bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of pooling samples on the efficiency of comparative studies using microarrays
Authors: Zhang Shu-Dong , Gant Timothy W. 
Published: October 2005

AbstractMotivation: Many biomedical experiments are carried out by pooling individual biological samples. However, pooling samples can potentially hide biological variance and give false confidence concerning the data significance. In the context of microarray experiments for detecting differentially expressed genes, recent publications have addressed the problem of the efficiency of sample pooling, and some approximate formulas were provided for the power and sample size calculations. It is desirable to have exact formulas for these calculations and have the approximate results checked against the exact ones. We show that the difference between the approximate and the exact results can be large.Results: In this study, we have characterized quantitatively the effect of pooling samples on the efficiency of microarray experiments for the detection of differential gene expression between two classes. We present exact formulas for calculating the power of microarray experimental designs involving sample pooling and technical replications. The formulas can be used to determine the total number of arrays and biological subjects required in an experiment to achieve the desired power at a given significance level. The conditions under which pooled design becomes preferable to non-pooled design can then be derived given the unit cost associated with a microarray and that with a biological subject. This paper thus serves to provide guidance on sample pooling and cost-effectiveness. The formulation in this paper is outlined in the context of performing microarray comparative studies, but its applicability is not limited to microarray experiments. It is also applicable to a wide range of biomedical comparative studies where sample pooling may be involved.Availability: A Java Webstart application can be accessed atContact: sdz1@le.ac.uk; twg1@le.ac.uk
Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX
Authors: Strömbäck Lena , Lambrix Patrick 
Published: October 2005

Abstract
Motivation: Analysis and simulation of pathway data is of high importance in bioinformatics. Standards for representation of information about pathways are necessary for integration and analysis of data from various sources. Recently, a number of representation formats for pathway data, SBML, PSI MI and BioPAX, have been proposed.
Results: In this paper we compare these formats and evaluate them with respect to their underlying models, information content and possibilities for easy creation of tools. The evaluation shows that the main structure of the formats is similar. However, SBML is tuned towards simulation models of molecular pathways while PSI MI is more suitable for representing details about particular interactions and experiments. BioPAX is the most general and expressive of the formats. These differences are apparent in allowed information and the structure for representation of interactions. We discuss the impact of these differences both with respect to information content in existing databases and computational properties for import and analysis of data.
Contact: lestr@ida.liu.se
A novel algorithm and web-based tool for comparing two alternative phylogenetic trees
Authors: Nye Tom M.W. , Liò Pietro , Gilks Walter R. 
Published: October 2005

Abstract
Summary: We describe an algorithm and software tool for comparing alternative phylogenetic trees. The main application of the software is to compare phylogenies obtained using different phylogenetic methods for some fixed set of species or obtained using different gene sequences from those species. The algorithm pairs up each branch in one phylogeny with a matching branch in the second phylogeny and finds the optimum 1-to-1 map between branches in the two trees in terms of a topological score. The software enables the user to explore the corresponding mapping between the phylogenies interactively, and clearly highlights those parts of the trees that differ, both in terms of topology and branch length.
Availability: The software is implemented as a Java applet at . It is also available on request from the authors.
Contact: thomas.nye@mrc-bsu.cam.ac.uk
Differential coexpression analysis using microarray data and its application to human cancer
Authors: Choi Jung Kyoon , Yu Ungsik , Yoo Ook Joon , Kim Sangsoo 
Published: October 2005

Abstract
Motivation: Microarrays have been used to identify differential expression of individual genes or cluster genes that are coexpressed over various conditions. However, alteration in coexpression relationships has not been studied. Here we introduce a model for finding differential coexpression from microarrays and test its biological validity with respect to cancer.
Results: We collected 10 published gene expression datasets from cancers of 13 different tissues and constructed 2 distinct coexpression networks: a tumor network and normal network. Comparison of the two networks showed that cancer affected many coexpression relationships. Functional changes such as alteration in energy metabolism, promotion of cell growth and enhanced immune activity were accompanied with coexpression changes. Coregulation of collagen genes that may control invasion and metastatic spread of tumor cells was also found. Cluster analysis in the tumor network identified groups of highly interconnected genes related to ribosomal protein synthesis, the cell cycle and antigen presentation. Metallothionein expression was also found to be clustered, which may play a role in apoptosis control in tumor cells. Our results show that this model would serve as a novel method for analyzing microarrays beyond the specific implications for cancer.
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: sskimb@ssu.ac.kr
Microarray phenotyping in Dictyostelium reveals a regulon of chemotaxis genes
Authors: Booth Ezgi O. , Driessche Nancy Van , Zhuchenko Olga , Kuspa Adam , Shaulsky Gad 
Published: October 2005

Abstract
Motivation: Coordinate regulation of gene expression can provide information on gene function. To begin a large-scale analysis of Dictyostelium gene function, we clustered genes based on their expression in wild-type and mutant strains and analyzed their functions.
Results: We found 17 modes of wild-type gene expression and refined them into 57 submodes considering mutant data. Annotation analyses revealed correlations between co-expression and function and an unexpected correlation between expression and function of genes involved in various aspects of chemotaxis. Co-regulation of chemotaxis genes was also found in published data from neutrophils. To test the predictive power of the analysis, we examined the phenotypes of mutations in seven co-regulated genes that had no published role in chemotaxis. Six mutants exhibited chemotaxis defects, supporting the idea that function can be inferred from co-expression. The clustering and annotation analyses provide a public resource for Dictyostelium functional genomics.
Supplementary information:
Contact: gadi@bcm.tmc.edu
Agricultural economics and distributional effects
Authors: Von Braun Joachim 
Published: October 2005

AbstractThe paper examines the main issues surrounding distributional effects in the domains of natural resource management and land policies, agricultural technology and research policies, agricultural market and trade policies, and consumer‐oriented policies, including standards, subsidies, and labeling. Agriculture is drifting into an ever more drastic bifurcation at a global level and within many countries. Correcting that bifurcation will require large investments in rural areas and rural people, in institutions, and in information and biological technologies accessible by the poor in the world's smallholder sector. Large and growing national and international inequalities related to agriculture and rural areas threaten peace, growth, and sustainable development.
Causes of rural economic development
Authors: Gardner Bruce L. 
Published: October 2005

AbstractUnderlying factors in the growth of agriculture as a sector and of rural incomes in developing countries are investigated, using data from 85 countries during 1960–2001. Hypotheses about growth are derived from both the general growth literature and the empirical literature on past agricultural growth in the United States and other industrial countries. The growth of agriculture as a sector is surprisingly independent of the growth of income per capita for those who work in that sector. Neither is necessary nor sufficient for the other. Agricultural economics is in many circumstances not the key discipline in understanding the economics of rural income and poverty.
Rural poverty dynamics: development policy implications
Authors: Barrett Christopher B. 
Published: October 2005

AbstractThis article explores the useful distinction between chronic and transitory poverty in understanding rural welfare dynamics, highlighting the possibility of poverty traps and their implications for “cargo net” policies to build up productive assets and “safety net” policies to protect such assets. We discuss the methodological difficulties in identifying and explaining either poverty traps or the critical thresholds that are their defining feature. A few empirical examples from sub‐Saharan Africa illustrate the likely existence of poverty traps that help to explain chronic rural poverty.
Is there a future for small farms?
Authors: Hazell Peter B. R. 
Published: October 2005

AbstractSmall farms are seriously challenged today in ways that make their future precarious. Marketing chains are changing and becoming more integrated and more demanding of quality and food safety. This is creating new opportunities for farmers who can compete and link to these markets, but threatens to leave many others behind. In developing countries, small farmers also face unfair competition from rich country farmers in many of their export and domestic markets. The viability of many is further undermined by the continuing shrinkage of their average farm size. And the spread of HIV/AIDS is further eroding the number of productive farm family workers, and leaving many children as orphans with limited knowledge about how to farm. Left to themselves, these forces will curtail opportunities for small farms, overly favor large farms, and lead to a premature and rapid exit of many small farms, adding to already serious problems of rural poverty and urban ghettos. If small farmers are to have a viable future, then there is a need for a concerted effort by governments, NGOs, and the private sector to create a more enabling economic environment for their development. Appropriate interventions could unleash significant benefits in the form of pro‐poor agricultural growth in many developing countries and more than pay for themselves in terms of their economic and social return. But they do not seem very likely at the moment and current trends are moving in the opposite direction.
A revival of large farms in Eastern Europe—how important are institutions?
Authors: Koester Ulrich 
Published: October 2005

AbstractContrary to expectations, large farms are still the dominant form of farm organization in most countries of the Commonwealth of Independent States and are important in some Central and Eastern countries. This paper analyzes the reasons for these failed expectations, focusing on the experience of Russia. The framework of institutional economics is applied to explain the reasons why the conventional approach, based on economies of scale and on‐farm transaction costs, does not apply to the evolution of farm size in the east (and even the west). Specific institutions, which are partly embedded and informal, and legal, but loosely enforced, suppress the birth of family farms in Russia and stimulate the growth of large farms, leading to holdings that are not observed in developed market economies. Hence, survival and growth of large farms are not necessarily based on comparative advantage of these farm organizations in a market economy environment.
Total factor productivity growth in agriculture: a Malmquist index analysis of 93 countries, 1980–2000
Authors: Coelli Tim J. , Rao D. S. Prasada 
Published: October 2005

AbstractIn this paper we examine the levels and trends in agricultural output and productivity in 93 developed and developing countries that account for a major portion of the world population and agricultural output. We make use of data drawn from the Food and Agriculture Organization of the United Nations and our study covers the period 1980–2000. Due to the nonavailability of reliable input price data, the study uses data envelopment analysis (DEA) to derive Malmquist productivity indices. The study examines trends in agricultural productivity over the period. Issues of catch‐up and convergence, or in some cases possible divergence, in productivity in agriculture are examined within a global framework. The paper also derives the shadow prices and value shares that are implicit in the DEA‐based Malmquist productivity indices, and examines the plausibility of their levels and trends over the study period.
Is small beautiful? Farm size, productivity, and poverty in Asian agriculture
Authors: Fan Shenggen , Chan‐Kang Connie 
Published: October 2005

AbstractSmall farms characterize agriculture in Asia. With the fragmentation of land holdings, the average size of farms fell in the region, while the number of small‐size holdings increased significantly. These small‐scale farmers play an important role for food security and poverty alleviation. However, whether and how these small farms can survive under globalization is a hotly debated topic. In particular, the traditional claim that “small is beautiful,” which is based on empirical observation that small farms present higher land productivity than large farms, is being challenged. It has been shown that a positive relationship also exists between farm size and labor productivity (and therefore income). To help these small farms prosper under increasing globalization, the governments have to change the “business as usual” attitude. Innovative land reform, for example, is crucial to secure property rights to farmers and to increase farm size. Equally important is the reform of public institutions in order to help small farmers to have access to credit, marketing, and technology. Moreover, promoting diversification in the production of high‐value commodities can play an important role in raising the small‐holders' income. Finally, policies that facilitate urban–rural migration and promote the development of the rural nonfarm sector are essential to help alleviate poverty among small‐farm households and among the rural poor in general.
Poverty amidst plenty: food insecurity in the United States
Authors: LeBlanc Michael , Kuhn Betsey , Blaylock James 
Published: October 2005

AbstractThe United States faces domestic food security issues that differ from those encountered by many countries. Yet, in 2001, 10.7% of U.S. households were estimated to be food insecure at some point during the year. Food security, poverty, and food insecurity are strongly linked by economic conditions. Job transitions, layoffs, and family disruptions result in periods of low income and vulnerability to food insecurity. Economic and food assistance programs have helped protect many U.S. households when the market economy has failed to do so. These programs have reduced vulnerability to falling income and food insecurity during economic downturns in the business cycle. However effective food assistance programs have been for reducing short‐term vulnerability, they do not enhance a household's ability to achieve sustainable food security. Prospects for improving long‐term food security are tied to the same economic forces shaping a household's income and budget, particularly those related to labor productivity and wages.
Agricultural biotechnology: implications for food security
Authors: Santaniello Vittorio 
Published: October 2005

AbstractIn 2015 under nourishment and famine will still be at higher levels than the targets set by the World Food Conference. Agricultural biotechnology is the major technological innovation to be made available to farmers after the end of the green revolution. The research activities of the biotech community, to provide solutions to the agricultural production problems, is intense and the results might be far reaching. The development of those technologies has been at times controversial but economic analysis of their impact have shown that producers and consumers, especially in developing countries, can benefit substantially. Although agricultural biotechnology is not a silver bullet to solve food insecurity problems, it can provide a significant help. Those technologies however need to be linked to the real needs of farmers and consumers.
The poverty of sustainability: rescuing economics from platitudes
Authors: Bromley Daniel W. 
Published: October 2005

AbstractThe idea of sustainability has become confused and incoherent. If sustainability is to regain a plausible pertinence to economic policy it must be understood to encompass two realms: (1) human interaction with nature; and (2) human interaction with others with respect to their interaction with nature. The on‐going redefinition of the purposes of nature requires that institutions—norms, rules‐property regimes—undergo constant evolution so that human action conduces to nondestructive action. Caution in the social realm is the greatest risk to environmental sustainability.
Under‐investing in public goods: evidence, causes, and consequences for agricultural development, equity, and the environment
Authors: López Ramón 
Published: October 2005

AbstractA common factor that explains why agriculture causes too much environmental degradation, grows too slowly, and has been ineffective in reducing rural poverty is the generalized tendency by governments to under invest in public goods despite the high rates of return to such investments. A large share of rural public expenditures is deviated to private goods (mostly subsidies to the wealthy), which generally have low or even negative rates of return. Behind such an obviously aberrant choice are political economy forces; a highly unequal political lobby market leads to government policies that are biased in favor of economic elites and detrimental for both the environment and rural development. Globalization may affect this important distortion on the allocation of government expenditures in various ways. One such way is by restricting the ability of governments to repress the political mobilization of the poor to counter the almost unchallenged power of the elites in the lobby market. This may contribute toward creating conditions that are more consistent with sustainable and socially equitable development.
Economic development and environmental management in the uplands of Southeast Asia: challenges for policy and institutional development
Authors: Rola Agnes C. , Coxhead Ian 
Published: October 2005

AbstractUsing a Philippine case study site, the forces driving the recent evolution of economic behavior and institutional arrangements in upland and forest margin areas of Southeast Asia are considered. In early modern development, subsistence agriculture using long‐phase forest–fallow rotations and regulated by customary law was replaced by more intensive, commercially oriented farming systems, a process heavily influenced by internal migration to the agricultural frontier. Traditional land and resource use institutions were quickly displaced during this shift—both de facto, through the actions of colonists, and de jure, through the state's assertion of ownership over forests and uplands and the introduction of private title to agricultural lands. Yet the effective implementation of natural resource use constraints lagged substantially behind the pace of agricultural development and forest exploitation, resulting in a period in which high demand for such resources coincided with virtually open access. These processes were noticeably subject to the influence of policies and reforms affecting markets, prices, and institutions.
Risk factors for non‐cardiac chest pain in the community
Authors: WISE J. L. , LOCKE G. R. , ZINSMEISTER A. R. , TALLEY N. J. 
Published: October 2005

SummaryBackground:  Non‐cardiac chest pain is a common and expensive condition. Risk factors for non‐cardiac chest pain are poorly understood and lack description in the USA community.Aim:  To explore risk factors and health‐seeking behaviour in non‐cardiac chest pain in a USA community.Methods:  Olmsted County, MN subjects who reported at least monthly or severe chest pain in response to a validated questionnaire were compared with controls. All the Mayo Clinic medical records were reviewed; those with cardiac disease or relevant organic conditions were excluded.Results:  Of 2118 eligible subjects, 1524 (72%) returned a questionnaire, 389 subjects (26%) reported any chest pain and 186 (12.2%) at least monthly or severe chest pain. Of these, 62 were excluded for a cardiac diagnosis or another organic cause. Thus, 124 subjects (9.1%, 95% CI: 7.6–10.8%) reported at least monthly or severe non‐cardiac chest pain, of which 65 (52.4%) had frequent reflux symptoms. Independent risk factors for non‐cardiac chest pain were obesity (OR 3.0, 95% CI: 1.64–5.50), family history of reflux (OR 2.8, 95% CI: 1.73–4.32), previous cigarette use (OR 2.0, 95% CI: 1.27–3.18), aspirin use (OR 1.5, 95% CI: 1.00–2.31) and use of antiarthritis medicines (OR 2.0, 95% CI: 1.27–3.16). Compared with subjects with non‐cardiac chest pain and associated gastro‐oesophageal reflux symptoms, subjects with non‐cardiac chest pain without associated gastro‐oesophageal reflux symptoms were less likely to have a family history of reflux, more likely to be younger, and less likely to be obese. Compared with controls, subjects with non‐cardiac chest pain without gastro‐oesophageal reflux symptoms were younger (OR 0.97, 95% CI: 0.95–0.99), reported higher somatic symptom scores (OR 1.1, 95% CI: 1.08–1.73) and were more likely to be obese (OR 2.6, 95% CI: 1.15–5.93).Conclusions:  Recurrent or severe non‐cardiac chest pain is common in the community. Half of the people with significant non‐cardiac chest pain have frequent reflux symptoms, thus, risk factors for non‐cardiac chest pain are similar to risk factors for gastro‐oesophageal reflux disease. People with non‐cardiac chest pain without reflux symptoms have a slightly different risk factor profile.
Effects of grapefruit juice on the pharmacokinetics of pitavastatin and atorvastatin
Authors: Ando Hitoshi , Tsuruoka Shuichi , Yanagihara Hayato , Sugimoto Koh‐ichi , Miyata Masaaki , Yamazoe Yasushi , Takamura Toshinari , Kaneko Shuichi , Fujimura Akio 
Published: October 2005

AimsTo compare the effects of grapefruit juice (GFJ) on the pharmacokinetics of pitavastatin and atorvastatin.MethodsIn a randomized, four‐phase crossover study, eight healthy subjects consumed either GFJ or water t.i.d. for 4 days in each trial. On each final day, a single dose of 4 mg pitavastatin or 20 mg atorvastatin was administered.ResultsGFJ increased the mean AUC0−24of atorvastatin acid by 83% (95% CI 23–144%) and that of pitavastatin acid by 13% (−3 to 29%).ConclusionsPitavastatin, unlike atorvastatin, appears to be scarcely affected by the CYP3A4‐mediated metabolism.