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102. The Invisible Hand of Social Capital: Narratives of First Generation College Students in Engineering.

Author

MARTIN, JULIE P.

Subjects
SOCIAL capital, ENGINEERING education, COLLEGE students, HIGHER education, DECISION making
Abstract

First generation college students can increase both the number and diversity of students in engineering. We use Lin's Network Theory of Social Capital, which describes relationships as being embedded with resources used to achieve a goal, as a framework for understanding undergraduate students' decisions to enroll in engineering studies. While much of the discourse on social capital in higher education focuses on inequalities and deficits experienced by first generation college students, our work helps to transition the discussion by highlighting the positive influence of education personnel as well as teachers and mentors associated with institutionalized programs. We use narrative analysis and two types of explicitly integrated complementary qualitative data to expand on Lin's theory. This paper presents an exemplar narrative describing what Lin calls the "invisible hand of social capital;" that is, when particularly resource-rich networks do not necessitate an individual knowingly mobilizing resources because information and resources are received in routine exchanges. Our findings support the need for continued proactive outreach, educational, and support systems that can serve as research-rich networks for first generation college students. [ABSTRACT FROM AUTHOR]

Published
2015

103. Characterizing Engineering Student Social Capital in Relation to Demographics.

Author

MARTIN, JULIE P., BROWN, SHANE, MILLER, MATTHEW K., and STEFL, SHANNON K.

Subjects
ENGINEERING education, ENGINEERING students, SOCIAL capital, DEMOGRAPHIC surveys, UNDERGRADUATES, CLUSTER analysis (Statistics)
Abstract

The primary goal of this paper is to explore the relationships between engineering undergraduate student demographic characteristics and the social capital these students utilize when making academic and career decisions. This multiinstitution study is carefully aligned with the Network Theory of Social Capital. Employing cluster analysis to characterize several key aspects of 1,410 undergraduate engineering students' social capital-namely, the composition and characterization of their social networks and indicators of their resource access-the authors explore latent patterns in the data, and uncover social capital profiles. These profiles are then related to demographic characteristics through additional statistical analyses. In particular, the paper investigates and challenges the theoretical notion regarding the significance of gender and race/ethnicity in students' social network characteristics and social capital indicators. Unlike other social capital work in education, this paper presents findings that gender and race/ethnicity are not significant or adequate for characterizing the social capital of engineering undergraduates. [ABSTRACT FROM AUTHOR]

Published
2015

106. Stigma-Based Rejection and the Detection of Signs of Acceptance

Author

Richman, Laura Smart, Martin, Julie, and Guadagno, Jennifer

Abstract

After people experience social rejection, one tactic to restore a sense of belonging is to selectively attend to and readily perceive cues that connote acceptance. The multimotive model of responses to rejection suggests that contextual features of the rejection are important determinants of how people are motivated to respond. According to this model, when rejection is construed as pervasive and chronic, people will be less likely to adopt strategies that promote belonging. Across two studies, we found that chronic rejection—in the context of stigmatization—predicted a slower response time to smiling faces and less recognition of affiliation-related words as compared to a nonstigmatized control group. These results suggest that, unlike more transitory forms of rejection, stigmatization leads to slower detection of signs of acceptance. These responses may hinder belonging repair and thus have important negative implications for health and well-being.

Published
2016
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107. Exploring the Theoretical Social Capital "Deficit" of First Generation College Students: Implications for Engineering Education.

Author

MARTIN, JULIE P., MILLER, MATTHEW K., and SIMMONS, DENISE R.

Subjects
SOCIAL capital, FIRST-generation college students, ENGINEERING students, SERVICES for college students, SOCIAL networks, ENGINEERING education in universities & colleges, YOUNG adults, HIGHER education, SOCIAL conditions of students
Abstract

This paper investigates social capital, that is, resources accrued through relationships, of engineering students based on their generational status in college. We administered a "Name and Resource Generator" instrument adapted from the field of sociology to a sample of 1,410 engineering undergraduates from five U.S. universities. Quantitative analysis of results revealed many statistically significant differences in the social capital characteristics and accessed resources for First Generation College students (FGC) compared to Continuing Generation College (CGC) students. While some of these results were theoretically anticipated, we also present unique findings regarding (1) the prevalence of available and accessed resources for FGC students, and (2) the type of individual (known as an "alter") providing the engineering-related resources. The retrospective nature of the study allowed us to draw conclusions about the nature of these resources and alter types both during and before undergraduate engineering studies. These results represent a significant theoretical contribution that engineering education stakeholders can use to enhance outreach, recruitment and retention efforts to help grow and diversify the field. [ABSTRACT FROM AUTHOR]

Published
2014

108. Engineering Student Social Capital in an Interactive Learning Environment.

Author

BROWN, SHANE, STREET, DAVID, and MARTIN, JULIE P.

Subjects
ENGINEERING students, SOCIAL capital, ACTIVE learning, TUTORS & tutoring, COLLEGE environment, CLASSROOM environment, ENGINEERING education in universities & colleges, YOUNG adults, HIGHER education
Abstract

College student access to resources has been shown to be important for learning, cognitive development, retention, and other outcomes. The framework of social capital, or resources embedded in social networks that are accessed by members of a network, captures the essence of this resource acquisition. One important source of social capital related to academic achievement is the interactive classroom environment, but social capital development in this setting has not been studied. The purpose of this research is to examine factors that influence social capital development in a setting where tutors are used in the lecture environment. Subject matter difficulty, approachability and accessibility of faculty and classroom environment were all factors that impacted students' choices related to accessing available social capital in this environment. Results can inform both social capital theory, in terms of development in an academic setting, and tutoring in comparable interactive learning environments. [ABSTRACT FROM AUTHOR]

Published
2014

109. Family Roles in Engineering Undergraduates' Academic and Career Choices: Does Parental Educational Attainment Matter?

Author

MARTIN, JULIE P., SIMMONS, DENISE R., and YU, SHIRLEY L.

Subjects
ENGINEERING students, PARENT participation in higher education, ENGINEERING education in universities & colleges, FIRST-generation college students, COLLEGE students' family relationships, VOCATIONAL guidance, HIGHER education
Abstract

The purpose of this paper is to examine in detail the roles that families, particularly parents, play in the academic and career choices of students majoring in engineering at the undergraduate level, with a particular emphasis on how roles may differ when considering the parental level of education. Previous studies have reported the various influences on students' decisions to enter and persist in engineering at the undergraduate level. Though the role of the family has been identified as an important influence, there remains a limited understanding of specific family roles. In this large qualitative study design, the authors use constructivist epistemology, an emergent design, and a basic interpretive approach. Semi-structured interviews were conducted with a sample of 118 engineering undergraduates enrolled at two universities and representing diversity in parental educational attainment. Based upon interview transcripts, six distinct family roles were identified in participants' academic and career choices. Variations in certain family roles were found with parental educational attainment. This study is innovative in that it significantly contributes to the knowledge base of family, especially parental, influences on engineering students by including the previously under-explored factor of parental educational attainment. Findings are synthesized into recommendations for developing recruitment and retention interventions for engineering undergraduates, particularly students with little or no familial experience with higher education. [ABSTRACT FROM AUTHOR]

Published
2014

110. Changes in predicted cardiovascular disease risk after biliopancreatic diversion surgery in severely obese patients.

Author

Piché, Marie-Ève, Martin, Julie, Cianflone, Katherine, Bastien, Marjorie, Marceau, Simon, Biron, Simon, Hould, Frédéric-Simon, and Poirier, Paul

Subjects
CARDIOVASCULAR diseases, PANCREATIC surgery, OVERWEIGHT persons, FOLLOW-up studies (Medicine), BODY mass index, BODY weight
Abstract

Objective: To determine the impact of biliopancreatic diversion with duodenal switch (BPD-DS) surgery on cardiovascular risk profile and predicted cardiovascular risk in severely obese patients. Materials/Methods: We compared 1-year follow-up anthropometric and metabolic profiles in severely obese who underwent BPD-DS (n=73) with controls (severely obese without surgery) (n=33). The 10-year predicted risk for coronary heart disease (CHD) was estimated using the Framingham risk-tool. We assigned 10-year and lifetime predicted risks to stratify subjects into 3 groups: 1) high short-term predicted risk (≥10% 10-year risk or diagnosed diabetes), 2) low short-term (<10% 10-year risk)/low lifetime predicted risk or 3) low short-term/high lifetime predicted risk. Results: During the follow-up period, body weight and body mass index decreased markedly in the surgical group (−52.1±1.9kg and −19.0±0.6kg/m2 respectively, p<0.001) vs. (−0.7±1.0kg and −0.3±0.4kg/m2, p=0.51). Weight loss in the surgical group was associated with a reduction in HbA1C (6.2% vs. 5.1%), HOMA-IR (61.5 vs. 9.3), all lipoprotein levels, as well as blood pressure (p<0.001). The 10-year CHD predicted risk decreased by 43% in women and 33% in men, whereas the estimated CHD risk in the non surgical group did not change. Before surgery, none of the women and only 18% of men showed low short-term/low lifetime predicted risk, whereas a significant proportion of subjects had high short-term predicted risk (36% in women and 12% in men). Following surgery, 52% of women and 55% of men have a low short-term/low lifetime predicted risk. Conclusions: These results highlight the cardiovascular benefits of BPD-DS and suggest a positive impact on predicted CHD risk in severely obese patients. Long-term studies are needed to confirm our results and to ascertain the effects on CHD risk estimates after BPD-DS surgery. [ABSTRACT FROM AUTHOR]

Published
2014
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113. Effect of bariatric surgery on airway response and lung function in obese subjects with asthma.

Author

Boulet, Louis-Philippe, Turcotte, Hélène, Martin, Julie, and Poirier, Paul

Abstract

Summary: Background: Obesity is a risk factor for self-reported asthma and makes asthma management more difficult. The effects of bariatric surgery on asthma in severely obese subjects remain to be documented. Methods: In this prospective study, 12 asthmatic patients with severe obesity were evaluated before, 6 and 12 months after bariatric surgery. Each had methacholine inhalation tests, measures of expiratory flows and lung volumes, measurements of C-reactive protein and questionnaires on asthma medication, asthma symptoms and co-morbid conditions. Eleven severely obese patients with asthma (considered as controls) underwent the same evaluations. Primary endpoint was airway responsiveness to methacholine and secondary endpoints were lung volumes and markers of systemic inflammation. Results: Mean body mass index decreased from 51.2 to 34.4 kg/m2 twelve months post-surgery. Mean PC20 methacholine improved from 0.84 to 6.2 mg/ml (P < 0.001); FEV1, FVC, FRC, FRC/TLC and ERV all improved (P ≤ 0.006). C-reactive protein decreased from 8.6 to 1.7 mg/L (P < 0.001) Asthma symptoms total score was significantly reduced (P = 0.03) and asthma medication needs decreased, ten patients being able to stop all asthma drugs. No significant changes of these parameters from baseline were observed in asthmatic controls. Improvements in airway responsiveness and lung volumes happened in parallel and correlated with reductions of body mass index (r = 0.58, P = 0.049), C-reactive protein levels (r = −0.74, P = 0.004). Conclusion: Airway responsiveness, lung volumes and asthma severity/control markedly improved with weight loss following bariatric surgery in severely obese patients. [Copyright &y& Elsevier]

Published
2012
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114. Plasma Adipokine and Hormone Changes in Mountaineers on Ascent to 5300 Meters.

Author

Smith, Jessica D., Cianflone, Katherine, Martin, Julie, Poirier, Paul, Broderick, Tom L., and Noël, Martin

Subjects
ACYLATION, WEIGHT loss, ADIPONECTIN, INTERLEUKIN-6, COMPLEMENT (Immunology), LIPOTROPIN, INFLAMMATION, HORMONES
Abstract

Objective: The current study evaluated multiple metabolic and inflammatory hormone responses in recreational climbers (7 men and 3 women, age 26–49 years) over 9 days. In particular, acylation-stimulating protein (ASP), which influences fat storage in adipose tissue, has not been measured at high altitude. Methods: Serial measurements were taken at sea level (SL), or 353 m, on day 0, 4000 m on day 3, 4750 m on day 6, and 5300 m on day 9 of the expedition. Results: Body mass index (BMI) decreased upon ascent to 5300 m from SL (SL 23.2 ± 1.5 kg/m2; 4000 m 23.2 ± 1.4 kg/m2; 4750 m 22.9 ± 1.3 kg/m2; 5300 m 22.3 ± 1.2 kg/m2; P < .001). Similarly, plasma non-esterified fatty acids and triglycerides increased, while HDL cholesterol decreased (P < .05 to < .001) from SL to 5300 m. Acylation-stimulating protein (SL 42.2 ± 40.2 nm; 4000 m 117.0 ± 69.6 nm; 4750 m 107.9 ± 44.5 nm; 5300 m 82.2 ± 20.2 nm; P = .019) and adiponectin (SL 10.4 ± 6.5 ng/mL, 4000 m 13.9 ± 8.5 ng/mL, 4750 m 18.3 ± 8.3 ng/mL, 5300 m 14.7 ± 8.0 ng/mL; P = .015) increased, as did insulin and Interleukin-6 (IL-6) levels (up to 71% and 168%, respectively; P < .05) with no change in leptin, complement C3 (C3), high sensitivity C-reactive protein (hsCRP) or cortisol levels throughout the mountain ascent from SL to 5300 m. Conclusion: Acylation-stimulating protein and adiponectin are increased during a 9-day period of high altitude (SL to 5300 m) exposure despite weight loss in healthy mountaineers. [ABSTRACT FROM AUTHOR]

Published
2011
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115. Characterization of the metabolic and physiologic response to chromium supplementation in subjects with type 2 diabetes mellitus.

Author

Cefalu, William T., Rood, Jennifer, Pinsonat, Patricia, Qin, Jianhua, Sereda, Olga, Levitan, Lilian, Anderson, Richard A., Zhang, Xian H., Martin, Julie M., Martin, Corby K., Wang, Zhong Q., and Newcomer, Bradley

Subjects
CHROMIUM in human nutrition, TYPE 2 diabetes, PHENOTYPES, COHORT analysis, LIPID metabolism, INSULIN resistance, DIETARY supplements
Abstract

Abstract: The objective of the study was to provide a comprehensive evaluation of chromium (Cr) supplementation on metabolic parameters in a cohort of type 2 diabetes mellitus subjects representing a wide phenotype range and to evaluate changes in “responders” and “nonresponders.” After preintervention testing to assess glycemia, insulin sensitivity (assessed by euglycemic clamps), Cr status, and body composition, subjects were randomized in a double-blind fashion to placebo or 1000 μg Cr. A substudy was performed to evaluate 24-hour energy balance/substrate oxidation and myocellular/intrahepatic lipid content. There was not a consistent effect of Cr supplementation to improve insulin action across all phenotypes. Insulin sensitivity was negatively correlated to soleus and tibialis muscle intramyocellular lipids and intrahepatic lipid content. Myocellular lipids were significantly lower in subjects randomized to Cr. At preintervention, responders, defined as insulin sensitivity change from baseline of at least 10% or greater, had significantly lower insulin sensitivity and higher fasting glucose and A1c when compared with placebo and nonresponders, that is, insulin sensitivity change from baseline of less than 10%. Clinical response was significantly correlated (P < .001) to the baseline insulin sensitivity, fasting glucose, and A1c. There was no difference in Cr status between responder and nonresponders. Clinical response to Cr is more likely in insulin-resistant subjects who have more elevated fasting glucose and A1c levels. Chromium may reduce myocellular lipids and enhance insulin sensitivity in subjects with type 2 diabetes mellitus who do respond clinically independent of effects on weight or hepatic glucose production. Thus, modulation of lipid metabolism by Cr in peripheral tissues may represent a novel mechanism of action. [Copyright &y& Elsevier]

Published
2010
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117. Phenotype of subjects with type 2 diabetes mellitus may determine clinical response to chromium supplementation.

Author

Wang, Zhong Q., Qin, Jianhua, Martin, Julie, Zhang, Xian H., Sereda, Olga, Anderson, Richard A., Pinsonat, Patricia, and Cefalu, William T.

Subjects
CHROMIUM, PHENOTYPES, TYPE 2 diabetes, INSULIN
Abstract

Abstract: Considerable controversy exists regarding the use of chromium (Cr) supplementation to modulate carbohydrate metabolism in subjects with diabetes. Recently, we reported that Cr supplementation, provided as 1000 μg/d as Cr picolinate, enhanced insulin sensitivity in subjects with type 2 diabetes mellitus. Our data agreed with some, but not all, studies that evaluated a similar dose and formulation in type 2 diabetes mellitus and suggested that subject selection and characteristics may be important considerations when assessing the clinical response. Thus, the goal of this study was to assess which metabolic or clinical characteristics, when obtained at baseline, best determine a clinical response to Cr when assessing changes in insulin sensitivity. Seventy-three subjects with type 2 diabetes mellitus were assessed in a double-blinded, randomized, placebo-controlled study. Subjects were assessed at baseline for glycemic control with glycated hemoglobin measures, oral glucose tolerance tests, and body weight and body fat measures (dual-energy x-ray absorptiometry). After baseline, insulin sensitivity in vivo was assessed with the use of hyperinsulinemic-euglycemic clamps. After the baseline clamp, subjects were randomized to receive Cr supplementation (1000 μg Cr/d provided as Cr picolinate) or placebo daily for 6 months. All study parameters were repeated after 6 months. The relationship of the baseline characteristics of the study subjects to the change in insulin sensitivity was determined. Sixty-three percent of the subjects with type 2 diabetes mellitus responded to the Cr treatment as compared with 30% with placebo. The only subject variable significantly associated with the clinical response to Cr was the baseline insulin sensitivity, as assessed with the hyperinsulinemic-euglycemic clamp (partial R 2 = .4038) (P = .0004). Subject phenotype appears to be very important when assessing the clinical response to Cr because baseline insulin sensitivity was found to account for nearly 40% of the variance in the clinical response to Cr. [Copyright &y& Elsevier]

Published
2007
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118. A retrospective evaluation of transthoracic biphasic electrical cardioversion for atrial fibrillation in dogs.

Author

Bright, Janice M., Martin, Julie M., and Mama, Khursheed

Subjects
HEART diseases, CARDIOVASCULAR diseases, HEART beat, STANDARD deviations
Abstract

Abstract: Objectives: To evaluate safety, efficacy, and clinical usefulness of biphasic transthoracic cardioversion for management of dogs with atrial fibrillation (AF). Background: In dogs AF is usually managed with heart rate control rather than by restoration of sinus rhythm (SR). However, restoration of SR has potential advantages of improving cardiac output and reducing ventricular filling pressures, and biphasic cardioversion provides an improved benefit/risk ratio compared to traditional monophasic cardioversion. Animals, materials and methods: Retrospective analysis of data from 39 dogs with spontaneous AF managed with biphasic transthoracic cardioversion was done. Conversion characteristics, adverse effects, and duration of SR were evaluated. Effects of heart disease and pretreatment with amiodarone on success of cardioversion and on duration of SR were also evaluated. Results: Restoration of SR was achieved in 36 of 39 dogs (92.3%). Presence of heart disease or atrial enlargement had no effect on cardioversion characteristics or ability to restore SR. Median duration of SR following cardioversion and treatment with amiodarone was 120 days. Dogs with lone AF remained in SR longer than those with heart disease. Conclusions: Biphasic cardioversion is safe and effective. Although duration of SR varied, a majority of dogs remained in SR long enough to benefit. [Copyright &y& Elsevier]

Published
2005
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119. Lake George… "The Queen of American Lakes".

Author

Martin, Julie A. and Borgos, Sharon

Abstract

Focuses on the reputation of Lake George in New York. Features of the lake; Details on the depth and richness of the region; Rank of the lake in the production of landlocked salmon.

Published
2002

120. Lymphoepithelial cysts of the pancreas a management dilemma

Author

Martin, Julie, Roberts, Keith J, Sheridan, Maria, Falk, Gavin A, Joyce, Daniel, Walsh, R Matthew, Smith, Andrew M, and Morris-Stiff, Gareth

Abstract

Pancreatic lymphoepithelial cysts (LECs) are rare, benign lesions that are typically unexpected post-operative pathological findings. We aimed to review clinical, radiological and pathological features of LECs that may allow their pre-operative diagnosis. Histopathology databases of two large pancreatic units were searched to identify LECs and notes reviewed to determine patient demographic details, mode of presentation, investigations, treatment and outcome. Five male and one female patients were identified. Their median age was 60 years. Lesions were identified on computed tomography performed for abdominal pain in two patients, and were incidentally observed in four patients. Five LECs were located in the tail and one in the body of the pancreas, with a median cyst size of 5 cm. Obtaining cyst fluid was difficult and a largely acellular aspirate was yielded. The pre-operative diagnosis was mucinous cystic neoplasm in all patients. This series of patients were treated distal pancreatectomy and splenectomy. A retrospective review of radiological examinations suggested that LECs have a relatively low signal on T2 imaging and a high signal intensity on T1 weighted images. LECs appear more common in elderly males, and are typically incidental, large, unilocular cysts. Close attention to signal intensity on MRI may allow pre-operative diagnosis of these lesions.

Published
2014
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121. A CALL TO METHODOLOGICAL ACTIVISM.

Author

Martin, Julie P., Stefl, Shannon K., and Slaton, Amy E.

Subjects
ACTIVISM, SCHOLARLY peer review
Abstract

The article focuses on research is political by this we mean that all research occurs inside the social systems by which resources, rewards, and other forms of influence and security are distributed in our culture. Topics include the no researcher-regardless of their topic or field-operates outside these social systems; no researcher sits above power or apart from its effects.

Published
2022

122. Exploring the Avyssos-Yali-Strogyli submarine volcanic complex at the the Avyssos-Yali-Strogyli submarine volcanic complex at the eastern edge of the Aegean Volcanic Arc edge of the Aegean Volcanic Arc

Author

Nomikou, Paraskevi, Croff Bell, Katherine L., Papanikolaou, Dimitros, Livanos, Isidoros, and Martin, Julie Fero

Abstract

The volcanic centers of Kos, Yali and Nisyros lie at the eastern edge of the Hellenic Volcanic Arc. Recent swath bathymetric surveys and seismic profiling, conducted by HCMR, led to the discovery of several submarine volcanic centers and massive underwater volcaniclastic deposits. Further research aboard the E/V “Nautilus” was conducted at the area in October 2010. Avyssos crater, located northeast of Strongyli islet, is believed to have been the original location of the massive eruption of Kos ignimbrite 160,000 years ago. Exploration of Avyssos showed that it the seafloor is mostly covered with fine-grained sediment full with traces of bioturbation. Hydrothermal activity was not evident at any point. Yali and Strongyli represent Late Pleistocene to Holocene volcanic islands that have developed between the islands of Kos and Tilos. ROV exploration of the eastern flank of Yali revealed wave-type sediment structures, as well as linear fractures at various depths. Several smaller craters were also discovered on the northwest slopes of Strongyli, aligned with ENE-WSW trending fractures with no signs of hydrothermal activity. Heavy biogenic encrustations cover the volcanic rock outcrops on the flanks of both Yali and Strongyli. Analysis of recovered samples will provide information about their relationship to the geology of the nearby islands.

Published
2013
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123. Morphological analysis and related volcanic features of the Kolumbo submarine volcanic chain (NE of Santorini Island, Aegean Volcanic Arc)

Author

Nomikou, Paraskevi, Carey, Steven, Croff Bell, Katherine L., Papanikolaou, Dimitros, Bejelou, Konstantina, Alexandri, Manna, Cantner, Kat, and Martin, Julie Fero

Abstract

Kolumbo submarine volcano is located in a small, elongated, rifted basin northeast of Santorini Island, Greece, and has been the site of recent submarine volcanism in the central Hellenic Volcanic Arc. It is the largest of a chain of nineteen volcanic cones occurring within this small rift zone and its most known eruption in 1650 A.D. had a serious impact on Santorini and the surrounding islands. According to previous studies, a range of ages is suggested for the activity along this volcanic line since many of the smaller volcanic cones seem to have been built above the present seafloor, while others are partly buried by Quaternary sediments. The ROVs Hercules and Argus of 0.E.T. (Ocean Exploration Trust) were used to explore the slopes, summits and craters of 17 of the 19 submarine volcanic centres identified on multibeam map of the area with E/V Nautilus (NA007) in August 2010. In this paper WC present some of the most interesting submarine morphological features along the Kolumbo Volcanic Chain.

Published
2013
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124. Impact of Bariatric Surgery on N-Terminal Fragment of the Prohormone Brain Natriuretic Peptide and Left Ventricular Diastolic Function

Author

Martin, Julie, Bergeron, Sébastien, Pibarot, Philippe, Bastien, Marjorie, Biertho, Laurent, Lescelleur, Odette, Bertrand, Fernand, Simard, Serge, and Poirier, Paul

Abstract

Obesity is often associated with left ventricular (LV) diastolic dysfunction (DD). Elevated N-terminal fragment of the prohormone brain natriuretic peptide (NT-proBNP) is considered a biomarker of LV dysfunction. Weight loss induced by bariatric surgery may improve LV DD, but conflicting results regarding NT-proBNP levels have been reported. Our objective was to determine the impact of bariatric surgery–induced weight loss on NT-proBNP levels and LV DD.

Published
2013
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125. Treatment of methicillin-resistant Staphylococcus aureusventilator-associated pneumonia with high-dose vancomycin or linezolid

Author

Hamilton, Leslie A., Christopher Wood, G., Magnotti, Louis J., Croce, Martin A., Martin, Julie B., Swanson, Joseph M., Boucher, Bradley A., and Fabian, Timothy C.

Abstract

The purpose of this study was to determine the clinical cure rate of high-dose vancomycin for the treatment of methicillin-resistant Staphylococcus aureus(MRSA) ventilator-associated pneumonia (VAP) in critically ill trauma patients. Recent trials suggest that a traditional dose of 1 g q12 hours results in unacceptable cure rates for MRSA VAP. Thus, more aggressive vancomycin dosing has the potential to improve efficacy. Based on pharmacokinetic principles, the goal initial dose at the study center has been 20 mgkg q12 hours or q8 hours since the 1990s.

Published
2012
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127. Pharmacocinétique de l’amikacine chez l’adulte : une hétérogénéité qui remet en cause le calcul de la dose basé sur le poids

Author

Bourguignon, Laurent, Goutelle, Sylvain, Gérard, Cécile, Guillermet, Anne, de Saint Martin, Julie Burdin, Maire, Pascal, and Ducher, Michel

Abstract

L’utilisation de l’amikacine est délicate en raison de sa toxicité et de sa variabilité pharmacocinétique. Cette variabilité est pratiquement ignorée chez l’adulte puisque seul le poids est utilisé dans le calcul de la dose à administrer.

Published
2009
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128. An Open-Label Clinical Trial Evaluating Safety and Pharmacokinetics of Two Dosing Schedules of Panitumumab in Patients with Solid Tumors

Author

Stephenson, Joe J., Gregory, Charles, Burris, Howard, Larson, Tim, Verma, Udit, Cohn, Allen, Crawford, Jeffrey, Cohen, Roger B., Martin, Julie, Lum, Peggy, Yang, Xinqun, and Amado, Rafael G.

Abstract

This study evaluated safety, pharmacokinetics, and efficacy of 2 dose schedules and 2 infusion times of panitumumab in patients with advanced solid malignancies.

Published
2009
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129. teacher-made ASSESSMENTS.

Author

Holler, Edward W., Gareis, Christopher R., Martin, Julie, Clouser, Ashley, and Miller, Steve

Subjects
RATING of students, LEARNING assessment, TEACHER-student relationships, LEARNING ability, CURRICULUM
Abstract

The article focuses on the development of teacher-made assessment in Grafton Middle School in York County, Virginia. It notes that the assessment aims to improve the learning and achievement of students and helps teachers to accurately determine degree of student learning in the classroom. Furthermore, a table of specification is an effective tool that teachers must have in assessing their students, for it provides grid on which attributes of the curriculum can be placed along the two axes.

Published
2008

130. A DNA Vaccine for Ebola Virus Is Safe and Immunogenic in a Phase I Clinical Trial

Author

Martin, Julie E., Sullivan, Nancy J., Enama, Mary E., Gordon, Ingelise J., Roederer, Mario, Koup, Richard A., Bailer, Robert T., Chakrabarti, Bimal K., Bailey, Michael A., Gomez, Phillip L., Andrews, Charla A., Moodie, Zoe, Gu, Lin, Stein, Judith A., Nabel, Gary J., and Graham, Barney S.

Abstract

ABSTRACTEbola viruses represent a class of filoviruses that causes severe hemorrhagic fever with high mortality. Recognized first in 1976 in the Democratic Republic of Congo, outbreaks continue to occur in equatorial Africa. A safe and effective Ebola virus vaccine is needed because of its continued emergence and its potential for use for biodefense. We report the safety and immunogenicity of an Ebola virus vaccine in its first phase I human study. A three-plasmid DNA vaccine encoding the envelope glycoproteins (GP) from the Zaire and Sudan/Gulu species as well as the nucleoprotein was evaluated in a randomized, placebo-controlled, double-blinded, dose escalation study. Healthy adults, ages 18 to 44 years, were randomized to receive three injections of vaccine at 2 mg (n= 5), 4 mg (n= 8), or 8 mg (n= 8) or placebo (n= 6). Immunogenicity was assessed by enzyme-linked immunosorbent assay (ELISA), immunoprecipitation-Western blotting, intracellular cytokine staining (ICS), and enzyme-linked immunospot assay. The vaccine was well-tolerated, with no significant adverse events or coagulation abnormalities. Specific antibody responses to at least one of the three antigens encoded by the vaccine as assessed by ELISA and CD4+T-cell GP-specific responses as assessed by ICS were detected in 20/20 vaccinees. CD8+T-cell GP-specific responses were detected by ICS assay in 6/20 vaccinees. This Ebola virus DNA vaccine was safe and immunogenic in humans. Further assessment of the DNA platform alone and in combination with replication-defective adenoviral vector vaccines, in concert with challenge and immune data from nonhuman primates, will facilitate evaluation and potential licensure of an Ebola virus vaccine under the Animal Rule.

Published
2006
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133. Familial immunodeficiency with cutaneous vasculitis, myoclonus, and cognitive impairment<FNR HREF="fn1"></FNR><FN ID="fn1">This article is a US Government work and, as such, is in the public domain in the United States of America.</FN><FNR HREF="fn2"></FNR><FN ID="fn2">Beverly N. Hay and Julie E. Martin contributed equally to this study.</FN>

Author

Hay, Beverly N., Martin, Julie E., Karp, Barbara, Davis, Joie, Darnell, Dirk, Solomon, Beth, Turner, Maria, Holland, Steven M., and Puck, Jennifer M.

Abstract

We report a family with five of six siblings (including identical male twins) with a novel constellation of immunologic and neurologic impairments. Affected subjects experienced severe dermatitis starting around 9 months of age, Stevens–Johnson syndrome in early childhood, and extreme elevations of IgE (9,400–43,000 IU/ml). The oldest sibling died at age 27 of respiratory failure following recurrent, severe pneumonias. All four surviving affected siblings have had chronic sinusitis or otitis, cutaneous vasculitis, and recurrent bacterial pneumonias leading to bronchiectasis. Neurologic features in all five siblings included oral motor deficits, dysarthria, low average IQ (70–80), and essential myoclonus. Four had documented ataxia and/or mild sensory loss with increased patellar but diminished ankle reflexes. The nonconsanguineous parents and one sibling had none of the above findings, consistent with autosomal recessive inheritance. This primary immunodeficiency with distinctive neurological impairments represents a new syndrome. Published 2003 Wiley-Liss, Inc.

Published
2004
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134. Impact of bariatric surgery on cardiac structure, function and clinical manifestations in morbid obesity

Author

Poirier, Paul, Martin, Julie, Marceau, Picard, Biron, Simon, and Marceau, Simon

Abstract

Obesity results from the excessive accumulation of fat. Risk of premature death is doubled compared to nonobese individuals, and risk of death from cardiovascular disease is increased fivefold. In patients with morbid obesity, a variety of adaptations and alterations in cardiac structure and function occur in the individual, as an excess amount of adipose tissue accumulates. The high long-term failure rate of diet intervention is well acknowledged by the clinician. Surgery for severe obesity has evolved during the last 40 years. Many surgical techniques have been described and abandoned. Nevertheless, numerous different techniques are still in use today. Weight loss has beneficial impacts on functional and structural cardiac status and will be reviewed in this report.

Published
2004
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135. Mechanical properties of a cryogenically mechanically alloyed polycarbonate–poly(aryl ether ether ketone) system

Author

Martin, Julie P. and Kander, Ronald G.

Abstract

The processing–property relationship of a model cryogenically mechanically alloyed polymer–polymer system [polycarbonate (PC) and poly(aryl ether ether ketone) (PEEK)] was investigated. PC and PEEK powders were cryogenically mechanically alloyed for 10 h, and the resulting two-phase powder particles were processed into testable coupons with a miniature ram-injection molder. The bulk mechanical properties of the coupons made from the mechanically alloyed powders and nonmechanically alloyed powders were investigated as a function of mechanical alloying and injection-molding parameters. The injection-molded coupons were mechanically tested in the three-point-bending mode. The results demonstrated that no measurable improvement was achieved in the energy to break, strain at failure, or failure strength in the coupons made from the mechanically alloyed materials in comparison with those of the coupons made from the nonmechanically alloyed powders. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 88: 1196–1202, 2003

Published
2003
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136. Responses of Primate Visual Cortical Neurons to Stimuli Presented by Flash, Saccade, Blink, and External Darkening

Author

Gawne, Timothy J. and Martin, Julie M.

Abstract

Our visual experience constitutes an unending chain of transient events, including those caused by saccadic eye movements, by blinks, and by localized or global changes in the external world. The categorical perception of objects is maintained across different classes of transient events, suggesting that the neural circuitry underlying visual perception responds to different transient events in a similar manner. However, different sorts of transients do have different perceptual impacts: for example, the sudden changes in a scene due to a saccade or a blink do not disturb our perceptual continuity of a visual scene as much as an external change does. We recorded the responses of 103 single visual cortical neurons in two rhesus monkeys (V1: n= 38, V2:n= 19, V3V/VP: n= 30, V4V:n= 16) to the onset and offset of a visual stimulus that was elicited by four different conditions: 1) stimulus flashed on and off while the eyes remain fixed; 2) stimulus turned on and off along with the entire scene (external darkening);3) stimulus constant, onset and offset induced by rapid saccadic eye movements; and 4) offset induced by an eyeblink. For most neurons the onset and offset of a visual stimulus elicited qualitatively similar responses regardless of condition. We found no systematic effect of different conditions across the neuronal population. Previously we have shown that when the visual scene is occluded by a blink V1 neuronal firing declines in a similar manner as when the external scene is darkened and the eyes left open. Here we show that this is also the case in V2, V3V/VP, and V4V. However, for a substantial minority of neurons, the response varied strongly as a function of the transient event. This overall pattern was the same in all four cortical areas studied here. We hypothesize that most neurons in visual cortex constitute a passive “filter bank”, analyzing the scene for specific details regardless of condition. However, there are neurons that respond in a qualitatively different manner depending on how a stimulus is presented, and we hypothesize that these signals may be important for determining the perceptual salience of a visual event.

Published
2002
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137. Responses of Primate Visual Cortical V4 Neurons to Simultaneously Presented Stimuli

Author

Gawne, Timothy J. and Martin, Julie M.

Abstract

We report here results from 45 primate V4 visual cortical neurons to the preattentive presentations of seven different patterns located in two separate areas of the same receptive field and to combinations of the patterns in the two locations. For many neurons, we could not determine any clear relationship for the responses to two simultaneous stimuli. However, for a substantial fraction of the neurons we found that the firing rate was well modeled as the maximum firing rate of each stimulus presented separately. It has previously been proposed that taking the maximum of the inputs (“MAX” operator) could be a useful operation for neurons in visual cortex, although there has until now been little direct physiological evidence for this hypothesis. Our results here provide direct support for the hypothesis that the MAX operator plays a significant (although certainly not exclusive) role in generating the receptive field properties of visual cortical neurons.

Published
2002
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139. The teaching of numeracy: What constitutes an effective approach?

Author

Bruce, Bob and Martin, Julie

Abstract

Askew and his colleagues (1997), put forward a range of important notions as to what might constitute effective approaches to the teaching of numeracy. In particular, they place great emphasis on the way in which teachers who make links between different areas of mathematics are seen to be effective teachers of numeracy. (Askew et al term this approach 'connectionist')The work reported here suggests that the notion of classifying a teacher as, say, connectionist is too simplistic. We report observations which suggest that effective teachers of numeracy incorporate a range of approaches into their teaching.

Published
2002
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140. Activity of Primate V1 Cortical Neurons During Blinks

Author

Gawne, Timothy J. and Martin, Julie M.

Abstract

Every time we blink our eyes, the image on the retina goes almost completely dark. And yet we hardly notice these interruptions, even though an external darkening is startling. Intuitively it would seem that if our perception is continuous, then the neuronal activity on which our perceptions are based should also be continuous. To explore this issue, we compared the responses of 63 supragranular V1 neurons recorded from two awake monkeys for four conditions: 1)constantstimulus, 2) during a reflexblink, 3) during a gapin the visual stimulus, and 4) during an external darkeningwhen an electrooptical shutter occluded the entire scene. We show here that the activity of neurons in visual cortical area V1 is essentially shut off during a blink. In the 100-ms epoch starting 70 ms after the stimulus was interrupted, the firing rate was 27.2 ± 2.7 spikes/s (SE) for a constant stimulus, 8.2 ± 0.9 spikes/s for a reflex blink, 17.3 ± 1.9 spikes/s for a gap, and 12.7 ± 1.4 spikes/s for an external darkening. The responses during a blink are less than during an external darkening (P< 0.05, t-test). However, many of these neurons responded with a transient burst of activity to the onset of an external darkening and not to a blink, suggesting that it is the suppression of this transient which causes us to ignore blinks. This is consistent with other studies where the presence of transient bursts of activity correlates with the perceived visibility of a stimulus.

Published
2000
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141. Angiotensin-Converting Enzyme Gene Polymorphism: Is There a Link to Nephropathy in Patients with Type 1 Diabetes?

Author

Martin, Julie K and Hayney, Mary S

Abstract

OBJECTIVE: To evaluate the association between the angiotensin-converting enzyme (ACE) gene polymorphism and diabetic nephropathy in patients with type 1 diabetes.DATA SOURCES: Citations were selected using the MEDLINE database. Only those citations involving human subjects and available in English were selected. Key search words included angiotensin-converting enzyme (ACE), polymorphism, nephropathy, and type 1 diabetes.STUDY SELECTION: Selection criteria consisted of all MEDLINE-referenced clinical trials, review articles, and editorial comments assessing the potential link between the ACE gene polymorphism and diabetic nephropathy in insulin-dependent diabetes mellitus published between January 1990 and February 1998.DATA SYNTHESIS: Because diabetic nephropathy is a serious complication of type 1 diabetes, focus has been placed on the early identification of and intervention with patients genetically susceptible to this complication. Because the ACE gene polymorphism has an effect on plasma ACE concentration variations among individuals, it has been investigated as a potential genetic marker for diabetic nephropathy. The best studies to date are reviewed in order to assess the utility of the ACE polymorphisms as a genetic marker of diabetic nephropathy in patients with type 1 diabetes, and to determine what implications this holds for drug treatment.CONCLUSIONS: Although the ACE gene polymorphism's potential link to diabetic nephropathy in patients with type 1 diabetes has been debated, the most definitive studies show that an association exists. Large epidemiologic studies must now be conducted to determine the implications this polymorphism holds for the best treatment strategies in the care of these patients.

Published
1999
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142. MIZORIBINE SERUM LEVELS ASSOCIATED WITH ENTEROTOXICITY IN THE DOG

Author

GREGORY, CLARE R., GOURLEY, IRA M., CAIN, GARY R., PATZ, JOHN D., IMONDI, KAREN A., and MARTIN, JULIE A.

Abstract

To prevent or minimize mizoribine enterotoxicity in organ transplant recipients and to differentiate mizoribine enterotoxicity from other causes of enteritis, serum levels of mizoribine that produced subclinical and clinical signs of enterotoxicity were determined in the dog. When mizoribine was administered orally at 12-hr intervals, half the dogs studied showed clinical evidence of gastrointestinal disturbances (vomiting, diarrhea, and anorexia) without histopathologic signs of enterotoxicity. Using a 24-hr oral-dose schedule, clinical signs of gastrointestinal disturbances and histopathologic evidence (mucosal degeneration, crypt degeneration, and necrosis) of enterotoxicity were encountered when the mean 12-hr mizoribine serum level was 0.97±0.4 μg/ml or greater. Histopathologic signs of enterotoxicity with repeated positive fecal occult blood assays and without clinical signs of gastrointestinal disturbances occurred when the mean 12-hr serum level was 0.53±0.17 μg/ml or greater. Oral administration of cyclosporine did not exacerbate mizoribine enterotoxicity in the dog when administered with mizoribine at a dose that produced histopathologic signs of enterotoxicity.

Published
1991

143. Defective haematopoiesis and vasculogenesis in transforming growth factor-β1 knock out mice

Author

Dickson, Marion C., Martin, Julie S., Cousins, Frances M., Kulkarni, Ashok B., Karlsson, Stefan, and Akhurst, Rosemary J.

Abstract

Transforming growth factor β1 (TGFβ1) is shown here to be required for yolk sac haematopoiesis and endothelial differentiation. Mice with a targeted mutation in the TGFβ1 gene were examined to determine the cause of prenatal lethality, which occurs in 50% of homozygous TGFβ1 null (TGFβ1−/−) conceptions. 50% of TGFβ1−/− and 25% of TGFβ1+/− conceptuses were found to die at around 10.5 dpc. The primary defects were restricted to extraembryonic tissues, namely the yolk sac vasculature and haematopoietic system. The embryos per se showed developmental retardation, oedema and necrosis, which were probably secondary to the extraembryonic lesions. The defect in vasculogenesis appeared to affect endothelial differentiation, rather than the initial appearance and outgrowth of endothelial cells. Initial differentiation of yolk sac mesoderm to endothelial cells occurred, but defective differentiation resulted in inadequate capillary tube formation, and weak vessels with reduced cellular adhesiveness. Defective haematopoiesis resulted in a reduced erythroid cell number within the yolk sac. Defective yolk sac vasculogenesis and haematopoiesis were present either together, or in isolation of each other. The phenotypes are consistent with the observation of abundant TGFβ1 gene expression in both endothelial and haematopoietic precursors. The data indicate that the primary effect of loss of TGFβ1 function in vivo is not increased haematopoietic or endothelial cell proliferation, which might have been expected by deletion of a negative growth regulator, but defective haematopoiesis and endothelial differentiation.

Published
1995
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144. Invasive Hemodynamic Monitoring in Pregnancy

Author

Martin, Julie M.

Abstract

When the pregnant woman develops an acute or critical illness requiring invasive hemodynamic monitoring, it is imperative to consider physiologic changes that occur during pregnancy that impact on assessment parameters. Awareness of both the alterations in these parameters and the changes in arterial blood gas values guide nursing care that continues to support perfusion and oxygenation needs unique to pregnancy. When critical care capabilities are not available in the labor and delivery unit, the obstetric patient is most often transferred to a medical or surgical intensive care unit. In such cases, consultation with obstetric staff is warranted.

Published
1992
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148. A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β Superfamily

Author

Korkut, Anil, Zaidi, Sobia, Kanchi, Rupa S., Rao, Shuyun, Gough, Nancy R., Schultz, Andre, Li, Xubin, Lorenzi, Philip L., Berger, Ashton C., Robertson, Gordon, Kwong, Lawrence N., Datto, Mike, Roszik, Jason, Ling, Shiyun, Ravikumar, Visweswaran, Manyam, Ganiraju, Rao, Arvind, Shelley, Simon, Liu, Yuexin, Ju, Zhenlin, Hansel, Donna, de Velasco, Guillermo, Pennathur, Arjun, Andersen, Jesper B., O'Rourke, Colm J., Ohshiro, Kazufumi, Jogunoori, Wilma, Nguyen, Bao-Ngoc, Li, Shulin, Osmanbeyoglu, Hatice U., Ajani, Jaffer A., Mani, Sendurai A., Houseman, Andres, Wiznerowicz, Maciej, Chen, Jian, Gu, Shoujun, Ma, Wencai, Zhang, Jiexin, Tong, Pan, Cherniack, Andrew D., Deng, Chuxia, Resar, Linda, Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, Knijnenburg, Theo, Kramer, Roger, Leinonen, Kalle, Liu, Yuexin, Miller, Michael, Reynolds, Sheila, Shmulevich, Ilya, Thorsson, Vesteinn, Zhang, Wei, Akbani, Rehan, Broom, Bradley M., Hegde, Apurva M., Ju, Zhenlin, Kanchi, Rupa S., Korkut, Anil, Li, Jun, Liang, Han, Ling, Shiyun, Liu, Wenbin, Lu, Yiling, Mills, Gordon B., Ng, Kwok-Shing, Rao, Arvind, Ryan, Michael, Wang, Jing, Weinstein, John N., Zhang, Jiexin, Abeshouse, Adam, Armenia, Joshua, Chakravarty, Debyani, Chatila, Walid K., de Bruijn, Ino, Gao, Jianjiong, Gross, Benjamin E., Heins, Zachary J., Kundra, Ritika, La, Konnor, Ladanyi, Marc, Luna, Augustin, Nissan, Moriah G., Ochoa, Angelica, Phillips, Sarah M., Reznik, Ed, Sanchez-Vega, Francisco, Sander, Chris, Schultz, Nikolaus, Sheridan, Robert, Sumer, S. Onur, Sun, Yichao, Taylor, Barry S., Wang, Jioajiao, Zhang, Hongxin, Anur, Pavana, Peto, Myron, Spellman, Paul, Benz, Christopher, Stuart, Joshua M., Wong, Christopher K., Yau, Christina, Hayes, D. Neil, Parker, Joel S., Wilkerson, Matthew D., Ally, Adrian, Balasundaram, Miruna, Bowlby, Reanne, Brooks, Denise, Carlsen, Rebecca, Chuah, Eric, Dhalla, Noreen, Holt, Robert, Jones, Steven J.M., Kasaian, Katayoon, Lee, Darlene, Ma, Yussanne, Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Mungall, Karen, Robertson, A. Gordon, Sadeghi, Sara, Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Tse, Kane, Wong, Tina, Berger, Ashton C., Beroukhim, Rameen, Cherniack, Andrew D., Cibulskis, Carrie, Gabriel, Stacey B., Gao, Galen F., Ha, Gavin, Meyerson, Matthew, Schumacher, Steven E., Shih, Juliann, Kucherlapati, Melanie H., Kucherlapati, Raju S., Baylin, Stephen, Cope, Leslie, Danilova, Ludmila, Bootwalla, Moiz S., Lai, Phillip H., Maglinte, Dennis T., Van Den Berg, David J., Weisenberger, Daniel J., Auman, J. Todd, Balu, Saianand, Bodenheimer, Tom, Fan, Cheng, Hoadley, Katherine A., Hoyle, Alan P., Jefferys, Stuart R., Jones, Corbin D., Meng, Shaowu, Mieczkowski, Piotr A., Mose, Lisle E., Perou, Amy H., Perou, Charles M., Roach, Jeffrey, Shi, Yan, Simons, Janae V., Skelly, Tara, Soloway, Matthew G., Tan, Donghui, Veluvolu, Umadevi, Fan, Huihui, Hinoue, Toshinori, Laird, Peter W., Shen, Hui, Zhou, Wanding, Bellair, Michelle, Chang, Kyle, Covington, Kyle, Creighton, Chad J., Dinh, Huyen, Doddapaneni, HarshaVardhan, Donehower, Lawrence A., Drummond, Jennifer, Gibbs, Richard A., Glenn, Robert, Hale, Walker, Han, Yi, Hu, Jianhong, Korchina, Viktoriya, Lee, Sandra, Lewis, Lora, Li, Wei, Liu, Xiuping, Morgan, Margaret, Morton, Donna, Muzny, Donna, Santibanez, Jireh, Sheth, Margi, Shinbrot, Eve, Wang, Linghua, Wang, Min, Wheeler, David A., Xi, Liu, Zhao, Fengmei, Hess, Julian, Appelbaum, Elizabeth L., Bailey, Matthew, Cordes, Matthew G., Ding, Li, Fronick, Catrina C., Fulton, Lucinda A., Fulton, Robert S., Kandoth, Cyriac, Mardis, Elaine R., McLellan, Michael D., Miller, Christopher A., Schmidt, Heather K., Wilson, Richard K., Crain, Daniel, Curley, Erin, Gardner, Johanna, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Penny, Robert, Shelton, Candace, Shelton, Troy, Sherman, Mark, Thompson, Eric, Yena, Peggy, Bowen, Jay, Gastier-Foster, Julie M., Gerken, Mark, Leraas, Kristen M., Lichtenberg, Tara M., Ramirez, Nilsa C., Wise, Lisa, Zmuda, Erik, Corcoran, Niall, Costello, Tony, Hovens, Christopher, Carvalho, Andre L., de Carvalho, Ana C., Fregnani, José H., Longatto-Filho, Adhemar, Reis, Rui M., Scapulatempo-Neto, Cristovam, Silveira, Henrique C.S., Vidal, Daniel O., Burnette, Andrew, Eschbacher, Jennifer, Hermes, Beth, Noss, Ardene, Singh, Rosy, Anderson, Matthew L., Castro, Patricia D., Ittmann, Michael, Huntsman, David, Kohl, Bernard, Le, Xuan, Thorp, Richard, Andry, Chris, Duffy, Elizabeth R., Lyadov, Vladimir, Paklina, Oxana, Setdikova, Galiya, Shabunin, Alexey, Tavobilov, Mikhail, McPherson, Christopher, Warnick, Ronald, Berkowitz, Ross, Cramer, Daniel, Feltmate, Colleen, Horowitz, Neil, Kibel, Adam, Muto, Michael, Raut, Chandrajit P., Malykh, Andrei, Barnholtz-Sloan, Jill S., Barrett, Wendi, Devine, Karen, Fulop, Jordonna, Ostrom, Quinn T., Shimmel, Kristen, Wolinsky, Yingli, Sloan, Andrew E., De Rose, Agostino, Giuliante, Felice, Goodman, Marc, Karlan, Beth Y., Hagedorn, Curt H., Eckman, John, Harr, Jodi, Myers, Jerome, Tucker, Kelinda, Zach, Leigh Anne, Deyarmin, Brenda, Hu, Hai, Kvecher, Leonid, Larson, Caroline, Mural, Richard J., Somiari, Stella, Vicha, Ales, Zelinka, Tomas, Bennett, Joseph, Iacocca, Mary, Rabeno, Brenda, Swanson, Patricia, Latour, Mathieu, Lacombe, Louis, Têtu, Bernard, Bergeron, Alain, McGraw, Mary, Staugaitis, Susan M., Chabot, John, Hibshoosh, Hanina, Sepulveda, Antonia, Su, Tao, Wang, Timothy, Potapova, Olga, Voronina, Olga, Desjardins, Laurence, Mariani, Odette, Roman-Roman, Sergio, Sastre, Xavier, Stern, Marc-Henri, Cheng, Feixiong, Signoretti, Sabina, Berchuck, Andrew, Bigner, Darell, Lipp, Eric, Marks, Jeffrey, McCall, Shannon, McLendon, Roger, Secord, Angeles, Sharp, Alexis, Behera, Madhusmita, Brat, Daniel J., Chen, Amy, Delman, Keith, Force, Seth, Khuri, Fadlo, Magliocca, Kelly, Maithel, Shishir, Olson, Jeffrey J., Owonikoko, Taofeek, Pickens, Alan, Ramalingam, Suresh, Shin, Dong M., Sica, Gabriel, Van Meir, Erwin G., Zhang, Hongzheng, Eijckenboom, Wil, Gillis, Ad, Korpershoek, Esther, Looijenga, Leendert, Oosterhuis, Wolter, Stoop, Hans, van Kessel, Kim E., Zwarthoff, Ellen C., Calatozzolo, Chiara, Cuppini, Lucia, Cuzzubbo, Stefania, DiMeco, Francesco, Finocchiaro, Gaetano, Mattei, Luca, Perin, Alessandro, Pollo, Bianca, Chen, Chu, Houck, John, Lohavanichbutr, Pawadee, Hartmann, Arndt, Stoehr, Christine, Stoehr, Robert, Taubert, Helge, Wach, Sven, Wullich, Bernd, Kycler, Witold, Murawa, Dawid, Wiznerowicz, Maciej, Chung, Ki, Edenfield, W. Jeffrey, Martin, Julie, Baudin, Eric, Bubley, Glenn, Bueno, Raphael, De Rienzo, Assunta, Richards, William G., Kalkanis, Steven, Mikkelsen, Tom, Noushmehr, Houtan, Scarpace, Lisa, Girard, Nicolas, Aymerich, Marta, Campo, Elias, Giné, Eva, Guillermo, Armando López, Van Bang, Nguyen, Hanh, Phan Thi, Phu, Bui Duc, Tang, Yufang, Colman, Howard, Evason, Kimberley, Dottino, Peter R., Martignetti, John A., Gabra, Hani, Juhl, Hartmut, Akeredolu, Teniola, Stepa, Serghei, Hoon, Dave, Ahn, Keunsoo, Kang, Koo Jeong, Beuschlein, Felix, Breggia, Anne, Birrer, Michael, Bell, Debra, Borad, Mitesh, Bryce, Alan H., Castle, Erik, Chandan, Vishal, Cheville, John, Copland, John A., Farnell, Michael, Flotte, Thomas, Giama, Nasra, Ho, Thai, Kendrick, Michael, Kocher, Jean-Pierre, Kopp, Karla, Moser, Catherine, Nagorney, David, O’Brien, Daniel, O’Neill, Brian Patrick, Patel, Tushar, Petersen, Gloria, Que, Florencia, Rivera, Michael, Roberts, Lewis, Smallridge, Robert, Smyrk, Thomas, Stanton, Melissa, Thompson, R. Houston, Torbenson, Michael, Yang, Ju Dong, Zhang, Lizhi, Brimo, Fadi, Ajani, Jaffer A., Angulo Gonzalez, Ana Maria, Behrens, Carmen, Bondaruk, Jolanta, Broaddus, Russell, Czerniak, Bogdan, Esmaeli, Bita, Fujimoto, Junya, Gershenwald, Jeffrey, Guo, Charles, Lazar, Alexander J., Logothetis, Christopher, Meric-Bernstam, Funda, Moran, Cesar, Ramondetta, Lois, Rice, David, Sood, Anil, Tamboli, Pheroze, Thompson, Timothy, Troncoso, Patricia, Tsao, Anne, Wistuba, Ignacio, Carter, Candace, Haydu, Lauren, Hersey, Peter, Jakrot, Valerie, Kakavand, Hojabr, Kefford, Richard, Lee, Kenneth, Long, Georgina, Mann, Graham, Quinn, Michael, Saw, Robyn, Scolyer, Richard, Shannon, Kerwin, Spillane, Andrew, Stretch, Jonathan, Synott, Maria, Thompson, John, Wilmott, James, Al-Ahmadie, Hikmat, Chan, Timothy A., Ghossein, Ronald, Gopalan, Anuradha, Levine, Douglas A., Reuter, Victor, Singer, Samuel, Singh, Bhuvanesh, Tien, Nguyen Viet, Broudy, Thomas, Mirsaidi, Cyrus, Nair, Praveen, Drwiega, Paul, Miller, Judy, Smith, Jennifer, Zaren, Howard, Park, Joong-Won, Hung, Nguyen Phi, Kebebew, Electron, Linehan, W. Marston, Metwalli, Adam R., Pacak, Karel, Pinto, Peter A., Schiffman, Mark, Schmidt, Laura S., Vocke, Cathy D., Wentzensen, Nicolas, Worrell, Robert, Yang, Hannah, Moncrieff, Marc, Goparaju, Chandra, Melamed, Jonathan, Pass, Harvey, Botnariuc, Natalia, Caraman, Irina, Cernat, Mircea, Chemencedji, Inga, Clipca, Adrian, Doruc, Serghei, Gorincioi, Ghenadie, Mura, Sergiu, Pirtac, Maria, Stancul, Irina, Tcaciuc, Diana, Albert, Monique, Alexopoulou, Iakovina, Arnaout, Angel, Bartlett, John, Engel, Jay, Gilbert, Sebastien, Parfitt, Jeremy, Sekhon, Harman, Thomas, George, Rassl, Doris M., Rintoul, Robert C., Bifulco, Carlo, Tamakawa, Raina, Urba, Walter, Hayward, Nicholas, Timmers, Henri, Antenucci, Anna, Facciolo, Francesco, Grazi, Gianluca, Marino, Mirella, Merola, Roberta, de Krijger, Ronald, Gimenez-Roqueplo, Anne-Paule, Piché, Alain, Chevalier, Simone, McKercher, Ginette, Birsoy, Kivanc, Barnett, Gene, Brewer, Cathy, Farver, Carol, Naska, Theresa, Pennell, Nathan A., Raymond, Daniel, Schilero, Cathy, Smolenski, Kathy, Williams, Felicia, Morrison, Carl, Borgia, Jeffrey A., Liptay, Michael J., Pool, Mark, Seder, Christopher W., Junker, Kerstin, Omberg, Larsson, Dinkin, Mikhail, Manikhas, George, Alvaro, Domenico, Bragazzi, Maria Consiglia, Cardinale, Vincenzo, Carpino, Guido, Gaudio, Eugenio, Chesla, David, Cottingham, Sandra, Dubina, Michael, Moiseenko, Fedor, Dhanasekaran, Renumathy, Becker, Karl-Friedrich, Janssen, Klaus-Peter, Slotta-Huspenina, Julia, Abdel-Rahman, Mohamed H., Aziz, Dina, Bell, Sue, Cebulla, Colleen M., Davis, Amy, Duell, Rebecca, Elder, J. Bradley, Hilty, Joe, Kumar, Bahavna, Lang, James, Lehman, Norman L., Mandt, Randy, Nguyen, Phuong, Pilarski, Robert, Rai, Karan, Schoenfield, Lynn, Senecal, Kelly, Wakely, Paul, Hansen, Paul, Lechan, Ronald, Powers, James, Tischler, Arthur, Grizzle, William E., Sexton, Katherine C., Kastl, Alison, Henderson, Joel, Porten, Sima, Waldmann, Jens, Fassnacht, Martin, Asa, Sylvia L., Schadendorf, Dirk, Couce, Marta, Graefen, Markus, Huland, Hartwig, Sauter, Guido, Schlomm, Thorsten, Simon, Ronald, Tennstedt, Pierre, Olabode, Oluwole, Nelson, Mark, Bathe, Oliver, Carroll, Peter R., Chan, June M., Disaia, Philip, Glenn, Pat, Kelley, Robin K., Landen, Charles N., Phillips, Joanna, Prados, Michael, Simko, Jeffry, Smith-McCune, Karen, VandenBerg, Scott, Roggin, Kevin, Fehrenbach, Ashley, Kendler, Ady, Sifri, Suzanne, Steele, Ruth, Jimeno, Antonio, Carey, Francis, Forgie, Ian, Mannelli, Massimo, Carney, Michael, Hernandez, Brenda, Campos, Benito, Herold-Mende, Christel, Jungk, Christin, Unterberg, Andreas, von Deimling, Andreas, Bossler, Aaron, Galbraith, Joseph, Jacobus, Laura, Knudson, Michael, Knutson, Tina, Ma, Deqin, Milhem, Mohammed, Sigmund, Rita, Godwin, Andrew K., Madan, Rashna, Rosenthal, Howard G., Adebamowo, Clement, Adebamowo, Sally N., Boussioutas, Alex, Beer, David, Giordano, Thomas, Mes-Masson, Anne-Marie, Saad, Fred, Bocklage, Therese, Landrum, Lisa, Mannel, Robert, Moore, Kathleen, Moxley, Katherine, Postier, Russel, Walker, Joan, Zuna, Rosemary, Feldman, Michael, Valdivieso, Federico, Dhir, Rajiv, Luketich, James, Mora Pinero, Edna M., Quintero-Aguilo, Mario, Carlotti, Carlos Gilberto, Dos Santos, Jose Sebastião, Kemp, Rafael, Sankarankuty, Ajith, Tirapelli, Daniela, Catto, James, Agnew, Kathy, Swisher, Elizabeth, Creaney, Jenette, Robinson, Bruce, Shelley, Carl Simon, Godwin, Eryn M., Kendall, Sara, Shipman, Cassaundra, Bradford, Carol, Carey, Thomas, Haddad, Andrea, Moyer, Jeffey, Peterson, Lisa, Prince, Mark, Rozek, Laura, Wolf, Gregory, Bowman, Rayleen, Fong, Kwun M., Yang, Ian, Korst, Robert, Rathmell, W. Kimryn, Fantacone-Campbell, J. Leigh, Hooke, Jeffrey A., Kovatich, Albert J., Shriver, Craig D., DiPersio, John, Drake, Bettina, Govindan, Ramaswamy, Heath, Sharon, Ley, Timothy, Van Tine, Brian, Westervelt, Peter, Rubin, Mark A., Lee, Jung Il, Aredes, Natália D., Mariamidze, Armaz, Weinstein, John N., Mishra, Lopa, and Akbani, Rehan

Abstract

We present an integromic analysis of gene alterations that modulate transforming growth factor β (TGF-β)-Smad-mediated signaling in 9,125 tumor samples across 33 cancer types in The Cancer Genome Atlas (TCGA). Focusing on genes that encode mediators and regulators of TGF-β signaling, we found at least one genomic alteration (mutation, homozygous deletion, or amplification) in 39% of samples, with highest frequencies in gastrointestinal cancers. We identified mutation hotspots in genes that encode TGF-β ligands (BMP5), receptors (TGFBR2, AVCR2A, and BMPR2), and Smads (SMAD2 and SMAD4). Alterations in the TGF-β superfamily correlated positively with expression of metastasis-associated genes and with decreased survival. Correlation analyses showed the contributions of mutation, amplification, deletion, DNA methylation, and miRNA expression to transcriptional activity of TGF-β signaling in each cancer type. This study provides a broad molecular perspective relevant for future functional and therapeutic studies of the diverse cancer pathways mediated by the TGF-β superfamily.

Published
2018
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149. The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

Author

Ricketts, Christopher J., De Cubas, Aguirre A., Fan, Huihui, Smith, Christof C., Lang, Martin, Reznik, Ed, Bowlby, Reanne, Gibb, Ewan A., Akbani, Rehan, Beroukhim, Rameen, Bottaro, Donald P., Choueiri, Toni K., Gibbs, Richard A., Godwin, Andrew K., Haake, Scott, Hakimi, A. Ari, Henske, Elizabeth P., Hsieh, James J., Ho, Thai H., Kanchi, Rupa S., Krishnan, Bhavani, Kwiatkowski, David J., Liu, Wenbin, Merino, Maria J., Mills, Gordon B., Myers, Jerome, Nickerson, Michael L., Reuter, Victor E., Schmidt, Laura S., Shelley, C. Simon, Shen, Hui, Shuch, Brian, Signoretti, Sabina, Srinivasan, Ramaprasad, Tamboli, Pheroze, Thomas, George, Vincent, Benjamin G., Vocke, Cathy D., Wheeler, David A., Yang, Lixing, Kim, William Y., Robertson, A. Gordon, Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, Knijnenburg, Theo, Kramer, Roger, Leinonen, Kalle, Liu, Yuexin, Miller, Michael, Reynolds, Sheila, Shmulevich, Ilya, Thorsson, Vesteinn, Zhang, Wei, Akbani, Rehan, Broom, Bradley M., Hegde, Apurva M., Ju, Zhenlin, Kanchi, Rupa S., Korkut, Anil, Li, Jun, Liang, Han, Ling, Shiyun, Liu, Wenbin, Lu, Yiling, Mills, Gordon B., Ng, Kwok-Shing, Rao, Arvind, Ryan, Michael, Wang, Jing, Weinstein, John N., Zhang, Jiexin, Abeshouse, Adam, Armenia, Joshua, Chakravarty, Debyani, Chatila, Walid K., de Bruijn, Ino, Gao, Jianjiong, Gross, Benjamin E., Heins, Zachary J., Kundra, Ritika, La, Konnor, Ladanyi, Marc, Luna, Augustin, Nissan, Moriah G., Ochoa, Angelica, Phillips, Sarah M., Reznik, Ed, Sanchez-Vega, Francisco, Sander, Chris, Schultz, Nikolaus, Sheridan, Robert, Sumer, S. Onur, Sun, Yichao, Taylor, Barry S., Wang, Jioajiao, Zhang, Hongxin, Anur, Pavana, Peto, Myron, Spellman, Paul, Benz, Christopher, Stuart, Joshua M., Wong, Christopher K., Yau, Christina, Hayes, D. Neil, Parker, Joel S., Wilkerson, Matthew D., Ally, Adrian, Balasundaram, Miruna, Bowlby, Reanne, Brooks, Denise, Carlsen, Rebecca, Chuah, Eric, Dhalla, Noreen, Holt, Robert, Jones, Steven J.M., Kasaian, Katayoon, Lee, Darlene, Ma, Yussanne, Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Mungall, Karen, Robertson, A. Gordon, Sadeghi, Sara, Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Tse, Kane, Wong, Tina, Berger, Ashton C., Beroukhim, Rameen, Cherniack, Andrew D., Cibulskis, Carrie, Gabriel, Stacey B., Gao, Galen F., Ha, Gavin, Meyerson, Matthew, Schumacher, Steven E., Shih, Juliann, Kucherlapati, Melanie H., Kucherlapati, Raju S., Baylin, Stephen, Cope, Leslie, Danilova, Ludmila, Bootwalla, Moiz S., Lai, Phillip H., Maglinte, Dennis T., Van Den Berg, David J., Weisenberger, Daniel J., Auman, J. Todd, Balu, Saianand, Bodenheimer, Tom, Fan, Cheng, Hoadley, Katherine A., Hoyle, Alan P., Jefferys, Stuart R., Jones, Corbin D., Meng, Shaowu, Mieczkowski, Piotr A., Mose, Lisle E., Perou, Amy H., Perou, Charles M., Roach, Jeffrey, Shi, Yan, Simons, Janae V., Skelly, Tara, Soloway, Matthew G., Tan, Donghui, Veluvolu, Umadevi, Fan, Huihui, Hinoue, Toshinori, Laird, Peter W., Shen, Hui, Zhou, Wanding, Bellair, Michelle, Chang, Kyle, Covington, Kyle, Creighton, Chad J., Dinh, Huyen, Doddapaneni, HarshaVardhan, Donehower, Lawrence A., Drummond, Jennifer, Gibbs, Richard A., Glenn, Robert, Hale, Walker, Han, Yi, Hu, Jianhong, Korchina, Viktoriya, Lee, Sandra, Lewis, Lora, Li, Wei, Liu, Xiuping, Morgan, Margaret, Morton, Donna, Muzny, Donna, Santibanez, Jireh, Sheth, Margi, Shinbrot, Eve, Wang, Linghua, Wang, Min, Wheeler, David A., Xi, Liu, Zhao, Fengmei, Hess, Julian, Appelbaum, Elizabeth L., Bailey, Matthew, Cordes, Matthew G., Ding, Li, Fronick, Catrina C., Fulton, Lucinda A., Fulton, Robert S., Kandoth, Cyriac, Mardis, Elaine R., McLellan, Michael D., Miller, Christopher A., Schmidt, Heather K., Wilson, Richard K., Crain, Daniel, Curley, Erin, Gardner, Johanna, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Penny, Robert, Shelton, Candace, Shelton, Troy, Sherman, Mark, Thompson, Eric, Yena, Peggy, Bowen, Jay, Gastier-Foster, Julie M., Gerken, Mark, Leraas, Kristen M., Lichtenberg, Tara M., Ramirez, Nilsa C., Wise, Lisa, Zmuda, Erik, Corcoran, Niall, Costello, Tony, Hovens, Christopher, Carvalho, Andre L., de Carvalho, Ana C., Fregnani, José H., Longatto-Filho, Adhemar, Reis, Rui M., Scapulatempo-Neto, Cristovam, Silveira, Henrique C.S., Vidal, Daniel O., Burnette, Andrew, Eschbacher, Jennifer, Hermes, Beth, Noss, Ardene, Singh, Rosy, Anderson, Matthew L., Castro, Patricia D., Ittmann, Michael, Huntsman, David, Kohl, Bernard, Le, Xuan, Thorp, Richard, Andry, Chris, Duffy, Elizabeth R., Lyadov, Vladimir, Paklina, Oxana, Setdikova, Galiya, Shabunin, Alexey, Tavobilov, Mikhail, McPherson, Christopher, Warnick, Ronald, Berkowitz, Ross, Cramer, Daniel, Feltmate, Colleen, Horowitz, Neil, Kibel, Adam, Muto, Michael, Raut, Chandrajit P., Malykh, Andrei, Barnholtz-Sloan, Jill S., Barrett, Wendi, Devine, Karen, Fulop, Jordonna, Ostrom, Quinn T., Shimmel, Kristen, Wolinsky, Yingli, Sloan, Andrew E., De Rose, Agostino, Giuliante, Felice, Goodman, Marc, Karlan, Beth Y., Hagedorn, Curt H., Eckman, John, Harr, Jodi, Myers, Jerome, Tucker, Kelinda, Zach, Leigh Anne, Deyarmin, Brenda, Hu, Hai, Kvecher, Leonid, Larson, Caroline, Mural, Richard J., Somiari, Stella, Vicha, Ales, Zelinka, Tomas, Bennett, Joseph, Iacocca, Mary, Rabeno, Brenda, Swanson, Patricia, Latour, Mathieu, Lacombe, Louis, Têtu, Bernard, Bergeron, Alain, McGraw, Mary, Staugaitis, Susan M., Chabot, John, Hibshoosh, Hanina, Sepulveda, Antonia, Su, Tao, Wang, Timothy, Potapova, Olga, Voronina, Olga, Desjardins, Laurence, Mariani, Odette, Roman-Roman, Sergio, Sastre, Xavier, Stern, Marc-Henri, Cheng, Feixiong, Signoretti, Sabina, Berchuck, Andrew, Bigner, Darell, Lipp, Eric, Marks, Jeffrey, McCall, Shannon, McLendon, Roger, Secord, Angeles, Sharp, Alexis, Behera, Madhusmita, Brat, Daniel J., Chen, Amy, Delman, Keith, Force, Seth, Khuri, Fadlo, Magliocca, Kelly, Maithel, Shishir, Olson, Jeffrey J., Owonikoko, Taofeek, Pickens, Alan, Ramalingam, Suresh, Shin, Dong M., Sica, Gabriel, Van Meir, Erwin G., Zhang, Hongzheng, Eijckenboom, Wil, Gillis, Ad, Korpershoek, Esther, Looijenga, Leendert, Oosterhuis, Wolter, Stoop, Hans, van Kessel, Kim E., Zwarthoff, Ellen C., Calatozzolo, Chiara, Cuppini, Lucia, Cuzzubbo, Stefania, DiMeco, Francesco, Finocchiaro, Gaetano, Mattei, Luca, Perin, Alessandro, Pollo, Bianca, Chen, Chu, Houck, John, Lohavanichbutr, Pawadee, Hartmann, Arndt, Stoehr, Christine, Stoehr, Robert, Taubert, Helge, Wach, Sven, Wullich, Bernd, Kycler, Witold, Murawa, Dawid, Wiznerowicz, Maciej, Chung, Ki, Edenfield, W. Jeffrey, Martin, Julie, Baudin, Eric, Bubley, Glenn, Bueno, Raphael, De Rienzo, Assunta, Richards, William G., Kalkanis, Steven, Mikkelsen, Tom, Noushmehr, Houtan, Scarpace, Lisa, Girard, Nicolas, Aymerich, Marta, Campo, Elias, Giné, Eva, Guillermo, Armando López, Van Bang, Nguyen, Hanh, Phan Thi, Phu, Bui Duc, Tang, Yufang, Colman, Howard, Evason, Kimberley, Dottino, Peter R., Martignetti, John A., Gabra, Hani, Juhl, Hartmut, Akeredolu, Teniola, Stepa, Serghei, Hoon, Dave, Ahn, Keunsoo, Kang, Koo Jeong, Beuschlein, Felix, Breggia, Anne, Birrer, Michael, Bell, Debra, Borad, Mitesh, Bryce, Alan H., Castle, Erik, Chandan, Vishal, Cheville, John, Copland, John A., Farnell, Michael, Flotte, Thomas, Giama, Nasra, Ho, Thai, Kendrick, Michael, Kocher, Jean-Pierre, Kopp, Karla, Moser, Catherine, Nagorney, David, O’Brien, Daniel, O’Neill, Brian Patrick, Patel, Tushar, Petersen, Gloria, Que, Florencia, Rivera, Michael, Roberts, Lewis, Smallridge, Robert, Smyrk, Thomas, Stanton, Melissa, Thompson, R. Houston, Torbenson, Michael, Yang, Ju Dong, Zhang, Lizhi, Brimo, Fadi, Ajani, Jaffer A., Gonzalez, Ana Maria Angulo, Behrens, Carmen, Bondaruk, Jolanta, Broaddus, Russell, Czerniak, Bogdan, Esmaeli, Bita, Fujimoto, Junya, Gershenwald, Jeffrey, Guo, Charles, Lazar, Alexander J., Logothetis, Christopher, Meric-Bernstam, Funda, Moran, Cesar, Ramondetta, Lois, Rice, David, Sood, Anil, Tamboli, Pheroze, Thompson, Timothy, Troncoso, Patricia, Tsao, Anne, Wistuba, Ignacio, Carter, Candace, Haydu, Lauren, Hersey, Peter, Jakrot, Valerie, Kakavand, Hojabr, Kefford, Richard, Lee, Kenneth, Long, Georgina, Mann, Graham, Quinn, Michael, Saw, Robyn, Scolyer, Richard, Shannon, Kerwin, Spillane, Andrew, Stretch, onathan, Synott, Maria, Thompson, John, Wilmott, James, Al-Ahmadie, Hikmat, Chan, Timothy A., Ghossein, Ronald, Gopalan, Anuradha, Levine, Douglas A., Reuter, Victor, Singer, Samuel, Singh, Bhuvanesh, Tien, Nguyen Viet, Broudy, Thomas, Mirsaidi, Cyrus, Nair, Praveen, Drwiega, Paul, Miller, Judy, Smith, Jennifer, Zaren, Howard, Park, Joong-Won, Hung, Nguyen Phi, Kebebew, Electron, Linehan, W. Marston, Metwalli, Adam R., Pacak, Karel, Pinto, Peter A., Schiffman, Mark, Schmidt, Laura S., Vocke, Cathy D., Wentzensen, Nicolas, Worrell, Robert, Yang, Hannah, Moncrieff, Marc, Goparaju, Chandra, Melamed, Jonathan, Pass, Harvey, Botnariuc, Natalia, Caraman, Irina, Cernat, Mircea, Chemencedji, Inga, Clipca, Adrian, Doruc, Serghei, Gorincioi, Ghenadie, Mura, Sergiu, Pirtac, Maria, Stancul, Irina, Tcaciuc, Diana, Albert, Monique, Alexopoulou, Iakovina, Arnaout, Angel, Bartlett, John, Engel, Jay, Gilbert, Sebastien, Parfitt, Jeremy, Sekhon, Harman, Thomas, George, Rassl, Doris M., Rintoul, Robert C., Bifulco, Carlo, Tamakawa, Raina, Urba, Walter, Hayward, Nicholas, Timmers, Henri, Antenucci, Anna, Facciolo, Francesco, Grazi, Gianluca, Marino, Mirella, Merola, Roberta, de Krijger, Ronald, Gimenez-Roqueplo, Anne-Paule, Piché, Alain, Chevalier, Simone, McKercher, Ginette, Birsoy, Kivanc, Barnett, Gene, Brewer, Cathy, Farver, Carol, Naska, Theresa, Pennell, Nathan A., Raymond, Daniel, Schilero, Cathy, Smolenski, Kathy, Williams, Felicia, Morrison, Carl, Borgia, Jeffrey A., Liptay, Michael J., Pool, Mark, Seder, Christopher W., Junker, Kerstin, Omberg, Larsson, Dinkin, Mikhail, Manikhas, George, Alvaro, Domenico, Bragazzi, Maria Consiglia, Cardinale, Vincenzo, Carpino, Guido, Gaudio, Eugenio, Chesla, David, Cottingham, Sandra, Dubina, Michael, Moiseenko, Fedor, Dhanasekaran, Renumathy, Becker, Karl-Friedrich, Janssen, Klaus-Peter, Slotta-Huspenina, Julia, Abdel-Rahman, Mohamed H., Aziz, Dina, Bell, Sue, Cebulla, Colleen M., Davis, Amy, Duell, Rebecca, Elder, J. Bradley, Hilty, Joe, Kumar, Bahavna, Lang, James, Lehman, Norman L., Mandt, Randy, Nguyen, Phuong, Pilarski, Robert, Rai, Karan, Schoenfield, Lynn, Senecal, Kelly, Wakely, Paul, Hansen, Paul, Lechan, Ronald, Powers, James, Tischler, Arthur, Grizzle, William E., Sexton, Katherine C., Kastl, Alison, Henderson, Joel, Porten, Sima, Waldmann, Jens, Fassnacht, Martin, Asa, Sylvia L., Schadendorf, Dirk, Couce, Marta, Graefen, Markus, Huland, Hartwig, Sauter, Guido, Schlomm, Thorsten, Simon, Ronald, Tennstedt, Pierre, Olabode, Oluwole, Nelson, Mark, Bathe, Oliver, Carroll, Peter R., Chan, June M., Disaia, Philip, Glenn, Pat, Kelley, Robin K., Landen, Charles N., Phillips, Joanna, Prados, Michael, Simko, Jeffry, Smith-McCune, Karen, VandenBerg, Scott, Roggin, Kevin, Fehrenbach, Ashley, Kendler, Ady, Sifri, Suzanne, Steele, Ruth, Jimeno, Antonio, Carey, Francis, Forgie, Ian, Mannelli, Massimo, Carney, Michael, Hernandez, Brenda, Campos, Benito, Herold-Mende, Christel, Jungk, Christin, Unterberg, Andreas, von Deimling, Andreas, Bossler, Aaron, Galbraith, Joseph, Jacobus, Laura, Knudson, Michael, Knutson, Tina, Ma, Deqin, Milhem, Mohammed, Sigmund, Rita, Godwin, Andrew K., Madan, Rashna, Rosenthal, Howard G., Adebamowo, Clement, Adebamowo, Sally N., Boussioutas, Alex, Beer, David, Giordano, Thomas, Mes-Masson, Anne-Marie, Saad, Fred, Bocklage, Therese, Landrum, Lisa, Mannel, Robert, Moore, Kathleen, Moxley, Katherine, Postier, Russel, Walker, Joan, Zuna, Rosemary, Feldman, Michael, Valdivieso, Federico, Dhir, Rajiv, Luketich, James, Pinero, Edna M. Mora, Quintero-Aguilo, Mario, Carlotti, Carlos Gilberto, Dos Santos, Jose Sebastião, Kemp, Rafael, Sankarankuty, Ajith, Tirapelli, Daniela, Catto, James, Agnew, Kathy, Swisher, Elizabeth, Creaney, Jenette, Robinson, Bruce, Shelley, Carl Simon, Godwin, Eryn M., Kendall, Sara, Shipman, Cassaundra, Bradford, Carol, Carey, Thomas, Haddad, Andrea, Moyer, Jeffey, Peterson, Lisa, Prince, Mark, Rozek, Laura, Wolf, Gregory, Bowman, Rayleen, Fong, Kwun M., Yang, Ian, Korst, Robert, Rathmell, W. Kimryn, Fantacone-Campbell, J. Leigh, Hooke, Jeffrey A., Kovatich, Albert J., Shriver, Craig D., DiPersio, John, Drake, Bettina, Govindan, Ramaswamy, Heath, Sharon, Ley, Timothy, Van Tine, Brian, Westervelt, Peter, Rubin, Mark A., Lee, Jung Il, Aredes, Natália D., Mariamidze, Armaz, Spellman, Paul T., Rathmell, W. Kimryn, and Linehan, W. Marston

Published
2018
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150. Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

Author

Campbell, Joshua D., Yau, Christina, Bowlby, Reanne, Liu, Yuexin, Brennan, Kevin, Fan, Huihui, Taylor, Alison M., Wang, Chen, Walter, Vonn, Akbani, Rehan, Byers, Lauren Averett, Creighton, Chad J., Coarfa, Cristian, Shih, Juliann, Cherniack, Andrew D., Gevaert, Olivier, Prunello, Marcos, Shen, Hui, Anur, Pavana, Chen, Jianhong, Cheng, Hui, Hayes, D. Neil, Bullman, Susan, Pedamallu, Chandra Sekhar, Ojesina, Akinyemi I., Sadeghi, Sara, Mungall, Karen L., Robertson, A. Gordon, Benz, Christopher, Schultz, Andre, Kanchi, Rupa S., Gay, Carl M., Hegde, Apurva, Diao, Lixia, Wang, Jing, Ma, Wencai, Sumazin, Pavel, Chiu, Hua-Sheng, Chen, Ting-Wen, Gunaratne, Preethi, Donehower, Larry, Rader, Janet S., Zuna, Rosemary, Al-Ahmadie, Hikmat, Lazar, Alexander J., Flores, Elsa R., Tsai, Kenneth Y., Zhou, Jane H., Rustgi, Anil K., Drill, Esther, Shen, Ronglei, Wong, Christopher K., Caesar-Johnson, Samantha J., Demchok, John A., Felau, Ina, Kasapi, Melpomeni, Ferguson, Martin L., Hutter, Carolyn M., Sofia, Heidi J., Tarnuzzer, Roy, Wang, Zhining, Yang, Liming, Zenklusen, Jean C., Zhang, Jiashan (Julia), Chudamani, Sudha, Liu, Jia, Lolla, Laxmi, Naresh, Rashi, Pihl, Todd, Sun, Qiang, Wan, Yunhu, Wu, Ye, Cho, Juok, DeFreitas, Timothy, Frazer, Scott, Gehlenborg, Nils, Getz, Gad, Heiman, David I., Kim, Jaegil, Lawrence, Michael S., Lin, Pei, Meier, Sam, Noble, Michael S., Saksena, Gordon, Voet, Doug, Zhang, Hailei, Bernard, Brady, Chambwe, Nyasha, Dhankani, Varsha, Knijnenburg, Theo, Kramer, Roger, Leinonen, Kalle, Liu, Yuexin, Miller, Michael, Reynolds, Sheila, Shmulevich, Ilya, Thorsson, Vesteinn, Zhang, Wei, Akbani, Rehan, Broom, Bradley M., Hegde, Apurva M., Ju, Zhenlin, Kanchi, Rupa S., Korkut, Anil, Li, Jun, Liang, Han, Ling, Shiyun, Liu, Wenbin, Lu, Yiling, Mills, Gordon B., Ng, Kwok-Shing, Rao, Arvind, Ryan, Michael, Wang, Jing, Weinstein, John N., Zhang, Jiexin, Abeshouse, Adam, Armenia, Joshua, Chakravarty, Debyani, Chatila, Walid K., de Bruijn, Ino, Gao, Jianjiong, Gross, Benjamin E., Heins, Zachary J., Kundra, Ritika, La, Konnor, Ladanyi, Marc, Luna, Augustin, Nissan, Moriah G., Ochoa, Angelica, Phillips, Sarah M., Reznik, Ed, Sanchez-Vega, Francisco, Sander, Chris, Schultz, Nikolaus, Sheridan, Robert, Sumer, S. Onur, Sun, Yichao, Taylor, Barry S., Wang, Jioajiao, Zhang, Hongxin, Anur, Pavana, Peto, Myron, Spellman, Paul, Benz, Christopher, Stuart, Joshua M., Wong, Christopher K., Yau, Christina, Hayes, D. Neil, Parker, Joel S., Wilkerson, Matthew D., Ally, Adrian, Balasundaram, Miruna, Bowlby, Reanne, Brooks, Denise, Carlsen, Rebecca, Chuah, Eric, Dhalla, Noreen, Holt, Robert, Jones, Steven J.M., Kasaian, Katayoon, Lee, Darlene, Ma, Yussanne, Marra, Marco A., Mayo, Michael, Moore, Richard A., Mungall, Andrew J., Mungall, Karen, Robertson, A. Gordon, Sadeghi, Sara, Schein, Jacqueline E., Sipahimalani, Payal, Tam, Angela, Thiessen, Nina, Tse, Kane, Wong, Tina, Berger, Ashton C., Beroukhim, Rameen, Cherniack, Andrew D., Cibulskis, Carrie, Gabriel, Stacey B., Gao, Galen F., Ha, Gavin, Meyerson, Matthew, Schumacher, Steven E., Shih, Juliann, Kucherlapati, Melanie H., Kucherlapati, Raju S., Baylin, Stephen, Cope, Leslie, Danilova, Ludmila, Bootwalla, Moiz S., Lai, Phillip H., Maglinte, Dennis T., Van Den Berg, David J., Weisenberger, Daniel J., Auman, J. Todd, Balu, Saianand, Bodenheimer, Tom, Fan, Cheng, Hoadley, Katherine A., Hoyle, Alan P., Jefferys, Stuart R., Jones, Corbin D., Meng, Shaowu, Mieczkowski, Piotr A., Mose, Lisle E., Perou, Amy H., Perou, Charles M., Roach, Jeffrey, Shi, Yan, Simons, Janae V., Skelly, Tara, Soloway, Matthew G., Tan, Donghui, Veluvolu, Umadevi, Fan, Huihui, Hinoue, Toshinori, Laird, Peter W., Shen, Hui, Zhou, Wanding, Bellair, Michelle, Chang, Kyle, Covington, Kyle, Creighton, Chad J., Dinh, Huyen, Doddapaneni, HarshaVardhan, Donehower, Lawrence A., Drummond, Jennifer, Gibbs, Richard A., Glenn, Robert, Hale, Walker, Han, Yi, Hu, Jianhong, Korchina, Viktoriya, Lee, Sandra, Lewis, Lora, Li, Wei, Liu, Xiuping, Morgan, Margaret, Morton, Donna, Muzny, Donna, Santibanez, Jireh, Sheth, Margi, Shinbrot, Eve, Wang, Linghua, Wang, Min, Wheeler, David A., Xi, Liu, Zhao, Fengmei, Hess, Julian, Appelbaum, Elizabeth L., Bailey, Matthew, Cordes, Matthew G., Ding, Li, Fronick, Catrina C., Fulton, Lucinda A., Fulton, Robert S., Kandoth, Cyriac, Mardis, Elaine R., McLellan, Michael D., Miller, Christopher A., Schmidt, Heather K., Wilson, Richard K., Crain, Daniel, Curley, Erin, Gardner, Johanna, Lau, Kevin, Mallery, David, Morris, Scott, Paulauskis, Joseph, Penny, Robert, Shelton, Candace, Shelton, Troy, Sherman, Mark, Thompson, Eric, Yena, Peggy, Bowen, Jay, Gastier-Foster, Julie M., Gerken, Mark, Leraas, Kristen M., Lichtenberg, Tara M., Ramirez, Nilsa C., Wise, Lisa, Zmuda, Erik, Corcoran, Niall, Costello, Tony, Hovens, Christopher, Carvalho, Andre L., de Carvalho, Ana C., Fregnani, José H., Longatto-Filho, Adhemar, Reis, Rui M., Scapulatempo-Neto, Cristovam, Silveira, Henrique C.S., Vidal, Daniel O., Burnette, Andrew, Eschbacher, Jennifer, Hermes, Beth, Noss, Ardene, Singh, Rosy, Anderson, Matthew L., Castro, Patricia D., Ittmann, Michael, Huntsman, David, Kohl, Bernard, Le, Xuan, Thorp, Richard, Andry, Chris, Duffy, Elizabeth R., Lyadov, Vladimir, Paklina, Oxana, Setdikova, Galiya, Shabunin, Alexey, Tavobilov, Mikhail, McPherson, Christopher, Warnick, Ronald, Berkowitz, Ross, Cramer, Daniel, Feltmate, Colleen, Horowitz, Neil, Kibel, Adam, Muto, Michael, Raut, Chandrajit P., Malykh, Andrei, Barnholtz-Sloan, Jill S., Barrett, Wendi, Devine, Karen, Fulop, Jordonna, Ostrom, Quinn T., Shimmel, Kristen, Wolinsky, Yingli, Sloan, Andrew E., De Rose, Agostino, Giuliante, Felice, Goodman, Marc, Karlan, Beth Y., Hagedorn, Curt H., Eckman, John, Harr, Jodi, Myers, Jerome, Tucker, Kelinda, Zach, Leigh Anne, Deyarmin, Brenda, Hu, Hai, Kvecher, Leonid, Larson, Caroline, Mural, Richard J., Somiari, Stella, Vicha, Ales, Zelinka, Tomas, Bennett, Joseph, Iacocca, Mary, Rabeno, Brenda, Swanson, Patricia, Latour, Mathieu, Lacombe, Louis, Têtu, Bernard, Bergeron, Alain, McGraw, Mary, Staugaitis, Susan M., Chabot, John, Hibshoosh, Hanina, Sepulveda, Antonia, Su, Tao, Wang, Timothy, Potapova, Olga, Voronina, Olga, Desjardins, Laurence, Mariani, Odette, Roman-Roman, Sergio, Sastre, Xavier, Stern, Marc-Henri, Cheng, Feixiong, Signoretti, Sabina, Berchuck, Andrew, Bigner, Darell, Lipp, Eric, Marks, Jeffrey, McCall, Shannon, McLendon, Roger, Secord, Angeles, Sharp, Alexis, Behera, Madhusmita, Brat, Daniel J., Chen, Amy, Delman, Keith, Force, Seth, Khuri, Fadlo, Magliocca, Kelly, Maithel, Shishir, Olson, Jeffrey J., Owonikoko, Taofeek, Pickens, Alan, Ramalingam, Suresh, Shin, Dong M., Sica, Gabriel, Van Meir, Erwin G., Zhang, Hongzheng, Eijckenboom, Wil, Gillis, Ad, Korpershoek, Esther, Looijenga, Leendert, Oosterhuis, Wolter, Stoop, Hans, van Kessel, Kim E., Zwarthoff, Ellen C., Calatozzolo, Chiara, Cuppini, Lucia, Cuzzubbo, Stefania, DiMeco, Francesco, Finocchiaro, Gaetano, Mattei, Luca, Perin, Alessandro, Pollo, Bianca, Chen, Chu, Houck, John, Lohavanichbutr, Pawadee, Hartmann, Arndt, Stoehr, Christine, Stoehr, Robert, Taubert, Helge, Wach, Sven, Wullich, Bernd, Kycler, Witold, Murawa, Dawid, Wiznerowicz, Maciej, Chung, Ki, Edenfield, W. Jeffrey, Martin, Julie, Baudin, Eric, Bubley, Glenn, Bueno, Raphael, De Rienzo, Assunta, Richards, William G., Kalkanis, Steven, Mikkelsen, Tom, Noushmehr, Houtan, Scarpace, Lisa, Girard, Nicolas, Aymerich, Marta, Campo, Elias, Giné, Eva, Guillermo, Armando López, Van Bang, Nguyen, Hanh, Phan Thi, Phu, Bui Duc, Tang, Yufang, Colman, Howard, Evason, Kimberley, Dottino, Peter R., Martignetti, John A., Gabra, Hani, Juhl, Hartmut, Akeredolu, Teniola, Stepa, Serghei, Hoon, Dave, Ahn, Keunsoo, Kang, Koo Jeong, Beuschlein, Felix, Breggia, Anne, Birrer, Michael, Bell, Debra, Borad, Mitesh, Bryce, Alan H., Castle, Erik, Chandan, Vishal, Cheville, John, Copland, John A., Farnell, Michael, Flotte, Thomas, Giama, Nasra, Ho, Thai, Kendrick, Michael, Kocher, Jean-Pierre, Kopp, Karla, Moser, Catherine, Nagorney, David, O’Brien, Daniel, O’Neill, Brian Patrick, Patel, Tushar, Petersen, Gloria, Que, Florencia, Rivera, Michael, Roberts, Lewis, Smallridge, Robert, Smyrk, Thomas, Stanton, Melissa, Thompson, R. 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Abstract

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smoking and/or human papillomavirus (HPV). SCCs harbor 3q, 5p, and other recurrent chromosomal copy-number alterations (CNAs), DNA mutations, and/or aberrant methylation of genes and microRNAs, which are correlated with the expression of multi-gene programs linked to squamous cell stemness, epithelial-to-mesenchymal differentiation, growth, genomic integrity, oxidative damage, death, and inflammation. Low-CNA SCCs tended to be HPV(+) and display hypermethylation with repression of TET1demethylase and FANCF, previously linked to predisposition to SCC, or harbor mutations affecting CASP8, RAS-MAPK pathways, chromatin modifiers, and immunoregulatory molecules. We uncovered hypomethylation of the alternative promoter that drives expression of the ΔNp63oncogene and embedded miR944. Co-expression of immune checkpoint, T-regulatory, and Myeloid suppressor cells signatures may explain reduced efficacy of immune therapy. These findings support possibilities for molecular classification and therapeutic approaches.

Published
2018
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