bluuebunny/crossref_metadata_2025 huggingface dataset:
An ontology for collaborative construction and analysis of cellular pathways
Authors: Demir E. , Babur O. , Dogrusoz U. , Gursoy A. , Ayaz A. , Gulesir G. , Nisanci G. , Cetin-Atalay R.
Published: February 2004

Motivation: As the scientific curiosity in genome studies shifts toward identification of functions of the genomes in large scale, data produced about cellular processes at molecular level has been accumulating with an accelerating rate. In this regard, it is essential to be able to store, integrate, access and analyze this data effectively with the help of software tools. Clearly this requires a strong ontology that is intuitive, comprehensive and uncomplicated.

Results: We define an ontology for an intuitive, comprehensive and uncomplicated representation of cellular events. The ontology presented here enables integration of fragmented or incomplete pathway information via collaboration, and supports manipulation of the stored data. In addition, it facilitates concurrent modifications to the data while maintaining its validity and consistency. Furthermore, novel structures for representation of multiple levels of abstraction for pathways and homologies is provided. Lastly, our ontology supports efficient querying of large amounts of data.

We have also developed a software tool named pathway analysis tool for integration and knowledge acquisition (PATIKA) providing an integrated, multi-user environment for visualizing and manipulating network of cellular events. PATIKA implements the basics of our ontology.

Availability: PATIKA version 1.0 beta is available upon request at http://www.patika.org
Advanced significance analysis of microarray data based on weighted resampling: a comparative study and application to gene deletions in Mycobacterium bovis
Authors: Kutalik Zoltan , Inwald Jacqueline , Gordon Steve V. , Hewinson R. Glyn , Butcher Philip , Hinds Jason , Cho Kwang-Hyun , Wolkenhauer Olaf
Published: February 2004

Motivation: When analyzing microarray data, non-biological variation introduces uncertainty in the analysis and interpretation. In this paper we focus on the validation of significant differences in gene expression levels, or normalized channel intensity levels with respect to different experimental conditions and with replicated measurements. A myriad of methods have been proposed to study differences in gene expression levels and to assign significance values as a measure of confidence. In this paper we compare several methods, including SAM, regularized t-test, mixture modeling, Wilk's lambda score and variance stabilization. From this comparison we developed a weighted resampling approach and applied it to gene deletions in Mycobacterium bovis.

Results: We discuss the assumptions, model structure, computational complexity and applicability to microarray data. The results of our study justified the theoretical basis of the weighted resampling approach, which clearly outperforms the others.

Availability: Algorithms were implemented using the statistical programming language R and available on the author's web-page.

Supplementary information: For additional material see http://www.sbi.uni-rostock.de/
Non-parametric, hypothesis-based analysis of microarrays for comparison of several phenotypes
Authors: Kowalski Jeanne , Drake Charles , Schwartz Ronald H. , Powell Jonathan
Published: February 2004

Motivation: We present a statistical framework for the analysis of high-dimensional microarray data, where the goal is to compare intensities among several groups based on as few as a single sample from each group. In this setting, it is of interest to compare gene expression among several phenotypes to define candidate genes that simultaneously characterize several criteria, simultaneously, among the comparison groups. We motivate the approach by a comparative microarray experiment in which clones of a cell were singly exposed to several distinct but related conditions. The experiment was conducted to elucidate genes involved in pathways leading to T cell clonal anergy.

Results: By integrating inference principles within a bioinformatics setting, we introduce a two-stage approach to select candidate genes that characterize several criteria. The method is unified in its non-parametric approach to inference and description. For inference, we construct a testable hypothesis based on the criteria of interest in a high-dimensional space, while preserving the dependence among genes. Upon rejecting the null, we estimate the cardinality of a set of individual candidate genes (or gene pairs) that depict the events of interest. With this estimate, we then select individual genes (or gene pairs) based upon a two-dimensional ranking that examines relations within and between genes, among comparison groups, using singular value decomposition in combination with inner product concepts.

Availability: The functions developed for obtaining results from our approach are available upon request. A detailed documentation of the methods and the experiment may be obtained from http://www.cancerbiostats.onc.jhmi.edu/Kowalski.htm
Is cross-validation valid for small-sample microarray classification?
Authors: Braga-Neto Ulisses M. , Dougherty Edward R.
Published: February 2004

Motivation: Microarray classification typically possesses two striking attributes: (1) classifier design and error estimation are based on remarkably small samples and (2) cross-validation error estimation is employed in the majority of the papers. Thus, it is necessary to have a quantifiable understanding of the behavior of cross-validation in the context of very small samples.

Results: An extensive simulation study has been performed comparing cross-validation, resubstitution and bootstrap estimation for three popular classification rules—linear discriminant analysis, 3-nearest-neighbor and decision trees (CART)—using both synthetic and real breast-cancer patient data. Comparison is via the distribution of differences between the estimated and true errors. Various statistics for the deviation distribution have been computed: mean (for estimator bias), variance (for estimator precision), root-mean square error (for composition of bias and variance) and quartile ranges, including outlier behavior. In general, while cross-validation error estimation is much less biased than resubstitution, it displays excessive variance, which makes individual estimates unreliable for small samples. Bootstrap methods provide improved performance relative to variance, but at a high computational cost and often with increased bias (albeit, much less than with resubstitution).

Availability and Supplementary information: A companion web site can be accessed at the URL http://ee.tamu.edu/~edward/cv_paper. The companion web site contains: (1) the complete set of tables and plots regarding the simulation study; (2) additional figures; (3) a compilation of references for microarray classification studies and (4) the source code used, with full documentation and examples.
A graph-theoretic modeling on GO space for biological interpretation of gene clusters
Authors: Lee Sung Geun , Hur Jung Uk , Kim Yang Seok
Published: February 2004

Motivation: With the advent of DNA microarray technologies, the parallel quantification of genome-wide transcriptions has been a great opportunity to systematically understand the complicated biological phenomena. Amidst the enthusiastic investigations into the intricate gene expression data, clustering methods have been the useful tools to uncover the meaningful patterns hidden in those data. The mathematical techniques, however, entirely based on the numerical expression data, do not show biologically relevant information on the clustering results.

Results: We present a novel methodology for biological interpretation of gene clusters. Our graph theoretic algorithm extracts common biological attributes of the genes within a cluster or a group of interest through the modified structure of gene ontology (GO) called GO tree. After genes are annotated with GO terms, the hierarchical nature of GO terms is used to find the representative biological meanings of the gene clusters. In addition, the biological significance of gene clusters can be assessed quantitatively by defining a distance function on the GO tree. Our approach has a complementary meaning to many statistical clustering techniques; we can see clustering problems from a different viewpoint by use of biological ontology. We applied this algorithm to the well-known data set and successfully obtained the biological features of the gene clusters with the quantitative biological assessment of clustering quality through GO Biological Process.

Availability: The software is available on request from the authors.
Knowledge discovery by automated identification and ranking of implicit relationships
Authors: Wren Jonathan D. , Bekeredjian Raffi , Stewart Jelena A. , Shohet Ralph V. , Garner Harold R.
Published: February 2004

Motivation: New relationships are often implicit from existing information, but the amount and growth of published literature limits the scope of analysis an individual can accomplish. Our goal was to develop and test a computational method to identify relationships within scientific reports, such that large sets of relationships between unrelated items could be sought out and statistically ranked for their potential relevance as a set.

Results: We first construct a network of tentative relationships between ‘objects’ of biomedical research interest (e.g. genes, diseases, phenotypes, chemicals) by identifying their co-occurrences within all electronically available MEDLINE records. Relationships shared by two unrelated objects are then ranked against a random network model to estimate the statistical significance of any given grouping. When compared against known relationships, we find that this ranking correlates with both the probability and frequency of object co-occurrence, demonstrating the method is well suited to discover novel relationships based upon existing shared relationships. To test this, we identified compounds whose shared relationships predicted they might affect the development and/or progression of cardiac hypertrophy. When laboratory tests were performed in a rodent model, chlorpromazine was found to reduce the progression of cardiac hypertrophy.

Supplementary information:  http://innovation.swmed.edu/IRIDESCENT/Supplemental_Info.htm
LDDist: a Perl module for calculating LogDet pair-wise distances for protein and nucleotide sequences
Authors: Thollesson Mikael
Published: February 2004

Summary:  LDDist is a Perl module implemented in C++ that allows the user to calculate LogDet pair-wise genetic distances for amino acid as well as nucleotide sequence data. It can handle site-to-site rate variation by treating a proportion of the sites as invariant and/or by assigning sites to different, presumably homogenous, rate categories. The rate-class assignments and invariant proportion can be set explicitly, or estimated by the program; the latter using either of two different capture–recapture methods. The assignment to rate categories in lieu of a phylogeny can be done using Shannon–Wiener index as a crude token for relative rate.

Availability:  LDDist and its companion Perl script PLD are freely available at http://artedi.ebc.uu.se/molev/software/LDDist.html
Predicting protein secondary structure by cascade-correlation neural networks
Authors: Wood Matthew J. , Hirst Jonathan D.
Published: February 2004

Summary: The back-propagation neural network algorithm is a commonly used method for predicting the secondary structure of proteins. Whilst popular, this method can be slow to learn and here we compare it with an alternative: the cascade-correlation architecture. Using a constructive algorithm, cascade-correlation achieves predictive accuracies comparable to those obtained by back-propagation, in shorter time.

Availability: A web server is available to a trained cascade-correlation neural network, with links to the source code for both algorithms.
SVM based method for predicting HLA-DRB1*0401 binding peptides in an antigen sequence
Authors: Bhasin Manoj , Raghava G. P. S.
Published: February 2004

Summary: Prediction of peptides binding with MHC class II allele HLA-DRB1*0401 can effectively reduce the number of experiments required for identifying helper T cell epitopes. This paper describes support vector machine (SVM) based method developed for identifying HLA-DRB1*0401 binding peptides in an antigenic sequence. SVM was trained and tested on large and clean data set consisting of 567 binders and equal number of non-binders. The accuracy of the method was 86% when evaluated through 5-fold cross-validation technique.

Available: A web server HLA-DR4Pred based on above approach is available at http://www.imtech.res.in/raghava/hladr4pred/ and http://bioinformatics.uams.edu/mirror/hladr4pred/ (Mirror Site).

Supplementary information:  http://www.imtech.res.in/raghava/hladr4pred/info.html
Metrics for comparing regulatory sequences on the basis of pattern counts
Authors: van Helden Jacques
Published: February 2004

Motivation: Upstream sequences contain short motifs, which mediate transcriptional regulation by specifically binding different transcription factors. The presence of common motifs in the regulatory regions of two genes might be considered as a clue for a potential co-regulation. A pattern count-based (dis)similarity metric between sequences could thus be used to classify genes according to their putative regulatory properties.

Results: We present here several metrics which rely on probability theory, and which aim at comparing sequences on the basis of pattern counts. We compare these metrics to several classical dissimilarity and similarity metrics, and illustrate their behaviour with a biological example.

Supplementary information: The data, results, and R routines used in this paper are freely available at http://rsat.ulb.ac.be/rsat/published_data/pattern_count_metrics_2003/
PIVOT: Protein Interacions VisualizatiOn Tool
Authors: Orlev Nir , Shamir Ron , Shiloh Yosef
Published: February 2004

Summary: Protein Interaction VisualizatiOn Tool (PIVOT) is a visualization tool for protein–protein interactions. It allows the user to create personal data sets of interactions by combining information from private and public data sources. The user can gradually access the interactions' data using a clear interactive map that is focused on the researcher's protein of interest, and is reshaped and expanded in response to his/her queries. It also offers several visual enhancements and intelligent queries that help the user efficiently study it. PIVOT allows the user to search the interactions data set for paths connecting proteins that are expected to co-operate. The user can also employ PIVOT to predict unknown interactions among proteins, based on interactions among their homologous proteins in other species.

Availability: Freely available for academic users, at http://www.cs.tau.ac.il/~rshamir/pivot

Supplementary information: A demonstration video clip is available at http://www.cs.tau.ac.il/~rshamir/pivot/Demo.avi
Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference
Authors: Altekar Gautam , Dwarkadas Sandhya , Huelsenbeck John P. , Ronquist Fredrik
Published: February 2004

Motivation: Bayesian estimation of phylogeny is based on the posterior probability distribution of trees. Currently, the only numerical method that can effectively approximate posterior probabilities of trees is Markov chain Monte Carlo (MCMC). Standard implementations of MCMC can be prone to entrapment in local optima. Metropolis coupled MCMC [(MC)3], a variant of MCMC, allows multiple peaks in the landscape of trees to be more readily explored, but at the cost of increased execution time.

Results: This paper presents a parallel algorithm for (MC)3. The proposed parallel algorithm retains the ability to explore multiple peaks in the posterior distribution of trees while maintaining a fast execution time. The algorithm has been implemented using two popular parallel programming models: message passing and shared memory. Performance results indicate nearly linear speed improvement in both programming models for small and large data sets.

Availability: MrBayes v3.0 is available at http://morphbank.ebc.uu.se/mrbayes/
The Jalview Java alignment editor
Authors: Clamp Michele , Cuff James , Searle Stephen M. , Barton Geoffrey J.
Published: February 2004

Summary: Multiple sequence alignment remains a crucial method for understanding the function of groups of related nucleic acid and protein sequences. However, it is known that automatic multiple sequence alignments can often be improved by manual editing. Therefore, tools are needed to view and edit multiple sequence alignments. Due to growth in the sequence databases, multiple sequence alignments can often be large and difficult to view efficiently. The Jalview Java alignment editor is presented here, which enables fast viewing and editing of large multiple sequence alignments.

Availability: The Jar file and source code for Jalview is freely available via the World Wide Web at http://www.jalview.org. A Jalview mailing list is also available by e-mailing majordomo@sanger.ac.uk with subscribe Jalview in the body of the mail.
SEPON, a Selection and Evaluation Pipeline for OligoNucleotides based on ESTs with a non-target Tm algorithm for reducing cross-hybridization in microarray gene expression experiments
Authors: Hornshøj Henrik , Stengaard Henrik , Panitz Frank , Bendixen Christian
Published: February 2004

Summary: SEPON, Selection and Evaluation Pipeline for OligoNucleotide generates n-mer oligonucleotide sequences from expressed sequence tags of non-annotated genomes for microarray gene-expression profiling. A non-target melting temperature (Tm) algorithm will reduce cross-hybridization by estimating Tm of oligonucleotide hybridization to non-specific targets (non-target Tm) and discard oligonucleotides with non-target Tm estimate above user-defined threshold. SEPON allows user-defined filtering, predicts exon location, assigns penalty based on 3′ distance, GC content, secondary structure Tm and non-target Tm and ranks oligonucleotides for optimal selection.

Availability: The program is freely available for non-commercial and academic use under the GNU General Public License and is obtained upon request to authors.

Supplementary information:  http://www.agrsci.dk/hag/sepon/
Gene specific siRNA selector
Authors: Levenkova Natasha , Gu Qingjuan , Rux John J.
Published: February 2004

Summary: Small interfering RNA (siRNA) is used in functional genomics applications to decrease the expression of a target gene, which may yield a biological effect that suggests a function for the target gene. The siRNA design tool scans a target gene for candidate siRNA sequences that satisfy user-adjustable rules. Selected candidates are then screened to identify those siRNA sequences that are specific to the gene of interest.

Availability: A web tool is freely available for academic or commercial use at http://bioinfo.wistar.upenn.edu/siRNA/siRNA.htm. Source code is available upon request.

Supplementary information: See http://bioinfo.wistar.upenn.edu/siRNA/siRNA.htm for additional documentation and help pages.
VisCoSe: visualization and comparison of consensus sequences
Authors: Spitzer Michael , Fuellen Georg , Cullen Paul , Lorkowski Stefan
Published: February 2004

Summary: We introduce visualization and comparison of consensus sequences (VisCoSe) as a WWW service and a stand-alone command line Perl script for visualizing and comparing consensus sequences of protein and nucleotide sequences. VisCoSe is the only interface available that simultaneously calculates consensus sequences of multiple data sets and automatically compares these consensus sequences. Furthermore, VisCoSe allows visualization of chemical properties of amino acids.

Availability:  http://viscose.ifg.uni-muenster.de/
HIVbase: a PC/Windows-based software offering storage and querying power for locally held HIV-1 genetic, experimental and clinical data
Authors: Lamers Susanna , Beason Scott , Dunlap Luke , Compton Robert , Salemi Marco
Published: February 2004

Background: Human immunodeficiency virus (HIV) research involves ongoing, repetitious sequencing of the HIV genome and the massive accumulation of associated investigational data. As a result, the storage of annotated DNA and/or protein sequences, as well as information retrieval, have become increasingly difficult tasks, with scientists extracting less information from their collected data than they should.

Objectives: Our objective was to design and develop a software package to aid researchers in the storage, analysis and exploration of their HIV-associated data.

Results: HIVbase contains familiar, easy-to-use interfaces and functionality for integrating many types of disparate data. The software contains tools that allow for the mass import of raw genetic data, eliminate repetitious sequence translations, have the ability to identify automatically and store HIV regions of interest from nucleic acid or protein sequences, allow for the export of data in commonly used analysis-ready formats, and for unique querying approaches.
Frequency Finder: a multi-source web application for collection of public allele frequencies of SNP markers
Authors: Nguyen Tu H. , Liu Chunyu , Gershon Elliot S. , McMahon Francis J.
Published: February 2004

Summary: Publicly available single nucleotide polymorphism (SNP) allele frequencies are an important resource for the selection of genetic markers that may be most useful for gene mapping and association studies. Data mining these allele frequencies through disparate public databases and Websites is time consuming and can result in inconsistent findings. We have developed a web-based software tool, Frequency Finder, to acquire SNP allele frequencies from multiple public data sources and return a summarized result to the user. Our software optimizes and automates the search of candidate markers, decreasing the amount of time it would take to extract pertinent data manually. We have included several methods to output the data, including on-screen and as a compressed text file. We show that Frequency Finder accurately retrieves available frequency data from the available sources. Using this tool, we detect significant differences between Asian, African and Caucasian populations in the allele frequency spectra of 246 097 SNPs. While limited to public databases that provide web-based access to allele frequencies, Frequency Finder provides a single, user-friendly interface for retrieving allele frequencies for large batches of SNPs from multiple data sources.

Availability: Frequency Finder is available for public use at http://mapgenetics.nimh.nih.gov/frequencyfinder and at http://bluegenes.bsd.uchicago.edu/frequencyfinder
Development and freedom
Authors: Prendergast Renee
Published: February 2004

This paper is an attempt to understand how Amartya Sen's thinking on development and freedom has evolved from his critique of welfare economics and his concern with underdevelopment and poverty. It is argued that Sen has done a great deal to rescue welfare economics from the consequences of methodological individualism by seeking an objective basis for comparisons of well‐being, by insisting on the need for interpersonal comparability and by creating a space for normative evaluations. Sen's contribution to the human development approach with its emphasis on positive freedom has also helped to provide a valuable counterweight to the dominant free market approach. However, some concerns are expressed that the approach does not give sufficient attention to long‐run dynamics and that the conception of capability employed is not helpful for the understanding of development
The Law: The Clinton Impeachment: Untangling the Web of Conflicting Considerations
Authors: KASSOP NANCY
Published: February 2004

Impeachment is a complex, tumultuous, and unpredictable process with multiple decision points where constitutional, legal, political, and institutional factors play equally critical and often irreconcilable roles. The Clinton impeachment illustrated that decisions at each step for each player produced benefits in one arena (e.g., political), but often at a cost in others (e.g., constitutional, institutional, or legal). Calculations (and miscalculations) were made by all players at every point. Ultimately, this vexing and inconsistent process may be exactly what the framers intended—to ensure that impeachments and removals would be rare and would succeed only when a slow, deliberative unfolding of tangled, decisional steps produced a bipartisan outcome.
The Polls: Public Attitudes toward the First Lady
Authors: COHEN JEFFREY E.
Published: February 2004

During Hillary Clinton's First Ladyship, public and poll interest in the First Lady surged as a function of Mrs. Clinton's active public, political, and policy presence. Does such an active First Lady have consequences for public evaluations of the president? I address this question by looking at “job approval” poll data on the First Lady and President Clinton. Although their polls are highly correlated, no causal connection between public evaluations of the First Lady and the president seems to exist.
The White House Counsel's Office
Authors: BORRELLI MARYANNE , HULT KAREN , KASSOP NANCY
Published: February 2004

The Office of White House Counsel sits at the intersection of law, politics, and policy. Its distinctive challenge is to advise the president to take actions that are both legally sound and politically astute. Often called “the president's lawyer,” the counsel's office serves, more accurately, as the “presidency's lawyer,” with tasks that extend well beyond the exclusively legal. Drawing on interviews with previous occupants of the office, the authors examine the unit's numerous activities, its place in the larger White House and executive branch, and the experiences of those who have served as counsel.
Lyndon Johnson, Community Action, and Management of the Administrative State
Authors: FLANAGAN RICHARD M.
Published: February 2004

The Community Action Program (CAP) was one of the highest‐profile but least successful of President Johnson's Great Society programs. Pluralist and neo‐Marxist theories hold that the origins of CAP and the problems that the program encountered were rooted in the politics of interest group and racial conflict, respectively. Drawing on archival evidence, this article turns attention to the important, yet forgotten, administrative dimension of CAP. The decentralized features of CAP were developed as a strategy to manage the federal bureaucracy and avoid conflict with Congress. Ultimately, CAP floundered as the decentralized control of the program freed it from the political control of the White House. The article concludes with a discussion of the problems presidents face in managing the federal bureaucracy and how the development of CAP reflects Johnson's management style in enacting domestic policy goals.
The Office of Communications
Authors: KUMAR MARTHA JOYNT
Published: February 2004

The Office of Communications is front and center in the White House effort to publicize the president and his policies. The importance of presidential communications can be seen in the manner in which the topic drives the agenda of daily staff meetings, the size of the commitment to it of White House and administration resources and people, and the way the function has insinuated itself into the operations of almost every White House office. While most White House offices are defined by the functions that come with the unit, the communications director's position is defined by his or her relationships with officials working inside and outside of the White House, including the president, the chief of staff, the press secretary, and officials in departments and agencies. There are three basic models for communications directors as they manage their operations: advocate with the press, strategist and planner, and events coordinator. At its minimum, the job entails events management, but its larger role is defining the message and strategic plan of a presidency.
The Little State Department: McGeorge Bundy and the National Security Council Staff, 1961‐65
Authors: PRESTON ANDREW
Published: February 2004

This article examines the alteration of the role, prerogatives, and power of the special assistant to the president for national security affairs, a position more commonly known as the national security adviser. Presidents Truman and Eisenhower conceived of and shaped the National Security Council(NSC) and its staff to be administrative in their responsibilities and character. Under President Kennedy, McGeorge Bundy utterly changed this, concentrating power and decision‐making authority in the hands of the special assistant and his NSC staff at the White House. From 1961, the special assistant and NSC staff ceased to be administrators and became policy formulators actively engaged in the policy‐making process. This transformation occurred largely at the expense of the State Department and had profound consequences for American foreign policy, particularly toward the conflict in Vietnam.
Congressional Support of the President: A Comparison of Foreign, Defense, and Domestic Policy Decision Making during and after the Cold War
Authors: PRINS BRANDON C. , MARSHALL BRYAN W.
Published: February 2004

Recent research on congressional‐executive relations has concluded that partisan and ideological forces explaining decision making in domestic policy have also become dominant in the realm of foreign policy. Accordingly, scholars have inferred the effective demise of the two‐presidencies. In this analysis, the authors compare models explaining bipartisan congressional support of the president on domestic issues with that of foreign and defense. Although factors relating to the congressional context tended to be influential in both policy areas, they found important differences in the effects of factors relating to the international context. They also found that congressional bipartisan support was significantly less likely on matters related to the purse strings and on issues such as trade. The contrasting effects of the explanatory factors across policy areas suggest the importance of both the two‐presidencies and resurgent Congress perspectives in explaining congressional‐executive interactions.
Losing Control: The Intraparty Consequences of Divided Government
Authors: ROSE MELODY
Published: February 2004

Divided government scholarship focuses either on evaluating divided government's correlation to legislative gridlock or on its tendency toward interparty squabbling. I argue that one overlooked aspect of divided government is its impact on intraparty dynamics: Divided government offers the controlling congressional party incentives to raise controversial issues to damage the coherence of the president's party. Revealing the tensions within the president's party serves to embarrass the president, increase the electoral chances of the majority party in Congress, and ultimately shift public policy. This phenomenon can be understood through Riker's theory of heresthetic. The contemporary debates between President Clinton and the Republican‐controlled Congress over abortion and gay rights provide ample evidence that this theory of divided government is compelling and war‐rants further consideration.
The Two Presidencies, 1984‐98: A Replication and Extension
Authors: SCHRAUFNAGEL SCOT , SHELLMAN STEPHEN M.
Published: February 2004

Aaron Wildavsky first proposed that presidents in the United States receive more support from Congress in foreign policy and thus can expect to wield more influence and discretion in this policy arena. Since that time, scholars have scrutinized Wildavsky's contention. A recent work by Fleisher et al., using a new measure of presidential support, argues convincingly that broad generalizations about the phenomenon of increased presidential support in foreign policy must be drawn tentatively. This article addresses the two‐presidencies thesis in three ways. First, the authors replicate a portion of Edwards's research to illustrate the reliability of our results. Second, the authors extend the data collection on more traditional measures used to test this thesis. Third, to address the issue of intermestic policy, the authors employ a new measure of presidential support that more carefully defines foreign and domestic policy actions. The analyses confirm the findings of Fleisher et al. and Edwards that the two‐presidencies phenomenon is largely idiographic.
The Contemporary Presidency: The Pressures of White House Work Life: “Naked in a Glass House”
Authors: KUMAR MARTHA JOYNT
Published: February 2004

The White House is a place where the work load is heavy, the hours are long, the pressures are great, and the benefits are manyfold. As hard as people say the work is, few would trade the time they spent working in the White House; nor is there a shortage of people wanting to work there. The pressures of White House work life relate to the volume and variety of the assignments, the heavy commitment of hours and days, the generous amount of criticism directed toward the president and individual White House staff members, and the narrow margin of error allowed to those working for the president. Although less numerous than the pressures, the benefits are an important component of White House work life. They revolve around the importance of the decisions made in a White House, the interesting people and situations one confronts when working in a White House, the increased likelihood of having an interesting and lucrative career after having the White House, and having a part in history as it is made.
The Law: The “Protective Return” Pocket Veto: Presidential Aggrandizement of Constitutional Power
Authors: SPITZER ROBERT J.
Published: February 2004

This article discusses the all‐but‐unknown practice of recent presidents to exercise a so‐called “protective return” veto, whereby presidents simultaneously exercise both a return veto and a pocket veto for individual bills. Defended by recent administrations as a defense of the existing pocket veto power, this article argues that it is in fact an attempt to create a practical absolute veto, a power rejected by the Constitution's founders. Veto history and evolution are examined to explain and analyze this effort to redefine the president's constitutional veto authority.
The Polls: Change and Stability in Public Assessments of Personal Traits, Bill Clinton, 1993‐99
Authors: COHEN JEFFREY E.
Published: February 2004

This article looks at changes in public perceptions of President Clinton's personal characteristics across his eight years in office. Utilizing a battery of questions that the Gallup Poll repeatedly asked of the public, we find that on issues of character, the public's views of Clinton became increasingly negative. In contrast, on issues of competence, public regard for Clinton rose. These findings are put into a theoretical context of the relationship between the president and the mass public rather than a narrow focus on Clinton's term in office.
Deregulation in the Electric Utility Industry: Excess Capacity and the Transition to a Long‐Run Competitive Market
Authors: Thompson Eric , Scott Frank , Berger Mark
Published: February 2004

ABSTRACT  Existing analyses of electricity deregulation have focused on situations where horizontal market power is present. This paper instead evaluates a market where a competitive outcome is more likely. Competitive market supply and demand curves for electricity have been simulated for a twenty‐state region. These simulated supply and demand curves are used to predict short‐run and long‐run prices for electric power. Many consumers will see a drop in the portion of their electric bills accounted for by the current economic costs of supplying them with electricity. Adjustments to consumers’ bills for stranded cost recovery will be determined by legislators and regulators on a state‐by‐state and utility‐by‐utility basis. Because of excess capacity that currently exists in the industry, the decline in prices will be greater in the short run than in the long run.
The Impact of Industrial Restructuring on Earnings Inequality: The Decline of Steel and Earnings in Pittsburgh
Authors: Beeson Patricia , Tannery Fredrick
Published: February 2004

ABSTRACT  Inter‐industry employment shifts were largely responsible for changes in the income distribution in the Pittsburgh region during the 1980s. Kernel density estimators were used, together with decomposition techniques developed by DiNardo et al. (1996) to show that industry shifts were responsible for over 90 percent of the earnings reductions at some points on the earnings distribution. Most of the losses at the lower end of the distribution occurred in the early 1980s as the economy plunged into a deep recession. The recovery in the later part of the decade brought little improvement as earnings in the lower part of the distribution continued to fall with the increase in employment of part‐time workers in the low‐wage trade and service sectors.
Interactions Between Economic Growth and Environmental Quality in U.S. Counties
Authors: Pagoulatos Angelos , Goetz Stephan J. , Debertin David L. , Johannson Tulin
Published: February 2004

ABSTRACT  Linkages among changes in employment, earnings per worker, and pollution per square mile are estimated for 3,036 U.S. counties for the period 1987 to 1995 using a three‐equation disequilibrium adjustment model. Counties with higher shares of African‐Americans experienced higher earnings growth rates over the period 1987‐1995, as did counties with proportionally more females. Counties in states with higher shares of unionized workers had higher earnings growth rates but generated fewer new jobs. Firm size had a significant and negative effect on earnings growth while higher costs of living were associated with higher earnings growth. Also, metro counties and counties in the Northeastern U.S. experienced higher earnings growth than their non‐metro counterparts and counties in other geographic regions. Statistically, faster job growth was found to accelerate the rate of earnings growth per worker. The authors conclude that counties concerned with job growth should recruit or attempt to spawn the creation of larger firms, recognizing that for some firms such a strategy may come at the cost of more rapid increases in pollution. Counties concerned with increasing the rate of growth in per worker earnings should instead focus on the creation of smaller firms.
50 Years AfterBrown v. Board of Education: The Promise and Challenge of Multicultural Education
Authors: Zirkel Sabrina , Cantor Nancy
Published: February 2004

We discuss the legacy of Brown for today's students and today's schools, and find that legacy is more psychological than legal. The decision does more to highlight issues of equity in education and how that influences students' identity, motivation, and aspirations than it does help us find legal means of addressing these concerns. The manuscripts presented in this issue articulate how today's students experience these issues. The manuscripts focus on several important aspects of interethnic contact in education: the processes by which interethnic contact leads to attitude and behavior change towards outgroup members, the effect of racial and ethnic integration on educational and developmental outcomes for students of color, and the promise that multicultural multiracial educational environments hold for all students.
The Benefits of Diversity in Education for Democratic Citizenship
Authors: Gurin Patricia , Nagda Biren (Ratnesh) A. , Lopez Gretchen E.
Published: February 2004

The social science statement in Brown v. Board of Education (1954) stressed that desegregation would benefit both African American and White children. Eventually, it was recognized that integration, rather than mere desegregation, was important for benefits to be realized. A parallel argument is made in the legal cases concerning affirmative action in higher education: educational benefits of diversity depend on curricular and co‐curricular experience with diverse peers, not merely on their co‐existence in the same institution (Gurin, P., 1999, Gurin, Dey, Hurtado, & Gurin, 2002). Positive benefits of diversity were demonstrated in a study comparing students in a curricular diversity program with students in a matched control group (n = 174), and in a longitudinal survey of University of Michigan students (n = 1670).
Developing a More Inclusive Social Identity: An Elementary School Intervention
Authors: Houlette Melissa A. , Gaertner Samuel L. , Johnson Kelly M. , Banker Brenda S. , Riek Blake M. , Dovidio John F.
Published: February 2004

School integration, stimulated by the 1954 Brown v. Board of Education
decision, has influenced students' social and educational experiences. Drawing on practice and theory, we focus on strategies for improving intergroup relations. In a series of sessions over four‐weeks, 830 first and second grade children participated in Green Circle program activities designed to widen their circles of inclusion to include people who are different from themselves. Although the intervention did not influence children's biases in sharing or how happy they would be playing with others who were different from themselves based on race, sex, and weight, it did lead them to be more inclusive in selecting their most preferred playmate. Implications for friendship development and improvement in intergroup attitudes are considered.

He drew a circle that shut me out‐

 Heretic, rebel, a thing to flout.

 But love and I had the wit to win‐

 We drew a circle that took him in.

               —Edwin Markham (1936, p. 67)
What Will You Think of Me? Racial Integration, Peer Relationships and Achievement Among White Students and Students of Color
Authors: Zirkel Sabrina
Published: February 2004

Brown v. Board of Education(1954) emphasized that segregation in schools leads the stigmatized students to withdraw from and lower their educational and professional aspirations. I consider this process in a modern sample by examining the relationship between the number of friends students report having at school and their goals and plans and their enjoyment of achievement activities in a sample of elementary and middle school students (N= 80). Students of color were more isolated at school, and this isolation was negatively correlated with interest in academic work. Among White students, however, no relationship between social isolation and interest in academic work was found. Discussion focuses on the role of the social climate in fostering or inhibiting achievement among students of color.
Interethnic Contact, Curriculum, and Attitudes in the First Year of College
Authors: Lopez Gretchen E.
Published: February 2004

Since Brown v. Board of Education (1954), social scientists have argued that education is important to change in racial attitudes given opportunities for interethnic contact. Students today are presented, also, with opportunities for interethnic learning through curriculum and extracurricular programming. The importance of contact, curriculum, and residence hall programs for the attitudes of first‐year college students from three ethnic groups was examined. Students (n = 791) completed surveys at the beginning and end of the year. Regressions tested the relationships of these first‐year experiences to intergroup attitudes (awareness of ethnic inequality, support for policies addressing ethnic inequality) at the end of the first year, controlling for initial attitudes and background. Contact and curriculum were related to attitudes for European American students.
Is There an Inherent Mismatch Between How Black and White Students Expect to Succeed in College and What Their Colleges Expect from Them?
Authors: Brower Aaron M. , Ketterhagen Annemarie
Published: February 2004

Students enter college with expectations about how they will succeed; likewise, colleges configure their courses, resources, and activities according to implicit expectations of how their students will succeed. Data from 1079 students at 6 universities was used to explore whether college‐success matches existed for Black students attending historically black colleges and universities (HBCUs) and for White students attending predominantly white institutions (PWIs), and whether mismatches existed for Black students attending PWIs. Results confirmed these matches and mismatches, and suggested that Black students worked harder to persist at PWIs. So while Brown aimed to provide educational access across color lines, this study's implications are that once students enter college, they must be supported as individuals who succeed along many paths.
Family Life and School Experience: Factors in the Racial Identity Development of Black Youth in White Communities
Authors: Tatum Beverly Daniel
Published: February 2004

Eighteen middle‐class Black college students were interviewed in‐depth about their experiences growing up in predominantly White communities. Using Cross's model of racial identity development as a theoretical framework for analysis, case studies of three women and two men are presented to highlight the impact of varied parental socialization practices and school experiences on racial identity development. For all, positive same‐race peer relationships, information about African‐American achievements, the availability of role models, and the encouragement of significant adults were important for academic success and the beginning resolution of identity conflicts. The implications of these findings for understanding aspects of school integration and for developing relevant school‐based interventions are considered.
Shift Happens: Spanish and English Transmission Between Parents and Their Children
Authors: Hurtado Aída , Vega Luis A.
Published: February 2004

We examined evidence for linguistic bands in Spanish/English language shift. Linguistic bands, defined as the degree of individuals' exposure to a language they may not speak but nonetheless comprehend, facilitate English/Spanish bilingualism and increase linguistic diversity rather than English monolingualism. Data for this study came from the National Chicano Survey (Arce, 1982), the California Identity Project (Hurtado, Hayes‐Bautista, Valdez, & Hernández, 1992), a statewide survey, and a California rural town convenience sample. Our findings strongly suggest that Spanish to English shift does occur from one generation of Latinos to another, but the existence of linguistic bands results, also, in stable English/Spanish bilingualism. Finally, we discuss consequences of advocating “English‐Only” policies and their effects on educational equity and social justice.
Students' of Color and European American Students' Stigma‐Relevant Perceptions of University Instructors
Authors: Brown Lisa M. , Dobbins Heather
Published: February 2004

In classrooms students of color may experience stigma (i.e., concern about being stereotyped) because negative stereotypes of their intellect are salient. Two studies included African American, European American, and Latina/Latino female and male undergraduates. Study 1 (n= 86) demonstrated while students of color generally had positive expectations of teachers, their expectations declined when imagining class with a European American instructor who would repeatedly versus never evaluate their work or an ethnically matched instructor across conditions. Study 2 (n= 136) revealed all students had more positive expectations of culturally tolerant versus culturally intolerant instructors. Students of color more than European American students perceived that intolerant instructors could grade them unfairly. We discuss implications for ethnically diverse classrooms.