Yield Of Varieties Research Articles

Synthesis of Filibuvir. Part II. Second-Generation Synthesis of a 6,6-Disubstituted 2H-Pyranone via Dieckmann Cyclization of a β-Acetoxy Ester

This paper describes an improved sequence for the conversion of an oxazolidinone (3) to a β-keto lactone (5). The primary drivers behind this change were the modest and variable yields observed in the intramolecular cyclization to generate the β-keto lactone. Changing the cyclization substrate from oxazolidinone to alkyl ester offered a significantly improved cyclization, as well as improvements in the alkyne hydrogenation. Selection of the optimal substrates for methanolysis and intermediate salt formation are also described.

Yield and economic performance of organic and conventional cotton-based farming systems--results from a field trial in India.

The debate on the relative benefits of conventional and organic farming systems has in recent time gained significant interest. So far, global agricultural development has focused on increased productivity rather than on a holistic natural resource management for food security. Thus, developing more sustainable farming practices on a large scale is of utmost importance. However, information concerning the performance of farming systems under organic and conventional management in tropical and subtropical regions is scarce. This study presents agronomic and economic data from the conversion phase (2007–2010) of a farming systems comparison trial on a Vertisol soil in Madhya Pradesh, central India. A cotton-soybean-wheat crop rotation under biodynamic, organic and conventional (with and without Bt cotton) management was investigated. We observed a significant yield gap between organic and conventional farming systems in the 1st crop cycle (cycle 1: 2007–2008) for cotton (−29%) and wheat (−27%), whereas in the 2nd crop cycle (cycle 2: 2009–2010) cotton and wheat yields were similar in all farming systems due to lower yields in the conventional systems. In contrast, organic soybean (a nitrogen fixing leguminous plant) yields were marginally lower than conventional yields (−1% in cycle 1, −11% in cycle 2). Averaged across all crops, conventional farming systems achieved significantly higher gross margins in cycle 1 (+29%), whereas in cycle 2 gross margins in organic farming systems were significantly higher (+25%) due to lower variable production costs but similar yields. Soybean gross margin was significantly higher in the organic system (+11%) across the four harvest years compared to the conventional systems. Our results suggest that organic soybean production is a viable option for smallholder farmers under the prevailing semi-arid conditions in India. Future research needs to elucidate the long-term productivity and profitability, particularly of cotton and wheat, and the ecological impact of the different farming systems.

Estimating maximum land use change potential from a regional biofuel industry

The maximum amount of land for growing switchgrass for ethanol is estimated for a region in the southeastern U.S. Breakeven capacities are calculated for land in row crops, hay, pasture and marginal land. Characteristics of land categories inform potential land use change impacts as well as switchgrass profitability. Variable yields within and across land categories are translated into distributions of switchgrass net revenue. Breakeven curves are generated for a range of switchgrass prices. These curves provide upper bounds for further analysis of actual switchgrass adoption in context of broader economic forces and possible policy mechanisms to minimize environmental impacts. A farm-gate price of $55Mg−1 is estimated for half of marginal and pasturelands to break even with switchgrass. At this price, only 20% of land in hay and a small fraction of row crop hectares break even. Half of hay and row crops hectares break even at approximately $90Mg−1 and $100Mg−1, respectively. At $60Mg−1, sufficient land area can profitably produce switchgrass for ethanol to displace approximately 10% of gasoline consumed in Georgia, North Carolina, and South Carolina; however, this price only indicates breakeven capacity implying that higher prices may be necessary to realize 10% displacement.

Synthetic Core Promoters for Pichia pastoris

Synthetic promoters are commonly used tools for circuit design or high level protein production. Promoter engineering efforts in yeasts, such as Saccharomyces cerevisiae and Pichia pastoris have mostly been focused on altering upstream regulatory sequences such as transcription factor binding sites. In higher eukaryotes synthetic core promoters, directly needed for transcription initiation by RNA Polymerase II, have been successfully designed. Here we report the first synthetic yeast core promoter for P. pastoris, based on natural yeast core promoters. Furthermore we used this synthetic core promoter sequence to engineer the core promoter of the natural AOX1 promoter, thereby creating a set of core promoters providing a range of different expression levels. As opposed to engineering strategies of the significantly longer entire promoter, such short core promoters can directly be added on a PCR primer facilitating library generation and are sufficient to obtain variable expression yields.

ChemInform Abstract: Coupling of Benzyl Halides with Aryl Grignard Reagents Catalyzed by Iron(III) Amine‐bis(phenolate) Complexes.

AbstractThe title reaction affords diarylmethanes (III) in highly variable yields and significant amounts of homo‐coupled by‐products.

Toward the Guidance of Transbronchial Biopsy: Identifying Pulmonary Nodules With Optical Coherence Tomography

Solitary pulmonary nodules (SPNs) frequently require transbronchial needle aspiration (TBNA) or biopsy to determine malignant potential, but have variable diagnostic yields. Confirming needle placement within SPNs during TBNA could significantly increase diagnostic yield. Optical coherence tomography (OCT) provides nondestructive, high-resolution, microstructural imaging with potential to distinguish SPN from parenchyma. We have developed needle-based OCT probes compatible with TBNA. Before OCT can play any significant role in guiding clinical TBNA, OCT interpretation criteria for differentiating SPN from lung parenchyma must be developed and validated. OCT of SPN and parenchyma was performed on 111 ex vivo resection specimens. OCT criteria for parenchyma and SPN were developed and validated in a blinded assessment. Six blinded readers (two pulmonologists, two pathologists, and two OCT experts) were trained on imaging criteria in a 15-min training session prior to interpreting the validation data set. OCT of lung parenchyma displayed evenly spaced signal-void alveolar spaces, signal-intense backreflections at tissue-air interfaces, or both. SPNs lacked both of these imaging features. Independent validation of OCT criteria by the six blinded readers demonstrated sensitivity and specificity of 95.4% and 98.2%, respectively. We have developed and validated OCT criteria for lung parenchyma and SPN with sensitivity and specificity > 95% in this ex vivo study. We anticipate that OCT could be a useful complementary imaging modality to confirm needle placement during TBNA to potentially increase diagnostic yield.

The Cre/loxP recombination system for production of infectious mouse polyomavirus

Murine polyomavirus mutants are frequently produced for experimental as well as therapy purposes. Commonly used methods for preparation of mutant viral genomes from recombinant vectors are laborious and give variable yields and quality. We describe an efficient and reproducible Cre/loxP-mediated recombination system that generates polyomavirus genomes from recombinant plasmid in vivo. We designed and constructed two variants of recombinant vectors containing the wild-type polyomavirus genome flanked by loxP homologous sites. The loxP sites were introduced either into the intronic region of early genes or between the two poly(A) signal sites of convergent transcriptional units. After cotransfection of the recombinant plasmids with the Cre-expressing vector into mouse 3T6 cells, we obtained infectious virus from the genome variant containing loxP site in the intronic region, but we failed to isolate any infectious virus from the viral genome containing loxP site between poly(A) signals. We show that the Cre/loxP-based method of polyomavirus production is simple, expedient, and reproducible and works with satisfactory efficiency.

Synthesis, characterization and biological evaluation of acetazolamide, cycloserine and isoniazid condensed some novel phthalimide derivatives

In the present study, a series of novel phthalimide derivatives synthesized because of its potent antimicrobial and antimycobacterial activity. Structurally modified phthalimide derivatives were prepared through condensation of substituted phthalic anhydride with corresponding acetazolamide, cycloserine and isoniazid with variable yields. Synthesized Compounds (6a–d), (7a–d) and (8a–d) analyzed for their structures, in vitro antimicrobial and antimycobacterial activity. Among the synthesized compounds, compound 6b, 7b and 8b was found to be the most potent against Gram-positive bacteria Bacillus subtilis , Gram-negative bacteria Escherichia coli , Mycobacterium tuberculosis CIP and M. tuberculosis H37Rv. A series of novel phthalimide derivatives of biological interest were synthesized and analyzed, suggests that it an interesting compound compared to the current therapeutic agents and are considered to investigate further for the same.

A 1D model for describing ion cyclotron resonance heating at arbitrary cyclotron harmonics in tokamak plasmas

Both at low and higher cyclotron harmonics, properly accounting for finite Larmor radius effects is crucial in many ion cyclotron resonance frequency heating scenario's creating high energy tails. This paper discusses an extension TOMCAT-U of the 1D TOMCAT tokamak plasma wave equation solver (Van Eester and Koch 1998 Plasma Phys. Control. Fusion 40 1949) to arbitrary harmonics and arbitrary wavelengths while only keeping leading order terms in equilibrium variation terms. Rather than adopting the particle position, the guiding center position is used as the independent variable when writing down an expression for the dielectric response that is suitable for numerical application. This choice of independent variable yields intuitive expressions involving the Kennel–Engelmann operator which can directly be linked to the corresponding expressions in the RF diffusion operator appearing in the Fokker–Planck equation. It also guarantees that a positive definite power transfer from waves to particles is ensured for any of the wave modes in a plasma in which all populations have a Maxwellian distribution, as is expected from first principles. Rather than relying on a truncated Taylor series expansion of the dielectric response, an integrodifferential approach that retains all finite Larmor radius effects is proposed. To keep the required computation time for this generalized description reasonable, tabulation of integrals is intensively used. Although the accent is on the presentation of the upgraded formalism as well as the adopted recursions and tabulations, a few examples are provided to illustrate the potential of the new wave code that relies on these tabulations.

Cryobiopsy: Should This Be Used in Place of Endobronchial Forceps Biopsies?

Forceps biopsies of airway lesions have variable yields. The yield increases when combining techniques in order to collect more material. With the use of cryotherapy probes (cryobiopsy) larger specimens can be obtained, resulting in an increase in the diagnostic yield. However, the utility and safety of cryobiopsy with all types of lesions, including flat mucosal lesions, is not established. Aims. Demonstrate the utility/safety of cryobiopsy versus forceps biopsy to sample exophytic and flat airway lesions. Settings and Design. Teaching hospital-based retrospective analysis. Methods. Retrospective analysis of patients undergoing cryobiopsies (singly or combined with forceps biopsies) from August 2008 through August 2010. Statistical Analysis. Wilcoxon signed-rank test. Results. The comparative analysis of 22 patients with cryobiopsy and forceps biopsy of the same lesion showed the mean volumes of material obtained with cryobiopsy were significantly larger (0.696 cm3 versus 0.0373 cm3, P = 0.0014). Of 31 cryobiopsies performed, one had minor bleeding. Cryopbiopsy allowed sampling of exophytic and flat lesions that were located centrally or distally. Cryobiopsies were shown to be safe, free of artifact, and provided a diagnostic yield of 96.77%. Conclusions. Cryobiopsy allows safe sampling of exophytic and flat airway lesions, with larger specimens, excellent tissue preservation and high diagnostic accuracy.

On the design of clone-based haplotyping

BackgroundHaplotypes are important for assessing genealogy and disease susceptibility of individual genomes, but are difficult to obtain with routine sequencing approaches. Experimental haplotype reconstruction based on assembling fragments of individual chromosomes is promising, but with variable yields due to incompletely understood parameter choices.ResultsWe parameterize the clone-based haplotyping problem in order to provide theoretical and empirical assessments of the impact of different parameters on haplotype assembly. We confirm the intuition that long clones help link together heterozygous variants and thus improve haplotype length. Furthermore, given the length of the clones, we address how to choose the other parameters, including number of pools, clone coverage and sequencing coverage, so as to maximize haplotype length. We model the problem theoretically and show empirically the benefits of using larger clones with moderate number of pools and sequencing coverage. In particular, using 140 kb BAC clones, we construct haplotypes for a personal genome and assemble haplotypes with N50 values greater than 2.6 Mb. These assembled haplotypes are longer and at least as accurate as haplotypes of existing clone-based strategies, whether in vivo or in vitro.ConclusionsOur results provide practical guidelines for the development and design of clone-based methods to achieve long range, high-resolution and accurate haplotypes.

Streptavidin binding bifunctional aptamers and their interaction with low molecular weight ligands

This paper describes the measurement of the binding affinities of two bifunctional RNA aptamers to their respective ligands. The aptamers comprise either a theophylline or malachite green binding sequence fused to a streptavidin binding sequence. These bifunctional aptamers are shown to bind simultaneously to both the small ligand and to streptavidin whether in free solution or on gold surfaces. Binding isotherms for both interactions were measured by different physiochemical techniques: surface plasmon resonance, fluorescence spectroscopy and dynamic light scattering. Both qualitatively and quantitatively there is little difference in binding affinities between the bifunctional aptamers and their monofunctional components. The respective Kd values for streptavidin binding in the monofunctional aptamer and in the theophylline bifunctional aptamer were 12nM and 65nM, respectively whilst the Kd values for theophylline binding in the monofunctional aptamer and the streptavidin bifunctional aptamer were 300nM and 120nM. These results are consistent with treating each aptamer sequence as a module that can be combined with others without significant loss of function. This allows for the use of streptavidin based immobilization strategies without either the cost of biotinylated dNTPs or the variable yields associated with the chemical biotinylation of RNA.

Naphthalene and Anthracene Cobaltates(1−): Useful Storable Sources of an Atomic Cobalt Anion

Reductions of CoBr(2) or cobaltocene by 3 equiv of potassium anthracene radical anion in tetrahydrofuran (THF) afford 60-80% yields of bis(anthracene)cobaltate(1-) (1), of interest as a readily accessible and quite labile source of spin-paired atomic Co(-). Although the unsolvated potassium salt of 1 is thermally unstable at 20 °C, the [K(18-crown-6)(THF)(2)](+) salt of 1 functions as a useful storable crystalline reagent for Co(-) in several reactions. Previously known classic cobaltates, [CoL(4)](-), for L = 1/2 (1,3-butadiene) (2), PF(3) (3), and P(OiPr)(3) (5), were obtained directly from 1 and structurally characterized for the first time. Anion 3 is noteworthy because it appears to possess the shortest known Co-P distance, av = 2.012(4) Å. Although the naphthalene analogue of 1 is not yet available as a pure substance, low-temperature reductions of CoBr(2) or cobaltocene by naphthalene radical anion in the presence of 1,5-cyclooctadiene (COD) afford variable yields (80-90% from CoCp(2)) of (naphthalene)(COD)cobaltate(1-) (10). Ready displacement of naphthalene in 10 by L = 1,3-butadiene, 2,2'-bipyridine, and COD occurs to give good yields of the respective [Co(L)(COD)](-), all of which have been structurally characterized. Both ligands in 10 are displaced by tert-butylisocyanide to afford [Co(CNtBu)(4)](-) (16), the first isolable and structurally characterized homoleptic alkylisocyanometalate. The molecular structure of 16 shows unprecedented bending of the isocyanides, av C-N-C = 137(2)°, for homoleptic isocyanide complexes.

A Mathematical Model Related To Chemostat With Variable Yields

In this paper, a three dimensional chemostat model with variable yields is studied. The properties of the steady state points, the local and global stability, the Hopf bifurcation and the positive invariant set for the system are investigated by qualitative analysis of differential equations.DOI: http://dx.doi.org/10.3329/dujs.v60i2.11482 Dhaka Univ. J. Sci. 60(2): 147-152, 2012 (July)

Gaps between farmer and attainable yields across rainfed sunflower growing regions of Argentina

We computed three estimators of attainable yield for each of between 5 and 8 rainfed sunflower-growing regions of Argentina using between 5 and 9 years of data over the 2000–2007 interval. The estimators were based on comparative yield trial (CYT) data for commercial hybrids, on individual commercial field (ICF) data, and on reporting district (RD) yield information. Contrasts between these estimators led us to prefer the attainable (CYT) yield estimator over the other two. Attainable (CYT) yields ranged from 2.21 to 2.83tha−1 across regions. Yield gaps between mean farmer (RD data) and attainable (CYT) yields were computed using best linear unbiased estimator (BLUE) values for both variables obtained using mixed linear models. These gaps were statistically significant (p≤0.05) for all 8 regions and ranged from 0.37 to 1.18tha−1 across regions, for a country average of 0.75tha−1, equivalent to 41% of the mean country yield of 1.85tha−1. We also used CYT data to examine the issue of recurrent, albeit infrequent, reports of unusually high yields. Mean yields for the top decile of comparative yield trial data ranged from 3.2 to 4.2tha−1 across regions, and the highest yields for this decile in any of the years of record ranged from 3.9 to 4.8tha−1 across regions. Individual commercial field yields were available for 5 regions. Gaps between BLUEs for this variable and attainable (CYT) yields were smaller than those between reporting district and attainable (CYT) yields, but were nevertheless significant in all 5 regions. A notable feature of reporting district, individual field, and yield trial data was their variability. At reporting district level within regions, contributions of spatial and temporal variability were roughly similar. The mean relative contribution of the trial effect to non-error variance of the CYT data exceeded 85% across regions, dominating the contributions of genotype and of genotype by trial effects. We conclude that the magnitude of mean farmer/attainable (CYT) yield gaps for this crop in Argentina justifies further research aimed at reducing regional gaps; and that CYT data can be used to generate an appropriate benchmark for attainable yields.

Competitive Exclusion for Chemostat Equations with Variable Yields

In this paper, we study the global dynamics of a chemostat model with a single nutrient and several competing species. Growth rates are not required to be proportional to food uptakes. Our approach is based on the construction of Lyapunov functions. The Lyapunov functions extend those used by Hsu (SIAM J. Appl. Math. 34:760–763, 1978) and by Wolkowicz and Lu (SIAM J. Appl. Math. 57:1019–1043, 1997) in the case when growth rates are proportional to food uptakes. Our result generalizes a large variety of previous results obtained by Lyapunov techniques.

An integrated model for assessment of sustainable agricultural residue removal limits for bioenergy systems

Agricultural residues have been identified as a significant potential resource for bioenergy production, but serious questions remain about the sustainability of harvesting residues. Agricultural residues play an important role in limiting soil erosion from wind and water and in maintaining soil organic carbon. Because of this, multiple factors must be considered when assessing sustainable residue harvest limits. Validated and accepted modeling tools for assessing these impacts include the Revised Universal Soil Loss Equation Version 2 (RUSLE2), the Wind Erosion Prediction System (WEPS), and the Soil Conditioning Index. Currently, these models do not work together as a single integrated model. Rather, use of these models requires manual interaction and data transfer. As a result, it is currently not feasible to use these computational tools to perform detailed sustainable agricultural residue availability assessments across large spatial domains or to consider a broad range of land management practices. This paper presents an integrated modeling strategy that couples existing datasets with the RUSLE2 water erosion, WEPS wind erosion, and Soil Conditioning Index soil carbon modeling tools to create a single integrated residue removal modeling system. This enables the exploration of the detailed sustainable residue harvest scenarios needed to establish sustainable residue availability. Using this computational tool, an assessment study of residue availability for the state of Iowa was performed. This study included all soil types in the state of Iowa, four representative crop rotation schemes, variable crop yields, three tillage management methods, and five residue removal methods. The key conclusions of this study are that under current management practices and crop yields nearly 26.5 million Mg of agricultural residue are sustainably accessible in the state of Iowa, and that through the adoption of no till practices residue removal could sustainably approach 40 million Mg. However, when considering the economics and logistics of residue harvest, yields below 2.25 Mg ha−1 are generally considered to not be viable for a commercial bioenergy system. Applying this constraint, the total agricultural residue resource available in Iowa under current management practices is 19 million Mg. Previously published results have shown residue availability from 22 million Mg to over 50 million Mg in Iowa.

Synthesis and antimycobacterial activity of some phthalimide derivatives

Structurally modified phthalimide derivatives were prepared through condensation of phthalic and tetrafluorophthalic anhydride with selected sulfonamides with variable yields. All compounds were screened for their antimycobacterium activity against Mycobacterium tuberculosis H37Ra (ATCC 25177) using a micro broth dilution technique. The fluorinated derivatives (compounds 2c, 2d, 2f and 2h) had antimycobacterium activity comparable with classical sulfonamide drugs. The minimum inhibitory concentration (MIC) of compounds 2c, 2d, 2f and 2h was greater than that of isoniazid (MIC<0.02μg/mL) and in vitro activity was greater than that of pyrazinamide, another first line antimycobacterium drug (MIC 50–100μg/mL). The new compounds could be considered new lead compounds in the treatment of multi-drug resistant tuberculosis.

Effects of farmers’ cultural practices on the weedy rice infestation and rice production

An on-farm trial was conducted at the Muda Agricultural Development Authority rice fields, Kedah, Peninsular Malaysia from November, 2003 to July, 2006 to study the impacts of farmers’ cultural practices on the weedy rice infestation and rice production. Five sample farmers (A, B, C, D and E) from five different sampling sites were selected on the basis of severity of weedy rice infestation on their fields in earlier seasons. Field observations and monitoring were carried out for collecting data and recording the agronomic practices done by the farmers from land preparation to harvesting of the crops. The number of weedy rice panicles per unit area was recorded from 50 sampling spots per plot using 1 × 1 m quadrat. Rice plants and the weedy rice within the quadrats were harvested. Data on grain yields and yield components were recorded. The collected data were analyzed statistically and mean differences in weed infestation were adjudged using standard error of means. Results revealed that the farmers used different rice varieties and applied different agronomic practices, which resulted in variable intensities of weedy rice infestations and production of variable rice grain yields. The farmers A and B, who followed transplanting and water seeding for crop establishment, applied pre-planting herbicides (2 to 3 times) during land preparation and used regular surveillance and monitoring (20 to 25 times) of their plots, had less weedy rice infestation (32.22 panicles/m2) and higher rice yields (6.70 to 8.88 t/ha). The farmers C, D and E, used wet direct seeding for crop establishment, applied no or less time of pre-planting herbicides (1 time) and had less field surveillance (10 to 15 times/season), had consequently a higher weedy rice panicle density (154.94 panicles/m2) and less rice yields (3.57 to 6.27 t/ha). Key words: Farmers’ cultural practice, weedy rice infestation, wet direct seeding, water seeding, transplanting.

Palladium(II)-catalyzed oxidative homo-coupling of 1,3-dimethyluracil derivatives

A palladium-catalyzed oxidative homo-coupling of 1,3-dimethyluracil was examined. Two types of uracil dimer, C5–C5′ linked dimer and C5–C6′ linked dimer were obtained in variable yields depending on the conditions along with a low yield of C5–C5′ and C6–C5′ linked uracil trimer.