bluuebunny/crossref_metadata_2025_split huggingface dataset:
An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis
Authors: Barker Jonathan A. , Thornton Janet M. 
Published: September 2003

Abstract
Motivation: Structural templates consisting of a few atoms in a specific geometric conformation provide a powerful tool for studying the relationship between protein structure and function. Current methods for template searching constrain template syntax and semantics by their design. Hence there is a need for a more flexible core algorithm upon which to build more sophisticated tools. Statistical analysis of structural similarity is still in its infancy when compared with its analogue in sequence alignment. In the context of template matching, there is an urgent need for normalization of scores so that results from templates with differing sensitivity may be compared directly.
Results: We introduce Jess, a fast and flexible algorithm for searching protein structures for small groups of atoms under arbitrary constraints on geometry and chemistry. We apply the algorithm to a set of manually derived enzyme active site templates, and derive an empirical measure for estimating the relative significance of hits encountered using differing templates.
Availability: Jess will be available in the near future under a restricted open source licence.
The effect of replication on gene expression microarray experiments
Authors: Pavlidis Paul , Li Qinghong , Noble William Stafford 
Published: September 2003

Abstract
Motivation: We examine the effect of replication on the detection of apparently differentially expressed genes in gene expression microarray experiments. Our analysis is based on a random sampling approach using real data sets from 16 published studies. We consider both the ability to find genes that meet particular statistical criteria as well as the stability of the results in the face of changing levels of replication.
Results: While dependent on the data source, our findings suggest that stable results are typically not obtained until at least five biological replicates have been used. Conversely, for most studies, 10–15 replicates yield results that are quite stable, and there is less improvement in stability as the number of replicates is further increased. Our methods will be of use in evaluating existing data sets and in helping to design new studies.
Supplementary information: http://microarray.cpmc.columbia.edu/pavlidis/pub/gxrep
ddbRNA: detection of conserved secondary structures in multiple alignments
Authors: di Bernardo Diego , Down Thomas , Hubbard Tim 
Published: September 2003

Abstract
Motivation: Structured non-coding RNAs (ncRNAs) have a very important functional role in the cell. No distinctive general features common to all ncRNA have yet been discovered. This makes it difficult to design computational tools able to detect novel ncRNAs in the genomic sequence.
Results: We devised an algorithm able to detect conserved secondary structures in both pairwise and multiple DNA sequence alignments with computational time proportional to the square of the sequence length. We implemented the algorithm for the case of pairwise and three-way alignments and tested it on ncRNAs obtained from public databases. On the test sets, the pairwise algorithm has a specificity greater than 97% with a sensitivity varying from 22.26% for Blast alignments to 56.35% for structural alignments. The three-way algorithm behaves similarly. Our algorithm is able to efficiently detect a conserved secondary structure in multiple alignments.
Availability: The executable file, the code and a PDF file containing the instructions, as well as the test data sets can be requested free of charge from the authors (dibernardo@tigem.it) or from the website http://www.tigem.it/research/dibernardo/default.htm
CGH-Plotter: MATLAB toolbox for CGH-data analysis
Authors: Autio Reija , Hautaniemi Sampsa , Kauraniemi Päivikki , Yli-Harja Olli , Astola Jaakko , Wolf Maija , Kallioniemi Anne 
Published: September 2003

Abstract
Summary: CGH-Plotter is a MATLAB toolbox with a graphical user interface for the analysis of comparative genomic hybridization (CGH) microarray data. CGH-Plotter provides a tool for rapid visualization of CGH-data according to the locations of the genes along the genome. In addition, the CGH-Plotter identifies regions of amplifications and deletions, using k-means clustering and dynamic programming. The application offers a convenient way to analyze CGH-data and can also be applied for the analysis of cDNA microarray expression data. CGH-Plotter toolbox is platform independent and requires MATLAB 6.1 or higher to operate.
Availability: http://sigwww.cs.tut.fi/TICSP/CGH-Plotter
Intergenic sequence inspector: searching and identifying bacterial RNAs
Authors: Pichon Christophe , Felden Brice 
Published: September 2003

Abstract
Summary:Intergenic Sequence Inspector (ISI) is a program that helps in identifying bacterial ribonucleic acids (RNAs). It automatically extracts, selects and visualizes candidate intergenic regions (IGRs) that bear conservations between phylogenetically related species, displaying sequence and structural signatures of RNA genes encompassing putative promoters, terminators, RNA secondary structure predictions and the G + C percent of the selected sequences. ISI is intentionally modular to analyze various bacterial genomes according to their intrinsic specificities and to the available data. ISI provides a sum of information to the user who can evaluate whether or not an IGR is susceptible to express RNAs.
Availability: The program can be downloaded at http://www.biochpharma.univ-rennes1.fr/ under the subsection 'Software'.
Imprinting in the endosperm: a possible role in preventing wide hybridization
Authors: Gutierrez-Marcos Jose F. , Pennington Paul D. , Costa Liliana M. , Dickinson Hugh G. 
Published: September 2003

Reproductive isolation is considered to play a key part in evolution, and plants and animals have developed a range of strategies that minimize gene flow between species. In plants, these strategies involve either pre–zygotic barriers, such as differences in floral structure and pollen–stigma recognition, or post–zygotic barriers, which are less well understood and affect aspects of seed development ranging from fertilization to maturation.In most angiosperms, a double fertilization event gives rise to a zygote and the endosperm: a triploid tissue with an unequal parental genomic contribution, which, like the placenta of mammals, provides reserves to the developing embryo. Interestingly, many aspects of endosperm development, again like the placenta, are regulated by a range of epigenetic mechanisms that are globally termed imprinting. Imprinted genes are characterized by their uniparental expression, the other parental allele being silenced. Normal development of the endosperm thus requires a highly specific balance of gene expression, from either the maternal or paternal genomes. Any alteration of this balance resulting from changes in allelic copy number, sequence or epigenetic imprints can cause endosperm failure and eventual seed abortion. In its widest sense, the endosperm thus serves as an accurate ‘sensor’ of compatibility between parents. A first step in understanding this important, yet complex system must clearly be the isolation and characterization of as wide a range as possible of imprinted genes.
Twinning in La0.95Sr0.05Ga0.9Mg0.1O2.92crystal studied by white-beam (Laue) X-ray microdiffraction
Authors: Savytskii D. I. , Trots D. M. , Vasylechko L. O. , Tamura N. , Berkowski M. 
Published: September 2003

The investigation of twin structure in La0.95Sr0.05Ga0.9Mg0.1O2.92perovskite-type crystals has been undertaken using the technique of white-beam X-ray microdiffraction. The sample shows definite twinning which is reflected in the Laue patterns as apparent splitting of the peaks. Reflections from the different domains were indexed separately. Positional shifts of twin domain spots with respect to the reference matrix spot, arising from the mutual misorientation of diffraction vectors, were measured on Laue patterns and compared with calculated values in order to solve the twin laws in this system. The dominant twin operations were found to be (12\bar{1}) and (10\bar{1}) mirror reflections.
Keeping Watch! Recounting Twenty‐Five Years of the Office of Chief Accountant, U.S. Securities and Exchange Commission, 1976–2001
Authors: Previts Gary J. , Roybark Helen M. , Coffman Edward N. 
Published: September 2003

This article adds to the literature of accounting regulation by providing background, including facts and circumstances relating to a quarter century of SEC activity preceding the events identified with the reshaping of the capital markets following the dot.com collapse and the attack on the World Trade Center, 11 September 2001. The subsequent collapse of Enron, the bankruptcy of Worldcom, the dissolution of Andersen, one of the Big Five accounting firms, and the passage in the United States of the Sarbanes‐Oxley Act, collectively have ushered in a new era of public–private capital market relationships. This study provides guidance and outlines topics useful to future researchers undertaking assessments of regulatory policies and the individuals involved in their administration.From 1976 to 2001 five individuals played a significant role in the development of the U.S. Securities and Exchange Commission's disclosure and reporting practices by virtue of their office and the collective influence of their views. A. Clarence Sampson (1976–87), Edmund Coulson (1988–91), Walter P. Schuetze (1992–95), Michael H. Sutton (1995–98) and Lynn E. Turner (1998–2001) directed accounting policy activities at the SEC during these years.
Corporate Governance and Gatekeeper Liability: the lessons from public authorities
Authors: Kirkbride James , Letza Steve 
Published: September 2003

(1) Under the requirements of the Local Government Act 1900, a system of promoting and regulating good governance in public authorities was introduced. The system involved the establishment of a Standards Board with agreed codes of conduct and enforcement mechanism through monitoring officers. All authority codes of conduct had to be approved by May 1902. The system was introduced under the headline of: “Reconnecting with the people – promoting good governance and ethical behaviour”. (2) In the mid‐1980s, the concept of “gatekeeper liability” was beginning to be promoted as a method of enhancing the regulation of boards of directors. The most influential work was that of Kraakman. Kraakman was concerned that a system of regulation was brought forward to respond to enforcement insufficiency in the area of corporate control. A notion of “gatekeeper” liability is one response.This paper explores the system of controlling governance in public authorities (1 above) and its relationship to the gatekeeper response advocated for private corporations (in 2 above). Through this analysis, a series of reflections and signposts are presented as lessons for the private sector and for the enhancement of good governance in that sector.
Public Saving and Policy Coordination in Aging Economies
Authors: Flodén Martin 
Published: September 2003

AbstractIn the coming decades, the share of people of working age will fall significantly in most developed countries. According to optimal taxation theory, public debts should be reduced before the baby‐boom generation retires. I find that if debts are instead maintained at current levels, welfare may be reduced substantially in countries with a large public sector and/or a large demographic change. Since population aging will be less dramatic in the United States than in Europe and Japan, capital will move from Europe and Japan to the United States. These capital movements will facilitate the US demographic transition but aggravate the transition in most European countries.
Early Mortality Declines at the Dawn of Modern Growth*
Authors: Boucekkine Raouf , Croix David de la , Licandro Omar 
Published: September 2003

AbstractWe explore the hypothesis that demographic changes which began in the seventeenth and eighteenth centuries are at the root of the acceleration in growth rates at the dawn of the modern age. During this period, life tables for Geneva and Venice show a decline in adult mortality; French marriage registers reveal an important increase in literacy; historians measure an acceleration of economic growth. We develop an endogenous growth model with a realistic survival law in which rising longevity increases individual incentives to invest in education and fosters growth. We quantitatively estimate that the observed improvements in adult mortality account for 70% of the growth acceleration in the pre‐industrial age.
Recent Technological and Economic Change among Industrialized Countries: Insights from Population Growth*
Authors: Beaudry Paul , Collard Fabrice 
Published: September 2003

AbstractCross‐country observations on the effects of population growth are used to show why differences in rates of growth in working‐age population may be a key to understanding differences in economic performance across industrialized countries over the period 1975–1997 versus 1960–1974. In particular, we argue that countries with lower rates of adult population growth adopted new capital‐intensive technologies more quickly than their high population growth counterparts, therefore allowing them to reduce their work time without deterioration of growth in output‐per‐adult.
Demographic and Economic Pressure on Emigration out of Africa*
Authors: Hatton Timothy J. , Williamson Jeffrey G. 
Published: September 2003

AbstractTwo of the main forces driving European emigration in the late nineteenth century were real wage gaps between sending and receiving regions and demographic booms in the low‐wage sending regions. Our new estimates of net migration for the countries of sub‐Saharan Africa show that exactly the same forces driving African across‐border migration are at work today. The results suggest that rapid growth in the cohort of potential young emigrants, population pressure on the resource base, and slow economic growth are likely to intensify the pressure for migration out of Africa and into high‐wage OECD countries over the next two decades.
Fiscal Implications of Immigration—A Net Present Value Calculation
Authors: Storesletten Kjetil 
Published: September 2003

AbstractFocusing on the net fiscal effects, the gain from admitting immigrants is computed for a welfare state with large expenditures and a large tax burden (Sweden). Prices and behavior are held constant, which allows a detailed analysis of the effects of immigration. The present value of future tax revenues minus outlays is potentially large; USD 23,500 per young working‐age immigrant, but an average new immigrant represents a net government loss of USD 20,500. The dominant factors are employment rates and age. For young working‐age immigrants, the “break‐even” participation rate for which the gain would be zero is 60%, well below the empirical rate for this group.
Liberalising Temporary Movement of Natural Persons: An Agenda for the Development Round
Authors: Winters L. Alan , Walmsley Terrie L. , Wang Zhen Kun , Grynberg Roman 
Published: September 2003

We discuss liberalising the temporary mobility of workers under Mode 4 of the GATS, particularly the movement of medium and low skilled service providers between developing and developed countries. Such mobility potentially offers huge returns: a flow equivalent to three per cent of developed countries’ skilled and unskilled work forces would generate an estimated increase in world welfare of over US$150 billion, shared fairly equally between developing and developed countries. The larger part of this emanates from the less‐skilled, essentially because losing higher‐skilled workers cuts output in developing countries severely. The mass migration of less skilled workers raises fears in developed countries for cultural identity, problems of assimilation and the drain on the public purse. These fears are hardly relevant to temporary movement, however. The biggest economic concern from temporary mobility is its competitive challenge to local less skilled workers. But as populations age and the average levels of training and education rise, developed countries will face an increasing scarcity of less skilled labour. Temporary mobility thus actually offers a strong communality of interest between developing and developed countries.The remainder of the paper looks at the GATS provisions on Mode 4 and the commitments that have been made under it. The paper reviews several official proposals for the Doha talks, including the very detailed one from India, and considers several countries’ existing schemes for the temporary movement of foreign workers. Many countries have long had bilateral foreign worker programmes, and some regional agreements provide for liberal and flexible movement. These show what is feasible and how concerns can be overcome. We caution that, to be useful, any WTO agreement must increase mobility, not just bureaucratise it.The paper concludes with some modest and practical proposals. We suggest, inter alia, that licensing firms to arrange the movement of labour is the most promising short‐term approach to increasing temporary mobility.
Channels of Entry and Preferred Destinations: The Circumvention of Denmark by Chinese Immigrants
Authors: Thunø Mette 
Published: September 2003

AbstractAs globalization spread during the 1990s, and especially since the turn of the millennium, European states have increasingly claimed their right to assert their sovereignty by regulating migration at the level of the individual (OECD, 2001: 76–81). Political parties have succeeded in gaining support on policy statements pertaining exclusively to migration. For example, recent legislation in Denmark restricts the categories of persons eligible as refugees to “Convention refugees” satisfying only the narrowest international criteria set out in the UN Refugee Convention. The civil rights of asylum seekers are restricted by prohibiting marriage while their applications are under review. To limit family reunification among immigrants, the present Danish Government has even prohibited immigrants with permanent residence status and Danish citizens from bringing non‐Danish spouses under age 24 into the country.These attempts at border enforcement and immigration control have been described by some critics as the endeavours of European Union (EU) members to build a “Fortress Europe” against immigrants from developing countries. Policy decisions and the implementation of various measures from finger printing to radar surveillance to control immigrants have corroborated such perceptions, but this paper will show that gaining entry to a highly controlled country such as Denmark from a poorer country such as the People's Republic of China (PRC) is fairly straightforward. Politicians may wish to convey the impression of being in control of international mobility by launching diverse anti‐immigration acts, but since the immigration embargo of the early 1970s all EU countries have received millions of immigrants, and increasingly permit or accept immigrants of various kinds to reside and work within their borders (Boeri et al., 2002). Immigration from developing countries is not evenly distributed throughout the EU, but rather targets specific destinations. This article will attempt to explain the direction of Chinese immigration flows to Europe in response to labour‐market demand, rather than as a consequence of “loopholes” in a country's legal or welfare provisions.By analysing historical and demographic data on the PRC Chinese in Denmark, I attempt to demonstrate that, despite being a European country with one of the lowest asylum rejection rates for PRC Chinese, the scope of Chinese asylum seekers and regular and irregular migrants arriving by way of family reunification remained limited in the 1990s compared to southern, central, and eastern European countries. My analysis of Danish data in relation to Chinese migration suggest that destinations related to the globalization of Chinese migration is more determined by labour and capital markets than the presumed attraction of social welfare benefits provided by a European welfare state such as Denmark.
Chinese Migration to Eastern Europe
Authors: Nyíri Pál 
Published: September 2003

AbstractMost of the work on the early history of Chinese migration to eastern Europe, that is, the first half of the twentieth century, has been written by Russian scholars. Contemporary sources — accounts of Russian travellers and government documents — are overwhelmingly preoccupied with migration to the Russian Asian territories. But the interest in Chinese immigration since the 1990s has resulted in considerable attention being paid to the historical background as well, notably by Larin (1998, 2000) and Saveliev (2002). Chinese scholarship on Chinese labour in Europe during World War I (e.g. S. Chen, 1986) only devotes little space to eastern Europe.Yet, Chinese migration to eastern Europe has a particular policy interest because in the past decade it has proven to be predictive of trends in Europe as a whole. A new flow of entrepreneurial migrants, who often had no connection to the historical, rural‐based chains of migration that produced the earlier Chinese migrant populations of western Europe, found it possible and profitable to do business and settle on the European periphery during a brief period of liberal migration controls. Erratic crackdowns on illegal migration in the absence of thought‐through migration regimes resulted in a volatile situation, periodically generating migration flows from one country in the region to another. These were facilitated by, and gave further rise to, networks of kinship and information spanning both eastern and western Europe.While this paper focuses on Hungary, it also attempts to review information on other eastern European countries (particularly Russia, Romania, Yugoslavia, and the Czech Republic) where it is available. In doing so, it intends to fill a gap in information on Chinese in eastern Europe until more substantial research is produced, as well as to highlight the common features of, and links between, Chinese migration into individual eastern European countries as well as into western Europe.