On Ribosome Load, Codon Bias and Protein Abundance

Different codons encoding the same amino acid are not used equally in protein-coding sequences. In bacteria, there is a bias towards codons with high translation rates. This bias is most pronounced in highly expressed proteins, but a recent study of synthetic GFP-coding sequences did not find a correlation between codon usage and GFP expression, suggesting that such correlation in natural sequences is not a simple property of translational mechanisms. Here, we investigate the effect of evolutionary forces on codon usage. The relation between codon bias and protein abundance is quantitatively analyzed based on the hypothesis that codon bias evolved to ensure the efficient usage of ribosomes, a precious commodity for fast growing cells. An explicit fitness landscape is formulated based on bacterial growth laws to relate protein abundance and ribosomal load. The model leads to a quantitative relation between codon bias and protein abundance, which accounts for a substantial part of the observed bias for E. coli. Moreover, by providing an evolutionary link, the ribosome load model resolves the apparent conflict between the observed relation of protein abundance and codon bias in natural sequences and the lack of such dependence in a synthetic gfp library. Finally, we show that the relation between codon usage and protein abundance can be used to predict protein abundance from genomic sequence data alone without adjustable parameters.

On Ribosome Load, Codon Bias and Protein Abundance

Different codons encoding the same amino acid are not used equally in protein-coding sequences. In bacteria, there is a bias towards codons with high translation rates. This bias is most pronounced in highly expressed proteins, but a recent study of synthetic GFP-coding sequences did not find a correlation between codon usage and GFP expression, suggesting that such correlation in natural sequences is not a simple property of translational mechanisms. Here, we investigate the effect of evolutionary forces on codon usage. The relation between codon bias and protein abundance is quantitatively analyzed based on the hypothesis that codon bias evolved to ensure the efficient usage of ribosomes, a precious commodity for fast growing cells. An explicit fitness landscape is formulated based on bacterial growth laws to relate protein abundance and ribosomal load. The model leads to a quantitative relation between codon bias and protein abundance, which accounts for a substantial part of the observed bias for E. coli. Moreover, by providing an evolutionary link, the ribosome load model resolves the apparent conflict between the observed relation of protein abundance and codon bias in natural sequences and the lack of such dependence in a synthetic gfp library. Finally, we show that the relation between codon usage and protein abundance can be used to predict protein abundance from genomic sequence data alone without adjustable parameters.

The Timeliness and Cost-Effectiveness of the Local and Regional Procurement of Food Aid

Local and regional procurement (LRP) of food aid is often claimed to lead to quicker and more cost-effective response. We generate timeliness and cost-effectiveness estimates by comparing US-funded LRP activities in nine countries against in-kind, transoceanic food aid shipments from the US to the same countries during the same timeframe. Procuring food locally or distributing cash or vouchers results in a time savings of nearly 14 weeks, a 62 percent gain. Cost-effectiveness varies significantly by commodity type. Procuring grains locally saved over 50 percent, on average, while local procurement of processed commodities was not always cost-effective. (C) 2013 Elsevier Ltd. All rights reserved.

Agricultural Policymaking: Interest Groups and Access to Governmental Officials

Conservation agriculture that focuses on soil recovery is both economically and environmentally sustainable. This lies in contrast with many of the current agricultural practices, which push for high production, which, in turn lead to over-depletion of the soil. Agricultural interest groups play a role in crafting farming policies with governmental officials. Therefore, my study examined three interest group types agribusinesses, farmer organizations, and environmental NGOs that seek to influence agricultural policy, specifically focusing on the federal farm bill, due to its large impact throughout the nation. The research in which data wasgathered through subject interviews, a literature review, and databases found that access to governmental officials affects the amount of influence a group can have. Access is contingent upon: 1) the number of networks (social, professional, and political), 2) amount of money spent through campaign contributions and lobbying expenditures, and 3) extent of business enterprises and subsidiaries. The evidence shows that there is a correlation between these variables and the extent of access. My research concludes that agribusiness interest groups have the most access to government officials, and thus have the greatest influence on agricultural policies. Because agribusinesses support subsidies of commodity-crops this indirectly impacts conservation agriculture, as the two programs compete in a zero-sum game for funding in the farm bills.

Potential and limitations of organic and fair trade cotton for improving livelihoods of smallholders: evidence from Central Asia

Cotton is a leading agricultural non-food commodity associated with soil degradation, water pollution and pesticide poisoning due to high levels of agrochemical inputs. Organic farming is often promoted as a means of addressing the economic, environmental and health risks of conventional cotton production, and it is slowly gaining ground in the global cotton market. Organic and fair trade cotton are widely seen as opportunities for smallholder farmers to improve their livelihoods thanks to higher returns, lower input costs and fewer risks. Despite an increasing number of studies comparing the profitability of organic and non-organic farming systems in developing and industrialized countries, little has been published on organic farming in Central Asia. The aim of this article is to describe the economic performance and perceived social and environmental impacts of organic cotton in southern Kyrgyzstan, drawing on a comparative field study conducted by the author in 2009. In addition to economic and environmental aspects, the study investigated farmers’ motivations toward and assessment of conversion to organic farming. Cotton yields on organic farms were found to be 10% lower, while input costs per unit were 42% lower; as a result, organic farmers’ cotton revenues were 20% higher. Due to lower input costs as well as organic and fair trade price premiums, the average gross margin from organic cotton was 27% higher. In addition to direct economic benefits, organic farmers enjoy other benefits, such as easy access to credit on favorable terms, provision of uncontaminated cottonseed cooking oil and cottonseed cake as animal feed, and marketing support as well as extension and training services provided by newly established organic service providers. The majority of organic farmers perceive improved soil quality, improved health conditions, and positively assess their initial decision to convert to organic farming. The major disadvantage of organic farming is the high manual labor input required. In the study area, where manual farm work is mainly women's work and male labor migration is widespread, women are most affected by this negative aspect of organic farming. Altogether, the results suggest that, despite the inconvenience of a higher workload, the advantages of organic farming outweigh its disadvantages and that conversion to organic farming improves the livelihoods of small-scale farmers.

Challenges for Participatory Conservation in Times of Global Change: Lessons from a Comparative Analysis and New Developments

Participatory approaches to conservation have been applied worldwide by governments and non-governmental organisations. However, results from a comparative analysis of the impacts of global change on management issues in 13 protected areas in Africa, Latin America, Asia, and Europe show that in many cases the involvement of local people has remained limited, and economic gains for local livelihoods have been limited or non-existent. Viewed from a ‘new institutionalist’ perspective and focusing on power relations and ideologies, the results of this study carried out within the framework of the Swiss National Centre of Competence in Research (NCCR) North-South show that in African cases local people do not feel part of the process and, therefore, become disengaged. In Asia, and even more so in Latin America, local indigenous peoples and their leaders support protected areas as a means to gain political rights over areas threatened by immigration. The European (Swiss) case is the only one where political rights and economic incentives present a context in which participation is of direct interest to local people. Meanwhile, recent debates on new global conservation developments in the context of climate change policy indicate a growing tendency to treat conservation as a commodity. We argue that this can have problematical effects on efforts to devolve power to the local level in the context of conservation.

Contemporary Hollywood And The Attention Economy

This thesis had two goals: to explore the transformation of Hollywood from the 1930s to present, and to investigate how Contemporary Hollywood functions in a growing attention economy. Evident in the types of films that it produces as well as its evolving industrial structure, Contemporary Hollywood significantly differs from the Classical Hollywood of the 1930s. New digital technologies like surround sound and computer-generated imagery (CGI) have allowed studios to create a different type of film like the blockbuster and to have more extensive control over their films. Additionally, growing exhibition and distribution platforms have also fundamentally altered the industrial landscape of Hollywood. In order to combat this more egalitarian distribution system, Contemporary Hollywood has turned to conglomeratization. But, what has caused such a radical shift in the form and function of Contemporary Hollywood and its films? This thesis argues that Hollywood is failing to thrive in this new media landscape¿not because of changing technologies¿but because of a changing consumer. Richard Lanham theorizes that we are living in a growing attention economy, where human attention is the most valuable commodity in such an information-saturated society. For the current consumer, there is near-constant media over-stimulation: he or she is exposed to any number of screens (mobile phones, laptops, tablets, televisions, etc.) at any given time. Because we can access anything from anywhere at anytime, we¿ve become somewhat schizophrenic and impatient in terms of the media that we consume in our lives.

The Crystallization Kinetics of Polylactic Acid (Pla) Processed Through Solid-State/Melt Extrusion

Polylactic acid (PLA) is a bio-derived, biodegradable polymer with a number of similar mechanical properties to commodity plastics like polyethylene (PE) and polyethylene terephthalate (PETE). There has recently been a great interest in using PLA to replace these typical petroleum-derived polymers because of the developing trend to use more sustainable materials and technologies. However, PLA¿s inherent slow crystallization behavior is not compatible with prototypical polymer processing techniques such as molding and extrusion, and in turn inhibits its widespread use in industrial applications. In order to make PLA into a commercially-viable material, there is a need to process the material in such a way that its tendency to form crystals is enhanced. The industry standard for producing PLA products is via twin screw extrusion (TSE), where polymer pellets are fed into a heated extruder, mixed at a temperature above its melting temperature, and molded into a desired shape. A relatively novel processing technique called solid-state shear pulverization (SSSP) processes the polymer in the solid state so that nucleation sites can develop and fast crystallization can occur. SSSP has also been found to enhance the mechanical properties of a material, but its powder output form is undesirable in industry. A new process called solid-state/melt extrusion (SSME), developed at Bucknell University, combines the TSE and SSSP processes in one instrument. This technique has proven to produce moldable polymer products with increased mechanical strength. This thesis first investigated the effects of the TSE, SSSP, and SSME polymer processing techniques on PLA. The study seeks to determine the process that yields products with the most enhanced thermal and mechanical properties. For characterization, percent crystallinity, crystallization half time, storage modulus, softening temperature, degradation temperature and molecular weight were analyzed for all samples. Through these characterization techniques, it was observed that SSME-processed PLA had enhanced properties relative to TSE- and SSSP-processed PLA. Because of the previous findings, an optimization study for SSME-processed PLA was conducted where throughput and screw design were varied. The optimization study determined PLA processed with a low flow rate and a moderate screw design in an SSME process produced a polymer product with the largest increase in thermal properties and a high retention of polymer structure relative to TSE-, SSSP-, and all other SSME-processed PLA. It was concluded that the SSSP part of processing scissions polymer chains, creating defects within the material, while the TSE part of processing allows these defects to be mixed thoroughly throughout the sample. The study showed that a proper SSME setup allows for both the increase in nucleation sites within the polymer and sufficient mixing, which in turn leads to the development of a large amount of crystals in a short period of time.

Hydrologic analysis of a limestone quarry using EPA's HELP Version 3.08 Model

Aggregates were historically a low cost commodity but with communities and governmental agencies reducing the amount of mining the cost is increasing dramatically. An awareness needs to be brought to communities that aggregate production is necessary for ensuring the existing infrastructure in today’s world. This can be accomplished using proven technologies in other areas and applying them to show how viable reclamation is feasible. A proposed mine reclamation, Douglas Township quarry (DTQ), in Dakota Township, MN was evaluated using Visual Hydrologic Evaluation of Landfill Performance (HELP) model. The HELP is commonly employed for estimating the water budget of a landfill, however, it was applied to determine the water budget of the DTQ following mining. Using an environmental impact statement as the case study, modeling predictions indicated the DTQ will adequately drain the water being put into the system. The height of the groundwater table will rise slightly due to the mining excavations but no ponding will occur. The application of HELP model determined the water budget of the DTQ and can be used as a viable option for mining companies to demonstrate how land can be reclaimed following mining operations.

ON THE DIGITAL-POLITICAL TOPOGRAPHY OF MUSIC

The persuasive power of music is often relegated to the dimension of pathos: that which moves us emotionally. Yet, the music commodity is now situated in and around the liminal spaces of digitality. To think about how music functions, how it argues across media, and how it moves us, we must examine its material and immaterial realities as they present themselves to us and as we so create them. This dissertation rethinks the relationship between rhetoric and music by examining the creation, performance, and distribution of music in its material and immaterial forms to demonstrate its persuasive power. While both Plato and Aristotle understood music as a means to move men toward virtue, Aristotle tells us in his Laws, through the Athenian Stranger, that the very best kinds of music can help guide us to truth. From this starting point, I assess the historical problem of understanding the rhetorical potential of music as merely that which directs or imitates the emotions: that which “Soothes the savage breast,” as William Congreve writes. By furthering work by Vickers and Farnsworth, who suggest that the Baroque fascination with applying rhetorical figures to musical figures is an insufficient framework for assessing the rhetorical potential of music, I demonstrate the gravity of musical persuasion in its political weight, in its violence—the subjective violence of musical torture at Guantanamo and the objective, ideological violence of music—and in what Jacques Attali calls the prophetic nature of music. I argue that music has a significant function, and as a non-discursive form of argumentation, works on us beyond affect. Moreover, with the emergence of digital music distribution and domestic digital recording technologies, the digital music commodity in its material and immaterial forms allows for ruptures in the former methods of musical composition, production, and distribution and in the political potential of music which Jacques Attali describes as being able to foresee new political realities. I thus suggest a new theoretical framework for thinking about rhetoric and music by expanding on Lloyd Bitzer’s rhetorical situation, by offering the idea of “openings” to the existing exigence, audience, and constraints. The prophetic and rhetorical power of music in the aleatoric moment can help provide openings from which new exigencies can be conceived. We must, therefore, reconsider the role of rhetorical-musical composition for the citizen, not merely as a tool for entertainment or emotional persuasion, but as an arena for engaging with the political.

Regulations on E-Commerce Consumer Protection Rules in China and Europe Compared – Same Same but Different?

This article provides a comprehensive overview of the regulations on e-commerce protection rules in China and the European Union. It starts by giving a general overview of different approaches towards consumer protection in e-commerce. This article then scrutinizes the current legal system in China by mainly focusing on SAIC’s “Interim Measures for the Administration of Online Commodity Trading and Relevant Service Activities”. The subsequent chapter covers the supervision of consumer protection in e-commerce in China, which covers both the regulatory objects of online commodity trading and the applied regulatory mechanisms. While the regulatory objects include operating agents, operating objects, operating behavior, electronic contracts, intellectual property and consumer protection, the regulatory mechanisms for e-commerce in China combines market mechanism and industry self-discipline under the government’s administrative regulation. Further, this article examines the current European legal system in online commodity trading. It outlines the aim and the scope of EU legislation in the respective field. Subsequently, the paper describes the European approach towards the supervision of consumer protection in e-commerce. As there is no central EU agency for consumer protection in e-commerce transactions, the EU stipulates a framework for Member States’ institutions, thereby creating a European supervisory network of Member States’ institutions and empowers private consumer organisations to supervise the market on their behalf. Moreover, the EU encourages the industry to self- or co-regulate e-commerce by providing incentives. Consequently, this article concludes that consumer protection may be achieved by different means and different systems. However, even though at first glance the Chinese and the European system appear to differ substantially, a closer look reveals tendencies of convergence between the two systems.

Exact Solutions to the Symmetric and Asymmetric Vehicle Routing Problem with Simultaneous Delivery and Pick-Up

In reverse logistics networks, products (e.g., bottles or containers) have to be transported from a depot to customer locations and, after use, from customer locations back to the depot. In order to operate economically beneficial, companies prefer a simultaneous delivery and pick-up service. The resulting Vehicle Routing Problem with Simultaneous Delivery and Pick-up (VRPSDP) is an operational problem, which has to be solved daily by many companies. We present two mixed-integer linear model formulations for the VRPSDP, namely a vehicle-flow and a commodity-flow model. In order to strengthen the models, domain-reducing preprocessing techniques, and effective cutting planes are outlined. Symmetric benchmark instances known from the literature as well as new asymmetric instances derived from real-world problems are solved to optimality using CPLEX 12.1.

Potential Economic Returns from Selling Beef in a Specified Value-Based Market

Three groups of steers--one theoretical group and two experimental groups—were evaluated for marketing cattle live, as boxed beef, and grade and yield when the live price was $71 to $73/cwt, grade and yield price $125/cwt for Choice yield grade 3 carcasses with $20/cwt discount for Select carcasses, and in a commodity-trim or close-trim boxed beef market. The results show that the value of highyielding steers can be significantly increased if sold in a close-trim boxed beef market. The close-trim premiums ranged from $5.06 per head for Select close-trim yield grade 4 carcasses to $87.18 per head for close-trim Choice yield grade 1 carcasses. A group of experimental steers averaging 82% Choice and 60% yield grades 1 and 2 returned an additional $104 in the close-trim boxed market compared with selling live for $73/cwt. Another group of experimental steers averaging 21% Choice, 18% Standard, and 93% yield grades 1 and 2 had $29 per head greater return than if the steers had been sold live for $71/cwt. These comparisons emphasize the importance of knowing how cattle will potentially grade before selecting an alternative marketing strategy. This prior knowledge is most important when the spread in price between Choice and Select is high. Producers need to learn more about their cattle to predict how the cattle may grade for a specified value-based market.

Use of Ultrasound Backfat Estimates to Form Marketing Groups Prior to Finishing for Feedlot Steers

An experiment was conducted using 95 Continental crossbred steers. The cattle were sorted by ultrasound 160 days before slaughter into a low backfat group (Low BF) and a higher backfat group (High BF). Half of the Low BF and half of the High BF were implanted whereas the other halves were not. Data from the experiment were used in two hypothetical markets. One market was a high yield beef program (HY) that did not allow the use of implants. The second market was a commodity beef program (CM) that allowed the use of implants. The cattle were priced as an unsorted group (ALL) and two sorted groups (Low BF and High BF) within the HY (non-implanted) and CM (implanted) markets. The CM program had a base price of $1.05/lb hot carcass weight (HCW) with a $0.15/lb HCW discount for quality grade (QG) Select and a $0.20/lb HCW discount for yield grade (YG) 4. The HY program used a base price of $1.07/lb HCW with premiums ($/lb HCW) paid for YG £ .9 (.15), 1.0 - 1.4 (.10), and 1.5 - 1.9 (.03). The carcasses were discounted ($/lb HCW) for YG 2.5 - 2.9 (.03), 3.0 - 3.9 (.15), and ³ 4.0 (.35). This data set provides good evidence that the end point at which to sell a group of cattle depends on the particular market. Sorting had an economic advantage over ALL in the HY Low BF and the CM High BF groups. The HY High BF cattle should have been sold sooner due to the discounts recieved for increased YG. The increased YG was directly affected by an increase in BF. Furthermore, the CM Low BF group should have been fed longer to increase the number of carcasses grading Choice.

Diet Roughage Ingredients for Newly Weaned Calves

Several commodity feeds that are high in fiber are available that may substitute for corn cobs in a complete starting ration. This study was designed to evaluate the use of soyhulls and sunflower meal as substitutes for corncobs as a roughage source for newly weaned calves. One-hundred-and-fifty calves from the ISU Rhodes Research Farm were weaned, weighed, sorted by sex, and stratified by weight to eight pens. Two pens of each sex were assigned to one of two diet treatments. Calves fed the corncob diet consumed two pounds more feed dry matter, gained 1.5 pounds more per day, and were more efficient the first 14 days on feed. The soyhull diet was quite fine in particle size, and some feed particle separation occurred in the bunk. Some compensatory performance may have occurred with the soyhull diet the second 14 days on feed, although no statistical differences existed. This suggests that palatability, feed presentation, and bunk characteristics are important considerations in selecting roughage sources for complete starting diets for newly weaned calves.