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Giordano R, Facina G, Bromberg S, Nazario A. Argon scalpel in the surgical treatment of breast cancer. Breast 2019. [DOI: 10.1016/s0960-9776(19)30376-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Giordano R, Bromberg S, Elias S, Nazário A, Waitzberg A, Sá R, Facina G. Abstract P2-14-24: Argon scalpel in the surgical treatment of breast cancer. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p2-14-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Summary: Surgery is a key part of the treatment of breast cancer. The adoption of electric scalpel began to be used in breast surgeries in 1970 and this equipment uses high frequency electric current to create the following effects: cutting, coagulation or mixing of the two. Data show a decrease in the intraoperative bleeding, however, can also increase complications, such as seroma and thermal lesions in the surgical flaps. A new technique that could be used is the coagulation with argon plasma which is a method of non-contact thermal hemostasis.
Objectives: to compare the electric scalpel with the scalpel by coagulation with argon plasma about aspects surgical and pathological.
Methods: this is a prospective cohort study in which 60 patients with breast cancer were selected at the Discipline of Breast Diseases of the Department of Gynecology of the Federal University of São Paulo (UNIFESP) at any clinical stage where the surgical treatment was indicated, from March 2014 to August 2014. The patients were consecutively selected and randomized into two groups: electric scalpel surgery (ES) and argon plasma coagulation surgery (APC). Inclusion criteria were: 18 to 90 years old patients with breast cancer at any clinical stage where surgical (conservative or radical) treatment was indicated. Intraoperative bleeding was assessed by measuring the weights of the compresses. The patients who underwent surgery were evaluated at 7, 14 and 30 postoperative days. In these returns, the appearance of the surgical wound, the presence and amount of seroma (in mL), hematoma or infection were analyzed. Surgical site infection was considered when there was erythema, increased local or systemic temperature, pain, suture dehiscence or presence of purulent exudate. The surgical specimen was studied in the Department of Pathological Anatomy of UNIFESP. The pathological analysis as recommended by the WHO and particular evaluations were carried out in order to observe the extent and degree of the thermal effect produced in surgical specimens by the two hemostatic techniques (ES and APC).
Results: The mean age of the patients was 56.0 years for the ES group and 54.9 for the APC. There was no significant difference between the groups regarding intraoperative bleeding. However, a statistically significant difference was observed when the days with drain were compared in the postoperative period, with a mean of 10.1 days for the SE group and 7.1 days for the APC group. The study demonstrated that the APC group had a significant greater thermal effect on the margins of the surgical specimen.
Table 1.Thermal effect on the margins of the surgical specimens by study group (p=0.032)Thermic EffectEletric N (%)Argon N (%)Total N (%)Absent7 (23.3)0 (0)7 (11.7)G110 (33.3)12 (40.0)22 (36.4)G211 (36.7)13 (43.3)24 (40.0)G32 (6.7)5 (16.7)7 (11.7)
Conclusions: the use of argon scalpel, when compared to the electric scalpel, allowed hemostasis to be performed adequately without altering the rates of bleeding, surgical time and postoperative complications, and reduced the number of days with the drain. The thermal effect on the surgical specimen was significant greater with the argon scalpel.
Citation Format: Giordano R, Bromberg S, Elias S, Nazário A, Waitzberg A, Sá R, Facina G. Argon scalpel in the surgical treatment of breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-14-24.
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Affiliation(s)
- R Giordano
- Federal University of Sao Paulo - UNIFESP, Sao Paulo, Brazil
| | - S Bromberg
- Federal University of Sao Paulo - UNIFESP, Sao Paulo, Brazil
| | - S Elias
- Federal University of Sao Paulo - UNIFESP, Sao Paulo, Brazil
| | - A Nazário
- Federal University of Sao Paulo - UNIFESP, Sao Paulo, Brazil
| | - A Waitzberg
- Federal University of Sao Paulo - UNIFESP, Sao Paulo, Brazil
| | - R Sá
- Federal University of Sao Paulo - UNIFESP, Sao Paulo, Brazil
| | - G Facina
- Federal University of Sao Paulo - UNIFESP, Sao Paulo, Brazil
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Bromberg S, Figueiredo P, Ades F. Abstract P3-13-05: Comparing conventional breast conserving surgery with the minimally invasive approach technique to treat early breast cancer - a retrospective case control study. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p3-13-05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background/Objective: The objective of the study was to compare the oncological safety and aesthetical results between the minimally invasive technique and the conventional breast conserving surgery. Breast conserving surgery was developed to avoid mastectomy and has become the standard of care in early stage breast cancer. Patient concerns with aesthetics have led to the development of oncoplastic surgical approaches. It has been demonstrated that the aesthetic success in breast cancer surgical treatment leads to improved sexual and social recovery. In patients that have no desire or no need for associated mammoplasty, minimally invasive treatments allow the maintenance of the breast pre-surgical appearance. The mínimally invasive technique is an oncoplastic surgery aimed to remove both the breast tumor and the sentinel lymph node through one incision, thus providing better aesthetic results than the conventional breast conservative two incision technique.
Methods: We retrospectively evaluated 2 cohorts of 60 consecutive early breast cancer patients ( invasive breast cancer measuring no more than 25mm and clinically axillary negative lymph nodes ) operated by either conventional breast conserving surgery (N=26) or one incision surgery (N=34). We selected patients that have no desire or no need for associated mammoplasty. We compared the mammary volume tissue removed; surgical time; number of dissected lymph nodes; surgical complications such as seroma, infection, and dehiscence of the surgical wound; and deformities, retractions, and subsequent aesthetic sequelae.
Results: In the minimally invasive technique group the breast volume removed was significantly lower than in the conventional surgery technique group as well as was the surgical time and the number of dissected lymph nodes.
Demographics and surgical results Minimally invasive surgery ( n=34)Conventional surgery (n=26)P valueAge 0.241Medium53.9(11.4)57.4(11.3) Range33 - 7634 - 85 Disease Stage 0.482I30(88.2)21(80.8) II4(11.8)5(19.2) Incision >0.99Axilla1 (3.1)0 (0.0) Periareolar21(65.6)17(65.4) Sulcus10(31.3)9(34.6) Breast dissected volume <0.001Medium16.3(8.5; 26.7)42.4(14.4; 112.2) Range2 - 905 - 270 Dissected lymph nodes <0.001Medium (IIQ)2(1-5)4(1-13) Range1 - 181 - 31 Surgical time (min) 0.010Medium130(105; 170)180(110; 240) Range30 - 22050 - 275
No cases required enlargement of the margins and aesthetical results were better in theminimally invasive technique with only incision group.
Conclusions: The minimally invasive approach to treat early breast cancer was shown to be similar to the conventional breast conserving surgery in terms of oncologic outcomes but providing better cosmetic result.
Citation Format: Bromberg S, Figueiredo P, Ades F. Comparing conventional breast conserving surgery with the minimally invasive approach technique to treat early breast cancer - a retrospective case control study [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-13-05.
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Affiliation(s)
- S Bromberg
- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - P Figueiredo
- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - F Ades
- Hospital Israelita Albert Einstein, São Paulo, Brazil
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Norouzi N, Carver S, Dear T, Bromberg S, Gray S, Kahan M, Aarabi P, Borgundvaag B. Evaluation of alcohol intoxication and withdrawal syndromes based on analysis of tremor signals. Biomed Signal Process Control 2017. [DOI: 10.1016/j.bspc.2016.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Muniz P, da Silva DAM, Bícego MC, Bromberg S, Pires-Vanin AMS. Sewage contamination in a tropical coastal area (São Sebastião Channel, SP, Brazil). Mar Pollut Bull 2015; 99:292-300. [PMID: 26231066 DOI: 10.1016/j.marpolbul.2015.07.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/19/2015] [Accepted: 07/21/2015] [Indexed: 06/04/2023]
Abstract
Urban effluent discharges in Brazilian coastal areas are a chronic problem and often lead to changes in the quality of the marine environment. São-Sebastião-Channel (SSC) is an important aquatic ecosystem to be monitored for urban sewage contamination due to the intense urban activities in that region, as well as the relative high biodiversity of marine organisms. In the area are present three submarine sewage outfalls, a commercial harbour and also the biggest oil terminal in Brazil. Total organic carbon (TOC), total nitrogen (TN), total sulphur (TS), steroids and linear alkylbenzenes (LABs) were measured in sediment samples collected in three strategic locations of the SSC in order to monitor urban sewage contamination. Total LAB and total sterols levels ranged from below DL-51.3 ng g(-1) and below DL-10.40 μg g(-1), respectively. Samples collected near sewage outfall in the central part of the SSC had higher concentrations of urban sewage-associated contaminants.
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Affiliation(s)
- P Muniz
- Oceanografía y Ecología Marina, Instituto de Ecología y Ciencias Ambientales (IECA), Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.
| | - D A M da Silva
- Environmental and Fisheries Science Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Boulevard East, Seattle, WA 98112, USA
| | - M C Bícego
- Instituto Oceanográfico da Universidade de São Paulo (IOUSP), Praça do Oceanográfico 191, Cidade Universitária, 05508-120 São Paulo, SP, Brazil
| | - S Bromberg
- Instituto Oceanográfico da Universidade de São Paulo (IOUSP), Praça do Oceanográfico 191, Cidade Universitária, 05508-120 São Paulo, SP, Brazil
| | - A M S Pires-Vanin
- Instituto Oceanográfico da Universidade de São Paulo (IOUSP), Praça do Oceanográfico 191, Cidade Universitária, 05508-120 São Paulo, SP, Brazil
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Carver S, Norouzi N, Bromberg S, Gray S, Kahan M, Aarabi P, Borgundvaag B. Time-frequency visualization of alcohol withdrawal tremors. Annu Int Conf IEEE Eng Med Biol Soc 2014; 2014:5474-5477. [PMID: 25571233 DOI: 10.1109/embc.2014.6944865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In this paper, we propose a signal processing method of assessing the severity tremors caused by alcohol withdrawal (AW) syndrome. We have developed an iOS application to calculate the Clinical Institute Withdrawal Assessment (CIWA) score which captures iPod movements using the built-in accelerometer in order to reliably estimate the tremor severity component of the score. We report on the characteristics of AW tremor, the accuracy of electronic assessment of tremor compared to expert clinician assessment, and the potential for using signal processing assessment to differentiate factitious from real tremor in patients seen in the emergency department, as well as in nurses mimicking a tremor. Our preliminary results are based on 84 recordings from 61 subjects (49 patients, 12 nurses). In general we found a linear relationship between energy measured by the accelerometer (in the 4.4-10 Hz range) and the expert rating of tremor severity. Additionally, we demonstrate that 75% of the recordings from patients with actual AW syndrome had a mean peak frequency higher than 7 Hz whereas only 17% of the nurses' factitious tremors were above 7 Hz, suggesting that tremor above 7 Hz could be a potential discriminator of real versus factitious tremors.
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Shimoyama M, Petri V, Pasko D, Bromberg S, Wu W, Chen J, Nenasheva N, Kwitek A, Twigger S, Jacob H. Using multiple ontologies to integrate complex biological data. Comp Funct Genomics 2011; 6:373-8. [PMID: 18629202 PMCID: PMC2447497 DOI: 10.1002/cfg.498] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2005] [Revised: 10/17/2005] [Accepted: 11/07/2005] [Indexed: 11/07/2022] Open
Abstract
The strength of the rat as a model organism lies in its utility in pharmacology, biochemistry and physiology research. Data resulting from such studies is difficult to represent in databases and the creation of user-friendly data mining tools has proved difficult. The Rat Genome Database has developed a comprehensive ontology-based data structure and annotation system to integrate physiological data along with environmental and experimental factors, as well as genetic and genomic information. RGD uses multiple ontologies to integrate complex biological information from the molecular level to the whole organism, and to develop data mining and presentation tools. This approach allows RGD to indicate not only the phenotypes seen in a strain but also the specific values under each diet and atmospheric condition, as well as gender differences. Harnessing the power of ontologies in this way allows the user to gather and filter data in a customized fashion, so that a researcher can retrieve all phenotype readings for which a high hypoxia is a factor. Utilizing the same data structure for expression data, pathways and biological processes, RGD will provide a comprehensive research platform which allows users to investigate the conditions under which biological processes are altered and to elucidate the mechanisms of disease.
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Affiliation(s)
- Mary Shimoyama
- Human and Molecular Genetics Center Medical College of Wisconsin Milwaukee WI 53226 USA
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Twigger SN, Shimoyama M, Bromberg S, Kwitek AE, Jacob HJ. The Rat Genome Database, update 2007--easing the path from disease to data and back again. Nucleic Acids Res 2007; 35:D658-62. [PMID: 17151068 PMCID: PMC1761441 DOI: 10.1093/nar/gkl988] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2006] [Accepted: 10/24/2006] [Indexed: 11/14/2022] Open
Abstract
The Rat Genome Database (RGD, http://rgd.mcw.edu) is one of the core resources for rat genomics and recent developments have focused on providing support for disease-based research using the rat model. Recognizing the importance of the rat as a disease model we have employed targeted curation strategies to curate genes, QTL and strain data for neurological and cardiovascular disease areas. This work has centered on rat but also includes data for mouse and human to create 'disease portals' that provide a unified view of the genes, QTL and strain models for these diseases across the three species. The disease curation efforts combined with normal curation activities have served to greatly increase the content of the database, particularly for biological information, including gene ontology, disease, pathway and phenotype ontology annotations. In addition to improving the features and database content, community outreach has been expanded to demonstrate how investigators can leverage the resources at RGD to facilitate their research and to elicit suggestions and needs for future developments. We have published a number of papers that provide additional information on the ontology annotations and the tools at RGD for data mining and analysis to better enable researchers to fully utilize the database.
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Affiliation(s)
- Simon N Twigger
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.
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Twigger SN, Pasko D, Nie J, Shimoyama M, Bromberg S, Campbell D, Chen J, dela Cruz N, Fan C, Foote C, Harris G, Hickmann B, Ji Y, Jin W, Li D, Mathis J, Nenasheva N, Nigam R, Petri V, Reilly D, Ruotti V, Schauberger E, Seiler K, Slyper R, Smith J, Wang W, Wu W, Zhao L, Zuniga-Meyer A, Tonellato PJ, Kwitek AE, Jacob HJ. Tools and strategies for physiological genomics: the Rat Genome Database. Physiol Genomics 2005; 23:246-56. [PMID: 16106031 PMCID: PMC4505745 DOI: 10.1152/physiolgenomics.00040.2005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The broad goal of physiological genomics research is to link genes to their functions using appropriate experimental and computational techniques. Modern genomics experiments enable the generation of vast quantities of data, and interpretation of this data requires the integration of information derived from many diverse sources. Computational biology and bioinformatics offer the ability to manage and channel this information torrent. The Rat Genome Database (RGD; http://rgd.mcw.edu) has developed computational tools and strategies specifically supporting the goal of linking genes to their functional roles in rat and, using comparative genomics, to human and mouse. We present an overview of the database with a focus on these unique computational tools and describe strategies for the use of these resources in the area of physiological genomics.
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Affiliation(s)
- Simon N Twigger
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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10
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de la Cruz N, Bromberg S, Pasko D, Shimoyama M, Twigger S, Chen J, Chen CF, Fan C, Foote C, Gopinath GR, Harris G, Hughes A, Ji Y, Jin W, Li D, Mathis J, Nenasheva N, Nie J, Nigam R, Petri V, Reilly D, Wang W, Wu W, Zuniga-Meyer A, Zhao L, Kwitek A, Tonellato P, Jacob H. The Rat Genome Database (RGD): developments towards a phenome database. Nucleic Acids Res 2005; 33:D485-91. [PMID: 15608243 PMCID: PMC540004 DOI: 10.1093/nar/gki050] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Rat Genome Database (RGD) (http://rgd.mcw.edu) aims to meet the needs of its community by providing genetic and genomic infrastructure while also annotating the strengths of rat research: biochemistry, nutrition, pharmacology and physiology. Here, we report on RGD's development towards creating a phenome database. Recent developments can be categorized into three groups. (i) Improved data collection and integration to match increased volume and biological scope of research. (ii) Knowledge representation augmented by the implementation of a new ontology and annotation system. (iii) The addition of quantitative trait loci data, from rat, mouse and human to our advanced comparative genomics tools, as well as the creation of new, and enhancement of existing, tools to enable users to efficiently browse and survey research data. The emphasis is on helping researchers find genes responsible for disease through the use of rat models. These improvements, combined with the genomic sequence of the rat, have led to a successful year at RGD with over two million page accesses that represent an over 4-fold increase in a year. Future plans call for increased annotation of biological information on the rat elucidated through its use as a model for human pathobiology. The continued development of toolsets will facilitate integration of these data into the context of rat genomic sequence, as well as allow comparisons of biological and genomic data with the human genomic sequence and of an increasing number of organisms.
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Affiliation(s)
- Norberto de la Cruz
- Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53213, USA
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11
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Kwitek AE, Gullings-Handley J, Yu J, Carlos DC, Orlebeke K, Nie J, Eckert J, Lemke A, Andrae JW, Bromberg S, Pasko D, Chen D, Scheetz TE, Casavant TL, Soares MB, Sheffield VC, Tonellato PJ, Jacob HJ. High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. Genome Res 2004; 14:750-7. [PMID: 15060019 PMCID: PMC383322 DOI: 10.1101/gr.1968704] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The laboratory rat is a major model organism for systems biology. To complement the cornucopia of physiological and pharmacological data generated in the rat, a large genomic toolset has been developed, culminating in the release of the rat draft genome sequence. The rat draft sequence used a variety of assembly packages, as well as data from the Radiation Hybrid (RH) map of the rat as part of their validation. As part of the Rat Genome Project, we have been building a high-density RH map to facilitate data integration from multiple maps and now to help validate the genome assembly. By incorporating vectors from our lab and several other labs, we have doubled the number of simple sequence length polymorphisms (SSLPs), genes, expressed sequence tags (ESTs), and sequence-tagged sites (STSs) compared to any other genome-wide rat map, a total of 24,437 elements. During the process, we also identified a novel approach for integrating the RH placement results from multiple maps. This new integrated RH map contains approximately 10 RH-mapped elements per Mb on the genome assembly, enabling the RH maps to serve as a scaffold for a variety of data visualization tools.
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Affiliation(s)
- Anne E Kwitek
- Human & Molecular Genetics Center and Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA.
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Twigger SN, Nie J, Ruotti V, Yu J, Chen D, Li D, Mathis J, Narayanasamy V, Gopinath GR, Pasko D, Shimoyama M, De La Cruz N, Bromberg S, Kwitek AE, Jacob HJ, Tonellato PJ. Integrative genomics: in silico coupling of rat physiology and complex traits with mouse and human data. Genome Res 2004; 14:651-60. [PMID: 15060006 PMCID: PMC383309 DOI: 10.1101/gr.1974504] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Integration of the large variety of genome maps from several organisms provides the mechanism by which physiological knowledge obtained in model systems such as the rat can be projected onto the human genome to further the research on human disease. The release of the rat genome sequence provides new information for studies using the rat model and is a key reference against which existing and new rat physiological results can be aligned. Previously, we described comparative maps of the rat, mouse, and human based on EST sequence comparisons combined with radiation hybrid maps. Here, we use new data and introduce the Integrated Genomics Environment, an extensive database of curated and integrated maps, markers, and physiological results. These results are integrated by using VCMapview, a java-based map integration and visualization tool. This unique environment allows researchers to relate results from cytogenetic, genetic, and radiation hybrid studies to the genome sequence and compare regions of interest between human, mouse, and rat. Integrating rat physiology with mouse genetics and clinical results from human by using the respective genomes provides a novel route to capitalize on comparative genomics and the strengths of model organism biology.
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Affiliation(s)
- Simon N Twigger
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA.
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Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Simons R, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Albà M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 2004; 428:493-521. [PMID: 15057822 DOI: 10.1038/nature02426] [Citation(s) in RCA: 1512] [Impact Index Per Article: 75.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2003] [Accepted: 02/20/2004] [Indexed: 01/16/2023]
Abstract
The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.
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Affiliation(s)
- Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA. http://www.hgsc.bcm.tmc.edu
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Abstract
What is the basis for the two-state cooperativity of protein folding? Since the 1950s, three main models have been put forward. 1. In 'helix-coil' theory, cooperativity is due to local interactions among near neighbours in the sequence. Helix-coil cooperativity is probably not the principal basis for the folding of globular proteins because it is not two-state, the forces are weak, it does not account for sheet proteins, and there is no evidence that helix formation precedes the formation of a hydrophobic core in the following pathways. 2. In the 'sidechain packing' model, cooperativity is attributed to the jigsaw-puzzle-like complementary fits of sidechains. This too is probably not the basis of folding cooperativity because exact models and experiments on homopolymers with sidechains give no evidence that sidechain freezing is two-state, sidechain complementarities in proteins are only weak trends, and the molten globule model predicted by this model is far more native-like than experiments indicate. 3. In the 'hydrophobic core collapse' model, cooperativity is due to the assembly of non-polar residues into a good core. Exact model studies show that this model gives two-state behaviour for some sequences of hydrophobic and polar monomers. It is based on strong forces. There is considerable experimental evidence for the kinetics this model predicts: the development of hydrophobic clusters and cores is concurrent with secondary structure formation. It predicts compact denatured states with sizes and degrees of disorder that are in reasonable agreement with experiments.
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Affiliation(s)
- H S Chan
- Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-1204, USA
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15
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Abstract
General principles of protein structure, stability, and folding kinetics have recently been explored in computer simulations of simple exact lattice models. These models represent protein chains at a rudimentary level, but they involve few parameters, approximations, or implicit biases, and they allow complete explorations of conformational and sequence spaces. Such simulations have resulted in testable predictions that are sometimes unanticipated: The folding code is mainly binary and delocalized throughout the amino acid sequence. The secondary and tertiary structures of a protein are specified mainly by the sequence of polar and nonpolar monomers. More specific interactions may refine the structure, rather than dominate the folding code. Simple exact models can account for the properties that characterize protein folding: two-state cooperativity, secondary and tertiary structures, and multistage folding kinetics--fast hydrophobic collapse followed by slower annealing. These studies suggest the possibility of creating "foldable" chain molecules other than proteins. The encoding of a unique compact chain conformation may not require amino acids; it may require only the ability to synthesize specific monomer sequences in which at least one monomer type is solvent-averse.
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Affiliation(s)
- K A Dill
- Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-1204, USA
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16
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Bromberg S, LiCata VJ, Mallikarachchi D, Allewell NM. Ligation alters the pathway of urea-induced denaturation of the catalytic trimer of Escherichia coli aspartate transcarbamylase. Protein Sci 1994; 3:1236-44. [PMID: 7987218 PMCID: PMC2142926 DOI: 10.1002/pro.5560030809] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We have examined the pathway and energetics of urea-induced dissociation and unfolding of the catalytic trimer (c3) of aspartate transcarbamylase from Escherichia coli at low temperature in the absence and presence of carbamyl phosphate (CP; a substrate), N-(phosphonacetyl)-L-Asp (PALA; a bisubstrate analog), and 2 anionic inhibitors, Cl- and ATP, by analytical gel chromatography supplemented by activity assays and ultraviolet difference spectroscopy. In the absence of active-site ligands and in the presence of ATP, c3 dissociates below 2 M urea into swollen c chains that then gradually unfold from 2 to 6 M urea with little apparent cooperativity. Linear extrapolation to 0 M urea of free energies determined in 3 independent types of experiments yields estimates for delta Gdissociation at 7.5 degrees C of about 7-10 kcal m-1 per interface. delta Gunfolding of dissociated chains when modeled as a 2-state process is estimated to be very small, on the order of -2 kcal m-1. The data are also consistent with the possibility that the unfolding of the dissociated monomer is a 1-state swelling process. In the presence of the ligands CP and PALA, and in the presence of Cl-, c3 dissociates at much higher urea concentrations, and trimer dissociation and unfolding occur simultaneously and apparently cooperatively, at urea concentrations that increase with the affinity of the ligand.
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Affiliation(s)
- S Bromberg
- Department of Biochemistry, University of Minnesota, St. Paul 55108
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17
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Abstract
What role does side-chain packing play in protein stability and structure? To address this question, we compare a lattice model with side chains (SCM) to a linear lattice model without side chains (LCM). Self-avoiding configurations are enumerated in 2 and 3 dimensions exhaustively for short chains and by Monte Carlo sampling for chains up to 50 main-chain monomers long. This comparison shows that (1) side-chain degrees of freedom increase the entropy of open conformations, but side-chain steric exclusion decreases the entropy of compact conformations, thus producing a substantial entropy that opposes folding; (2) there is side-chain "freezing" or ordering, i.e., a sharp decrease in entropy, near maximum compactness; and (3) the different types of contacts among side chains (s) and main-chain elements (m) have different frequencies, and the frequencies have different dependencies on compactness. mm contacts contribute significantly only at high densities, suggesting that main-chain hydrogen bonding in proteins may be promoted by compactness. The distributions of mm, ms, and ss contacts in compact SCM configurations are similar to the distributions in protein structures in the Brookhaven Protein Data Bank. We propose that packing in proteins is more like the packing of nuts and bolts in a jar than like the pairwise matching of jigsaw puzzle pieces.
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Affiliation(s)
- S Bromberg
- Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-1204
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Bromberg S, Burz DS, Allewell NM. Use of analytical gel chromatography to analyze tertiary and quaternary structural changes in E. coli aspartate transcarbamylase. J Biochem Biophys Methods 1990; 20:143-56. [PMID: 2179387 DOI: 10.1016/0165-022x(90)90073-l] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
E. coli aspartate transcarbamylase (ATCase) is a large (310 kDa) protein that undergoes major changes in quaternary structure when substrates and regulatory nucleotides bind. We have used analytical gel chromatography to detect quaternary structure changes in both the holoenzyme and its catalytic subunit (c3), to characterize the quaternary structure of single site mutant proteins and to monitor urea-induced dissociation and unfolding of c3. Binding of the bisubstrate analog PALA (N-(phosphonacetyl)-L-aspartate) to ATCase and c3 has been shown to alter s20.w by -3.3% and + 1.4%, respectively [Howlett, G.J. and Schachman, H.K. (1977), Biochemistry 23, 5077-5083]. The corresponding changes in the chromatographic partition coefficient (sigma) are -2.6 +/- 0.3% and 5.5 +/- 1.9% on Sephacryl S400HR and S200, respectively. Partition coefficients of mutant ATCases with single site mutations in the c chain differ from those of the wild-type protein by +/- 0.5% in small zone experiments; for example, mutations Arg 269----Gly and Glu 239----Gln alter the partition coefficient by 0.4% and -0.5%, respectively. The partition coefficient of mutant Glu 50----Gln is identical to the wild type enzyme. In the presence of saturating PALA, partition coefficients of Glu 50----Gln and Arg 269----Gly, but not Glu 239----Gln are identical to those of the wild type. Results for Glu 239----Gln are consistent with measurements of activity, small angle X-ray scattering and sedimentation coefficient that indicate that mutations at this site shift the quaternary structure towards the R state [Ladjimi and Kantrowitz (1988), Biochemistry 27, 276-83; Vachette and Hervé, cited by Kantrowitz and Lipscomb (1988), Science 241, 669-674; Newell and Schachman (1988), FASEB J. 2, A551]. Results for Glu 50----Gln are also consistent with measurements of activity (Ladjimi et al. (1988), Biochemistry 27, 268-276). The changes in tertiary and quaternary structure that result from urea-induced denaturation of c3 result in larger changes in the partition coefficient. Dissociation into folded monomers in 1-1.75 M urea is accompanied by a 4.6% increase in partition coefficient, while denaturation at greater than 5 M urea gives rise to a 43% decrease on S-300 Sephacryl. The bisubstrate analog PALA suppresses dissociation and increases the cooperativity of the unfolding reaction.
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Affiliation(s)
- S Bromberg
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06457
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Abstract
It is the authors' premise that caregivers of the suicidal elderly patient are at times guided by a paternalism that is not always in the best interests of the patient. They advocate instead care based on greater respect for the autonomy of the patient. A case of a suicidal, recently widowed man is presented, and historical and ethical considerations of bereavement and suicide are discussed.
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20
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Abstract
The sequence specificity of the Tetrahymena DNA-adenine methylase was determined by nearest-neighbor analyses of in vivo and in vitro methylated DNA. In vivo all four common bases were found to the 5' side of N6-methyladenine, but only thymidine was 3'. Homologous DNA already methylated in vivo and heterologous Micrococcus luteus DNA were methylated in vitro by a partially purified DNA-adenine methylase activity isolated from Tetrahymena macronuclei. The in vitro-methylated sequence differed from the in vivo sequence in that both thymidine and cytosine were 3' nearest neighbors of N6-methyladenine.
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Goodwin JS, Bromberg S, Staszak C, Kaszubowski PA, Messner RP, Neal JF. Effect of physical stress on sensitivity of lymphocytes to inhibition by prostaglandin E2. The Journal of Immunology 1981. [DOI: 10.4049/jimmunol.127.2.518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Abstract
Physical stress is associated with depressed cellular immune function. We have found that lymphocytes from subjects undergoing either of 2 stressful events, cardiac surgery or childbirth, are more sensitive to inhibition by PGE2. For example, the concentration of PGE2 required for 50% inhibition of 3H-thymidine incorporation (ID50) into phytohemagglutinin-stimulated lymphocytes from patients undergoing cardiac surgery went from 1.5 X 10(-8) M on the day before surgery to 3 X 10(-9) M on the day after surgery. This increase in sensitivity to PGE2 was accompanied by a significantly decreased lymphocyte proliferative response (27 to 68% of control, depending on mitogen dose) and a 50% increase in the percentage of E rosette-positive cells with receptors for the Fc portion of IgG. The increased sensitivity to PGE and the depressed mitogen responses returned to preoperative values by day 10. The depressed mitogen responses of the postoperative patients were completely restored to normal by removal of glass-adherent cells before culture. In addition, the responses of the postoperative patients and the women in labor were partially restored by the addition of indomethacin, a prostaglandin synthetase inhibitor, to the cultures. Thus it would appear that physical stress causes lymphocytes to become more sensitive to prostaglandin E2, and the increased sensitivity to inhibition by this immunomodulator is responsible in part for the depressed cellular immune function after physical stress.
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22
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Goodwin JS, Bromberg S, Staszak C, Kaszubowski PA, Messner RP, Neal JF. Effect of physical stress on sensitivity of lymphocytes to inhibition by prostaglandin E2. J Immunol 1981; 127:518-22. [PMID: 6265552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Physical stress is associated with depressed cellular immune function. We have found that lymphocytes from subjects undergoing either of 2 stressful events, cardiac surgery or childbirth, are more sensitive to inhibition by PGE2. For example, the concentration of PGE2 required for 50% inhibition of 3H-thymidine incorporation (ID50) into phytohemagglutinin-stimulated lymphocytes from patients undergoing cardiac surgery went from 1.5 X 10(-8) M on the day before surgery to 3 X 10(-9) M on the day after surgery. This increase in sensitivity to PGE2 was accompanied by a significantly decreased lymphocyte proliferative response (27 to 68% of control, depending on mitogen dose) and a 50% increase in the percentage of E rosette-positive cells with receptors for the Fc portion of IgG. The increased sensitivity to PGE and the depressed mitogen responses returned to preoperative values by day 10. The depressed mitogen responses of the postoperative patients were completely restored to normal by removal of glass-adherent cells before culture. In addition, the responses of the postoperative patients and the women in labor were partially restored by the addition of indomethacin, a prostaglandin synthetase inhibitor, to the cultures. Thus it would appear that physical stress causes lymphocytes to become more sensitive to prostaglandin E2, and the increased sensitivity to inhibition by this immunomodulator is responsible in part for the depressed cellular immune function after physical stress.
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Glover D, Gerety M, Bromberg S, Fullam S, DiVasto P, Kaufman A. Diethylstilbestrol in the treatment of rape victims. West J Med 1976; 125:331-4. [PMID: 1032235 PMCID: PMC1237330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Despite growing controversy surrounding its use as a "morning after pill," diethylstilbestrol (DES) is prescribed liberally for rape victims. Guidelines for its use in these patients is lacking. Of 150 consecutive rape victims treated at a university medical center, 63 (42 percent) received prescriptions for DES. Of the 55 (87 percent) on whom follow-up was obtained, in 40 (73 percent) there were substantial side effects-nausea or vomiting, or both. At least six (11 percent) did not complete therapy because of these side effects. The authors offer guidelines for use of DES for rape victims and a plan for patient education and follow-up.
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Goffi FS, Bromberg S, Reis L, Neves DP, Almeida AL, Guimarães JS, Hashiba K. [Insular neoplasms of the pancreas. Surgical aspects]. AMB Rev Assoc Med Bras 1975; 21:67-71. [PMID: 166418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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