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1. A knowledge graph representation learning approach to predict novel kinase-substrate interactions

Author

Gavali, Sachin, Ross, Karen, Chen, Chuming, Cowart, Julie, and Wu, Cathy H.

Subjects
Quantitative Biology - Quantitative Methods, Computer Science - Artificial Intelligence, Quantitative Biology - Molecular Networks
Abstract

The human proteome contains a vast network of interacting kinases and substrates. Even though some kinases have proven to be immensely useful as therapeutic targets, a majority are still understudied. In this work, we present a novel knowledge graph representation learning approach to predict novel interaction partners for understudied kinases. Our approach uses a phosphoproteomic knowledge graph constructed by integrating data from iPTMnet, Protein Ontology, Gene Ontology and BioKG. The representation of kinases and substrates in this knowledge graph are learned by performing directed random walks on triples coupled with a modified SkipGram or CBOW model. These representations are then used as an input to a supervised classification model to predict novel interactions for understudied kinases. We also present a post-predictive analysis of the predicted interactions and an ablation study of the phosphoproteomic knowledge graph to gain an insight into the biology of the understudied kinases.

Published
2022

3. Exploring Graduate Students' Understanding of Research: Links between Identity and Research Conceptions

Author

Ross, Karen, Dennis, Barbara, Zhao, Pengfei, and Li, Peiwei

Abstract

We are in an era that calls for increasing "training" in educational research methodologies. When the National Research Council (2004) calls for training in educational research that is "rigorous" and "relevant," the focus strongly emphasizes WHAT should be taught instead of WHO is being engaged in the learning. Similarly, most of the research on teaching educational inquiry explores the "what" and not the "who" of the learning. In contrast, we explore conceptualizations of "research" as expressed by graduate students in a research methodology course, as well as the way that student narratives illustrate their own identity claims in relation to research. We develop the analytical concept of "pragmatic fissures" to explain the tension often present between the way students conceptualize research and the way they perceive themselves in relation to the research process. We suggest that these pragmatic fissures provide an opportunity for expanding pedagogical approaches to course delivery, as well as approaches to methodology textbook design. In the spirit of post-perspectives aimed at challenging the "methods" approach to research learning (St. Pierre, 2014), we welcome an opportunity for thinking about research instruction as more locally and organically connected to the lived experiences and conceptual make-up of students engaged in the learning process.

Published
2017

5. The Roles and Responsibilities of Action Research Networks in Times of Crisis: Lessons from the Action Research Network of the Americas

Author

Call-Cummings, Meagan, Hauber-Ozer, Melissa, Rowell, Lonnie, and Ross, Karen

Abstract

Against the backdrop of the COVID-19 pandemic, we explore the perceived roles of action research networks during times of crisis and then consider our own experiences grappling with our responsibilities as members of the Action Research Network of the Americas (ARNA) in highlighting and building solidarity through its Knowledge Democracy Initiative and Social Solidarity Project. To critically reflect on our work, we consider the usefulness of Gaventa's (1991) three strategies for knowledge democratization to action research networks in "perilous" times and the responsibility of action research scholars-advocates-activists-participants to anchor our work in an ethos of knowledge democracy. In conclusion, we issue a call to embrace critical, participatory forms of action research, and creative, new pathways for the work of knowledge democracy.

Published
2020
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11. Promoting Science Literacy through an Interdisciplinary Approach

Author

Ross, Karen, Hooten, Mary Ann, and Cohen, Glenn

Abstract

Recognition of the value of a scientifically literate citizenry has driven American science education reform since the 1950s. We have seen some improvement in the comprehension of science facts in the past 10-20 years, but far less improvement in Americans' understanding of the nature of science. College science courses are ideal venues for promoting science literacy. However, in an effort to condense a complicated subject into a single semester, the nature of science is often lost amidst the facts presented in a freshman survey course, often the entirety of a non-science major's experience in science. We argue that an interdisciplinary approach that integrates the sciences and the humanities can attract non-science majors, increasing these students' exposure to scientific concepts by relating them to students' existing interests and knowledge. This fosters science literacy by teaching students that science is a process of human inquiry with a distinct methodology, instead of simply a litany of facts. We recommend that a successful interdisciplinary course should present an engaging topic with which students can identify, incorporate opportunities for student research, and offer site visits to working laboratories.

Published
2013

12. Promoting Change within the Constraints of Conflict: Case Study of Sadaka Reut in Israel

Author

Ross, Karen

Abstract

This article explores the approach to transformative education utilized by Sadaka Reut, a binational civil society organization in Israel that works with Jewish and Palestinian youth. I examine three central tools Sadaka Reut uses to achieve its goal of educating youth for social change: using personal experiences as the basis for discussion; emphasizing personal-structural links; and implementing uninational activities within a binational framework. I argue that though the organization's approach holds potential for appealing to a broad audience and for fostering transformation amongst participants, the strength of dominant discourses in Israeli society places significant constraints on Sadaka Reut's work and limits possibilities for widespread success.

Published
2013

13. Educational Attainment and Attitudes towards War in Muslim Countries Contemplating War: The Cases of Jordan, Lebanon, Pakistan, and Turkey

Author

Shafiq, M. Najeeb and Ross, Karen

Abstract

This study addresses the little understood relationship between educational attainment and public attitudes towards war in four predominantly Muslim countries contemplating war: Jordan, Lebanon, Pakistan, and Turkey. The multivariate analysis using public opinion data suggests that the educational attainment of respondents has no statistically significant association with believing that war is necessary for obtaining justice. In a separate analysis, there is no statistically significant association between educational attainment and believing that U.N. approval is necessary before using military force to deal with an international threat. This study suggests that there is some validity to concerns raised by the U.K.'s Department for International Development and UNICEF that education may not be contributing to peaceful conflict resolution. (Contains 3 tables, 2 figures, and 15 footnotes.) [This study was supported by Indiana University's Proffitt Grant Program.]

Published
2009

14. State and Local Implementation of the 'No Child Left Behind Act'. Volume VII--Title I School Choice and Supplemental Educational Services: Final Report

Author

Office of Planning, Evaluation and Policy Development (ED), Policy and Program Studies Service, Vernez, Georges, Naftel, Scott, Ross, Karen, Le Floch, Kerstin Carlson, Beighley, Christopher, and Gill, Brian

Abstract

This report presents trends on the implementation of Title I parental choice options from the National Longitudinal Study of No Child Left Behind (NLS-NCLB) and the Study of State Implementation of Accountability and Teacher Quality Under No Child Left Behind (SSI-NCLB). The report uses data from state-level interviews; surveys of a nationally representative sample of district officials, principals and teachers; surveys of parents in eight school districts; and surveys of supplemental educational service providers in 16 districts to examine the implementation across the country of the school choice and supplemental educational service components of Title I through 2006-07. It is based on data collected in 2004-05 and 2006-07, updating findings from the interim report that was based on data collected in 2004-05. Most districts reported that they offered Title I public school choice and supplemental educational services if they were required to do so, and the number of students participating in both options increased substantially from the initial implementation of NCLB to the most recent year with available data. However, only a small proportion of eligible students actually participated in school choice or supplemental educational services, and participation rates have remained relatively constant. Four notable issues appeared to continue to contribute to low participation rates, in spite of the progress that had been made on some of these issues: (1) Supply of options for both Title I public school choice and supplemental educational services was limited at the secondary level; (2) Approximately half of districts continued to be unable to notify parents of students eligible for Title I public school choice of that option before the beginning of the school year; (3) A majority of parents of students eligible for Title I public school choice and more than one-third of parents of students eligible for supplemental educational services continued to say they were not notified of those options, even though the districts documented that written notifications had been sent out; and (4) Even when parents said they were notified, nine out of 10 parents of students eligible for Title I public school choice and nearly half of parents of students eligible for Title I supplemental educational services chose not to participate, primarily due to satisfaction with the child's current school. The report concludes that, although there continue to be issues around availability of Title I public school choice and supplemental educational services and timely notification of and communication with parents, it is parents of eligible students who ultimately decide whether they want to avail themselves of the options offered to their children. To date, parents have shown a low propensity to do so for both public school choice and supplemental educational services. Three appendices are included: (1) Description of NLS-NCLB and SSI-NCLB Methodologies; (2) Standard Error Exhibits; and (3) Supplemental Exhibits. (Contains 34 footnotes and 88 exhibits.)

Published
2009

15. State and Local Implementation of the 'No Child Left Behind Act.' Volume IV--Title I School Choice and Supplemental Educational Services: Interim Report

Author

Office of Planning, Evaluation and Policy Development (ED), Policy and Program Studies Service, Gill, Brian, McCombs, Jennifer Sloan, Naftel, Scott, Ross, Karen, Song, Mengli, Harmon, Jennifer, and Vernez, Georges

Abstract

This report presents findings on the implementation of parental choice options from the first year of the National Longitudinal Study of "No Child Left Behind" (NLS-"NCLB") and the Study of State Implementation of Accountability and Teacher Quality Under "No Child Left Behind" (SSI-"NCLB"). The report uses data from state-level interviews, from surveys of a nationally representative sample of district officials, principals, and teachers, surveys of parents in eight school districts, surveys of supplemental educational service providers in 16 districts, and student-level demographic and achievement data in nine districts, to examine the implementation across the country of the school choice and supplemental educational service components of Title I through 2004-05. This report addresses three broad areas in evaluating the Title I provisions for providing school choice and supplemental services for students in low-performing schools: (1) Who is eligible to participate in parental school choice and supplemental educational services under Title I of "NCLB," what choices are made available, and who participates? (2) How are states, districts and schools providing information to make parents aware of their options? What information do parents have and use to make decisions about their school choice and supplemental service options? and (3) How do states, districts, and schools support, monitor, and collaborate in the implementation of supplemental educational services under Title I? Two appendixes are included: (1) Description of NLS-"NCLB" and SSI-"NCLB" Methodologies; and (2) Standard Error Exhibits. (Contains 77 exhibits.) [For the report highlights, see ED613405.]

Published
2008

16. Family Support during the Transition to Adulthood. Policy Brief #3

Author

National Poverty Center, Schoeni, Robert, and Ross, Karen

Abstract

Robert Schoeni and Karen Ross, in their chapter in "On the Frontier of Adulthood," examine several issues related to this material support: how much time and money youth receive from their parents between the ages of 18 and 34, the difference in support between high and low-income families, and the changing patterns of support over the last 30 years. In one of the first empirical attempts to estimate the amount of assistance that children receive during young adulthood, the authors find that parents contribute, on average, $2,200 annually over the 17-year period, and that this support has increased substantially in the last decades. (Contains 3 figures.)

Published
2004

17. The Effects of the Washington State Education Reform on Schools and Classrooms. CSE Technical Report.

Author

California Univ., Los Angeles. Center for the Study of Evaluation., Center for Research on Evaluation, Standards, and Student Testing, Los Angeles, CA., Stecher, Brian M., Barron, Sheila L., Chun, Tammi, and Ross, Karen

Abstract

The effects of Washington state education reforms on schools and classrooms were studied through surveys completed by about 150 elementary and middle school principals and about 400 writing and mathematics teachers in grades 4 and 7, the grades in which students take the Washington Assessment of Student Learning (WASL) tests. The surveys asked about the respondents' familiarity with the reform and their opinions about it. Principals were also asked about the implementation of the reform, including changes to standards, curriculum, and assessments. Teachers were asked about participation in professional development and changes in their classroom practices. Surveys showed districts and schools in transition, with change not always occurring uniformly. Principals and teachers had studied the reform, and believed they understood it. Teachers were changing classroom practices with the most visible changes being those related to the WASL results. Mathematics teachers and elementary school teachers had made more changes than writing teachers and middle school teachers. The surveys also show a mixed picture about the relationship between school practices and WASL scores. Four appendixes contain examples of essential academic learning requirements for writing and mathematics, survey items included in the regression analyses, and results of the regression analyses. (Contains 35 tables, 20 figures, and 29 references.) (SLD)

Published
2000

20. The glycan structure dictionary—a dictionary describing commonly used glycan structure terms.

Author

Vora, Jeet, primary, Navelkar, Rahi, additional, Vijay-Shanker, K, additional, Edwards, Nathan, additional, Martinez, Karina, additional, Ding, Xiying, additional, Wang, Tianyi, additional, Su, Peng, additional, Ross, Karen, additional, Lisacek, Frederique, additional, Hayes, Catherine, additional, Kahsay, Robel, additional, Ranzinger, Rene, additional, Tiemeyer, Michael, additional, and Mazumder, Raja, additional

Published
2023
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25. Ethnic stereotypes and television : an examination of white students' attitudes towards ethnic stereotypes and television in six Midlands colleges

Author

Ross, Karen

Subjects
305, HT Communities. Classes. Races, PN1990 Broadcasting
Abstract

This research study sets out to identify and examine the ways in which the white majority have traditionally comprehended ethnic minority coninunities with particular reference to the role played by television in representing such coninunities. In the British context, television has come to dominate social and cultural life to the extent that the Reithian principles for television (that is, to educate, inform and entertain) have become crucially important in the maintenance, if not absolute creation, of notions of national culture. Given the concentration of ethnic minority corrinunities in mainly inner-city areas, for the majority of white people, their only contact with such corrrnunities is through the vicarious experience afforded by television. The medium's role in representing ethnic coninunities honestly and realistically is thus vital and if for no other reason deserves careful examination. My principal hypothesis is that television, through its characterisations of ethnic minority comunities, maintains, reinforces and perpetuates stereotypical assumptions already held by the white majority about such corrinunities, which hinder the pursuit of a harmonious and multi-cultural society. In order to test this hypothesis, a survey was conducted with 650 white students attending further education colleges in the Midlands which sought to ascertain their attitudes towards ethnic stereotypes and television. Professionals working in the television industry were also interviewed and a short monitoring study of contemporary television fiction was later conducted. The survey findings suggest, inter alia, that young white people do make stereotypical judgments about ethnic minority people which conform to traditional assumptions; that inter-ethnic friendship tends to mediate the propensity to make more unfavourable assessments of ethnicallyspecific characteristics; and that the perception of ethnic minority coninunities in the real world closely parallel those which exist in the world of television fiction. The specific merit of this study lies in its detailed examination of a significant and important sample population, the study both identifying general attitudes towards ethnic minority coninunities and also relating these general beliefs to student attitudes towards the ethnic portraits typically found in television. The study is thus able to establish that the ethnic stereotypes which exist in the popular white consciousness are regularly rehearsed through the contemporary medium of television.

Published
1990

26. Spectrums of Participation: A Framework of Possibility for Participatory Inquiry and Inquirers

Author

Call-Cummings, Meagan and Ross, Karen

Subjects
ideal type, participatory action research, epistemology, participation, partizipative Handlungsforschung, Partizipation, Einschränkungen, constraints, Epistemologie, Idealtypus
Abstract

Anhand von Beispielen aus unseren eigenen Forschungen versuchen wir, die ontologischen und erkenntnistheoretischen Verpflichtungen zu identifizieren, die wir als partizipative Forscher*innen haben, und wir erörtern, wie unterschiedlich sich Sozialforschung in verschiedenen Kontexten gestalten kann. Wir wenden uns der grundlegenden Literatur zur partizipativen Handlungsforschung sowie zu Philosophien und Theorien von Partizipation zu, um die Annahmen zu entschlüsseln, die unseren Erwartungen an eine "gute" Partizipation zugrunde liegen könnten. Entgegen binären Konzeptualisierungen verstehen wir Partizipation als eine Reihe erkenntnistheoretischer Verpflichtungen und nicht als eine Reihe von Methoden, die, wenn sie angewandt würden, irgendwie zu einer Summe von "gut genug" führen könnten. Letztlich ist unser Ziel, einen Beitrag zu den laufenden Diskussionen über Möglichkeiten der Partizipation für diejenigen zu leisten, die gerne partizipativ arbeiten würden, dies aber aufgrund verschiedener Beschränkungen für nicht machbar halten., Using examples from our own inquiry experiences, we seek to identify the ontological and epistemological commitments we have as participatory researchers and to discuss how participation in social inquiry can look different in varied contexts. We turn to foundational literature on participatory action research as well as philosophies and theories of participation to unpack assumptions that may underlie our expectations of what "counts" as "good" participation. Our goal is to add nuance to and push back against binary conceptualizations of participation and to move toward understanding participation as a set of epistemological commitments rather than a set of methods that, if used, may somehow add up to a sum of "good enough." Ultimately, our goal is to contribute to ongoing discussions around the possibilities of participation for those who may be drawn to participatory inquiry but who may feel like it is not viable because of various constraints.

Published
2022

28. Reclaiming Impact in Qualitative Research

Author

Ross, Karen

Subjects
dialogue, Impact, transformation, Dialog, Intersubjektivität, qualitative Forschung, intersubjectivity, qualitative research
Abstract

Sowohl in der akademischen als auch in der praktischen Literatur wird der Begriff Impact sehr weit gefasst. In Verbindung mit (uni-)direktionalen Beziehungen zwischen Variablen und methodologischen Rahmen, die auf einen positivistischen Ansatz ausgerichtet sind, wird der Begriff jedoch sehr viel enger ausgelegt. Eine solche verengte Konzeptualisierung ist problematisch insbesondere im Zusammenhang mit Initiativen, die interne, individuelle Veränderungen abzielen. Ich schlage daher vor, Impact neu zu konzeptualisieren, um menschliches Handeln anzuerkennen und Wandel ganzheitlicher erforschen zu können. Im Rahmen post-positivistischer qualitativer Forschung sollte der Begriff zurückerobert werden, da qualitative Methoden das Potenzial haben, ein dialogisches Verständnis von Impact und des intersubjektiven Kontextes, durch den Wandel entsteht zu erhellen., In both academic and practitioner literature, the term "impact" is conceptualized broadly. Yet the application of impact is construed much more narrowly, in association with (uni)-directional relationships between variables and methodological frameworks oriented towards a positivist approach. Such a conceptualization is problematic, particularly in the context of initiatives that have a goal of internal, individual transformation. Thus, I suggest reconceptualizing impact to acknowledge human agency and explore change more holistically. I argue for a reclaiming of impact by the post-positivist qualitative research community, given the potential of qualitative methodologies to elucidate dialogic understandings of impact and the intersubjective context through which transformation emerges.

Published
2022

29. 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

31. 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

35. Additional file 2 of The IS6 family, a clinically important group of insertion sequences including IS26

Author

Varani, Alessandro, Susu He, Siguier, Patricia, Ross, Karen, and Chandler, Michael

Abstract

Additional file 2: Figure S2. Alignment of a representative sample of the transposases of IS6 family members including members of each major clade. Alignment was by Clustal [129] and the graphic output from SnapGene. The figure shows the probable zinc finger N-terminal extension (consecutive CxxC motifs), the helix-turn-helix domain (HTH) and the catalytic domain (DDE K/R).

Published
2021
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36. Additional file 1 of The IS6 family, a clinically important group of insertion sequences including IS26

Author

Varani, Alessandro, Susu He, Siguier, Patricia, Ross, Karen, and Chandler, Michael

Subjects
parasitic diseases, population characteristics
Abstract

Additional file 1: Figure S1a-g. Left (IRL) and right IRR and a combined IRL + IRR inverted terminal repeats for each clade are shown in WebLogo format [25]. Figure S1h. The last section shows an alignment of the ends of clade Aiv adjusted by hand.

Published
2021
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37. 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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39. Protein Ontology: a controlled structured network of protein entities

Author

Natale, Darren A., Arighi, Cecilia N., Blake, Judith A., Bult, Carol J., Christie, Karen R., Cowart, Julie, DʼEustachio, Peter, Diehl, Alexander D., Drabkin, Harold J., Helfer, Olivia, Huang, Hongzhan, Masci, Anna Maria, Ren, Jia, Roberts, Natalia V., Ross, Karen, Ruttenberg, Alan, Shamovsky, Veronica, Smith, Barry, Yerramalla, Meher Shruti, Zhang, Jian, AlJanahi, Aisha, Çelen, Irem, Gan, Cynthia, Lv, Mengxi, Schuster-Lezell, Emily, and Wu, Cathy H.

Published
2014
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40. Cleavage of protease-activated receptors on an immortalized oral epithelial cell line by Porphyromonas gingivalis gingipains

Author

Giacaman, Rodrigo A., Asrani, Anil C., Herzberg, Mark C., and Ross, Karen F.

Subjects
Cytokines -- Health aspects, Cytokines -- Genetic aspects, Cytokines -- Research, Gram-negative bacteria -- Health aspects, Gram-negative bacteria -- Genetic aspects, Gram-negative bacteria -- Research, Keratinocytes -- Physiological aspects, Keratinocytes -- Genetic aspects, Keratinocytes -- Research, Biological sciences
Abstract

Porphyromonas gingivalis activates protease-activated receptors (PARs) on oral keratinocytes, resulting in downstream signalling for an innate immune response. Activation depends on P. gingivalis gingipains, but could be confounded by lipopolysaccharide signalling through Toll-like receptors. We therefore hypothesized that P. gingivalis cleaves oral keratinocyte PARs in an Arg-(Rgp) or Lys- (Kgp) gingipain-specific manner to upregulate pro-inflammatory cytokines. Immortalized human oral keratinocytes (TERT-2) were incubated with wild-type P. gingivalis (ATCC 33277) or strains from a panel of isogenic gingipain deletion mutants: Kgp-deficient (KDP 129); Rgp-deficient (KDP 133); or Kgp-and Rgp-deficient (KDP 136). After incubation with P. gingivalis, keratinocytes were probed with specific antibodies against the N-terminus of PAR-1 and PAR-2. Using flow cytometry and immunofluorescence, receptor cleavage was marked by loss of specific antibody binding to the respective PARs. TERT-2 cells constitutively expressed high levels of PAR-1 and PAR-2, and lower levels of PAR-3. P. gingivalis ATCC 33277 cleaved PAR-1 and PAR-2 in a dose-dependent manner, while the receptors were unaffected by the protease-negative double mutant (KDP 136) at all m.o.i, tested. The single Kgp-negative mutant preferentially cleaved PAR-l, whereas the Rgp-negative mutant cleaved PAR-2. Wild-type or Kgp-negative mutant cleavage of PAR-1 upregulated expression of IL-1 [alpha], IL-1 [beta], IL-6 and TNF-[alpha]; the Rgp-negative mutant did not modulate these cytokines. Selective cleavage of PAR-1 on oral epithelial cells by P. gingivalis Rgp therefore upregulates expression of pro-inflammatory cytokines. DOI 10.1099/mic.0.029132-0

Published
2009

41. Feminist Data Studies

Author

Luka, Mary Elizabeth, Leurs, K.H.A., Ross, Karen, LS Gender and Postcolonial Studies, ICON - Gender Studies, and Afd Media, Data & Citizenship

Subjects
Taverne
Abstract

This entry explores intersectional data-analysis rooted in social justice in the social sciences and humanities. The datalogical turn foregrounds the proliferation of algorithmic processing and data as an emergent regime of power/knowledge in the digital datafication of everyday life. Big data, digital methods and data studies are buzzwords that privilege modes of knowledge production to elevate quantitative, abstracted and disembodied approaches over qualitative data approaches. However, database technologies and human experiences are always necessarily mutually constituted (Metcalf & Crawford, 2016). Infrastructures, categorizations and algorithmic processing are commonly black-boxed and therefore invisible with the consequence that data generated is never raw, but always cooked (Bowker 2006). These processes are not devoid of different forms of cultural prejudices and discriminations, rather they are often used to exacerbate gendered, sexed, racialized, classed power hierarchies. Sub-topics to be discussed in this entry include feminist ethics of care and alternative data studies (Leurs, 2017; Luka & Millette, 2018); examinations of digital infrastructures including e-waste (Hogan, 2015) and assemblages of hardware and software (Bivens, 2017); and critiques of data gathering and data visualizations (Haraway, 1997; Kennedy et al., 2016).

Published
2020

42. 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

43. Chapter 6. The media world versus the real world of women and political representation : Questioning differences and struggling for answers

Author

Ross, Karen, Jansen, Marloes, and Bürger, Tobias

Subjects
Medievetenskap, media representations, journalism, comparative media research, political news, news media, Genusstudier, Gender Studies, women and the media, women politicians, newsrooms, the GEM dataset, media and politics, gender equality, Media Studies
Abstract

The chapter "The mediaworld versus the real world of women and political representation: Questioning differences and struggling for answers", by Karen Ross, Marloes Jansen and Tobias Bürger, addresses the long-standing question of women’s voice in political news. The authors test the relationship of women, politics, and news with the incidence of women politicians as elected representatives, in two ways: first, by considering the extent to which women politicians are visible across the broad news landscape and second, by considering their visibility in news stories which are explicitly political in orientation. What the authors find is a global and systematic pattern of underrepresentation of women politicians in the news compared with their actual numbers in legislatures across the world. Their analysis suggests that the “real” world of politics seems to be more gender-equal than the media world of mainstream news. The chapter goes on to consider possible reasons to explain this difference, including the role played by socio-cultural factors such as a nation’s broad equality commitment and the extent to which the gender balance in newsrooms, including in senior editorial positions, has an impact on the visibility of women politicians in news content. The project Comparing Gender and Media Equality across the Globe has been fundedby the Swedish Research Council (2016–2020) and is based at the Department of Journalism, Media and Communication (JMG) at the University of Gothenburg, Sweden.The GEM dataset and its codebook are free to use and can be downloaded in variousformats. For access, contact JMG. Please ensure that proper attribution is given when citing the dataset.

Published
2020

45. 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

46. 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

47. piNET: a versatile web platform for downstream analysis and visualization of proteomics data

Author

Shamsaei, Behrouz, primary, Chojnacki, Szymon, primary, Pilarczyk, Marcin, primary, Najafabadi, Mehdi, primary, Niu, Wen, primary, Chen, Chuming, primary, Ross, Karen, primary, Matlock, Andrea, primary, Muhlich, Jeremy, primary, Chutipongtanate, Somchai, primary, Zheng, Jie, primary, Turner, John, primary, Vidović, Dušica, primary, Jaffe, Jake, primary, MacCoss, Michael, primary, Wu, Cathy, primary, Pillai, Ajay, primary, Ma’ayan, Avi, primary, Schürer, Stephan, primary, Kouril, Michal, primary, Medvedovic, Mario, primary, and Meller, Jarek, primary

Published
2020
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49. GlyGen data model and processing workflow

Author

Kahsay, Robel, primary, Vora, Jeet, primary, Navelkar, Rahi, primary, Mousavi, Reza, primary, Fochtman, Brian C, primary, Holmes, Xavier, primary, Pattabiraman, Nagarajan, primary, Ranzinger, Rene, primary, Mahadik, Rupali, primary, Williamson, Tatiana, primary, Kulkarni, Sujeet, primary, Agarwal, Gaurav, primary, Martin, Maria, primary, Vasudev, Preethi, primary, Garcia, Leyla, primary, Edwards, Nathan, primary, Zhang, Wenjin, primary, Natale, Darren A, primary, Ross, Karen, primary, Aoki-Kinoshita, Kiyoko F, primary, Campbell, Matthew P, primary, York, William S, primary, and Mazumder, Raja, primary

Published
2020
Full Text
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