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5. Rhetoric versus Reality: What We Know and What We Need to Know about Vouchers and Charter Schools. Updated Edition

Author

RAND Education, Santa Monica, CA., Gill, Brian, Timpane, P. Mike, Ross, Karen E., Gill, Brian, Timpane, P. Mike, Ross, Karen E., and RAND Education, Santa Monica, CA.

Abstract

Education vouchers and charter schools are two of the most prominent and far-reaching forms of family-choice policies currently in evidence in the nation's elementary and secondary schools. As such, they present important challenges to the traditional provision of public education in schools that are created, governed, funded, and operated by state and local authorities. This update of Chapters One and Three of a book originally published in 2001 reviews the theoretical foundations for vouchers and charter schools and the empirical evidence of their effectiveness as set forth in hundreds of recent reports and studies. It incorporates a substantial amount of new evidence on achievement effects, and it also examines the ways in which multiple dimensions of policy design--such as targeting, funding levels and limitations, admissions policies, academic standards and assessments, and accountability--will determine the nature and extent of any specific program's impact. A comprehensive assessment is made of what is known about the effects of vouchers and charters in terms of not only academic achievement, but also family choice, equitable access, racial/ethnic integration, and civic socialization. The book discusses the important empirical questions that are as yet unresolved and considers the prospects for answering them in the future. Finally, it explores the details of the design of voucher and charter policies, concluding with recommendations for policymakers who are considering their enactment. [For the 2001 edition of this book, see ED461917.]

Published
2007

6. Rhetoric Versus Reality: What We Know and What We Need To Know about Vouchers and Charter Schools.

Author

Rand Corp., Santa Monica, CA., Gill, Brian P., Timpane, P. Michael, Ross, Karen E., Brewer, Dominic J., Gill, Brian P., Timpane, P. Michael, Ross, Karen E., Brewer, Dominic J., and Rand Corp., Santa Monica, CA.

Abstract

Two proposals for education reform are school vouchers and charter schools, both of which have raised controversy with regard to their effectiveness and efficiency. At the present time, there is insufficient evidence to provide a crisp, clear bottom-line judgment of the wisdom of voucher and charter programs. This book identifies and articulates the range of empirical questions that ought to be answered to assess the wisdom of policies promoting vouchers or charter schools. It examines the existing empirical evidence on these questions, providing a broad assessment of what is currently known about the effects of vouchers and charters in terms of academic achievement. Important unresolved empirical questions are discussed, and prospects for answering them in the future are considered. Many questions cannot be answered at all because of lack of research, notably matters involving total demand, supply response of educational providers, and the final impact on public schools. Design details of voucher and charter policies are also explored. Recommendations include enacting a program of vigorous research, that is not confined to choice programs. Better information on the performance of conventional public schools and alternative reform models is also needed. (Contains 319 references.) (RT)

Published
2001

7. Overview of the COVID-19 text mining tool interactive demonstration track in BioCreative VII

Author

Barcelona Supercomputing Center, Chatr-aryamontri, Andrew, Hirschman, Lynette, Ross, Karen E, Oughtred, Rose, Krallinger, Martin, Dolinski, Kara, Tyers, Mike, Korves, Tonia, Arighi, Cecilia N, Barcelona Supercomputing Center, Chatr-aryamontri, Andrew, Hirschman, Lynette, Ross, Karen E, Oughtred, Rose, Krallinger, Martin, Dolinski, Kara, Tyers, Mike, Korves, Tonia, and Arighi, Cecilia N

Abstract

The coronavirus disease 2019 (COVID-19) pandemic has compelled biomedical researchers to communicate data in real time to establish more effective medical treatments and public health policies. Nontraditional sources such as preprint publications, i.e. articles not yet validated by peer review, have become crucial hubs for the dissemination of scientific results. Natural language processing (NLP) systems have been recently developed to extract and organize COVID-19 data in reasoning systems. Given this scenario, the BioCreative COVID-19 text mining tool interactive demonstration track was created to assess the landscape of the available tools and to gauge user interest, thereby providing a two-way communication channel between NLP system developers and potential end users. The goal was to inform system designers about the performance and usability of their products and to suggest new additional features. Considering the exploratory nature of this track, the call for participation solicited teams to apply for the track, based on their system’s ability to perform COVID-19-related tasks and interest in receiving user feedback. We also recruited volunteer users to test systems. Seven teams registered systems for the track, and >30 individuals volunteered as test users; these volunteer users covered a broad range of specialties, including bench scientists, bioinformaticians and biocurators. The users, who had the option to participate anonymously, were provided with written and video documentation to familiarize themselves with the NLP tools and completed a survey to record their evaluation. Additional feedback was also provided by NLP system developers. The track was well received as shown by the overall positive feedback from the participating teams and the users., National Institutes of Health Office of Research Infrastructure Programs (R01OD010929 to M.T. and K.D.); Canadian Institutes of Health Research (FDN-167277 to M.T.); Canada Research Chair in Systems and Synthetic Biology (to M.T.); National Institutes of Health (2U24HG007822-08, 1R35 GM141873-01 to K.E.R. and C.N.A); Spanish Plan for the Advancement of Language Technology and Proyectos I+D+i2020-AI4PROFHEALTH (PID2020-119266RA-I00 to M.K.); MITRE (W56KGU-18-D-0004 to L.H. and T.K.). The views, opinions and/or findings contained in this report are those of the authors and should not be construed as an official government position, policy or decision., Peer Reviewed, Postprint (published version)

Published
2022

10. RESTful API for iPTMnet: a resource for protein post-translational modification network discovery

Author

Gavali, Sachin, Cowart, Julie, Chen, Chuming, Ross, Karen E, Arighi, Cecilia, and Wu, Cathy H

Subjects
Docker, RESTful API, Phosphoproteomics, Computational Biology, Proteins, Rust, Data Mining, Original Article, Post-Translational Modification, iPTMnet, Web Service, Cloud, Protein Processing, Post-Translational, Software
Abstract

iPTMnet is a bioinformatics resource that integrates protein post-translational modification (PTM) data from text mining and curated databases and ontologies to aid in knowledge discovery and scientific study. The current iPTMnet website can be used for querying and browsing rich PTM information but does not support automated iPTMnet data integration with other tools. Hence, we have developed a RESTful API utilizing the latest developments in cloud technologies to facilitate the integration of iPTMnet into existing tools and pipelines. We have packaged iPTMnet API software in Docker containers and published it on DockerHub for easy redistribution. We have also developed Python and R packages that allow users to integrate iPTMnet for scientific discovery, as demonstrated in a use case that connects PTM sites to kinase signaling pathways.

Published
2020

11. Alterations in the Global Proteome and Phosphoproteome in Third Generation EGFR TKI Resistance Reveal Drug Targets to Circumvent Resistance

Author

Zhang, Xu, primary, Maity, Tapan K., additional, Ross, Karen E., additional, Qi, Yue, additional, Cultraro, Constance M., additional, Bahta, Meriam, additional, Pitts, Stephanie, additional, Keswani, Meghana, additional, Gao, Shaojian, additional, Nguyen, Khoa Dang P., additional, Cowart, Julie, additional, Kirkali, Fatos, additional, Wu, Cathy, additional, and Guha, Udayan, additional

Published
2021
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12. Uncovering novel cell cycle players through the inactivation of securin in budding yeast

Author

Sarin, Sumeet, Ross, Karen E., Boucher, Lorrie, Green, Yvette, Tyers, Mike, and Cohen-Fix, Orna

Subjects
Genetics -- Research, Biological sciences
Abstract

Budding yeast securin/Pds1p, an inhibitor of the anaphase activator separase/Esp1p, is involved in several checkpoint pathways and in promoting Esp1p's nuclear localization. Using a modified synthetic genetic array (SGA) screen for genes that become essential in the absence of Pds1p, we uncovered roles for uncharacterized genes in cell cycle processes, including Esp1p activation.

Published
2004

13. The role of Cdh1p in maintaining genomic stability in budding yeast

Author

Ross, Karen E. and Cohen-Fix, Orna

Subjects
Genomes -- Physiological aspects, Chromosomes -- Genetic aspects, Proteins -- Genetic aspects, Mitosis -- Genetic aspects, Ubiquitin -- Physiological aspects, Ubiquitin -- Genetic aspects, Genetic regulation -- Physiological aspects, Cell cycle -- Genetic aspects, Biodegradation -- Genetic aspects, Chemical inhibitors -- Physiological aspects, Genetic research -- Analysis, Biological sciences
Abstract

Cdh1p, a substrate specificity factor for the cell cycle-regulated ubiquitin ligase, the anaphase-promoting complex/cyclosome (APC/C), promotes exit from mitosis by directing the degradation of a number of proteins, including the mitotic cyclins. Here we present evidence that Cdh1p activity at the M/[G.sub.1] transition is important not only for mitotic exit but also for high-fidelity chromosome segregation in the subsequent cell cycle. CDH1 showed genetic interactions with MAD2 and PDS1, genes encoding components of the mitotic spindle assembly checkpoint that acts at metaphase to prevent premature chromosome segregation. Unlike cdh1[DELTA] and mad2[DELTA] single mutants, the mad2[DELTA] cdh1[DELTA] double mutant grew slowly and exhibited high rates of chromosome and plasmid loss. Simultaneous deletion of PDS1 and EDH1 caused extensive chromosome missegregation and cell death. Our data suggest that at least part of the chromosome loss can be attributed to kinetochore/spindle problems. Our data further suggest that Cdh1p and Sic1p, a Cdc28p/Clb inhibitor, have overlapping as well as nonoverlapping roles in ensuring proper chromosome segregation. The severe growth defects of both mad2[DELTA] cdh1[DELTA] and pds1[DELTA] cdh1[DELTA] strains were rescued by overexpressing Swe1p, a [G.sub.2]/M inhibitor of the cyclin-dependent kinase, Cdc28p/Clb. We propose that the failure to degrade cyclins at the end of mitosis leaves cdh1[DELTA] mutant strains with abnormal Cdc28p/ Clb activity that interferes with proper chromosome segregation.

Published
2003

14. Dephosphorylation of cyclin-dependent kinases by type 2C protein phosphatases

Author

Cheng, Aiyang, Ross, Karen E., Kaldis, Philipp, and Solomon, Mark J.

Subjects
Cytochemistry -- Research, Protein kinases -- Research, Phosphorylation -- Physiological aspects, Phosphatases -- Physiological aspects, Cell cycle -- Research, Biological sciences
Abstract

The dephosphorylation of a Thr-169 phosphorylated form of Cdc28p in crude yeast lysates has been characterized in order to identify the Cdc28p phosphatase. Type 2C protein phosphatase(PP2C)-like activities take care of the dephosphorylation of Cdc29p in yeast extracts. Identification of the basic kinases and phosphatases acting on the major phosphorylation sites of the cyclin-dependent kinases (CDKs) controlling cell cycle progression has been completed with the determination of PP2Cs as the main protein phosphatases opposing Cdk-activating kinase (CAK).

Published
1999

18. Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources

Author

Huang, Liang-Chin, primary, Ross, Karen E., additional, Baffi, Timothy R., additional, Drabkin, Harold, additional, Kochut, Krzysztof J., additional, Ruan, Zheng, additional, D’Eustachio, Peter, additional, McSkimming, Daniel, additional, Arighi, Cecilia, additional, Chen, Chuming, additional, Natale, Darren A., additional, Smith, Cynthia, additional, Gaudet, Pascale, additional, Newton, Alexandra C., additional, Wu, Cathy, additional, and Kannan, Natarajan, additional

Published
2018
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29. Who Is Leading Our Schools? An Overview of School Administrators and Their Careers

Author

RAND CORP SANTA MONICA CA, Gates, Susan M., Ringel, Jeanne S., Santibanez, Lucrecia, Ross, Karen E., Chung, Catherine H., RAND CORP SANTA MONICA CA, Gates, Susan M., Ringel, Jeanne S., Santibanez, Lucrecia, Ross, Karen E., and Chung, Catherine H.

Abstract

The recently passed No Child Left Behind legislation reflects the increasing visibility and importance of school administration in the larger education reform effort. But just when the role of school administrators is being emphasized, policymakers and the public are becoming increasingly concerned that there is or soon will be a short- age of qualified individuals to fill formal school and district management positions. This concern stems primarily from the perception that a large number of people are leaving school administrative positions, that districts are having a hard time replacing those who leave, and that replacements often lack the skills necessary to succeed in school administration. To know whether the United States is indeed facing a crisis in the recruitment and retention of school administrators, the Wallace-Readers Digest Funds asked RAND to conduct a systematic analysis of the career patterns of school administrators, including the moves they make into and out of the profession and the factors that might be expected to influence those moves.

Published
2003

30. Rhetoric Versus Reality. What We Know and What We Need to Know About Vouchers and Charter Schools

Author

RAND CORP SANTA MONICA CA, Gill, Brian P., Timpane, P. M., Ross, Karen E., Brewer, Dominic J., RAND CORP SANTA MONICA CA, Gill, Brian P., Timpane, P. M., Ross, Karen E., and Brewer, Dominic J.

Abstract

Education vouchers and charter schools are two of the most prominent and far-reaching forms of family choice policies currently in evidence in the nation's elementary and secondary schools. As such, they present important challenges to the traditional provision of public education in schools that are created, governed, funded, and operated by state and local authorities. This book reviews the theoretical foundations for vouchers and charter schools and the empirical evidence of their effectiveness as set forth in hundreds of recent reports and studies. The literature analyzed includes studies that directly examine voucher and charter schools, in the United States and abroad, and, where relevant, comparisons between existing public and private schools. This book also examines the ways in which multiple dimensions of policy design such as targeting, funding levels and limitations, admissions policies, academic standards and assessments, and accountability-will determine the nature and extent of any specific program's impact. The findings will be of interest to policymakers, researchers, and educators at every level of the education system who must assess numerous proposals for vouchers, charter schools, and other forms of family choice in education.

Published
2001

31. Dephosphorylation of cyclin-dependent kinases by type 2C protein phosphatases.

Author

Aiyang Cheng, Ross, Karen E., Kaldis, Philipp, and Solomon, Mark J.

Subjects
*DEPHOSPHORYLATION, *CYCLIN-dependent kinases, *PHOSPHOPROTEIN phosphatases, *CELL cycle, *GENETIC overexpression
Abstract

Activating phosphorylation of cyclin-dependent protein kinases (CDKs) is necessary for their kinase activity and cell cycle progression. This phosphorylation is carried out by the Cdk-activating kinase (CAK); in contrast, little is known about the corresponding protein phosphatase. We show that type 2C protein phosphatases (PP2Cs) are responsible for this dephosphorylation of Cdc28p, the major budding yeast CDK. Two yeast PP2Cs, Ptc2p and Ptc3p, display Cdc28p phosphatase activity in vitro and in vivo, and account for ~90% of Cdc28p phosphatase activity in yeast extracts. Overexpression of PTC2 or PTC3 results in synthetic lethality in strains temperature-sensitive for yeast CAK1, and disruptions of PTC2 and PTC3 suppress the growth defect of a cak1 mutant. Furthermore, PP2C-like enzymes are the predominant phosphatases toward human Cdk2 in HeLa cell extracts, indicating that the substrate specificity of PP2Cs toward CDKs is evolutionarily conserved. [ABSTRACT FROM AUTHOR]

Published
2015

34. Activating Phosphorylation of the Saccharomyces cerevisiaeCyclin-dependent Kinase, Cdc28p, Precedes Cyclin Binding

Author

Ross, Karen E., Kaldis, Philipp, and Solomon, Mark J.

Abstract

Eukaryotic cell cycle progression is controlled by a family of protein kinases known as cyclin-dependent kinases (Cdks). Two steps are essential for Cdk activation: binding of a cyclin and phosphorylation on a conserved threonine residue by the Cdk-activating kinase (CAK). We have studied the interplay between these regulatory mechanisms during the activation of the major Saccharomyces cerevisiaeCdk, Cdc28p. We found that the majority of Cdc28p was phosphorylated on its activating threonine (Thr-169) throughout the cell cycle. The extent of Thr-169 phosphorylation was similar for monomeric Cdc28p and Cdc28p bound to cyclin. By varying the order of the addition of cyclin and Cak1p, we determined that Cdc28p was activated most efficiently when it was phosphorylated before cyclin binding. Furthermore, we found that a Cdc28pT169Amutant, which cannot be phosphorylated, bound cyclin less well than wild-type Cdc28p in vivo. These results suggest that unphosphorylated Cdc28p may be unable to bind tightly to cyclin. We propose that Cdc28p is normally phosphorylated by Cak1p before it binds cyclin. This activation pathway contrasts with that in higher eukaryotes, in which cyclin binding appears to precede activating phosphorylation.

Published
2000
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35. Perspectives on tracking data reuse across biodata resources.

Author

Ross KE, Bastian FB, Buys M, Cook CE, D'Eustachio P, Harrison M, Hermjakob H, Li D, Lord P, Natale DA, Peters B, Sternberg PW, Su AI, Thakur M, Thomas PD, and Bateman A

Abstract

Motivation: Data reuse is a common and vital practice in molecular biology and enables the knowledge gathered over recent decades to drive discovery and innovation in the life sciences. Much of this knowledge has been collated into molecular biology databases, such as UniProtKB, and these resources derive enormous value from sharing data among themselves. However, quantifying and documenting this kind of data reuse remains a challenge., Results: The article reports on a one-day virtual workshop hosted by the UniProt Consortium in March 2023, attended by representatives from biodata resources, experts in data management, and NIH program managers. Workshop discussions focused on strategies for tracking data reuse, best practices for reusing data, and the challenges associated with data reuse and tracking. Surveys and discussions showed that data reuse is widespread, but critical information for reproducibility is sometimes lacking. Challenges include costs of tracking data reuse, tensions between tracking data and open sharing, restrictive licenses, and difficulties in tracking commercial data use. Recommendations that emerged from the discussion include: development of standardized formats for documenting data reuse, education about the obstacles posed by restrictive licenses, and continued recognition by funding agencies that data management is a critical activity that requires dedicated resources., Availability and Implementation: Summaries of survey results are available at: https://docs.google.com/forms/d/1j-VU2ifEKb9C-sW6l3ATB79dgHdRk5v_lESv2hawnso/viewanalytics (survey of data providers) and https://docs.google.com/forms/d/18WbJFutUd7qiZoEzbOytFYXSfWFT61hVce0vjvIwIjk/viewanalytics (survey of users)., Competing Interests: A.B. is Editor-in-Chief of Bioinformatics Advances, but was not involved in the editorial process of this manuscript., (© The Author(s) 2024. Published by Oxford University Press.)

Published
2024
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36. Scalable Text Mining Assisted Curation of Post-Translationally Modified Proteoforms in the Protein Ontology.

Author

Ross KE, Natale DA, Arighi C, Chen SC, Huang H, Li G, Ren J, Wang M, Vijay-Shanker K, and Wu CH

Abstract

The Protein Ontology (PRO) defines protein classes and their interrelationships from the family to the protein form (proteoform) level within and across species. One of the unique contributions of PRO is its representation of post-translationally modified (PTM) proteoforms. However, progress in adding PTM proteoform classes to PRO has been relatively slow due to the extensive manual curation effort required. Here we report an automated pipeline for creation of PTM proteoform classes that leverages two phosphorylation-focused text mining tools (RLIMS-P, which detects mentions of kinases, substrates, and phosphorylation sites, and eFIP, which detects phosphorylation-dependent protein-protein interactions (PPIs)) and our integrated PTM database, iPTMnet. By applying this pipeline, we obtained a set of ~820 substrate-site pairs that are suitable for automated PRO term generation with literature-based evidence attribution. Inclusion of these terms in PRO will increase PRO coverage of species-specific PTM proteoforms by 50%. Many of these new proteoforms also have associated kinase and/or PPI information. Finally, we show a phosphorylation network for the human and mouse peptidyl-prolyl cis-trans isomerase (PIN1/Pin1) derived from our dataset that demonstrates the biological complexity of the information we have extracted. Our approach addresses scalability in PRO curation and will be further expanded to advance PRO representation of phosphorylated proteoforms.

Published
2016

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