Phylogenetic MCMC algorithms are misleading on mixtures of trees   总被引：2，自引：0，他引：2  

Mossel E  Vigoda E 《Science (New York, N.Y.)》2005,309(5744):2207-2209

Markov chain Monte Carlo (MCMC) algorithms play a critical role in the Bayesian approach to phylogenetic inference. We present a theoretical analysis of the rate of convergence of many of the widely used Markov chains. For N characters generated from a uniform mixture of two trees, we prove that the Markov chains take an exponentially long (in N) number of iterations to converge to the posterior distribution. Nevertheless, the likelihood plots for sample runs of the Markov chains deceivingly suggest that the chains converge rapidly to a unique tree. Our results rely on novel mathematical understanding of the log-likelihood function on the space of phylogenetic trees. The practical implications of our work are that Bayesian MCMC methods can be misleading when the data are generated from a mixture of trees. Thus, in cases of data containing potentially conflicting phylogenetic signals, phylogenetic reconstruction should be performed separately on each signal.  相似文献   

Observation of polymer conformation hysteresis in extensional flow     

Schroeder CM  Babcock HP  Shaqfeh ES  Chu S 《Science (New York, N.Y.)》2003,301(5639):1515-1519

Highly extensible Escherichia coli DNA molecules in planar extensional flow were visualized in dilute solution by fluorescence microscopy. For a narrow range of flow strengths, the molecules were found in either a coiled or highly extended conformation, depending on the deformation history of the polymer. This conformation hysteresis persists for many polymer relaxation times and is due to conformation-dependent hydrodynamic forces. Polymer conformational free-energy landscapes were calculated from computer simulations and show two free-energy minima for flow strengths near the coil-stretch transition. Hysteresis cycles may directly influence bulk-solution stresses and the development of stress-strain relations for dilute polymer flows.  相似文献   

School food environments and the obesity issue: content,structural determinants,and agency in Canadian high schools     

Anthony Winson 《Agriculture and Human Values》2008,25(4):499-511

To understand the phenomenon of the rapidly increasing prevalence of overweight and obese children and youth, it is especially important to examine the school food environment, the role of structural factors in shaping this environment, and the resulting nutrition and health outcomes. The paper examines research on school food environments in the US and Canada. It notes evidence of widespread availability of poor nutrition products in both environments and delineates reasons for the situation, and examines initiatives presently being undertaken in a number of jurisdictions in both countries to encourage healthy eating in schools. Empirical data are presented from a pilot study of high schools in the Canadian province of Ontario. The study documents the extent of student purchasing of nutrient-poor foods and beverages, and the structural factors internal and external to the school that appear responsible for the availability of such products in food environments in this critical institutional sphere. The paper also examines positive local initiatives in high schools that seek to encourage healthy eating in schools.

Anthony WinsonEmail:

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Anthony Winson PhD   is a professor in the department of sociology and anthropology at the University of Guelph. He has written on agriculture, food and rural development, and restructuring issues related to Canada and the Third World for more than 20 years. Among his books are The Intimate Commodity: Food and the Development of the Agro-Industrial Complex in Canada (Garamond 1993) and, more recently, Contingent Work, Disrupted Lives (University of Toronto 2002, with Belinda Leach) which examines economic restructuring, the changing world of work, and the factors underlying sustainability in small manufacturing-dependent rural communities in several regions of Ontario. This book won the John Porter Book Prize of the Canadian Sociology and Anthropology Association for 2003. Dr. Winson’s current work is focused on the analysis of factors shaping the contemporary Canadian food environment and their role in producing what has been termed the “epidemic of obesity.” Particular attention is being paid to supermarkets and schools as part of broader-ranging research on the political economic context of the food environment.  相似文献   

The illusion of control: industrialized agriculture,nature, and food safety   总被引：1，自引：0，他引：1  

Diana Stuart 《Agriculture and Human Values》2008,25(2):177-181

I explore the role of nature in the agrifood system and how attempts to fit food production into a large-scale manufacturing model has lead to widespread outbreaks of food borne illness. I illustrate how industrial processing of leafy greens is related to the outbreak of E. coli 0157:H7 associated with spinach in the fall of 2006. I also use this example to show how industry attempts to create the illusion of control while failing to address weaknesses in current processing systems. The leafy greens industry has focused efforts on sterilizing the growing environment and adopting new technologies, while neglecting to change the concentrated structure of processing systems. Repeated breakdowns in these systems illustrate a widening fault line between attempted and failed control of nature in industrial food production.

Diana StuartEmail:

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Growth and fatty acid composition of sesame (<Emphasis Type="Italic">Sesamum indicum</Emphasis> L.) genotypes as influence by planting dates and nitrogen fertilization in semiarid region of Northwest,Pakistan     

Shahzad Ali  Amanullah Jan  Jia Zhikuan  Amir Sohail  Cai Tie  Wei Ting  Zhang Peng  Manzoor  Irshad Ahmad  Mati Ur Rahman  Ren Xiaolong  Liu Xiaoli  Xu Yue Yue 《Russian Agricultural Sciences》2016,42(3-4):224-229

A field experiment was conducted on silty clay loam soil in the years 2011–2012. Two sesame (Sesamum indicum L.) cultivars (Local Black and Local White) were evaluated using various 3 different sowing dates (20th June, 10th and 30th July) and four agrotechnical level (0, 40, 80 and 120 kg N ha^–1) at New Developmental Farm The University of Agriculture, Peshawar, Pakistan. The objective of this study was to evaluate the effects of sowing dates on growth, yield and oil fatty acid composition of two sesame cultivars grown under different nitrogen fertilization. Results showed that cv. Local Black was characterized by significantly higher content of oil (47%), seed yield (696 kg ha^–1) and oil yield (335 kg ha^–1) while cv. Local White had higher palmitic acid (8%) and linoleic acid (38.7%). Yield and its main components were positively affected by the earlier sowing date. With regard to fatty acid composition, a decrease in oleic and stearic acid and an increase in linoleic and palmitic acid were observed. At early sowing, oleic and palmitic acid decreased whereas linoleic and stearic acid increased. The decrease in the oleic/linoleic acid ratio observed at early sowing, suggests a possible role of temperature on the activity of oleate desaturase in the developing seeds. Intensive technology of cultivation (120 kg N ha^–1), compared to the economical technology (40 kg N ha^–1), significantly increased the seed yield of both sesame cultivars. This was due to higher number of branches, Capsules m^–2, capsules plant^–1, seeds capsule^–1 and 1000 seed weight (g). The intensive technology of cultivation had a beneficial effect on the content of palmitic acid, linolenic acid and oleic acid in sesame seed.  相似文献   

Improved remote sensing detection of wheat powdery mildew using dual-green vegetation indices     

Wei Feng  Wenying Shen  Li He  Jianzhao Duan  Binbin Guo  Yingxue Li  Chenyang Wang  Tiancai Guo 《Precision Agriculture》2016,17(5):608-627

In this study, we investigated the possibility of using ground-based remote sensing technology to estimate powdery mildew disease severity in winter wheat. Using artificially inoculated fields, potted plants, and disease nursery tests, we measured the powdery mildew canopy spectra of varieties of wheat at different levels of incidence and growth stages to investigate the disease severity. The results showed that the powdery mildew sensitive bands were between 580 and 710 nm. The best two-band vegetation index that correlated with wheat powdery mildew between 400 and 1000 nm wavelength were the normalized spectrum 570–590 and 536–566 nm bands for the ratio index, and 568–592 and 528–570 nm for the normalized difference index. The coefficients of determination (R ²) for both were almost the same. The optimum dual-green vegetation index was constructed based on a calculation of the ratio and normalized difference between the normalized spectrum within the two green bands. The coefficients of determination (R ²) of DGSR (584, 550) (dual-green simple ratio) and DGND (584, 550) (dual-green normalized difference) were both 0.845. The inverse models of disease severity performed well in the test process at the canopy scale, and indicated that, compared with the traditional vegetation indices of Lwidth, mND705, ND (SDr, SDb), SIPI, and GNDVI, the novel dual-green indices greatly improved the remote sensing detection of wheat powdery mildew disease. Following these results, combined disease severity and canopy spectra were shown to be of enormous value when applied to the accurate monitoring, prevention, and control of crop diseases.  相似文献   

Conserving copalillo: The creation of sustainable Oaxacan wood carvings     

Michael Chibnik  Silvia Purata 《Agriculture and Human Values》2007,24(1):17-28

Most accounts of the effect of the global marketplace on deforestation in Africa, Asia, and Latin America emphasize the demand for timber used in industrial processes and the conversion of tropical forests to pastures for beef cattle. In recent years, numerous scholars and policymakers have suggested that developing a market for non-timber forest products (NTFPs) might slow the pace of habitat destruction. Although increased demand for NTFPs rarely results in massive deforestation, the depletion of the raw materials needed to make particular products is common. Many rural households in the Mexican state of Oaxaca have prospered over the past three decades through the sale of brightly-painted, whimsical wood carvings (alebrijes) to international tourists and the owners of ethnic arts shops in the United States, Canada, and Europe. This paper examines a promising project aimed at providing Oaxacan alebrije-makers with a reliable, legal, and sustainable supply of wood. The ecologists, artisans, merchants, and forest owners involved in the project face formidable obstacles. Gaining permission to harvest wood from land belonging to Oaxacan communities requires the negotiation of a complex social, legal, economic, and political landscape. Artisans’ decisions about where to obtain wood rest largely on price, quality, and reliability of the supplier; they are willing to pay a premium for ecologically sustainable wood only if the additional cost can be passed on to consumers. Nonetheless, a group of carvers has begun to buy sustainably harvested wood. This arrangement has economic advantages for both the alebrije-makers and the owners of the forests where the wood is produced. Michael Chibnik is Professor of Anthropology at the University of Iowa. He has conducted fieldwork in Belize, Peru, Mexico, and in various parts of the United States. His research interests include economic anthropology, artisans, work organization, agricultural decision-making, and political ecology. He is the author of Crafting Tradition: The Making and Marketing of Oaxacan Wood Carvings (University of Texas Press, 2003) and Risky Rivers: The Economics and Politics of Floodplain Farming in Amazonia (University of Arizona Press, 1994), and editor of Farm Work and Fieldwork: American Agriculture in Anthropological Perspective (Cornell University Press, 1987). Dr. Silvia E. Purata is a Mexican ethnoecologist based in Xalapa, Veracruz. She is a member of People and Plants International, an organization that works to integrate conservation and the use of natural resources. Purata has conducted research on the methods indigenous peoples use to extract non-timber forest products (NTFPs) in tropical forests and the fate of such systems in varying socioeconomic circumstances. She has also been working on the promotion of forest certification in the Selva Maya.  相似文献   

Bans,tests, and alchemy: Food safety regulation and the Uganda fish export industry     

Stefano Ponte 《Agriculture and Human Values》2007,24(2):179-193

Contemporary regulation of food safety incorporates principles of quality management and systemic performance objectives that used to characterize private standards. Conversely, private standards are covering ground that used to be the realm of regulation. The nature of the two is becoming increasingly indistinguishable. The case study of the Ugandan fish export industry highlights how management methods borrowed from private standards can be applied to public regulation to achieve seemingly conflicting objectives. In the late 1990s, the EU imposed repeated bans on fish imported from Uganda on the basis of food safety concerns. However, the EU did not provide scientific proof that the fish were actually “unsafe.” Rather, the poor performance of Uganda’s regulatory and monitoring system was used as justification. Only by fixing “the system” (of regulations and inspections) and performing the ritual of laboratory testing for all consignments for export to the EU did the Ugandan industry regain its status as a “safe” source of fish. Yet, gaps and inconsistencies abound in the current Ugandan fish safety management system. Some operations are by necessity carried out as “rituals of verification.” Given the importance of microbiological tests and laboratories in the compliance system, “alchemic rituals” provide an appropriate metaphor. These rituals are part and parcel of a model that reassures the EU fish-eating public that all is under control in Uganda from boat to point of export. As a consequence, actual non-compliance from boat to landing site allows the fishery to survive as an artisanal operation. Stefano Ponte is Senior Researcher at the Danish Institute for International Studies, Copenhagen. His research focuses on the role of standards, regulation and quality conventions in the governance of agro-food value chains, with particular focus on Africa. He is co-author of Trading Down: Africa, Value Chains and the Global Economy and The Coffee Paradox: Global Markets, Commodity Trade and the Elusive Promise of Development.  相似文献   

Reverse leasing and power dynamics among blue agave farmers in western Mexico     

Sarah Bowen  Peter R. W. Gerritsen 《Agriculture and Human Values》2007,24(4):473-488

We examine changing production relations in the Mexican tequila industry to explore the ways in which large industrial firms are using “reverse leasing arrangements,” a form of contract farming, to extend their control over small agave farmers. Under these arrangements, smallholders rent their parcels to contracting companies who bring in capital, machinery, labor, and other agricultural inputs. Smallholders do not have access to their land, nor do they make any of the management decisions. We analyze the factors that have led some producers to participate in reverse leasing arrangements, while allowing other producers to continue farming independently. In addition, we look at the ways in which farmers are responding to these new production relations and constraints and the strategies that they are using to regain control over the production process.

Sarah BowenEmail:

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Consumption strategies in Mexican rural households: pursuing food security with quality     

Kirsten Appendini  Ma. Guadalupe Quijada 《Agriculture and Human Values》2016,33(2):439-454

Food quality is an important issue on the global agenda, particularly in high- and middle-income economies, but of little concern in designing Mexico’s food policy. Food policy has focused on quantity and in the case of maize, on satisfying domestic demand by supporting large commercial agriculture and importing from abroad. However, and as argued in this paper, obtaining a food staple (maize-tortilla) of quality is also an important issue for rural households and contributes to motivating continued smallholder production. Based on case studies in the rural district of Atlacomulco, in the state of Mexico, as well as in two regions of the state of Chiapas, this paper analyzes the production and consumption strategies of rural households. We focus on goals of food security and quality and note differential trends among households of varying characteristics and local contexts. We find that the motivation of small-scale producers to grow maize should be supported by Mexico’s food policy.  相似文献