bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ethics, Market and Government Failure, and Globalization: Perspectives on Debt and Finance
Authors: Stiglitz J. E. 
Published: June 2006

AbstractThis chapter looks at the ethical aspects of globalization during the 1990s. It argues that in the way that they have sought to shape globalization, the advanced industrial countries and some of the multilateral institutions that they control have violated some basic ethical norms. Three central issues in the context of global finance are analyzed: the design of debt contracts between developed and developing countries and other aspects of lending behavior; the consequences of excessive debt; and broader issues associated with the global reserve system. Three types of ethical problems are discussed: (1) where markets (or international institutions) take advantage of their “power” and the weaknesses of the developing country to pursue their own interests at the expense of or risk to those in the developing countries; (2) where international financial institutions provide advice that works to the disadvantage of the developing countries; and (3) where the markets, and especially the international financial institutions, have not done as much as they could for the well-being of the developed countries.
Helping the Poor to Help Themselves: Debt Relief or Aid?
Authors: Arslanalp Serkan , Henry Peter Blair 
Published: June 2006

AbstractThis chapter discusses the central economic question of debt relief: does debt relief work to promote economic growth? This seemingly straightforward question — often taken for granted by debt campaigners — merits closer attention to ensure that relief bears constructive and sustainable outcomes. It is argued that debt relief is highly effective at promoting growth in countries suffering from a “debt overhang”, where reducing debt levels will stimulate investment and net resource transfers from abroad, but less effective in countries where infrastructure is weak and where net resource transfers are already positive.
Odious Debt
Authors: Jayachandran Seema , Kremer Michael 
Published: June 2006

Abstract
This chapter discusses the problem of illegitimate debt from a new angle. Instead of focusing on borrowers, it focuses on the role and incentives of creditors who lend to questionable governments for illicit purposes. This approach follows a theme that runs throughout the book: responsibility for bad loans should lie with lenders as much as borrowers. It is argued that as long as borrowing countries are obligated to repay bad debts, lenders will have no incentive to avoid bad loans. Furthermore, once a loan is made to an odious regime, no tribunal can be entrusted to label it as such, and charges of favoritism will always be made against the tribuna's decision.
Dealing Comprehensively, and Justly, with Sovereign Debt
Authors: Boorman Jack 
Published: June 2006

AbstractThis chapter discusses ideas for resolving debt crises. It argues that a narrow focus on debt relief in HIPCs is insufficient and that the activist community and lenders must look to finding broader measures of foreign aid and creating a fair trading environment. In the end, finding the “right” level of debt relief is impossible and ignores the more important aim of delivering a better life to impoverished people. Support is given to a proposal floated by the IMF for a sovereign debt restructuring mechanism (SDRM) to resolve pending debt crises in developing countries.
The IMF's SDRM—Simply Disastrous Rescheduling Management?
Authors: Raffer Kunibert 
Published: June 2006

AbstractThis chapter argues that that the IMF's sovereign debt restructuring mechanism (SDRM) is misguided in several ways. Most importantly, the SDRM proposal leaves the IMF itself in the position of having to make two crucial decisions: whether to endorse a stay of payments to creditors, and what amount of debt is “sustainable”, i.e., how much debt should be written off. This decision-making capacity creates a conflict of interest, as the IMF itself is almost always a creditor to countries experiencing debt crises. As an alternative to the IMF's SDRM, a mechanism modeled on Chapter 9 of the US bankruptcy code is proposed, which applies to municipalities and resolves some of the knotty problems of dealing with public (as compared with private) insolvency. This approach would rely on ad hoc panels formed by the debtor and creditor committees and therefore would not require that the IMF serve as arbitrator.
The Jubilee 2000 Campaign: A Brief Overview
Authors: Pettifor Ann 
Published: June 2006

Abstract
This chapter describes what is perhaps the most powerful innovation for achieving debt relief for the poor since the mid-1990s: the mobilization of civil societies. The Jubilee 2000 movement was extraordinary — uniting tens of millions of people and spanning nations and continents — all in the name of reducing the burden of developing-country debt. The movement's history and analysis of its successes and failures underscores the importance of civil society groups in the debate over debt and their potential role in promoting and implementing solutions.
Exceeding Our Grasp
Authors: Stanford P. Kyle 
Published: June 2006

AbstractThe incredible achievements of modern scientific theories lead most of us to embrace scientific realism: the view that our best theories offer us at least roughly accurate descriptions of otherwise inaccessible parts of the world like genes, atoms, and the big bang. This book argues that careful attention to the history of scientific investigation invites a challenge to this view that is not well represented in contemporary debates about the nature of the scientific enterprise. The historical record of scientific inquiry, the book suggests, is characterized by the problem of unconceived alternatives. Past scientists have routinely failed even to conceive of alternatives to their own theories and lines of theoretical investigation, alternatives that were both well-confirmed by the evidence available at the time and sufficiently serious as to be ultimately accepted by later scientific communities. The book supports this claim with a detailed investigation of the mid-to-late 19th-century theories of inheritance and generation proposed in turn by Charles Darwin, Francis Galton, and August Weismann. It goes on to argue that this historical pattern strongly suggests that there are equally well-confirmed and scientifically serious alternatives to our own best theories that remain currently unconceived. Moreover, this challenge is more serious than those rooted in either the so-called pessimistic induction or the underdetermination of theories by evidence, in part because existing realist responses to these latter challenges offer no relief from the problem of unconceived alternatives itself.
Realism, Pessimism, and Underdetermination
Authors: Stanford P. Kyle 
Published: June 2006

AbstractThis chapter begins with a discussion of scientific realism. It then looks at some reasons that have been given for doubting that the pessimistic induction and the underdetermination of theories by evidence really should lead us to withhold belief in the claims of the best scientific theories. It is argued that the most powerful challenge to scientific realism has yet to be formulated, but emerges naturally from a systematic consideration of the reasons that the much more famous challenges offered by the pessimistic induction, and that the underdetermination of theories by evidence have left scientific realists unconvinced of their significance.
Chasing Duhem
Authors: Stanford P. Kyle 
Published: June 2006

AbstractNearly a century ago, French physicist Pierre Duhem offered a characteristically lucid and provocative articulation of the challenge to the power of scientific methods to uncover theoretical truths about the natural world. What seems to have worried Duhem is the eliminative character of many important scientific inferences: often in science, perhaps even typically, we arrive at a decision to accept or believe a given theory because we take ourselves to have convincingly eliminated or discredited any and all of its proposed rivals or competing explanations of the available evidence. But as Duhem saw, such an eliminative inferential procedure will only guide us to the truth about nature if the truth is among these competitors in the first place. It is argued that eliminative inferences are only reliable when we can be reasonably sure that we have considered all of the most likely, plausible, or reasonable alternatives before we proceed to eliminate all but one of them (or, in the limiting case, simply rest content with the lone contender). But the history of science shows that we have repeatedly failed to conceive of (and therefore consider) alternatives to our best theories that were both well confirmed by the evidence available at the time and sufficiently plausible as to be later accepted by actual scientific communities. The historical record suggests that in science we are typically unable to exhaust the space of likely, plausible, or reasonable candidate theoretical explanations for a given set of phenomena before proceeding to eliminate all but a single contender, but this is just what would be required for such eliminative inferences to be reliable.
Galton and the Stirp Theory
Authors: Stanford P. Kyle 
Published: June 2006

AbstractThis chapter begins with a discussion of Galton's transfusion experiments and his development of the “stirp” theory of inheritance. It then discusses Galton's understanding of “correlation” and “ variable influences” in development. It is argued that just as Darwin failed to conceive of the very possibility of any common-cause mechanism for inheritance, after surmounting this conceptual obstacle Galton failed in turn to conceive of any alternatives to the maturational and invariant aspects of his own account of particulate inheritance.
August Weismann's Theory of the Germ‐Plasm
Authors: Stanford P. Kyle 
Published: June 2006

AbstractThis chapter focuses on August Weismann's theory of the germ-plasm. It is argued that both Weismann's failure to conceive of any alternative to the disintegration of the idioplasm as the mechanism of ontogenetic differentiation and nuclear control, and his failure to conceive of any genuinely facultative capacity on the part of the germ-plasm suggest that Weismann never conceived of the quite general possibility that the germ-plasm could itself serve as what we might call a productive rather than an expendable resource for the cell and/or the organism.
History Revisited
Authors: Stanford P. Kyle 
Published: June 2006

AbstractThis chapter examines the most influential recent efforts by scientific realists to blunt or block the pessimistic induction by engaging the details of the history of science itself, including the first serious efforts to recruit those details to the realist cause. It argues that the most promising and influential realist replies to the historical challenge (including those of Clyde Hardin and Alexander Rosenberg, Philip Kitcher, Stathis Psillos, Jarrett Leplin, and John Worrall) ultimately manage to achieve only Pyrrhic victories for realism, that is, “defences” of scientific realism that are forced to concede to the realist's opponent either just the substantive points that were in dispute between them or everything he/she needs for a convincing historical case against realism itself. Both the problem of unconceived alternatives and the pessimistic induction itself survive even the best recent efforts to defend realism from the specter of the historical record.
Selective Confirmation and the Historical Record
Authors: Stanford P. Kyle 
Published: June 2006

AbstractThe preceding chapter showed that the best remaining hope for defending realism from the challenges of history seems to lie with the strategy of “selective confirmation.” On this strategy, we defend only some parts or components of past theories as responsible for (and therefore confirmed by) their successes, while abandoning others as idle, merely presuppositional, or otherwise not involved in the empirical successes those theories managed to achieve, and therefore never genuinely confirmed by those successes in the first place. This chapter argues that without some prospectively applicable and historically reliable criterion for distinguishing idle and/or genuinely confirmed parts of our theories from others, the strategy of selective confirmation offers no refuge for the scientific realist. Without such a criterion, we can have no confidence in our ability to pick out the parts of theories needed for (and thus selectively confirmed by) their successes while those theories are live contenders. We will therefore not be in a position to identify those parts or features of our own theories we may safely regard as accurate descriptions of the natural world (even though we know that not all are), and thus the realist's opponent will again be entitled to the conclusion that was wanted all along. Such criteria are just what existing appeals to selective confirmation do not (and perhaps cannot) provide.
Science without Realism?
Authors: Stanford P. Kyle 
Published: June 2006

AbstractThis chapter addresses the question of whether there is any sense to be made of science without scientific realism. That is, it will try to identify whether there is any coherent positive view we might take of our successful scientific theories if we abandon the presumption that they must be approximately true descriptions of nature's innermost recesses and secret domains. A long and distinguished minority tradition has embraced a view entitled “instrumentalism,” which instead regards even our best scientific theories merely as effective tools or instruments for achieving our practical goals. It is argued that the problem of unconceived alternatives promises to breathe new life into this instrumentalist tradition: not into its discredited semantic theses, but into its positive conception of the status of scientific theories.
caGrid: design and implementation of the core architecture of the cancer biomedical informatics grid
Authors: Saltz Joel , Oster Scott , Hastings Shannon , Langella Stephen , Kurc Tahsin , Sanchez William , Kher Manav , Manisundaram Arumani , Shanbhag Krishnakant , Covitz Peter 
Published: June 2006

Abstract
Motivation: The complexity of cancer is prompting researchers to find new ways to synthesize information from diverse data sources and to carry out coordinated research efforts that span multiple institutions. There is a need for standard applications, common data models, and software infrastructure to enable more efficient access to and sharing of distributed computational resources in cancer research. To address this need the National Cancer Institute (NCI) has initiated a national-scale effort, called the cancer Biomedical Informatics Grid (caBIG™), to develop a federation of interoperable research information systems.
Results: At the heart of the caBIG approach to federated interoperability effort is a Grid middleware infrastructure, called caGrid. In this paper we describe the caGrid framework and its current implementation, caGrid version 0.5. caGrid is a model-driven and service-oriented architecture that synthesizes and extends a number of technologies to provide a standardized framework for the advertising, discovery, and invocation of data and analytical resources. We expect caGrid to greatly facilitate the launch and ongoing management of coordinated cancer research studies involving multiple institutions, to provide the ability to manage and securely share information and analytic resources, and to spur a new generation of research applications that empower researchers to take a more integrative, trans-domain approach to data mining and analysis.
Availability: The caGrid version 0.5 release can be downloaded from . The operational test bed Grid can be accessed through the client included in the release, or through the caGrid-browser web application .
Contact: joel.saltz@osumc.edu
Intramolecular surface contacts contain information about protein–protein interface regions
Authors: de Vries Sjoerd J. , Bonvin Alexandre M. J. J. 
Published: June 2006

Abstract
Motivation: Some amino acids clearly show preferences over others in protein–protein interfaces. These preferences, or so-called interface propensities can be used for a priori interface prediction. We investigated whether the prediction accuracy could be improved by considering not single but pairs of residues in an interface. Here we present the first systematic analysis of intramolecular surface contacts in interface prediction.
Results: We show that preferences do exist for contacts within and around an interface region within one molecule: specific pairs of amino acids are more often occurring than others. Using intramolecular contact propensities in a blind test, higher average scores were assigned to interface residues than to non-interface residues. This effect persisted as small but significant when the contact propensities were corrected to eliminate the influence of single amino acid interface propensity. This indicates that intramolecular contact propensities may replace interface propensities in protein–protein interface prediction.
Availability: The source code is available on request from the authors.
Contact: a.m.j.j.bonvin@chem.uu.nl
Supplementary Information: Supplementary data are available at Bioinformatics online.
A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS
Authors: Bellew Matthew , Coram Marc , Fitzgibbon Matthew , Igra Mark , Randolph Tim , Wang Pei , May Damon , Eng Jimmy , Fang Ruihua , Lin ChenWei , Chen Jinzhi , Goodlett David , Whiteaker Jeffrey , Paulovich Amanda , McIntosh Martin 
Published: June 2006

Abstract
Motivation: Comparing two or more complex protein mixtures using liquid chromatography mass spectrometry (LC-MS) requires multiple analysis steps to locate and quantitate natural peptides within a single experiment and to align and normalize findings across multiple experiments.
Results: We describe msInspect, an open-source application comprising algorithms and visualization tools for the analysis of multiple LC-MS experimental measurements. The platform integrates novel algorithms for detecting signatures of natural peptides within a single LC-MS measurement and combines multiple experimental measurements into a peptide array, which may then be mined using analysis tools traditionally applied to genomic array analysis. The platform supports quantitation by both label-free and isotopic labeling approaches. The software implementation has been designed so that many key components may be easily replaced, making it useful as a workbench for integrating other novel algorithms developed by a growing research community.
Availability: The msInspect software is distributed freely under an Apache 2.0 license. The software as well as a Zip file with all peptide feature files and scripts needed to generate the tables and figures in this article are available at
Contact: mmcintos@fhcrc.org
Supplementary Information: Supplementary materials are available at (select ‘Published Experiments’ from the list of Projects and then ‘msInspect Paper’).
JADE: a distributed Java application for deleterious genomic mutation (DGM) estimation
Authors: Li J.-L. , Li M.-X. , Guo Y.-F. , Deng H.-Y. , Deng H.-W. 
Published: June 2006

Abstract
Summary: The characterization of deleterious genomic mutation (DGM) is of central significance for evolutionary biology and genetic studies. Fitness moment method has been developed to efficiently characterize DGM from natural population directly. In order to enable researchers to employ this method for theoretical and empirical research on characterizing DGM, we here present a distributed Java Application for DGM Estimation (JADE).
Availability:
Contact: Jinlong.Li@sbri.org
Transcriptome network component analysis with limited microarray data
Authors: Galbraith Simon J. , Tran Linh M. , Liao James C. 
Published: June 2006

Abstract
Summary: Network component analysis (NCA) is a method to deduce transcription factor (TF) activities and TF-gene regulation control strengths from gene expression data and a TF-gene binding connectivity network. Previously, this method could analyze a maximum number of regulators equal to the total sample size because of the identifiability limit in data decomposition. As such, the total number of source signal components was limited to the total number of experiments rather than the total number of biological regulators. However, networks that have less transcriptome data points than the number of regulators are of interest. Thus it is imperative to develop a theoretical basis that allows realistic source signal extraction based on relatively few data points. On the other hand, such methods would inherently increase numerical challenges leading to multiple solutions. Therefore, solutions to both the problems are needed.
Results: We have improved NCA for transcription factor activity (TFA) estimation, based on the observation that most genes are regulated by only a few TFs. This observation leads to the derivation of a new identifiability criterion which is tested during numerical iteration that allows us to decompose data when the number of TFs is greater than the number of experiments. To show that our method works with real microarray data and has biological utility, we analyze Saccharomyces cerevisiae cell cycle microarray data (73 experiments) using a TF-gene connectivity network (96 TFs) derived from ChIP-chip binding data. We compare the results of NCA analysis with the results obtained from ChIP-chip regression methods, and we show that NCA and regression produce TFAs that are qualitatively similar, but the NCA TFAs outperform regression in statistical tests. We also show that NCA can extract subtle TFA signals that correlate with known cell cycle TF function and cell cycle phase. Overall we determined that 31 TFs have statistically periodic TFAs in one or more experiments, 75% of which are known cell cycle regulators. In addition, we find that the 12 TFAs that are periodic in two or more experiments correspond to well-known cell cycle regulators. We also investigated TFA sensitivity to the choice of connectivity network we constructed two networks using different ChIP-chip p-value cut-offs.
Availability: The NCA Toolbox for MATLAB is available at
Contact: liaoj@seas.ucla.edu
Evolutionary simulations to detect functional lineage-specific genes
Authors: Dupanloup Isabelle , Kaessmann Henrik 
Published: June 2006

Abstract
Motivation: Supporting the functionality of recent duplicate gene copies is usually difficult, owing to high sequence similarity between duplicate counterparts and shallow phylogenies, which hamper both the statistical and experimental inference.
Results: We developed an integrated evolutionary approach to identify functional duplicate gene copies and other lineage-specific genes. By repeatedly simulating neutral evolution, our method estimates the probability that an ORF was selectively conserved and is therefore likely to represent a bona fide coding region. In parallel, our method tests whether the accumulation of non-synonymous substitutions reveals signatures of selective constraint. We show that our approach has high power to identify functional lineage-specific genes using simulated and real data. For example, a coding region of average length (∼1400 bp), restricted to hominoids, can be predicted to be functional in ∼94–100% of cases. Notably, the method may support functionality for instances where classical selection tests based on the ratio of non-synonymous to synonymous substitutions fail to reveal signatures of selection. Our method is available as an automated tool, ReEVOLVER, which will also be useful to systematically detect functional lineage-specific genes of closely related species on a large scale.
Availability: ReEVOLVER is available at .
Contact: Henrik.Kaessmann@unil.ch
Supplementary Data: Supplementary Data are available at Bioinformatics online.