bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 95: Phylogenetic classification, structural evolution, and functional divergence of the ABC-type transporters: Inferences derived from CDTree/Cn3D software applications
Authors: Song James S. , Derbyshire Myra K. , Lu Fu , Jackson John D. , Yamashita Roxanne A. , Marchler-Bauer Aron , Bryant Stephen H. 
Published: February 2011

Abstract
The NCBI's Conserved Domain Database (CDD; http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml), is a collection of annotated multiple sequence alignment models representing ancient conserved protein domains, basic units of protein function and protein evolution. Domain models are annotated with functional sites and can be viewed as sequence alignments together with corresponding 3D structure using the CDTree/Cn3D software applications. CDTree/Cn3D is a domain hierarchy editor which lets the user view and examine conserved domain hierarchies interactively and in great detail. A domain hierarchy is a structured collection of domain models reflecting the domain family's molecular evolution. Here we present our current, functionally annotated evolutionary classifications of the nucleotide-binding domain, transmembrane domain, and periplasmic binding proteins of the ABC (ATP binding cassette)-type transport systems which are involved in the transport of a wide variety of substrates such as sugars, ions, peptides, and more complex organic molecules across membranes. Mutations in ABC transporters cause or contribute to multi-drug resistance, cystic fibrosis, and a range of other human diseases. Using CDTree/Cn3D functionality, subfamilies present in diverse organisms were inferred from the multiple sequence alignments, phylogenetic trees, and the domain architectures of the proteins involved. Furthermore subfamilies, some of which are only comprised of uncharacterized proteins, were annotated with molecular and cellular function and the location of conserved sites, as available in the literature and evident from protein 3D structure. We demonstrate the utility of CDTree/Cn3D in studying the molecular evolution of protein and domain families, and in accelerating the discovery of orthologous groups. CDTree/Cn3D are freely available for download via the CDD website. A version of CDTree, which supports both Mac OSX and Windows operating systems, has recently been made available.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 95.
Abstract 952: Nitric oxide donor sulindac inhibits photocarcinogenesis by modulating epithelial mesenchymal transition and mitogen activated protein kinase signaling in SKH-1 hairless mouse skin
Authors: Singh Tripti , Kapur Puneet , Chaudhary Sandeep C. , Elmets Craig A. , Kopelovich Levy , Athar Mohammad 
Published: February 2011

Abstract
Nitric oxide (NO)-releasing non-steroid anti-inflammatory drugs (NO-NSAIDs) have been shown to have anti-proliferative, proapoptotic and cancer inhibitory properties. Here, we have investigated the effects of NO-donor sulindac on UVB-induced skin cancer development in SKH-1 hairless mice. Mice (6-8 weeks old) were divided into three groups of ten mice each, which received either vehicle (acetone), vehicle+UVB (180mJ/cm 2) or topical application of NO-sulindac (5mg/mouse)+UVB after dissolving in acetone. Mice-treated with NO-sulindac developed significantly less number of tumors (60%) compared with non-NO-sulindac treated mice and tumor volume was also less by 90% on termination of the experiment at week 30th. Immunohistochemical and western blot analyses revealed that the expression levels of proliferation markers such as proliferating cell nuclear antigen (PCNA) and cell cycle regulatory cyclin D1 were markedly diminished in tumors of NO-sulindac treated mice. However, the treatment of NO-sulindac resulted in enhanced apoptosis in skin tumors as ascertained by the increased terminal deoxynucleotidyl transferase-mediated nick end labeling (TUNEL) assay, reduced Bcl-2 and enhanced Bax expression levels in the tumors and tumor uninvolved skin. To investigate the effects of NO-sulindac on the progression of benign lesions to invasive carcinomas, we examined squamous cell carcinomas (SCC) for various epithelial-mesenchymal transition (EMT) markers. NO-sulindac decreased the expression of mesenchymal markers such as Fibronectin, N-cadherin, SNAI, Slug and Twist whereas the epithelial polarity marker E-cadherin was found to be increased compared to the SCCs of non-NO-sulindac treated group. Down regulation of EMT by NO-sulindac was associated with a remarkable diminution of UVB-induced phosphorylation MAPK proteins such as, extracellular signal-regulated kinase 1/2 (Erk 1/2), c-Jun-NH2 terminal kinase 1/2 (JNK1/2) and p38 in both UVB-exposed skin and skin tumors. Together our results suggest that NO-sulindac is a potential chemopreventive agent for photocarcinogenesis and that inhibition of photocarcinogenesis by NO-sulindac is associated with the inhibition of EMT and MAPK protein expression in skin tumors.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 952.
Abstract 960: Use of MMTV-Neu/P53 KO transgenic mice to screen for potential chemopreventive agents
Authors: Lubet Ronald A. , Juliana Margaret , Iwata Kenneth , Grubbs Clinton 
Published: February 2011

Abstract
The MMTV-Neu transgenic mouse develops Neu over-expressing ER− mammary cancers. Since human ER− Neu over-expressing mammary cancers often also have mutations in P53, a heterozygous KO of P53 was incorporated into the model. We have used this model to examine a wide variety of potential chemopreventive agents. The agents were routinely administered to virgin female MMTV-Neu/P53 KO mice beginning when they were 60 days of age. Initiation of treatment with the agents at this time is later than that often employed by other investigators (usually 35 days of age). Mice were routinely monitored until 360 days of age. It was found that both RXR agonists (Targretin, UAB-30) and EGFR 1 and/or 2 inhibitors (Tarceva, Lapatinib) were highly effective in preventing the development of these cancers. These results agree with previously published results by Dr. Powell Brown and colleagues. It was also observed that a wide variety of agents were ineffective; including Atorvastatin, rosiglitazone (a PPAR gamma agonist), SAHA (an HDAC inhibitor) and a soy isoflavones mixture. In separate studies, mice bearing small palpable mammary tumors were treated for five days with these various agents, and examined for alterations in potential biomarkers; including proliferation. As previously shown by our lab in an ER+ rat model of mammary cancer, effective agents (e.g., Iressa and Targretin) strongly inhibited cancer cell proliferation, whereas ineffective agents failed to significantly inhibit proliferation. Such a short-term assay might be employed to determine potential chemopreventive compounds. This model, therefore, appears useful in identifying agents that will prevent the development of breast cancer that over-express Neu. This is important since Neu over-expressing ER− cancers have a relatively poor prognosis, and Neu over-expressing ER+ tumors are relatively unresponsive to standard hormonal therapies (e.g., tamoxifen and aromatase inhibitors). Supported by NCI Contract Number HHSN261200433001C.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 960.
Abstract 969: Revising and updating NCI's best practices for biospecimen resources
Authors: Vaught Jimmie , Lockhart Nicole , Yassin Rihab , Myers Kimberly , Lim Mark David , Fore Ian , Sawyer Sherilyn , Moore Helen , Compton Carolyn 
Published: February 2011

Abstract
In 2007 the NCI Office of Biorepositories and Biospecimen Research (OBBR) published the NCI Best Practices for Biospecimen Resources (http://biospecimens.cancer.gov/practices/). The Best Practices were originally published following a public comment period on the Federal Register and internal review by several National Institutes of Health offices. The Best Practices do not comprise detailed laboratory procedures and are intended to be adapted, as appropriate, based on the mission and scientific needs of individual biospecimen resources. The Best Practices were developed to address the heterogeneity and the generally unknown or uneven quality of biospecimens used for research, which can lead to unreliable and irreproducible results. In addition to these technical and operational issues, many ethical, legal and policy guidelines and concerns must be addressed when conducting research involving the use of biospecimens from patients and other research participants.
The revised version of the Best Practices is intended to respond to comments received from the biospecimen resource community over the past 2 years, and provide more current and detailed recommendations related to biospecimen and data quality. Major revisions include the addition of new sections on biospecimen resource management and operations and conflicts of interest, and expansion of recommendations related to custodianship and informed consent based on the consensus findings of the 2007 NCI-hosted Workshop on Custodianship and Ownership Issues in Biospecimen Research, addition of current references throughout the document, and harmonization with current Federal guidance documents and recommendations from international biospecimen organizations.
The revised Best Practices will be launched using an interactive Web format, to provide a mechanism for more frequent updates and encourage feedback from the community. The Best Practices will continue to evolve as the field of biospecimen biology advances; novel scientific, technological, and clinical practices develop; and new ethical and legal policies and regulations emerge. Results from biospecimen research initiatives will inform future versions of the Best Practices as the community moves toward the development of evidence-based standard operating procedures that are both specimen type specific and analysis platform specific. The NCI is committed to maintaining current and scientifically accurate best practices for biospecimen resources and will continue to solicit input from stakeholders in the cancer research community.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 969.
Abstract 972: Mythbusters: Cancer research in jeopardy
Authors: Kennedy Jane , Boutte Angela , Cargen Lynne , Crowe Stephanie , Hanson Caroline , Hardin Gail , Hallock Kathy , Lancaster Diane , Lee Patricia , Markham Nick , Martin Pamela , McCollum Dan , McCullough Nancy , Moses Jeanne , Obenauf Ardeth , Piper Gary , Piper Janet , Shaw Aubie K. , Weiss Jacob 
Published: February 2011

Abstract
In the United States, less than 5% of eligible adult cancer patients participate in clinical trials. Lack of information and commonly held beliefs or myths are among the biggest barriers to enrollment in cancer clinical trials. Additionally, traditional methods of education can be intimidating, frightening or even boring and the most difficult time to educate patients about cancer clinical trials is at the time of diagnosis. Thus, there is a need to develop novel strategies to educate individuals and the community about clinical trials prior to a cancer diagnosis.
The Vanderbilt-Ingram Cancer Center Patient Advocacy Program and the Vanderbilt Postdoctoral Association collaborated to develop and deliver an innovative, interactive pilot program aimed at dispelling myths commonly associated with cancer clinical trials. Patient advocates, researchers, and clinicians scripted and participated in a “Jeopardy” game show format to provide factual information in a relaxed and entertaining environment.
For a community audience of 50, a response to each myth was surveyed electronically prior to the presentation. After the preliminary response of audience members was noted, an expert clarified each myth by presenting factual information. After the presentation of ten myths, a post-test was administered to assess changes in knowledge.
We found that audience knowledge was significantly increased by 20%. 96% of audience members indicated that the game show format was an effective method for learning. 87% indicated that they would discuss cancer clinical trials with family, friends or co-workers. We conclude that “Mythbusters: Cancer Research in Jeopardy” is an effective learning tool and significantly increases community knowledge about cancer clinical trials. The results of this pilot will provide a model for effective community education and may ultimately impact participation in cancer clinical trials.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 972.
Abstract 98: Automated cell tracking and interaction analysis in intra-vital two-photon microscopy image data
Authors: Klauschen Frederick , Meier-Schellersheim Martin , Mandl Judith , Qi Hai , Ishii Masaru , Dietel Manfred , Germain Ronald N. , Denkert Carsten 
Published: February 2011

Abstract
The development of two-photon fluorescence microscopy has enabled researchers to investigate dynamic biological processes such as cell migration and interaction behavior with high spatio-temporal resolution in vivo. However, the development of computational high-throughput methods for automated and standardized quantitative analysis of the resulting 4-D image data has lagged behind the experimental advances.
Here, we introduce a novel approach for automated cell migration analysis (“cell tracking”) combined with cellular interaction analysis in 4-D intra-vital two-photon fluorescence microscopy data. Our method accounts for variations of image quality and allows for rapid, standardized, quantitative analysis and comparison of the relevant features in large data sets by integrating adaptive image segmentation and cell tracking modules. It may be used for quantitative data analysis and model validation in basic and tumor immunology studies about, for instance, lymphocyte migration and interaction dynamics in tumor or lymphoid tissues. We demonstrate the utility of our approach by applying our method to the quantification of in-vivo T-cell movement and T-/B- and dendritic cell interaction dynamics in lymph nodes and present results on the impact of a (SAP-) knock-out mutant on synapse formation and T cell function complementing the findings of a recent study.
Such measurements that may yield important information about the molecular mechanisms determining cellular migration and interaction behavior would be very difficult to perform with conventional approaches that rely on manual/semi-automated analyses. Our method should thus be highly valuable to investigators working with cell-biological microscopy who are interested in quantifying cell migration behavior not only, but especially in the context of dynamic interactions between immune and/or cancer cells.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 98.
Abstract 982: Increasing HPV vaccine utilization among Hispanic girls to reduce cervical cancer disparities
Authors: Hull Pamela C. , Sanderson Maureen , Khabele Dineo , Canedo Juan 
Published: February 2011

Abstract
Incidence and mortality rates from cervical cancer are higher in Hispanic women compared to non-Hispanic white women. The purpose of this pilot study is to implement and assess a multilevel, culturally- and linguistically-appropriate social marketing intervention targeting the Hispanic population to increase utilization of the HPV vaccine among Hispanic girls ages 9-18 in Nashville/Davidson County, Tennessee. The specific aims are to (1) pre-test and disseminate culturally- and linguistically-appropriate media messages to promote use of the HPV vaccine in the target population; (2) provide information, referral and follow-up reminders to families to encourage initiation and completion of HPV vaccine series; and (3) assess the impact of the intervention by comparing changes in HPV vaccine utilization rates for Hispanic girls in partner clinics and in the state Immunization Registry. This pilot translational research study draws on Rogers’ Diffusion of Innovation theory. We employ the methodology of Community-Based Prevention Marketing, which combines social marketing theories and techniques with community-based participatory research (CBPR) approaches. The intervention uses a combination of Spanish-language media_radio, newspaper and printed brochures_to disseminate the messages throughout the community. A trained lay health promoter (promotora de salud) at Progreso Community Center receives phone calls to answer general questions about the vaccine and eligibility requirements for the VFC program, refers patients to appropriate locations to obtain the vaccine, and provides follow-up reminders. In this presentation we will present how formative research findings were used to develop the intervention and preliminary baseline intervention data. Targeted interventions to Hispanic communities such as this one to encourage use of a new cervical cancer vaccine could help eradicate ethnic disparities in cervical cancer. The study contributes valuable knowledge to the dearth of research on possible barriers for Hispanics to use this vaccine or about culturally- and linguistically-appropriate social marketing strategies for HPV vaccine use among Hispanics.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 982.
Abstract 984: Planning for caHUB, NCI's cancer human biobank
Authors: Compton Carolyn , Dickherber Anthony , Fore Ian , Lockhart Nicole , Lim Mark David , Moore Helen , Myers Kimberly , Rogers Joyce , Sawyer Sherilyn , Tuovinen Priyanga , Vaught Jimmie 
Published: February 2011

Abstract
Many high-profile NCI initiatives are significantly impacted by biospecimen availability and quality. One of the newly delineated developmental pathways for transforming scientific discoveries into new clinical modalities for oncology, defined by NCI's Translational Research Working Group, is entirely biospecimen-based and is similarly impacted. Both direct experience with these initiatives as well as broader input from the scientific community, including recent results from a market research survey, have indicated a striking unmet need for high-quality human biospecimens. In response to this need, the Office of Biorepositories and Biospecimen Research (OBBR) is planning for the implementation of the cancer Human Biobank (caHUB). No centralized resource of this type exists at this time. This initiative will take advantage of resources already developed by the NCI, including the OBBR Biospecimen Research Network (BRN) and the NCI Best Practices for Biospecimen Resources (http://biospecimens.cancer.gov/practices/).
The OBBR is engaging in a detailed process with a variety of planning groups, to address the requirements for implementation of caHUB. caHUB will acquire and make available to the research community biospecimens that have been collected according to the highest technical and ethical standards; provide biospecimen reference samples that serve as benchmarks for specimen integrity and molecular type; conduct research that supports evidence-based biospecimen best practices; and create opportunities for collaboration and information exchange across the research enterprise. caHUB will ensure the quality of its inventory by acquiring biospecimens that have been collected and processed according to evidence-based standard operating procedures, annotated with comprehensive clinical, molecular, and collection data, and procured from patients who received high-quality care. caHUB proposes to contract with military, community, and academic institutions to collect biospecimens and their associated data. Through a caBIG®-compliant public network, caHUB will make specimens and data available to a broad research community, including academia, government, private foundations, and biotechnology and pharmaceutical industries, and enable new collaborations among researchers in all areas of investigation, thereby accelerating the pace of discovery and innovation.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 984.
Abstract 988: A diet and exercise intervention in women being treated for breast cancer
Authors: Djuric Zora , Ellsworth Jennifer , Rapai Mary , Weldon Anne , Kim Jihye , Sen Ananda 
Published: February 2011

Abstract
Increases in body fat have been documented to occur in breast cancer patients during chemotherapy and radiation treatment. This is a matter of concern that can impact on health status in survivorship, especially given the difficulties in achieving weight loss once a gain has occurred. Weight gain and obesity have also been linked with recurrence. In this pilot study we investigated the feasibility of recruiting women early in their breast cancer treatment to a study that sought to prevent body fat gain. The study randomized women to receive written materials only or telephone counseling. The goals of the counseling were to decrease fat intake, increase fruit and vegetable intakes and to include at least 30 minutes of moderate to vigorous exercise daily. The counseling stressed self-monitoring of these behaviors. A total of 40 women were enrolled within 2 weeks of starting chemotherapy. This was 53% of the women who were referred to the study by their oncologists over 8 months. Baseline BMI was a mean of 27 (range 18-43 kg/m2) and 19 women were in the normal BMI range. Only 11 women had a body fat percentage in the recommended range. Retention of subjects for 12 months was 75% overall but it was better in the written arm (17 of 20 women) than in the telephone arm (13 of 20 women). Body fat increased in the written arm from 39.2 to 40.8% but it decreased from 39.0 to 37.3% in the telephone arm. Other objective measures also improved in the telephone arm such as blood pressure and leptin levels. Both total and moderate/vigorous activity increased more in the telephone arm than in the written arm. Improvements in dietary intakes at 12 months were noted in the telephone arm but not in the written arm. This preliminary data indicates that telephone support is helpful for making lifestyle changes that prevent body fat gain during treatment for breast cancer. Subject satisfaction with the study was high. The prevention of body fat gain during treatment for breast cancer is therefore feasible, and this approach could be useful for maximizing health in survivorship. Supported by the University of Michigan Metabolomics and Obesity Center, the Michigan Diabetes Research and Training Center, the Barbara Padnos Breast Cancer Research Fund and the Michigan Institute for Clinical and Health Research.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 988.