain yield under drought

High yield growth of patterned vertically aligned carbon nanotubes using inkjet-printed catalyst.

PubMed

Beard, James D; Stringer, Jonathan; Ghita, Oana R; Smith, Patrick J

2013-10-09

This study reports on the fabrication of vertically aligned carbon nanotubes localized at specific sites on a growth substrate by deposition of a nanoparticle suspension using inkjet printing. Carbon nanotubes were grown with high yield as vertically aligned forests to a length of approximately 400 μm. The use of inkjet printing for catalyst fabrication considerably improves the production rate of vertically aligned patterned nanotube forests compared with conventional patterning techniques, for example, electron beam lithography or photolithography.

Simultaneous achievement of high ethanol yield and titer in Clostridium thermocellum

DOE PAGES

Tian, Liang; Papanek, Beth; Olson, Daniel G.; ...

2016-06-02

Background Biofuel production from plant cell walls offers the potential for sustainable and economically attractive alternatives to petroleum-based products. Fuels from cellulosic biomass are particularly promising, but would benefit from lower processing costs. Clostridium thermocellum can rapidly solubilize and ferment cellulosic biomass, making it a promising candidate microorganism for consolidated bioprocessing for biofuel production, but increases in product yield and titer are still needed. Results We started with an engineered C. thermocellum strain where the central metabolic pathways to products other than ethanol had been deleted. After two stages of adaptive evolution, an evolved strain was selected with improved yieldmore » and titer. On chemically defined medium with crystalline cellulose as substrate, the evolved strain produced 22.4 ± 1.4 g/L ethanol from 60 g/L cellulose. Moreover, the resulting yield was about 0.39 gETOH/gGluc eq, which is 75 % of the maximum theoretical yield. Genome resequencing, proteomics, and biochemical analysis were used to examine differences between the original and evolved strains. Conclusions A two step selection method successfully improved the ethanol yield and the titer. Finaly, this evolved strain has the highest ethanol yield and titer reported to date for C. thermocellum, and is an important step in the development of this microbe for industrial applications.« less

Dakota Diamond: An exceptionally high yielding, cold chipping potato cultivar with long-term storage potential

USDA-ARS?s Scientific Manuscript database

Dakota Diamond (ND5822C-7) is a medium to late maturing cultivar with uniformly sized tubers and very high yield potential. It resulted from the cross of ND4103-2 and “Dakota Pearl”. Dakota Diamond is comprised of approximately 23.3% wild potato species germplasm. It combines the characteristics ...

Absolute quantum yield measurement of powder samples.

PubMed

Moreno, Luis A

2012-05-12

quantum yield calculation. 5. Corrected quantum yield calculation. 6. Chromaticity coordinates calculation using Report Generator program. The Hitachi F-7000 Quantum Yield Measurement System offer advantages for this application, as follows: High sensitivity (S/N ratio 800 or better RMS). Signal is the Raman band of water measured under the following conditions: Ex wavelength 350 nm, band pass Ex and Em 5 nm, response 2 sec), noise is measured at the maximum of the Raman peak. High sensitivity allows measurement of samples even with low quantum yield. Using this system we have measured quantum yields as low as 0.1 for a sample of salicylic acid and as high as 0.8 for a sample of magnesium tungstate. Highly accurate measurement with a dynamic range of 6 orders of magnitude allows for measurements of both sharp scattering peaks with high intensity, as well as broad fluorescence peaks of low intensity under the same conditions. High measuring throughput and reduced light exposure to the sample, due to a high scanning speed of up to 60,000 nm/minute and automatic shutter function. Measurement of quantum yield over a wide wavelength range from 240 to 800 nm. Accurate quantum yield measurements are the result of collecting instrument spectral response and integrating sphere correction factors before measuring the sample. Large selection of calculated parameters provided by dedicated and easy to use software. During this video we will measure sodium salicylate in powder form which is known to have a quantum yield value of 0.4 to 0.5.

Validity and reproducibility of self-reported working hours among Japanese male employees.

PubMed

Imai, Teppei; Kuwahara, Keisuke; Miyamoto, Toshiaki; Okazaki, Hiroko; Nishihara, Akiko; Kabe, Isamu; Mizoue, Tetsuya; Dohi, Seitaro

2016-07-22

Working long hours is a potential health hazard. Although self-reporting of working hours in various time frames has been used in epidemiologic studies, its validity is unclear. The objective of this study was to examine the validity and reproducibility of self-reported working hours among Japanese male employees. The participants were 164 male employees of four large-scale companies in Japan. For validity, the Spearman correlation between self-reported working hours in the second survey and the working hours recorded by the company was calculated for the following four time frames: daily working hours, monthly overtime working hours in the last month, average overtime working hours in the last 3 months, and the frequency of long working months (≥45 h/month) within the last 12 months. For reproducibility, the intraclass correlation between the first (September 2013) and second surveys (December 2013) was calculated for each of the four time frames. The Spearman correlations between self-reported working hours and those based on company records were 0.74, 0.81, 0.85, and 0.89 for daily, monthly, 3-monthly, and yearly time periods, respectively. The intraclass correlations for self-reported working hours between the two questionnaire surveys were 0.63, 0.66, 0.73, and 0.87 for the respective time frames. The results of the present study among Japanese male employees suggest that the validity of self-reported working hours is high for all four time frames, whereas the reproducibility is moderate to high.

RNA isolation from loquat and other recalcitrant woody plants with high quality and yield.

PubMed

Morante-Carriel, Jaime; Sellés-Marchart, Susana; Martínez-Márquez, Ascensión; Martínez-Esteso, María José; Luque, Ignacio; Bru-Martínez, Roque

2014-05-01

RNA isolation is difficult in plants that contain large amounts of polysaccharides and polyphenol compounds. To date, no commercial kit has been developed for the isolation of high-quality RNA from tissues with these characteristics, especially for fruit. The common protocols for RNA isolation are tedious and usually result in poor yields when applied to recalcitrant plant tissues. Here an efficient RNA isolation protocol based on cetyltrimethylammonium bromide (CTAB) and two successive precipitations with 10 M lithium chloride (LiCl) was developed specifically for loquat fruits, but it was proved to work efficiently in other tissues of loquat and woody plants. The RNA isolated by this improved protocol was not only of high purity and integrity (A260/A280 ratios ranged from 1.90 to 2.04 and A260/A230 ratios were>2.0) but also of high yield (up to 720 μg on average [coefficient of variation=21%] total RNA per gram fresh tissue). The protocol was tested on loquat fruit (different stages of development, postharvest, ripening, and bruising), leaf, root, flower, stem, and bud; quince fruit and root; grapevine cells in liquid culture; and rose petals. The RNA obtained with this method is amenable to enzymatic treatments and can be efficiently applied for research on gene characterization, expression, and function. Copyright © 2014 Elsevier Inc. All rights reserved.

Reproducibility of radiomics for deciphering tumor phenotype with imaging

NASA Astrophysics Data System (ADS)

Zhao, Binsheng; Tan, Yongqiang; Tsai, Wei-Yann; Qi, Jing; Xie, Chuanmiao; Lu, Lin; Schwartz, Lawrence H.

2016-03-01

Radiomics (radiogenomics) characterizes tumor phenotypes based on quantitative image features derived from routine radiologic imaging to improve cancer diagnosis, prognosis, prediction and response to therapy. Although radiomic features must be reproducible to qualify as biomarkers for clinical care, little is known about how routine imaging acquisition techniques/parameters affect reproducibility. To begin to fill this knowledge gap, we assessed the reproducibility of a comprehensive, commonly-used set of radiomic features using a unique, same-day repeat computed tomography data set from lung cancer patients. Each scan was reconstructed at 6 imaging settings, varying slice thicknesses (1.25 mm, 2.5 mm and 5 mm) and reconstruction algorithms (sharp, smooth). Reproducibility was assessed using the repeat scans reconstructed at identical imaging setting (6 settings in total). In separate analyses, we explored differences in radiomic features due to different imaging parameters by assessing the agreement of these radiomic features extracted from the repeat scans reconstructed at the same slice thickness but different algorithms (3 settings in total). Our data suggest that radiomic features are reproducible over a wide range of imaging settings. However, smooth and sharp reconstruction algorithms should not be used interchangeably. These findings will raise awareness of the importance of properly setting imaging acquisition parameters in radiomics/radiogenomics research.

Metaresearch for Evaluating Reproducibility in Ecology and Evolution.

PubMed

Fidler, Fiona; Chee, Yung En; Wintle, Bonnie C; Burgman, Mark A; McCarthy, Michael A; Gordon, Ascelin

2017-03-01

Recent replication projects in other disciplines have uncovered disturbingly low levels of reproducibility, suggesting that those research literatures may contain unverifiable claims. The conditions contributing to irreproducibility in other disciplines are also present in ecology. These include a large discrepancy between the proportion of "positive" or "significant" results and the average statistical power of empirical research, incomplete reporting of sampling stopping rules and results, journal policies that discourage replication studies, and a prevailing publish-or-perish research culture that encourages questionable research practices. We argue that these conditions constitute sufficient reason to systematically evaluate the reproducibility of the evidence base in ecology and evolution. In some cases, the direct replication of ecological research is difficult because of strong temporal and spatial dependencies, so here, we propose metaresearch projects that will provide proxy measures of reproducibility.

Evidence for a weakening strength of temperature-corn yield relation in the United States during 1980-2010.

PubMed

Leng, Guoyong

2017-12-15

Temperature is known to be correlated with crop yields, causing reduction of crop yield with climate warming without adaptations or CO 2 fertilization effects. The historical temperature-crop yield relation has often been used for informing future changes. This relationship, however, may change over time following alternations in other environmental factors. Results show that the strength of the relationship between the interannual variability of growing season temperature and corn yield (R GST_CY ) has declined in the United States between 1980 and 2010 with a loss in the statistical significance. The regression slope which represents the anomalies in corn yield that occur in association with 1 degree temperature anomaly has decreased significantly from -6.9%/K of the first half period to -2.4%/K--3.5%/K of the second half period. This implies that projected corn yield reduction will be overestimated by a fact of 2 in a given warming scenario, if the corn-temperature relation is derived from the earlier historical period. Changes in R GST_CY are mainly observed in Midwest Corn Belt and central High Plains, but are partly reproduced by 11 process-based crop models. In Midwest rain-fed systems, the decrease of negative temperature effects coincides with an increase in water availability by precipitation. In irrigated areas where water stress is minimized, the decline of beneficial temperature effects is significantly related to the increase in extreme hot days. The results indicate that an extrapolation of historical yield response to temperature may bias the assessment of agriculture vulnerability to climate change. Efforts to reduce climate impacts on agriculture should pay attention not only to climate change, but also to changes in climate-crop yield relations. There are some caveats that should be acknowledged as the analysis is restricted to the changes in the linear relation between growing season mean temperature and corn yield for the specific study period

Maximization of DRAM yield by control of surface charge and particle addition during high dose implantation

NASA Astrophysics Data System (ADS)

Horvath, J.; Moffatt, S.

1991-04-01

Ion implantation processing exposes semiconductor devices to an energetic ion beam in order to deposit dopant ions in shallow layers. In addition to this primary process, foreign materials are deposited as particles and surface films. The deposition of particles is a major cause of IC yield loss and becomes even more significant as device dimensions are decreased. Control of particle addition in a high-volume production environment requires procedures to limit beamline and endstation sources, control of particle transport, cleaning procedures and a well grounded preventative maintenance philosophy. Control of surface charge by optimization of the ion beam and electron shower conditions and measurement with a real-time charge sensor has been effective in improving the yield of NMOS and CMOS DRAMs. Control of surface voltages to a range between 0 and -20 V was correlated with good implant yield with PI9200 implanters for p + and n + source-drain implants.

[Simultaneously preparation of grams of high purity tyrosol, crenulatin and salidroside from Rhodiola crenulata].

PubMed

Luo, Xin; Wang, Xue-jing; Li, Shi-ping; Zhang, Qiao; Zhao, Yi-wu; Huang Wen-zhe; Wang, Zhen-zhong; Xiao, Wei

2015-04-01

Tyrosol, crenulatin and salidroside are the main active constituents of Rhodiola crenulata, with extensive pharmacological activities. In the study, grams of high purity tyrosol, crenulatin and salidroside were simultaneously separated from R. crenulata by the first time. Firstly, R. crenulata was extracted by 70% alcohol. Then, with the yields of three compounds as the index, the macroporous resin was optimized. At last, grams of high purity tyrosol, crenulatin and salidroside were isolated by D-101 macroporousresin, purified by column chromatography. Detected by HPLC, the purity of three compounds were higher than 98%. This method has the advantages of simple process and operation, less dosage of organic solvent, highly yield and reproducibility, suitable for the simultaneously preparation of tyrosol, crenulatin and salidroside.

Influence of Yield Stress Determination in Anisotropic Hardening Model on Springback Prediction in Dual-Phase Steel

NASA Astrophysics Data System (ADS)

Lee, J.; Bong, H. J.; Ha, J.; Choi, J.; Barlat, F.; Lee, M.-G.

2018-05-01

In this study, a numerical sensitivity analysis of the springback prediction was performed using advanced strain hardening models. In particular, the springback in U-draw bending for dual-phase 780 steel sheets was investigated while focusing on the effect of the initial yield stress determined from the cyclic loading tests. The anisotropic hardening models could reproduce the flow stress behavior under the non-proportional loading condition for the considered parametric cases. However, various identification schemes for determining the yield stress of the anisotropic hardening models significantly influenced the springback prediction. The deviations from the measured springback varied from 4% to 13.5% depending on the identification method.

Prognostic Value and Reproducibility of Pretreatment CT Texture Features in Stage III Non-Small Cell Lung Cancer

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

Fried, David V.; Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston, Houston, Texas; Tucker, Susan L.

2014-11-15

Purpose: To determine whether pretreatment CT texture features can improve patient risk stratification beyond conventional prognostic factors (CPFs) in stage III non-small cell lung cancer (NSCLC). Methods and Materials: We retrospectively reviewed 91 cases with stage III NSCLC treated with definitive chemoradiation therapy. All patients underwent pretreatment diagnostic contrast enhanced computed tomography (CE-CT) followed by 4-dimensional CT (4D-CT) for treatment simulation. We used the average-CT and expiratory (T50-CT) images from the 4D-CT along with the CE-CT for texture extraction. Histogram, gradient, co-occurrence, gray tone difference, and filtration-based techniques were used for texture feature extraction. Penalized Cox regression implementing cross-validation wasmore » used for covariate selection and modeling. Models incorporating texture features from the 33 image types and CPFs were compared to those with models incorporating CPFs alone for overall survival (OS), local-regional control (LRC), and freedom from distant metastases (FFDM). Predictive Kaplan-Meier curves were generated using leave-one-out cross-validation. Patients were stratified based on whether their predicted outcome was above or below the median. Reproducibility of texture features was evaluated using test-retest scans from independent patients and quantified using concordance correlation coefficients (CCC). We compared models incorporating the reproducibility seen on test-retest scans to our original models and determined the classification reproducibility. Results: Models incorporating both texture features and CPFs demonstrated a significant improvement in risk stratification compared to models using CPFs alone for OS (P=.046), LRC (P=.01), and FFDM (P=.005). The average CCCs were 0.89, 0.91, and 0.67 for texture features extracted from the average-CT, T50-CT, and CE-CT, respectively. Incorporating reproducibility within our models yielded 80.4% (±3.7% SD), 78.3% (±4.0% SD

Reproducibility of cine displacement encoding with stimulated echoes (DENSE) cardiovascular magnetic resonance for measuring left ventricular strains, torsion, and synchrony in mice.

PubMed

Haggerty, Christopher M; Kramer, Sage P; Binkley, Cassi M; Powell, David K; Mattingly, Andrea C; Charnigo, Richard; Epstein, Frederick H; Fornwalt, Brandon K

2013-08-27

Advanced measures of cardiac function are increasingly important to clinical assessment due to their superior diagnostic and predictive capabilities. Cine DENSE cardiovascular magnetic resonance (CMR) is ideal for quantifying advanced measures of cardiac function based on its high spatial resolution and streamlined post-processing. While many studies have utilized cine DENSE in both humans and small-animal models, the inter-test and inter-observer reproducibility for quantification of advanced cardiac function in mice has not been evaluated. This represents a critical knowledge gap for both understanding the capabilities of this technique and for the design of future experiments. We hypothesized that cine DENSE CMR would show excellent inter-test and inter-observer reproducibility for advanced measures of left ventricular (LV) function in mice. Five normal mice (C57BL/6) and four mice with depressed cardiac function (diet-induced obesity) were imaged twice, two days apart, on a 7T ClinScan MR system. Images were acquired with 15-20 frames per cardiac cycle in three short-axis (basal, mid, apical) and two long-axis orientations (4-chamber and 2-chamber). LV strain, twist, torsion, and measures of synchrony were quantified. Images from both days were analyzed by one observer to quantify inter-test reproducibility, while inter-observer reproducibility was assessed by a second observer's analysis of day-1 images. The coefficient of variation (CoV) was used to quantify reproducibility. LV strains and torsion were highly reproducible on both inter-observer and inter-test bases with CoVs ≤ 15%, and inter-observer reproducibility was generally better than inter-test reproducibility. However, end-systolic twist angles showed much higher variance, likely due to the sensitivity of slice location within the sharp longitudinal gradient in twist angle. Measures of synchrony including the circumferential (CURE) and radial (RURE) uniformity of strain indices, showed excellent

High yield antibiotic producing mutants of Streptomyces erythreus induced by low energy ion implantation

NASA Astrophysics Data System (ADS)

Yu, Chen; Zhixin, Lin; Zuyao, Zou; Feng, Zhang; Duo, Liu; Xianghuai, Liu; Jianzhong, Tang; Weimin, Zhu; Bo, Huang

1998-05-01

Conidia of Streptomyces erythreus, an industrial microbe, were implanted by nitrogen ions with energy of 40-60 keV and fluence from 1 × 10 11 to 5 × 10 14 ions/cm 2. The logarithm value of survival fraction had good linear relationship with the logarithm value of fluence. Some mutants with a high yield of erythromycin were induced by ion implantation. The yield increment was correlated with the implantation fluence. Compared with the mutation results induced by ultraviolet rays, mutation effects of ion implantation were obvious having higher increasing erythromycin potency and wider mutation spectrum. The spores of Bacillus subtilis were implanted by arsenic ions with energy of 100 keV. The distribution of implanted ions was measured by Rutherford Backscattering Spectrometry (RBS) and calculated in theory. The mechanism of mutation induced by ion implantation was discussed.

Reproducibility of the measurement of sweet taste preferences.

PubMed

Asao, Keiko; Luo, Wendy; Herman, William H

2012-12-01

Developing interventions to prevent and treat obesity are medical and public health imperatives. Taste is a major determinant of food intake and reliable methods to measure taste preferences need to be established. This study aimed to establish the short-term reproducibility of sweet taste preference measurements using 5-level sucrose concentrations in healthy adult volunteers. We defined sweet taste preference as the geometric mean of the preferred sucrose concentration determined from two series of two-alternative, forced-choice staircase procedures administered 10min apart on a single day. We repeated the same procedures at a second visit 3-7days later. Twenty-six adults (13 men and 13 women, age 33.2±12.2years) completed the measurements. The median number of pairs presented for each series was three (25th and 75th percentiles: 3, 4). The intraclass correlation coefficients between the measurements was 0.82 (95% confidence interval [CI]: 0.63-0.92) within a few days. This study showed high short-term reproducibility of a simple, 5-level procedure for measuring sweet taste preferences. This method may be useful for assessing sweet taste preferences and the risks resulting from those preferences. Copyright © 2012 Elsevier Ltd. All rights reserved.

Tensile strength/yield strength (TS/YS) ratios of high-strength steel (HSS) reinforcing bars

NASA Astrophysics Data System (ADS)

Tavio, Anggraini, Retno; Raka, I. Gede Putu; Agustiar

2018-05-01

The building codes such as American Concrete Institute (ACI) 318M-14 and Standard National Indonesia (SNI) 2847:2013 require that the ratio of tensile strength (TS) and yield strength (YS) should not less than 1.25. The requirement is based on the assumption that a capability of a structural member to develop inelastic rotation capacity is a function of the length of the yield region. This paper reports an investigation on various steel grades, namely Grades 420, 550, 650, and 700 MPa, to examine the impact of different TS/YS ratios if it is less or greater than the required value. Grades 550, 650, and 700 MPa were purposely selected with the intention to examine if these higher grades are still promising to be implemented in special structural systems since they are prohibited by the building codes for longitudinal reinforcement, whereas Grade 420 MPa bars are the maximum limit of yield strength of reinforcing bars that is allowable for longitudinal reinforcement of special structural systems. Tensile tests of these steel samples were conducted under displacement controlled mode to capture the complete stress-strain curves and particularly the post-yield response of the steel bars. From the study, it can be concluded that Grade 420 performed higher TS/YS ratios and they were able to reach up to more than 1.25. However, the High Strength Still (HSS) bars (Grades 550, 600, and 700 MPa) resulted in lower TS/YS ratios (less than 1.25) compared with those of Grade 420 MPa.

Investigation of Ozone Yield of Air Fed Ozonizer by High Pressure Homogeneous Dielectric Barrier Discharge

DTIC Science & Technology

2013-07-01

31st ICPIG, July 14-19, 2013, Granada , Spain Investigation of ozone yield of air fed ozonizer by high pressure homogeneous dielectric barrier...Phenomena in Ionized Gases (31st) (ICPIG) Held in Granada , Spain on 14-19 July 2013 14. ABSTRACT We succeed in generating an atmospheric and high...8-98) Prescribed by ANSI Std Z39-18 31st ICPIG, July 14-19, 2013, Granada , Spain size and thickness are 100 cm2 and 2 mm respectively. The

Altered Tuber Yield in Genetically Modified High-Amylose and Oil Potato Lines Is Associated With Changed Whole-Plant Nitrogen Economy

PubMed Central

Pourazari, Fereshteh; Andersson, Mariette; Weih, Martin

2018-01-01

Breeding for improved crop quality traits can affect non-target traits related to growth and resource use, and these effects may vary in different cultivation conditions (e. g., greenhouse vs. field). The objectives of this study are to investigate the growth and whole-plant nitrogen (N) economy of two genetically modified (GM) potato lines compared to their non-GM parental varieties and when grown in different cultivation conditions. A high-amylose GM potato line and its parent were grown under field and greenhouse conditions for one growing season in Sweden; and a GM oil potato line and its parent were grown in greenhouse conditions only. Tuber yield, above ground biomass, N uptake efficiency and other plant N economy traits were assessed. In both cultivation conditions, the GM lines produced between 1.5 and two times more tubers as compared with their parents. In the greenhouse, fresh tuber yield and N uptake efficiency were unaffected by the genetic modifications, but the GM-lines produced less tuber biomass per plant-internal N compared to their parents. In the field, the fresh tuber yield was 40% greater in the high-amylose line as compared with its parent; the greater fresh tuber yield in the high-amylose GM line was accomplished by higher water allocation to the harvested tubers, and associated with increased N recovery from soil (+20%), N uptake efficiency (+53%), tuber N content (+20%), and N accumulation (+120%) compared with the non-GM parent. The cultivation conditions influenced the yield and N economy. For example, the final fresh above-ground plant biomass and N pool were considerably higher in the greenhouse conditions, whilst the tuber yield was higher in the field conditions. In conclusion, the genetic modification inducing high accumulation of amylose in potato tubers affected several non-target traits related to plant N economy, and increased the plant N uptake and accumulation efficiency of the field-grown plants. Due to strongly increased

A Framework for Reproducible Latent Fingerprint Enhancements.

PubMed

Carasso, Alfred S

2014-01-01

Photoshop processing of latent fingerprints is the preferred methodology among law enforcement forensic experts, but that appproach is not fully reproducible and may lead to questionable enhancements. Alternative, independent, fully reproducible enhancements, using IDL Histogram Equalization and IDL Adaptive Histogram Equalization, can produce better-defined ridge structures, along with considerable background information. Applying a systematic slow motion smoothing procedure to such IDL enhancements, based on the rapid FFT solution of a Lévy stable fractional diffusion equation, can attenuate background detail while preserving ridge information. The resulting smoothed latent print enhancements are comparable to, but distinct from, forensic Photoshop images suitable for input into automated fingerprint identification systems, (AFIS). In addition, this progressive smoothing procedure can be reexamined by displaying the suite of progressively smoother IDL images. That suite can be stored, providing an audit trail that allows monitoring for possible loss of useful information, in transit to the user-selected optimal image. Such independent and fully reproducible enhancements provide a valuable frame of reference that may be helpful in informing, complementing, and possibly validating the forensic Photoshop methodology.

A Framework for Reproducible Latent Fingerprint Enhancements

PubMed Central

Carasso, Alfred S.

2014-01-01

Photoshop processing1 of latent fingerprints is the preferred methodology among law enforcement forensic experts, but that appproach is not fully reproducible and may lead to questionable enhancements. Alternative, independent, fully reproducible enhancements, using IDL Histogram Equalization and IDL Adaptive Histogram Equalization, can produce better-defined ridge structures, along with considerable background information. Applying a systematic slow motion smoothing procedure to such IDL enhancements, based on the rapid FFT solution of a Lévy stable fractional diffusion equation, can attenuate background detail while preserving ridge information. The resulting smoothed latent print enhancements are comparable to, but distinct from, forensic Photoshop images suitable for input into automated fingerprint identification systems, (AFIS). In addition, this progressive smoothing procedure can be reexamined by displaying the suite of progressively smoother IDL images. That suite can be stored, providing an audit trail that allows monitoring for possible loss of useful information, in transit to the user-selected optimal image. Such independent and fully reproducible enhancements provide a valuable frame of reference that may be helpful in informing, complementing, and possibly validating the forensic Photoshop methodology. PMID:26601028

Parameter optimization for reproducible cardiac 1 H-MR spectroscopy at 3 Tesla.

PubMed

de Heer, Paul; Bizino, Maurice B; Lamb, Hildo J; Webb, Andrew G

2016-11-01

frequency selective excitation water suppression (7.0%). Using the optimized parameters an intrasession limits of agreement of the myocardial triglyceride content of -0.11% to +0.04%, and an intersession of -0.15% to +0.9%, were achieved. The coefficient of variation was 5% for the intrasession reproducibility and 6.5% for the intersession reproducibility. Using approaches designed to optimize SNR and minimize the variation in inter-average signal intensities and frequencies/phases, a protocol was developed to perform cardiac MR spectroscopy on a clinical 3T system with high reproducibility. J. Magn. Reson. Imaging 2016;44:1151-1158. © 2016 International Society for Magnetic Resonance in Medicine.

Facile Growth of High-Yield Gold Nanobipyramids Induced by Chloroplatinic Acid for High Refractive Index Sensing Properties.

PubMed

Fang, Caihong; Zhao, Guili; Xiao, Yanling; Zhao, Jun; Zhang, Zijun; Geng, Baoyou

2016-11-14

Au nanobipyramids (NBPs) have attracted great attention because of their unique localized surface plasmon resonance properties. However, the current growth methods always have low yield or suffer tedious process. Developing new ways to direct synthesis of high-yield Au NBPs using common agents is therefore desirable. Here, we employed chloroplatinic acid as the key shape-directing agent for the first time to grow Au NBPs using a modified seed-mediated method at room temperature. H 2 PtCl 6 was added both during the seed preparation and in growth solution. Metallic Pt, reduced from chloroplatinic acid, will deposit on the surface of the seed nanoparticles and the Au nanocrystals and thus plays a critical role for the formation of Au NBPs. Additionally, the reductant, precursor, and surfactant are all cheap and commonly used. Furthermore, the Au NBPs offer narrow size distribution, two sharp tips, and a shared basis. Au NBPs therefore show much higher refractive index sensitivities than that of the Au nanorods. The refractive index sensitivities and lager figure of merit values of Au NBPs exhibit an increase of 63% and 321% respectively compared to the corresponding values of Au nanorod sample.

Co-solvent pretreatment reduces costly enzyme requirements for high sugar and ethanol yields from lignocellulosic biomass.

PubMed

Nguyen, Thanh Yen; Cai, Charles M; Kumar, Rajeev; Wyman, Charles E

2015-05-22

We introduce a new pretreatment called co-solvent-enhanced lignocellulosic fractionation (CELF) to reduce enzyme costs dramatically for high sugar yields from hemicellulose and cellulose, which is essential for the low-cost conversion of biomass to fuels. CELF employs THF miscible with aqueous dilute acid to obtain up to 95 % theoretical yield of glucose, xylose, and arabinose from corn stover even if coupled with enzymatic hydrolysis at only 2 mgenzyme  gglucan (-1) . The unusually high saccharification with such low enzyme loadings can be attributed to a very high lignin removal, which is supported by compositional analysis, fractal kinetic modeling, and SEM imaging. Subsequently, nearly pure lignin product can be precipitated by the evaporation of volatile THF for recovery and recycling. Simultaneous saccharification and fermentation of CELF-pretreated solids with low enzyme loadings and Saccharomyces cerevisiae produced twice as much ethanol as that from dilute-acid-pretreated solids if both were optimized for corn stover. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The construction of a two-dimensional reproducing kernel function and its application in a biomedical model.

PubMed

Guo, Qi; Shen, Shu-Ting

2016-04-29

There are two major classes of cardiac tissue models: the ionic model and the FitzHugh-Nagumo model. During computer simulation, each model entails solving a system of complex ordinary differential equations and a partial differential equation with non-flux boundary conditions. The reproducing kernel method possesses significant applications in solving partial differential equations. The derivative of the reproducing kernel function is a wavelet function, which has local properties and sensitivities to singularity. Therefore, study on the application of reproducing kernel would be advantageous. Applying new mathematical theory to the numerical solution of the ventricular muscle model so as to improve its precision in comparison with other methods at present. A two-dimensional reproducing kernel function inspace is constructed and applied in computing the solution of two-dimensional cardiac tissue model by means of the difference method through time and the reproducing kernel method through space. Compared with other methods, this method holds several advantages such as high accuracy in computing solutions, insensitivity to different time steps and a slow propagation speed of error. It is suitable for disorderly scattered node systems without meshing, and can arbitrarily change the location and density of the solution on different time layers. The reproducing kernel method has higher solution accuracy and stability in the solutions of the two-dimensional cardiac tissue model.

High diagnostic yield of clinical exome sequencing in Middle Eastern patients with Mendelian disorders.

PubMed

Yavarna, Tarunashree; Al-Dewik, Nader; Al-Mureikhi, Mariam; Ali, Rehab; Al-Mesaifri, Fatma; Mahmoud, Laila; Shahbeck, Noora; Lakhani, Shenela; AlMulla, Mariam; Nawaz, Zafar; Vitazka, Patrik; Alkuraya, Fowzan S; Ben-Omran, Tawfeg

2015-09-01

Clinical exome sequencing (CES) has become an increasingly popular diagnostic tool in patients with heterogeneous genetic disorders, especially in those with neurocognitive phenotypes. Utility of CES in consanguineous populations has not yet been determined on a large scale. A clinical cohort of 149 probands from Qatar with suspected Mendelian, mainly neurocognitive phenotypes, underwent CES from July 2012 to June 2014. Intellectual disability and global developmental delay were the most common clinical presentations but our cohort displayed other phenotypes, such as epilepsy, dysmorphism, microcephaly and other structural brain anomalies and autism. A pathogenic or likely pathogenic mutation, including pathogenic CNVs, was identified in 89 probands for a diagnostic yield of 60%. Consanguinity and positive family history predicted a higher diagnostic yield. In 5% (7/149) of cases, CES implicated novel candidate disease genes (MANF, GJA9, GLG1, COL15A1, SLC35F5, MAGE4, NEUROG1). CES uncovered two coexisting genetic disorders in 4% (6/149) and actionable incidental findings in 2% (3/149) of cases. Average time to diagnosis was reduced from 27 to 5 months. CES, which already has the highest diagnostic yield among all available diagnostic tools in the setting of Mendelian disorders, appears to be particularly helpful diagnostically in the highly consanguineous Middle Eastern population.

Fluctuation and reproducibility of exposure and effect of insulin glargine in healthy subjects.

PubMed

Becker, R H A; Frick, A D; Teichert, L; Nosek, L; Heinemann, L; Heise, T; Rave, K

2008-11-01

Low diurnal fluctuation and high day-to-day reproducibility in exposure and effect characterize beneficial basal insulin products. Two insulin glargine (LANTUS) formulations [without (R) or with polysorbate-20 (T)], added to minimize unfolding of proteins and subsequent formation of fibril structures, were assessed for equivalence in exposure and effect, and aspects of fluctuation and reproducibility in time-concentration and time-action profiles. A dose of 0.4 U/kg was subcutaneously administered to 24 healthy subjects in a two-sequence (R-T-R-T or T-R-T-R), randomized, four-way crossover trial utilizing 30-h Biostator-based euglycaemic glucose clamps. Identical serum insulin glargine concentration and time-action profiles established average, individual and population equivalence in insulin exposure and effect. Point estimates for 24-h area under the curve for insulin (INS-AUC(0-24) (h)) and glucose infusion rates (GIR-AUC(0-24) (h)) were 97% [90% confidence interval (CI): 91-103%] and 100% (88-114%), respectively. Within-subject variability (coefficient of variation) for INS-AUC(0-24) (h) and GIR-AUC(0-24) (h) were 19% (95% CI: 14-25%) and 34% (24-43%), respectively. The diurnal relative fluctuation of the serum insulin glargine concentration was 20% (95% CI: 19-21%). Insulin glargine in either formulation presents with a high day-to-day reproducibility of a uniform release after injection enabling an effective basal insulin supplementation.

Study of optimal extraction conditions for achieving high yield and antioxidant activity of tomato seed oil.

PubMed

Shao, Dongyan; Atungulu, Griffiths G; Pan, Zhongli; Yue, Tianli; Zhang, Ang; Li, Xuan

2012-08-01

Value of tomato seed has not been fully recognized. The objectives of this research were to establish suitable processing conditions for extracting oil from tomato seed by using solvent, determine the impact of processing conditions on yield and antioxidant activity of extracted oil, and elucidate kinetics of the oil extraction process. Four processing parameters, including time, temperature, solvent-to-solid ratio and particle size were studied. A second order model was established to describe the oil extraction process. Based on the results, increasing temperature, solvent-to-solid ratio, and extraction time increased oil yield. In contrast, larger particle size reduced the oil yield. The recommended oil extraction conditions were 8 min of extraction time at temperature of 25 °C, solvent-to-solids ratio of 5/1 (v/w) and particle size of 0.38 mm, which gave oil yield of 20.32% with recovery rate of 78.56%. The DPPH scavenging activity of extracted oil was not significantly affected by the extraction parameters. The inhibitory concentration (IC(50) ) of tomato seed oil was 8.67 mg/mL which was notably low compared to most vegetable oils. A 2nd order model successfully described the kinetics of tomato oil extraction process and parameters of extraction kinetics including initial extraction rate (h), equilibrium concentration of oil (C(s) ), and the extraction rate constant (k) could be precisely predicted with R(2) of at least 0.957. The study revealed that tomato seed which is typically treated as a low value byproduct of tomato processing has great potential in producing oil with high antioxidant capability. The impact of processing conditions including time, temperature, solvent-to-solid ratio and particle size on yield, and antioxidant activity of extracted tomato seed oil are reported. Optimal conditions and models which describe the extraction process are recommended. The information is vital for determining the extraction processing conditions for industrial

Chimeric Mice with Competent Hematopoietic Immunity Reproduce Key Features of Severe Lassa Fever.

PubMed

Oestereich, Lisa; Lüdtke, Anja; Ruibal, Paula; Pallasch, Elisa; Kerber, Romy; Rieger, Toni; Wurr, Stephanie; Bockholt, Sabrina; Pérez-Girón, José V; Krasemann, Susanne; Günther, Stephan; Muñoz-Fontela, César

2016-05-01

Lassa fever (LASF) is a highly severe viral syndrome endemic to West African countries. Despite the annual high morbidity and mortality caused by LASF, very little is known about the pathophysiology of the disease. Basic research on LASF has been precluded due to the lack of relevant small animal models that reproduce the human disease. Immunocompetent laboratory mice are resistant to infection with Lassa virus (LASV) and, to date, only immunodeficient mice, or mice expressing human HLA, have shown some degree of susceptibility to experimental infection. Here, transplantation of wild-type bone marrow cells into irradiated type I interferon receptor knockout mice (IFNAR-/-) was used to generate chimeric mice that reproduced important features of severe LASF in humans. This included high lethality, liver damage, vascular leakage and systemic virus dissemination. In addition, this model indicated that T cell-mediated immunopathology was an important component of LASF pathogenesis that was directly correlated with vascular leakage. Our strategy allows easy generation of a suitable small animal model to test new vaccines and antivirals and to dissect the basic components of LASF pathophysiology.

Reflectance confocal microscopy and features of melanocytic lesions: an internet-based study of the reproducibility of terminology.

PubMed

Pellacani, Giovanni; Vinceti, Marco; Bassoli, Sara; Braun, Ralph; Gonzalez, Salvador; Guitera, Pascale; Longo, Caterina; Marghoob, Ashfaq A; Menzies, Scott W; Puig, Susana; Scope, Alon; Seidenari, Stefania; Malvehy, Josep

2009-10-01

To test the interobserver and intraobserver reproducibility of the standard terminology for description and diagnosis of melanocytic lesions in in vivo confocal microscopy. A dedicated Web platform was developed to train the participants and to allow independent distant evaluations of confocal images via the Internet. Department of Dermatology, University of Modena and Reggio Emilia, Modena, Italy. The study population was composed of 15 melanomas, 30 nevi, and 5 Spitz/Reed nevi. Six expert centers were invited to participate at the study. Intervention Evaluation of 36 features in 345 confocal microscopic images from melanocytic lesions. Interobserved and intraobserved agreement, by calculating the Cohen kappa statistics measure for each descriptor. High overall levels of reproducibility were shown for most of the evaluated features. In both the training and test sets there was a parallel trend of decreasing kappa values as deeper anatomic skin levels were evaluated. All of the features, except 1, used for melanoma diagnosis, including roundish pagetoid cells, nonedged papillae, atypical cells in basal layer, cerebriform clusters, and nucleated cells infiltrating dermal papillae, showed high overall levels of reproducibility. However, less-than-ideal reproducibility was obtained for some descriptors, such as grainy appearance of the epidermis, junctional thickening, mild atypia in basal layer, plump bright cells, small bright cells, and reticulated fibers in the dermis. Conclusion The standard consensus confocal terminology useful for the evaluation of melanocytic lesions was reproducibly recognized by independent observers.

Analysis of a large dataset of mycorrhiza inoculation field trials on potato shows highly significant increases in yield.

PubMed

Hijri, Mohamed

2016-04-01

An increasing human population requires more food production in nutrient-efficient systems in order to simultaneously meet global food needs while reducing the environmental footprint of agriculture. Arbuscular mycorrhizal fungi (AMF) have the potential to enhance crop yield, but their efficiency has yet to be demonstrated in large-scale crop production systems. This study reports an analysis of a dataset consisting of 231 field trials in which the same AMF inoculant (Rhizophagus irregularis DAOM 197198) was applied to potato over a 4-year period in North America and Europe under authentic field conditions. The inoculation was performed using a liquid suspension of AMF spores that was sprayed onto potato seed pieces, yielding a calculated 71 spores per seed piece. Statistical analysis showed a highly significant increase in marketable potato yield (ANOVA, P < 0.0001) for inoculated fields (42.2 tons/ha) compared with non-inoculated controls (38.3 tons/ha), irrespective of trial year. The average yield increase was 3.9 tons/ha, representing 9.5 % of total crop yield. Inoculation was profitable with a 0.67-tons/ha increase in yield, a threshold reached in almost 79 % of all trials. This finding clearly demonstrates the benefits of mycorrhizal-based inoculation on crop yield, using potato as a case study. Further improvements of these beneficial inoculants will help compensate for crop production deficits, both now and in the future.

Metaresearch for Evaluating Reproducibility in Ecology and Evolution

PubMed Central

Fidler, Fiona; Chee, Yung En; Wintle, Bonnie C.; Burgman, Mark A.; McCarthy, Michael A.; Gordon, Ascelin

2017-01-01

Abstract Recent replication projects in other disciplines have uncovered disturbingly low levels of reproducibility, suggesting that those research literatures may contain unverifiable claims. The conditions contributing to irreproducibility in other disciplines are also present in ecology. These include a large discrepancy between the proportion of “positive” or “significant” results and the average statistical power of empirical research, incomplete reporting of sampling stopping rules and results, journal policies that discourage replication studies, and a prevailing publish-or-perish research culture that encourages questionable research practices. We argue that these conditions constitute sufficient reason to systematically evaluate the reproducibility of the evidence base in ecology and evolution. In some cases, the direct replication of ecological research is difficult because of strong temporal and spatial dependencies, so here, we propose metaresearch projects that will provide proxy measures of reproducibility. PMID:28596617

Estimation of genetic parameters and selection of high-yielding, upright common bean lines with slow seed-coat darkening.

PubMed

Alvares, R C; Silva, F C; Melo, L C; Melo, P G S; Pereira, H S

2016-11-21

Slow seed coat darkening is desirable in common bean cultivars and genetic parameters are important to define breeding strategies. The aims of this study were to estimate genetic parameters for plant architecture, grain yield, grain size, and seed-coat darkening in common bean; identify any genetic association among these traits; and select lines that associate desirable phenotypes for these traits. Three experiments were set up in the winter 2012 growing season, in Santo Antônio de Goiás and Brasília, Brazil, including 220 lines obtained from four segregating populations and five parents. A triple lattice 15 x 15 experimental design was used. The traits evaluated were plant architecture, grain yield, grain size, and seed-coat darkening. Analyses of variance were carried out and genetic parameters such as heritability, gain expected from selection, and correlations, were estimated. For selection of superior lines, a "weight-free and parameter-free" index was used. The estimates of genetic variance, heritability, and gain expected from selection were high, indicating good possibility for success in selection of the four traits. The genotype x environment interaction was proportionally more important for yield than for the other traits. There was no strong genetic correlation observed among the four traits, which indicates the possibility of selection of superior lines with many traits. Considering simultaneous selection, it was not possible to join high genetic gains for the four traits. Forty-four lines that combined high yield, more upright plant architecture, slow darkening grains, and commercial grade size were selected.

Female fecundity variation affects reproducibility of experiments on host plant preference and acceptance in a phytophagous insect

PubMed Central

Schäpers, Alexander; Petrén, Hampus; Wheat, Christopher W.; Wiklund, Christer

2017-01-01

Reproducibility is a scientific cornerstone. Many recent studies, however, describe a reproducibility crisis and call for assessments of reproducibility across scientific domains. Here, we explore the reproducibility of a classic ecological experiment—that of assessing female host plant preference and acceptance in phytophagous insects, a group in which host specialization is a key driver of diversification. We exposed multiple cohorts of Pieris napi butterflies from the same population to traditional host acceptance and preference tests on three Brassicaceae host species. Whereas the host plant rank order was highly reproducible, the propensity to oviposit on low-ranked hosts varied significantly even among cohorts exposed to similar conditions. Much variation could be attributed to among-cohort variation in female fecundity, a trait strongly correlated both to female size and to the size of the nuptial gift a female receives during mating. Small males provide small spermatophores, and in our experiment small females that mated with small males had a disproportionally low propensity to oviposit on low-ranked hosts. Hence, our results provide empirical support to the theoretical prediction that female host utilization is strongly affected by non-genetic, environmental variation, and that such variation can affect the reproducibility of ecological experiments even under seemingly identical conditions. PMID:28202813

Faster, More Reproducible DESI-MS for Biological Tissue Imaging

NASA Astrophysics Data System (ADS)

Tillner, Jocelyn; Wu, Vincen; Jones, Emrys A.; Pringle, Steven D.; Karancsi, Tamas; Dannhorn, Andreas; Veselkov, Kirill; McKenzie, James S.; Takats, Zoltan

2017-10-01

A new, more robust sprayer for desorption electrospray ionization (DESI) mass spectrometry imaging is presented. The main source of variability in DESI is thought to be the uncontrolled variability of various geometric parameters of the sprayer, primarily the position of the solvent capillary, or more specifically, its positioning within the gas capillary or nozzle. If the solvent capillary is off-center, the sprayer becomes asymmetrical, making the geometry difficult to control and compromising reproducibility. If the stiffness, tip quality, and positioning of the capillary are improved, sprayer reproducibility can be improved by an order of magnitude. The quality of the improved sprayer and its potential for high spatial resolution imaging are demonstrated on human colorectal tissue samples by acquisition of images at pixel sizes of 100, 50, and 20 μm, which corresponds to a lateral resolution of 40-60 μm, similar to the best values published in the literature. The high sensitivity of the sprayer also allows combination with a fast scanning quadrupole time-of-flight mass spectrometer. This provides up to 30 times faster DESI acquisition, reducing the overall acquisition time for a 10 mm × 10 mm rat brain sample to approximately 1 h. Although some spectral information is lost with increasing analysis speed, the resulting data can still be used to classify tissue types on the basis of a previously constructed model. This is particularly interesting for clinical applications, where fast, reliable diagnosis is required. [Figure not available: see fulltext.

Control of Emission Color of High Quantum Yield CH3NH3PbBr3 Perovskite Quantum Dots by Precipitation Temperature.

PubMed

Huang, He; Susha, Andrei S; Kershaw, Stephen V; Hung, Tak Fu; Rogach, Andrey L

2015-09-01

Emission color controlled, high quantum yield CH 3 NH 3 PbBr 3 perovskite quantum dots are obtained by changing the temperature of a bad solvent during synthesis. The products for temperatures between 0 and 60 °C have good spectral purity with narrow emission line widths of 28-36 nm, high absolute emission quantum yields of 74% to 93%, and short radiative lifetimes of 13-27 ns.

Consistency and reproducibility of the VMAT plan delivery using three independent validation methods

PubMed Central

Chandraraj, Varatharaj; Manickam, Ravikumar; Esquivel, Carlos; Supe, Sanjay S; Papanikolaou, Nikos

2010-01-01

The complexity of VMAT delivery requires new methods and potentially new tools for the commissioning of these systems. It appears that great consideration is needed for quality assurance (QA) of these treatments since there are limited devices that are dedicated to the QA of rotational delivery. In this present study, we have evaluated the consistency and reproducibility of one prostate and one lung VMAT plans for 31 consecutive days using three different approaches: 1) MLC DynaLog files, 2) in vivo measurements using the multiwire ionization chamber DAVID, and 3) using PTWseven29 2D ARRAY with the OCTAVIUS phantom at our Varian Clinac linear accelerator. Overall, the three methods of testing the reproducibility and consistency of the VMAT delivery were in agreement with each other. All methods showed minimal daily deviations that contributed to clinically insignificant dose variations from day to day. Based on our results, we conclude that the VMAT delivery using a Varian 2100CD linear accelerator equipped with 120 MLC is highly reproducible. PACS numbers: 87.55.Qr and 87.56.Fc

Selection of strawberry cultivars with tolerance to Tetranychus urticae (Acari: Tetranychidae) and high yield under different managements.

PubMed

Costa, A F; Teodoro, P E; Bhering, L L; Fornazier, M J; Andrade, J S; Martins, D S; Zanuncio Junior, J S

2017-04-28

Tetranychus urticae Koch (Acari: Tetranychidae) is considered the main pest of strawberry. Several factors can favor its development, among them the genotype susceptibility and cropping system. The aims of this study were to evaluate the agronomic performance of strawberry cultivars under different managements and to identify strawberry cultivars that meet tolerance to T. urticae and high fruit yield. Thirteen cultivars of strawberry ('Albion', 'Aleluia', 'Aromas', 'Camarosa', 'Camino Real', 'Campinas', 'Diamante', 'Dover', 'Festival', 'Seascape', 'Toyonoka', 'Tudla', and 'Ventana') under three managements (open field, low tunnel, and high tunnel) were evaluated. The T. urticae attack to different cultivars was influenced by managements, being low tunnel the one that provided higher infestations in the most evaluated cultivars. 'Camarosa' was the cultivar with the lower incidence of pest and 'Dover' had the higher infestation. The genotype most suitable for growing under different managements is the 'Festival' genotype, since it meets tolerance to T. urticae, high fruit yield, and phenotypic stability.

46 CFR 56.80-10 - Forming (reproduces 129.2).

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 2 2010-10-01 2010-10-01 false Forming (reproduces 129.2). 56.80-10 Section 56.80-10 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING PIPING SYSTEMS AND APPURTENANCES Bending and Forming § 56.80-10 Forming (reproduces 129.2). (a) Piping components may be formed...

46 CFR 56.80-10 - Forming (reproduces 129.2).

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 2 2011-10-01 2011-10-01 false Forming (reproduces 129.2). 56.80-10 Section 56.80-10 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING PIPING SYSTEMS AND APPURTENANCES Bending and Forming § 56.80-10 Forming (reproduces 129.2). (a) Piping components may be formed...

Reproducibility of preclinical animal research improves with heterogeneity of study samples

PubMed Central

Vogt, Lucile; Sena, Emily S.; Würbel, Hanno

2018-01-01

Single-laboratory studies conducted under highly standardized conditions are the gold standard in preclinical animal research. Using simulations based on 440 preclinical studies across 13 different interventions in animal models of stroke, myocardial infarction, and breast cancer, we compared the accuracy of effect size estimates between single-laboratory and multi-laboratory study designs. Single-laboratory studies generally failed to predict effect size accurately, and larger sample sizes rendered effect size estimates even less accurate. By contrast, multi-laboratory designs including as few as 2 to 4 laboratories increased coverage probability by up to 42 percentage points without a need for larger sample sizes. These findings demonstrate that within-study standardization is a major cause of poor reproducibility. More representative study samples are required to improve the external validity and reproducibility of preclinical animal research and to prevent wasting animals and resources for inconclusive research. PMID:29470495

Composting in small laboratory pilots: Performance and reproducibility

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

Lashermes, G.; Barriuso, E.; Le Villio-Poitrenaud, M.

2012-02-15

Highlights: Black-Right-Pointing-Pointer We design an innovative small-scale composting device including six 4-l reactors. Black-Right-Pointing-Pointer We investigate the performance and reproducibility of composting on a small scale. Black-Right-Pointing-Pointer Thermophilic conditions are established by self-heating in all replicates. Black-Right-Pointing-Pointer Biochemical transformations, organic matter losses and stabilisation are realistic. Black-Right-Pointing-Pointer The organic matter evolution exhibits good reproducibility for all six replicates. - Abstract: Small-scale reactors (<10 l) have been employed in composting research, but few attempts have assessed the performance of composting considering the transformations of organic matter. Moreover, composting at small scales is often performed by imposing a fixed temperature, thus creatingmore » artificial conditions, and the reproducibility of composting has rarely been reported. The objectives of this study are to design an innovative small-scale composting device safeguarding self-heating to drive the composting process and to assess the performance and reproducibility of composting in small-scale pilots. The experimental setup included six 4-l reactors used for composting a mixture of sewage sludge and green wastes. The performance of the process was assessed by monitoring the temperature, O{sub 2} consumption and CO{sub 2} emissions, and characterising the biochemical evolution of organic matter. A good reproducibility was found for the six replicates with coefficients of variation for all parameters generally lower than 19%. An intense self-heating ensured the existence of a spontaneous thermophilic phase in all reactors. The average loss of total organic matter (TOM) was 46% of the initial content. Compared to the initial mixture, the hot water soluble fraction decreased by 62%, the hemicellulose-like fraction by 68%, the cellulose-like fraction by 50% and the lignin-like fractions by 12% in the

Highly Sensitive, Uniform, and Reproducible Surface-Enhanced Raman Spectroscopy Substrate with Nanometer-Scale Quasi-periodic Nanostructures.

PubMed

Jin, Yuanhao; Wang, Yingcheng; Chen, Mo; Xiao, Xiaoyang; Zhang, Tianfu; Wang, Jiaping; Jiang, Kaili; Fan, Shoushan; Li, Qunqing

2017-09-20

We introduce a simple and cost-effective approach for fabrication of effective surface-enhanced Raman spectroscopy (SERS) substrates. It is shown that the as-fabricated substrates show excellent SERS effects in various probe molecules with high sensitivity, that is, picomolar level detection, and also good reliability. With a SERS enhancement factor beyond 10 8 and excellent reproducibility (deviation less than 5%) of signal intensity, the fabrication of the SERS substrate is realized on a four-inch wafer and proven to be effective in pesticide residue detection. The SERS substrate is realized first through the fabrication of quasi-periodic nanostructured silicon with dimension features in tens of nanometers using superaligned carbon nanotubes networks as an etching mask, after which a large amount of hot spots with nanometer gaps are formed through deposition of a gold film. With rigorous nanostructure design, the enhanced performance of electromagnetic field distribution for nanostructures is optimized. With the advantage of cost-effective large-area preparation, it is believed that the as-fabricated SERS substrate could be used in a wide variety of actual applications where detection of trace amounts is necessary.

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.

Modelling predicts that tolerance to drought during reproductive development will be required for high yield potential and stability of wheat in Europe

NASA Astrophysics Data System (ADS)

Semenov, Mikhail A.; Stratonovitch, Pierre; Paul, Matthew J.

2017-04-01

Short periods of extreme weather, such as a spell of high temperature or drought during a sensitive stage of development, could result in substantial yield losses due to reduction in grain number and grain size. In a modelling study (Stratonovitch & Semenov 2015), heat tolerance around flowering in wheat was identified as a key trait for increased yield potential in Europe under climate change. Ji et all (Ji et al. 2010) demonstrated cultivar specific responses of yield to drought stress around flowering in wheat. They hypothesised that carbohydrate supply to anthers may be the key in maintaining pollen fertility and grain number in wheat. It was shown in (Nuccio et al. 2015) that genetically modified varieties of maize that increase the concentration of sucrose in ear spikelets, performed better under non-drought and drought conditions in field experiments. The objective of this modelling study was to assess potential benefits of tolerance to drought during reproductive development for wheat yield potential and yield stability across Europe. We used the Sirius wheat model to optimise wheat ideotypes for 2050 (HadGEM2, RCP8.5) climate scenarios at selected European sites. Eight cultivar parameters were optimised to maximise mean yields, including parameters controlling phenology, canopy growth and water limitation. At those sites where water could be limited, ideotypes sensitive to drought produced substantially lower mean yields and higher yield variability compare with tolerant ideotypes. Therefore, tolerance to drought during reproductive development is likely to be required for wheat cultivars optimised for the future climate in Europe in order to achieve high yield potential and yield stability.

Evidence for a weakening strength of temperature-corn yield relation in the United States during 1980–2010

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

Leng, Guoyong

Temperature is known to be correlated with crop yields, causing reduction of crop yield with climate warming without adaptations or CO2 fertilization effects. The historical temperature-crop yield relation has often been used for informing future changes. This relationship, however, may change over time following alternations in other environmental factors. Results show that the strength of the relationship between the interannual variability of growing season temperature and corn yield (RGST_CY) has declined in the United States between 1980 and 2010 with a loss in the statistical significance. The regression slope which represents the anomalies in corn yield that occur in associationmore » with 1 degree temperature anomaly has decreased significantly from -6.9%/K of the first half period to -2.4%/K~-3.5%/K of the second half period. This implies that projected corn yield reduction will be overestimated by a fact of 2 in a given warming scenario, if the corn-temperature relation is derived from the earlier historical period. Changes in RGST_CY are mainly observed in Midwest Corn Belt and central High Plains, and are well reproduced by 11 process-based crop models. In Midwest rain-fed systems, the decrease of negative temperature effects coincides with an increase in water availability by precipitation. In irrigated areas where water stress is minimized, the decline of beneficial temperature effects is significantly related to the increase in extreme hot days. The results indicate that an extrapolation of historical yield response to temperature may bias the assessment of agriculture vulnerability to climate change. Efforts to reduce climate impacts on agriculture should pay attention not only to climate change, but also to changes in climate-crop yield relations. There are some caveats that should be acknowledged as the analysis is restricted to the changes in the linear relation between growing season mean temperature and corn yield for the specific study

Repeatability and reproducibility of optic nerve head perfusion measurements using optical coherence tomography angiography

NASA Astrophysics Data System (ADS)

Chen, Chieh-Li; Bojikian, Karine D.; Xin, Chen; Wen, Joanne C.; Gupta, Divakar; Zhang, Qinqin; Mudumbai, Raghu C.; Johnstone, Murray A.; Chen, Philip P.; Wang, Ruikang K.

2016-06-01

Optical coherence tomography angiography (OCTA) has increasingly become a clinically useful technique in ophthalmic imaging. We evaluate the repeatability and reproducibility of blood perfusion in the optic nerve head (ONH) measured using optical microangiography (OMAG)-based OCTA. Ten eyes from 10 healthy volunteers are recruited and scanned three times with a 68-kHz Cirrus HD-OCT 5000-based OMAG prototype system (Carl Zeiss Meditec Inc., Dublin, California) centered at the ONH involving two separate visits within six weeks. Vascular images are generated with OMAG processing by detecting the differences in OCT signals between consecutive B-scans acquired at the same retina location. ONH perfusion is quantified as flux, vessel area density, and normalized flux within the ONH for the prelaminar, lamina cribrosa, and the full ONH. Coefficient of variation (CV) and intraclass correlation coefficient (ICC) are used to evaluate intravisit and intervisit repeatability, and interobserver reproducibility. ONH perfusion measurements show high repeatability [CV≤3.7% (intravisit) and ≤5.2% (intervisit)] and interobserver reproducibility (ICC≤0.966) in all three layers by three metrics. OCTA provides a noninvasive method to visualize and quantify ONH perfusion in human eyes with excellent repeatability and reproducibility, which may add additional insight into ONH perfusion in clinical practice.

Validity and reproducibility of self-reported working hours among Japanese male employees

PubMed Central

Imai, Teppei; Kuwahara, Keisuke; Miyamoto, Toshiaki; Okazaki, Hiroko; Nishihara, Akiko; Kabe, Isamu; Mizoue, Tetsuya; Dohi, Seitaro

2016-01-01

Objective: Working long hours is a potential health hazard. Although self-reporting of working hours in various time frames has been used in epidemiologic studies, its validity is unclear. The objective of this study was to examine the validity and reproducibility of self-reported working hours among Japanese male employees. Methods: The participants were 164 male employees of four large-scale companies in Japan. For validity, the Spearman correlation between self-reported working hours in the second survey and the working hours recorded by the company was calculated for the following four time frames: daily working hours, monthly overtime working hours in the last month, average overtime working hours in the last 3 months, and the frequency of long working months (≥45 h/month) within the last 12 months. For reproducibility, the intraclass correlation between the first (September 2013) and second surveys (December 2013) was calculated for each of the four time frames. Results: The Spearman correlations between self-reported working hours and those based on company records were 0.74, 0.81, 0.85, and 0.89 for daily, monthly, 3-monthly, and yearly time periods, respectively. The intraclass correlations for self-reported working hours between the two questionnaire surveys were 0.63, 0.66, 0.73, and 0.87 for the respective time frames. Conclusions: The results of the present study among Japanese male employees suggest that the validity of self-reported working hours is high for all four time frames, whereas the reproducibility is moderate to high. PMID:27265530

Dysplastic naevus: histological criteria and their inter-observer reproducibility.

PubMed

Hastrup, N; Clemmensen, O J; Spaun, E; Søndergaard, K

1994-06-01

Forty melanocytic lesions were examined in a pilot study, which was followed by a final series of 100 consecutive melanocytic lesions, in order to evaluate the inter-observer reproducibility of the histological criteria proposed for the dysplastic naevus. The specimens were examined in a blind fashion by four observers. Analysis by kappa statistics showed poor reproducibility of nuclear features, while reproducibility of architectural features was acceptable, improving in the final series. Consequently, we cannot apply the combined criteria of cytological and architectural features with any confidence in the diagnosis of dysplastic naevus, and, until further studies have documented that architectural criteria alone will suffice in the diagnosis of dysplastic naevus, we, as pathologists, shall avoid this term.

Reproducible and controllable induction voltage adder for scaled beam experiments

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

Sakai, Yasuo; Nakajima, Mitsuo; Horioka, Kazuhiko

2016-08-15

A reproducible and controllable induction adder was developed using solid-state switching devices and Finemet cores for scaled beam compression experiments. A gate controlled MOSFET circuit was developed for the controllable voltage driver. The MOSFET circuit drove the induction adder at low magnetization levels of the cores which enabled us to form reproducible modulation voltages with jitter less than 0.3 ns. Preliminary beam compression experiments indicated that the induction adder can improve the reproducibility of modulation voltages and advance the beam physics experiments.

Data Identifiers and Citations Enable Reproducible Science

NASA Astrophysics Data System (ADS)

Tilmes, C.

2011-12-01

Modern science often involves data processing with tremendous volumes of data. Keeping track of that data has been a growing challenge for data center. Researchers who access and use that data don't always reference and cite their data sources adequately for consumers of their research to follow their methodology or reproduce their analyses or experiments. Recent research has led to recommendations for good identifiers and citations that can help address this problem. This paper will describe some of the best practices in data identifiers, reference and citation. Using a simplified example scenario based on a long term remote sensing satellite mission, it will explore issues in identifying dynamic data sets and the importance of good data citations for reproducibility. It will describe the difference between granule and collection level identifiers, using UUIDs and DOIs to illustrate some recommendations for developing identifiers and assigning them during data processing. As data processors create data products, the provenance of the input products and precise steps that led to their creation are recorded and published for users of the data to see. As researchers access the data from an archive, they can use the provenance to help understand the genesis of the data, which could have effects on their usage of the data. By citing the data on publishing their research, others can retrieve the precise data used in their research and reproduce the analyses and experiments to confirm the results. Describing the experiment to a sufficient extent to reproduce the research enforces a formal approach that lends credibility to the results, and ultimately, to the policies of decision makers depending on that research.

MULTI-KEV X-RAY YIELDS FROM HIGH-Z GAS TARGETS FIELDED AT OMEGA

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

Kane, J O; Fournier, K B; May, M J

2010-11-04

The authors report on modeling of x-ray yield from gas-filled targets shot at the OMEGA laser facility. The OMEGA targets were 1.8 mm long, 1.95 mm in diameter Be cans filled with either a 50:50 Ar:Xe mixture, pure Ar, pure Kr or pure Xe at {approx} 1 atm. The OMEGA experiments heated the gas with 20 kJ of 3{omega} ({approx} 350 nm) laser energy delivered in a 1 ns square pulse. the emitted x-ray flux was monitored with the x-ray diode based DANTE instruments in the sub-keV range. Two-dimensional x-ray images (for energies 3-5 keV) of the targets were recordedmore » with gated x-ray detectors. The x-ray spectra were recorded with the HENWAY crystal spectrometer at OMEGA. Predictions are 2D r-z cylindrical with DCA NLTE atomic physics. Models generally: (1) underpredict the Xe L-shell yields; (2) overpredict the Ar K-shell yields; (3) correctly predict the Xe thermal yields; and (4) greatly underpredict the Ar thermal yields. However, there are spreads within the data, e.g. the DMX Ar K-shell yields are correctly predicted. The predicted thermal yields show strong angular dependence.« less

Intrathoracic Fat Measurements Using Multidetector Computed Tomography (MDCT): Feasibility and Reproducibility

PubMed Central

Stojanovska, Jadranka; Ibrahim, El-Sayed H.; Chughtai, Aamer R.; Jackson, Elizabeth A.; Gross, Barry H.; Jacobson, Jon A.; Tsodikov, Alexander; Daneshvar, Brian; Long, Benjamin D.; Chenevert, Thomas L.; Kazerooni, Ella A.

2017-01-01

Intrathoracic fat volume, more specifically, epicardial fat volume, is an emerging imaging biomarker of adverse cardiovascular events. The purpose of this work is to show the feasibility and reproducibility of intrathoracic fat volume measurement applied to contrast-enhanced multidetector computed tomography images. A retrospective cohort study of 62 subjects free of cardiovascular disease (55% females, age = 49 ± 11 years) conducted from 2008 to 2011 formed the study group. Intrathoracic fat volume was defined as all fat voxels measuring −50 to −250 Hounsfield Unit within the intrathoracic cavity from the level of the pulmonary artery bifurcation to the heart apex. The intrathoracic fat was separated into epicardial and extrapericardial fat by tracing the pericardium. The measurements were obtained by 2 readers and compared for interrater reproducibility. The fat volume measurements for the study group were 141 ± 72 cm3 for intrathoracic fat, 58 ± 27 cm3 for epicardial fat, and 84 ± 50 cm3 for extrapericardial fat. There was no statistically significant difference in intrathoracic fat volume measurements between the 2 readers, with correlation coefficients of 0.88 (P = .55) for intrathoracic fat volume and −0.12 (P = .33) for epicardial fat volume. Voxel-based measurement of intrathoracic fat, including the separation into epicardial and extrapericardial fat, is feasible and highly reproducible from multidetector computed tomography scans. PMID:28626797

High process yield rates of thermoplastic nanofluidic devices using a hybrid thermal assembly technique.

PubMed

Uba, Franklin I; Hu, Bo; Weerakoon-Ratnayake, Kumuditha; Oliver-Calixte, Nyote; Soper, Steven A

2015-02-21

Over the past decade, thermoplastics have been used as alternative substrates to glass and Si for microfluidic devices because of the diverse and robust fabrication protocols available for thermoplastics that can generate high production rates of the desired structures at low cost and with high replication fidelity, the extensive array of physiochemical properties they possess, and the simple surface activation strategies that can be employed to tune their surface chemistry appropriate for the intended application. While the advantages of polymer microfluidics are currently being realized, the evolution of thermoplastic-based nanofluidic devices is fraught with challenges. One challenge is assembly of the device, which consists of sealing a cover plate to the patterned fluidic substrate. Typically, channel collapse or substrate dissolution occurs during assembly making the device inoperable resulting in low process yield rates. In this work, we report a low temperature hybrid assembly approach for the generation of functional thermoplastic nanofluidic devices with high process yield rates (>90%) and with a short total assembly time (16 min). The approach involves thermally sealing a high T(g) (glass transition temperature) substrate containing the nanofluidic structures to a cover plate possessing a lower T(g). Nanofluidic devices with critical feature sizes ranging between 25-250 nm were fabricated in a thermoplastic substrate (T(g) = 104 °C) and sealed with a cover plate (T(g) = 75 °C) at a temperature significantly below the T(g) of the substrate. Results obtained from sealing tests revealed that the integrity of the nanochannels remained intact after assembly and devices were useful for fluorescence imaging at high signal-to-noise ratios. The functionality of the assembled devices was demonstrated by studying the stretching and translocation dynamics of dsDNA in the enclosed thermoplastic nanofluidic channels.

High-yield sol-gel synthesis of well-dispersed, colorless ZrO(2) nanocrystals.

PubMed

Mizuno, Mikihisa; Sasaki, Yuichi; Lee, Sungkil; Katakura, Hitoshi

2006-08-15

A 93% high-yield synthesis of well-dispersed, colorless zirconium dioxide (ZrO(2)) nanocrystals is reported. In this synthesis, hydrolysis and condensation reactions of zirconium(IV) tert-butoxide in the presence of oleic acid (100 degrees C) formed ZrO(2) precursors. The ZrO(2) precursors were made of -Zr-O-Zr- networks surrounded by oleic acid molecules. Annealing (280 degrees C) the precursors dispersed in dioctyl ether caused crystallization of the -Zr-O-Zr- networks, thereby generating 4 nm ZrO(2) nanocrystals stabilized with oleic acid. The particles were highly crystalline and tetragonal phase. A dense ZrO(2) nanocrystal dispersion in toluene (280 mg/mL) showed a transmittance of about 90% (3 mm optical path length) in the whole visible region.

GeoTrust Hub: A Platform For Sharing And Reproducing Geoscience Applications

NASA Astrophysics Data System (ADS)

Malik, T.; Tarboton, D. G.; Goodall, J. L.; Choi, E.; Bhatt, A.; Peckham, S. D.; Foster, I.; Ton That, D. H.; Essawy, B.; Yuan, Z.; Dash, P. K.; Fils, G.; Gan, T.; Fadugba, O. I.; Saxena, A.; Valentic, T. A.

2017-12-01

Recent requirements of scholarly communication emphasize the reproducibility of scientific claims. Text-based research papers are considered poor mediums to establish reproducibility. Papers must be accompanied by "research objects", aggregation of digital artifacts that together with the paper provide an authoritative record of a piece of research. We will present GeoTrust Hub (http://geotrusthub.org), a platform for creating, sharing, and reproducing reusable research objects. GeoTrust Hub provides tools for scientists to create `geounits'--reusable research objects. Geounits are self-contained, annotated, and versioned containers that describe and package computational experiments in an efficient and light-weight manner. Geounits can be shared on public repositories such as HydroShare and FigShare, and also using their respective APIs reproduced on provisioned clouds. The latter feature enables science applications to have a lifetime beyond sharing, wherein they can be independently verified and trust be established as they are repeatedly reused. Through research use cases from several geoscience laboratories across the United States, we will demonstrate how tools provided from GeoTrust Hub along with Hydroshare as its public repository for geounits is advancing the state of reproducible research in the geosciences. For each use case, we will address different computational reproducibility requirements. Our first use case will be an example of setup reproducibility which enables a scientist to set up and reproduce an output from a model with complex configuration and development environments. Our second use case will be an example of algorithm/data reproducibility, where in a shared data science model/dataset can be substituted with an alternate one to verify model output results, and finally an example of interactive reproducibility, in which an experiment is dependent on specific versions of data to produce the result. Toward this we will use software and data

Enhancing biomass energy yield from pilot-scale high rate algal ponds with recycling.

PubMed

Park, J B K; Craggs, R J; Shilton, A N

2013-09-01

This paper investigates the effect of recycling on biomass energy yield in High Rate Algal Ponds (HRAPs). Two 8 m(3) pilot-scale HRAPs treating primary settled sewage were operated in parallel and monitored over a 2-year period. Volatile suspended solids were measured from both HRAPs and their gravity settlers to determine biomass productivity and harvest efficiency. The energy content of the biomass was also measured. Multiplying biomass productivity and harvest efficiency gives the 'harvestable biomass productivity' and multiplying this by the energy content defines the actual 'biomass energy yield'. In Year 1, algal recycling was implemented in one of the ponds (HRAPr) and improved harvestable biomass productivity by 58% compared with the control (HRAPc) without recycling (HRAPr: 9.2 g/m(2)/d; HRAPc: 5.8 g/m(2)/d). The energy content of the biomass grown in HRAPr, which was dominated by Pediastrun boryanum, was 25% higher than the control HRAPc which contained a mixed culture of 4-5 different algae (HRAPr: 21.5 kJ/g; HRAPc: 18.6 kJ/g). In Year 2, HRAPc was then seeded with the biomass harvested from the P. boryanum dominated HRAPr. This had the effect of shifting algal dominance from 89% Dictyosphaerium sp. (which is poorly-settleable) to over 90% P. boryanum in 5 months. Operation of this pond was then switched to recycling its own harvested biomass, which maintained P. boryanum dominance for the rest of Year 2. This result confirms, for the first time in the literature, that species control is possible for similarly sized co-occurring algal colonies in outdoor HRAP by algal recycling. With regard to the overall improvement in biomass energy yield, which is a critical parameter in the context of algal cultivation for biofuels, the combined improvements that recycling triggered in biomass productivity, harvest efficiency and energy content enhanced the harvested biomass energy yield by 66% (HRAPr: 195 kJ/m(2)/day; HRAPc: 118 kJ/m(2)/day). Copyright © 2013

In search of annual legumes to improve forage sorghum yield and nutritive value in the southern high plains

USDA-ARS?s Scientific Manuscript database

Livestock production is significant in the Southern High Plains of the USA and demand is increasing for greater forage dry matter (DM) yield with increased nutritive value. Forage sorghum (FS)[Sorghum bicolor (L.) Moench] is commonly used, although, it is low in crude protein (CP) and high in fiber....

Optimizing Hill Seeding Density for High-Yielding Hybrid Rice in a Single Rice Cropping System in South China

PubMed Central

Wang, Danying; Chen, Song; Wang, Zaiman; Ji, Chenglin; Xu, Chunmei; Zhang, Xiufu; Chauhan, Bhagirath Singh

2014-01-01

Mechanical hill direct seeding of hybrid rice could be the way to solve the problems of high seeding rates and uneven plant establishment now faced in direct seeded rice; however, it is not clear what the optimum hill seeding density should be for high-yielding hybrid rice in the single-season rice production system. Experiments were conducted in 2010 and 2011 to determine the effects of hill seeding density (25 cm×15 cm, 25 cm×17 cm, 25 cm×19 cm, 25 cm×21 cm, and 25 cm×23 cm; three to five seeds per hill) on plant growth and grain yield of a hybrid variety, Nei2you6, in two fields with different fertility (soil fertility 1 and 2). In addition, in 2012 and 2013, comparisons among mechanical hill seeding, broadcasting, and transplanting were conducted with three hybrid varieties to evaluate the optimum seeding density. With increases in seeding spacing from 25 cm×15 cm to 25 cm×23 cm, productive tillers per hill increased by 34.2% and 50.0% in soil fertility 1 and 2. Panicles per m2 declined with increases in seeding spacing in soil fertility 1. In soil fertility 2, no difference in panicles per m2 was found at spacing ranging from 25 cm×17 cm to 25 cm×23 cm, while decreases in the area of the top three leaves and aboveground dry weight per shoot at flowering were observed. Grain yield was the maximum at 25 cm×17 cm spacing in both soil fertility fields. Our results suggest that a seeding density of 25 cm×17 cm was suitable for high-yielding hybrid rice. These results were verified through on-farm demonstration experiments, in which mechanical hill-seeded rice at this density had equal or higher grain yield than transplanted rice. PMID:25290342

Effect of yield curves and porous crush on hydrocode simulations of asteroid airburst

NASA Astrophysics Data System (ADS)

Robertson, D. K.; Mathias, D. L.

2017-03-01

Simulations of asteroid airburst are being conducted to obtain best estimates of damage areas and assess sensitivity to variables for asteroid characterization and mitigation efforts. The simulations presented here employed the ALE3D hydrocode to examine the breakup and energy deposition of asteroids entering the Earth's atmosphere, using the Chelyabinsk meteor as a test case. This paper examines the effect of increasingly complex material models on the energy deposition profile. Modeling the meteor as a rock having a single strength can reproduce airburst altitude and energy deposition reasonably well but is not representative of real rock masses (large bodies of material). Accounting for a yield curve that includes different tensile, shear, and compressive strengths shows that shear strength determines the burst altitude. Including yield curves and compaction of porous spaces in the material changes the detailed mechanics of the breakup but only has a limited effect on the burst altitude and energy deposition. Strong asteroids fail and create peak energy deposition close to the altitude at which ram dynamic pressure equals the material strength. Weak asteroids, even though they structurally fail at high altitude, require the increased pressure at lower altitude to disrupt and disperse the rubble. As a result, a wide range of weaker asteroid strengths produce peak energy deposition at a similar altitude.

Reproducible research in vadose zone sciences

USDA-ARS?s Scientific Manuscript database

A significant portion of present-day soil and Earth science research is computational, involving complex data analysis pipelines, advanced mathematical and statistical models, and sophisticated computer codes. Opportunities for scientific progress are greatly diminished if reproducing and building o...

An Open Science and Reproducible Research Primer for Landscape Ecologists

EPA Science Inventory

In recent years many funding agencies, some publishers, and even the United States government have enacted policies that encourage open science and strive for reproducibility; however, the knowledge and skills to implement open science and enable reproducible research are not yet...

Xenon Sputter Yield Measurements for Ion Thruster Materials

NASA Technical Reports Server (NTRS)

Williams, John D.; Gardner, Michael M.; Johnson, Mark L.; Wilbur, Paul J.

2003-01-01

In this paper, we describe a technique that was used to measure total and differential sputter yields of materials important to high specific impulse ion thrusters. The heart of the technique is a quartz crystal monitor that is swept at constant radial distance from a small target region where a high current density xenon ion beam is aimed. Differential sputtering yields were generally measured over a full 180 deg arc in a plane that included the beam centerline and the normal vector to the target surface. Sputter yield results are presented for a xenon ion energy range from 0.5 to 10 keV and an angle of incidence range from 0 deg to 70 deg from the target surface normal direction for targets consisting of molybdenum, titanium, solid (Poco) graphite, and flexible graphite (grafoil). Total sputter yields are calculated using a simple integration procedure and comparisons are made to sputter yields obtained from the literature. In general, the agreement between the available data is good. As expected for heavy xenon ions, the differential and total sputter yields are found to be strong functions of angle of incidence. Significant under- and over-cosine behavior is observed at low- and high-ion energies, respectively. In addition, strong differences in differential yield behavior are observed between low-Z targets (C and Ti) and high-Z targets (Mo). Curve fits to the differential sputter yield data are provided. They should prove useful to analysts interested in predicting the erosion profiles of ion thruster components and determining where the erosion products re-deposit.

Past crops yield dynamics reconstruction from tree-ring chronologies in the forest-steppe zone based on low- and high-frequency components

NASA Astrophysics Data System (ADS)

Babushkina, Elena A.; Belokopytova, Liliana V.; Shah, Santosh K.; Zhirnova, Dina F.

2018-05-01

Interrelations of the yield variability of the main crops (wheat, barley, and oats) with hydrothermal regime and growth of conifer trees ( Pinus sylvestris and Larix sibirica) in forest-steppes were investigated in Khakassia, South Siberia. An attempt has been made to understand the role and mechanisms of climatic impact on plants productivity. It was found that amongst variables describing moisture supply, wetness index had maximum impact. Strength of climatic response and correlations with tree growth are different for rain-fed and irrigated crops yield. Separated high-frequency variability components of yield and tree-ring width have more pronounced relationships between each other and with climatic variables than their chronologies per se. Corresponding low-frequency variability components are strongly correlated with maxima observed after 1- to 5-year time shift of tree-ring width. Results of analysis allowed us to develop original approach of crops yield dynamics reconstruction on the base of high-frequency variability component of the growth of pine and low-frequency one of larch.

Respiratory effort correction strategies to improve the reproducibility of lung expansion measurements

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

Du, Kaifang; Reinhardt, Joseph M.; Christensen, Gary E.

2013-12-15

correlated with respiratory effort difference (R = 0.744 for ELV in the cohort with tidal volume difference greater than 100 cc). In general for all subjects, global normalization, ETV and ELV significantly improved reproducibility compared to no effort correction (p = 0.009, 0.002, 0.005 respectively). When tidal volume difference was small (less than 100 cc), none of the three effort correction strategies improved reproducibility significantly (p = 0.52, 0.46, 0.46 respectively). For the cohort (N = 13) with tidal volume difference greater than 100 cc, the average gamma pass rate improves from 57.3% before correction to 66.3% after global normalization, and 76.3% after ELV. ELV was found to be significantly better than global normalization (p = 0.04 for all subjects, and p = 0.003 for the cohort with tidal volume difference greater than 100 cc).Conclusions: All effort correction strategies improve the reproducibility of the authors' pulmonary ventilation measures, and the improvement of reproducibility is highly correlated with the changes in respiratory effort. ELV gives better results as effort difference increase, followed by ETV, then global. However, based on the spatial and temporal heterogeneity in the lung expansion rate, a single scaling factor (e.g., global normalization) appears to be less accurate to correct the ventilation map when changes in respiratory effort are large.« less

Enhancement of yield strength in zirconium metal through high-pressure induced structural phase transition

NASA Astrophysics Data System (ADS)

Zhao, Yusheng; Zhang, Jianzhong

2007-11-01

We report here a high-pressure phase-transition induced strengthening in ultrapure zirconium metal. The determined yield strength shows more than sixfold abrupt increase at the transition pressure of Pc=6GPa, from σyα≈180MPa in the low-pressure phase of α-Zr to σyω≈1180MPa in the high-pressure phase of ω-Zr. The observed enhancement provides an alternate route for material strengthening and is the most significant among the known strengthening techniques for metals. Our findings support the theoretical simulations of the substantial covalent bonding and "rougher" corrugation of slip planes for dislocations in the ω-phase of zirconium.

Diffusion Properties and 3D Architecture of Human Lower Leg Muscles Assessed with Ultra-High-Field-Strength Diffusion-Tensor MR Imaging and Tractography: Reproducibility and Sensitivity to Sex Difference and Intramuscular Variability.

PubMed

Fouré, Alexandre; Ogier, Augustin C; Le Troter, Arnaud; Vilmen, Christophe; Feiweier, Thorsten; Guye, Maxime; Gondin, Julien; Besson, Pierre; Bendahan, David

2018-05-01

Purpose To demonstrate the reproducibility of the diffusion properties and three-dimensional structural organization measurements of the lower leg muscles by using diffusion-tensor imaging (DTI) assessed with ultra-high-field-strength (7.0-T) magnetic resonance (MR) imaging and tractography of skeletal muscle fibers. On the basis of robust statistical mapping analyses, this study also aimed at determining the sensitivity of the measurements to sex difference and intramuscular variability. Materials and Methods All examinations were performed with ethical review board approval; written informed consent was obtained from all volunteers. Reproducibility of diffusion tensor indexes assessment including eigenvalues, mean diffusivity, and fractional anisotropy (FA) as well as muscle volume and architecture (ie, fiber length and pennation angle) were characterized in lower leg muscles (n = 8). Intramuscular variability and sex differences were characterized in young healthy men and women (n = 10 in each group). Student t test, statistical parametric mapping, correlation coefficients (Spearman rho and Pearson product-moment) and coefficient of variation (CV) were used for statistical data analysis. Results High reproducibility of measurements (mean CV ± standard deviation, 4.6% ± 3.8) was determined in diffusion properties and architectural parameters. Significant sex differences were detected in FA (4.2% in women for the entire lower leg; P = .001) and muscle volume (21.7% in men for the entire lower leg; P = .008), whereas architecture parameters were almost identical across sex. Additional differences were found independently of sex in diffusion properties and architecture along several muscles of the lower leg. Conclusion The high-spatial-resolution DTI assessed with 7.0-T MR imaging allows a reproducible assessment of structural organization of superficial and deep muscles, giving indirect information on muscle function. © RSNA, 2018 Online supplemental material is

The relation of the yield stress of high-pressure anvils to the pressure attained at yielding and the ultimate attainable pressure

NASA Technical Reports Server (NTRS)

Panda, P. C.; Ruoff, A. L.

1979-01-01

A sensitive microprofilometer was used to determine the onset of yielding in the anvils of a supported opposed anvil device for the case of 3% cobalt-cemented tungsten carbide as the anvil material. In addition, it is shown how the commencement of yielding in boron carbide pistons, the yield strength being known, can be used to obtain the transition pressure to a conducting phase in gallium phosphide. The transition pressures of bismuth and gallium phosphide are obtained and it is found that these transitions are extremely close to the maximum attainable pressure in, respectively, a maraging steel and a 3% cobalt-cemented tungsten carbide.

A new paradigm for reproducing and analyzing N-body simulations of planetary systems

NASA Astrophysics Data System (ADS)

Rein, Hanno; Tamayo, Daniel

2017-05-01

The reproducibility of experiments is one of the main principles of the scientific method. However, numerical N-body experiments, especially those of planetary systems, are currently not reproducible. In the most optimistic scenario, they can only be replicated in an approximate or statistical sense. Even if authors share their full source code and initial conditions, differences in compilers, libraries, operating systems or hardware often lead to qualitatively different results. We provide a new set of easy-to-use, open-source tools that address the above issues, allowing for exact (bit-by-bit) reproducibility of N-body experiments. In addition to generating completely reproducible integrations, we show that our framework also offers novel and innovative ways to analyse these simulations. As an example, we present a high-accuracy integration of the Solar system spanning 10 Gyr, requiring several weeks to run on a modern CPU. In our framework, we can not only easily access simulation data at predefined intervals for which we save snapshots, but at any time during the integration. We achieve this by integrating an on-demand reconstructed simulation forward in time from the nearest snapshot. This allows us to extract arbitrary quantities at any point in the saved simulation exactly (bit-by-bit), and within seconds rather than weeks. We believe that the tools we present in this paper offer a new paradigm for how N-body simulations are run, analysed and shared across the community.

Semiconductor Seeded Nanorods with Graded Composition Exhibiting High Quantum-Yield, High Polarization, and Minimal Blinking.

PubMed

Hadar, Ido; Philbin, John P; Panfil, Yossef E; Neyshtadt, Shany; Lieberman, Itai; Eshet, Hagai; Lazar, Sorin; Rabani, Eran; Banin, Uri

2017-04-12

Seeded semiconductor nanorods represent a unique family of quantum confined materials that manifest characteristics of mixed dimensionality. They show polarized emission with high quantum yield and fluorescence switching under an electric field, features that are desirable for use in display technologies and other optical applications. So far, their robust synthesis has been limited mainly to CdSe/CdS heterostructures, thereby constraining the spectral tunability to the red region of the visible spectrum. Herein we present a novel synthesis of CdSe/Cd 1-x Zn x S seeded nanorods with a radially graded composition that show bright and highly polarized green emission with minimal intermittency, as confirmed by ensemble and single nanorods optical measurements. Atomistic pseudopotential simulations elucidate the importance of the Zn atoms within the nanorod structure, in particular the effect of the graded composition. Thus, the controlled addition of Zn influences and improves the nanorods' optoelectronic performance by providing an additional handle to manipulate the degree confinement beyond the common size control approach. These nanorods may be utilized in applications that require the generation of a full, rich spectrum such as energy-efficient displays and lighting.

Specific Yield--Column drainage and centrifuge moisture content

USGS Publications Warehouse

Johnson, A.I.; Prill, R.C.; Morris, D.A.

1963-01-01

The specific yield of a rock or soil, with respect to water, is the ratio of (1) the volume of water which, after being saturated, it will yield by gravity to (2) its own volume. Specific retention represents the water retained against gravity drainage. The specific yield and retention when added together are equal to the total interconnected porosity of the rock or soil. Because specific retention is more easily determined than specific yield, most methods for obtaining yield first require the determination of specific retention. Recognizing the great need for developing improved methods of determining the specific yield of water-bearing materials, the U.S. Geological Survey and the California Department of Water Resources initiated a cooperative investigation of this subject. The major objectives of this research are (1) to review pertinent literature on specific yield and related subjects, (2) to increase basic knowledge of specific yield and rate of drainage and to determine the most practical methods of obtaining them, (3) to compare and to attempt to correlate the principal laboratory and field methods now commonly used to obtain specific yield, and (4) to obtain improved estimates of specific yield of water-bearing deposits in California. An open-file report, 'Specific yield of porous media, an annotated bibliography,' by A. I. Johnson, D. A. Morris, and R. C. Prill, was released in 1960 in partial fulfillment of the first objective. This report describes the second phase of the specific-yield study by the U.S. Geological Survey Hydrologic Laboratory at Denver, Colo. Laboratory research on column drainage and centrifuge moisture equivalent, two methods for estimating specific retention of porous media, is summarized. In the column-drainage study, a wide variety of materials was packed into plastic columns of 1- to 8-inch diameter, wetted with Denver tap water, and drained under controlled conditions of temperature and humidity. The effects of cleaning the

77 FR 55880 - Prudential Short Duration High Yield Fund, Inc. and Prudential Investments LLC; Notice of...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-11

... High Yield Fund, Inc. (``Initial Fund'') and Prudential Investments LLC (``PI'' or the ``Adviser... investment company currently advised or to be advised in the future by PI (including any successor in... 2(a)(9) of the Act) with PI (such entities, together with PI, the ``Advisers'') that decides in the...