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102. An Open Trial of Metacognitive Remediation Therapy and Pharmacotherapy to Promote Smoking Cessation among Individuals with Psychotic-Spectrum Disorders

Author

Breitborde, Nicholas J. K., primary, Keller-Hamilton, Brittney, additional, Moe, Aubrey M., additional, Pine, Jacob G., additional, Nelson, Nicholas, additional, Weiss, David, additional, Hogan, Tory, additional, Quisenberry, Amanda, additional, Teferra, Andreas, additional, and Ferketich, Amy K., additional

Published
2021
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103. Multi-tissue integrative analysis of personal epigenomes

Author

Rozowsky, Joel, Drenkow, Jorg, Yang, Yucheng, Gursoy, Gamze, Galeev, Timur, Borsari, Beatrice, Epstein, Charles, Xiong, Kun, Xu, Jinrui, Gao, Jiahao, Yu, Keyang, Berthel, Ana, Chen, Zhanlin, Navarro, Fabio, Liu, Jason, Sun, Maxwell, Wright, James, Chang, Justin, Cameron, Christopher, Shoresh, Noam, Gaskell, Elizabeth, Adrian, Jessika, Aganezov, Sergey, Balderrama-Gutierrez, Gabriela, Banskota, Samridhi, Corona, Guillermo, Chee, Sora, Chhetri, Surya, Martins, Gabriel, Danyko, Cassidy, Davis, Carrie, Farid, Daniel, Farrell, Nina, Gabdank, Idan, Gofin, Yoel, Gorkin, David, Gu, Mengting, Hecht, Vivian, Hitz, Benjamin, Issner, Robbyn, Kirsche, Melanie, Kong, Xiangmeng, Lam, Bonita, Li, Shantao, Li, Bian, Li, Tianxiao, Li, Xiqi, Lin, Khine, Luo, Ruibang, Mackiewicz, Mark, Moore, Jill, Mudge, Jonathan, Nelson, Nicholas, Nusbaum, Chad, Popov, Ioann, Pratt, Henry, Qiu, Yunjiang, Ramakrishnan, Srividya, Raymond, Joe, Salichos, Leonidas, Scavelli, Alexandra, Schreiber, Jacob, Sedlazeck, Fritz, See, Lei, Sherman, Rachel, Shi, Xu, Shi, Minyi, Sloan, Cricket, Strattan, J. Seth, Tan, Zhen, Tanaka, Forrest, Vlasova, Anna, Wang, Jun, Werner, Jonathan, Williams, Brian, Xu, Min, Yan, Chengfei, Yu, Lu, Zaleski, Christopher, Zhang, Jing, Cherry, J. Michael, Mendenhall, Eric, Noble, William, Weng, Zhiping, Levine, Morgan, Dobin, Alexander, Wold, Barbara, Mortazavi, Ali, Ren, Bing, Gillis, Jesse, Myers, Richard, Snyder, Michael, Choudhary, Jyoti, Milosavljevic, Aleksandar, Schatz, Michael, Guigo, Roderic, Bernstein, Bradley, Gingeras, Thomas, Gerstein, Mark, Rozowsky, Joel, Drenkow, Jorg, Yang, Yucheng, Gursoy, Gamze, Galeev, Timur, Borsari, Beatrice, Epstein, Charles, Xiong, Kun, Xu, Jinrui, Gao, Jiahao, Yu, Keyang, Berthel, Ana, Chen, Zhanlin, Navarro, Fabio, Liu, Jason, Sun, Maxwell, Wright, James, Chang, Justin, Cameron, Christopher, Shoresh, Noam, Gaskell, Elizabeth, Adrian, Jessika, Aganezov, Sergey, Balderrama-Gutierrez, Gabriela, Banskota, Samridhi, Corona, Guillermo, Chee, Sora, Chhetri, Surya, Martins, Gabriel, Danyko, Cassidy, Davis, Carrie, Farid, Daniel, Farrell, Nina, Gabdank, Idan, Gofin, Yoel, Gorkin, David, Gu, Mengting, Hecht, Vivian, Hitz, Benjamin, Issner, Robbyn, Kirsche, Melanie, Kong, Xiangmeng, Lam, Bonita, Li, Shantao, Li, Bian, Li, Tianxiao, Li, Xiqi, Lin, Khine, Luo, Ruibang, Mackiewicz, Mark, Moore, Jill, Mudge, Jonathan, Nelson, Nicholas, Nusbaum, Chad, Popov, Ioann, Pratt, Henry, Qiu, Yunjiang, Ramakrishnan, Srividya, Raymond, Joe, Salichos, Leonidas, Scavelli, Alexandra, Schreiber, Jacob, Sedlazeck, Fritz, See, Lei, Sherman, Rachel, Shi, Xu, Shi, Minyi, Sloan, Cricket, Strattan, J. Seth, Tan, Zhen, Tanaka, Forrest, Vlasova, Anna, Wang, Jun, Werner, Jonathan, Williams, Brian, Xu, Min, Yan, Chengfei, Yu, Lu, Zaleski, Christopher, Zhang, Jing, Cherry, J. Michael, Mendenhall, Eric, Noble, William, Weng, Zhiping, Levine, Morgan, Dobin, Alexander, Wold, Barbara, Mortazavi, Ali, Ren, Bing, Gillis, Jesse, Myers, Richard, Snyder, Michael, Choudhary, Jyoti, Milosavljevic, Aleksandar, Schatz, Michael, Guigo, Roderic, Bernstein, Bradley, Gingeras, Thomas, and Gerstein, Mark

Abstract

Evaluating the impact of genetic variants on transcriptional regulation is a central goal in biological science that has been constrained by reliance on a single reference genome. To address this, we constructed phased, diploid genomes for four cadaveric donors (using long-read sequencing) and systematically charted noncoding regulatory elements and transcriptional activity across more than 25 tissues from these donors. Integrative analysis revealed over a million variants with allele-specific activity, coordinated, locus-scale allelic imbalances, and structural variants impacting proximal chromatin structure. We relate the personal genome analysis to the ENCODE encyclopedia, annotating allele- and tissue-specific elements that are strongly enriched for variants impacting expression and disease phenotypes. These experimental and statistical approaches, and the corresponding EN-TEx resource, provide a framework for personalized functional genomics.

Published
2021

107. Access to Optimal Emergency Care for Children

Author

Brown, Kathleen M., primary, Ackerman, Alice D., additional, Ruttan, Timothy K., additional, Snow, Sally K., additional, Conners, Gregory P., additional, Callahan, James, additional, Gross, Toni, additional, Joseph, Madeline, additional, Lee, Lois, additional, Mack, Elizabeth, additional, Marin, Jennifer, additional, Mazor, Suzan, additional, Paul, Ronald, additional, Timm, Nathan, additional, Dietrich, Ann M., additional, Alade, Kiyetta H., additional, Amato, Christopher S., additional, Atanelov, Zaza, additional, Auerbach, Marc, additional, Barata, Isabel A., additional, Benjamin, Lee S., additional, Berg, Kathleen T., additional, Brown, Kathleen, additional, Chang, Cindy, additional, Chow, Jessica, additional, Chumpitazi, Corrie E., additional, Claudius, Ilene A., additional, Easter, Joshua, additional, Foster, Ashley, additional, Fox, Sean M., additional, Gausche-Hill, Marianne, additional, Gerardi, Michael J., additional, Goodloe, Jeffrey M., additional, Heniff, Melanie, additional, Homme, James (Jim) L., additional, Ishimine, Paul T., additional, John, Susan D., additional, Joseph, Madeline M., additional, Lam, Samuel Hiu-Fung, additional, Lawson, Simone L., additional, Lee, Moon O., additional, Li, Joyce, additional, Lin, Sophia D., additional, Martini, Dyllon Ivy, additional, Mellick, Larry Bruce, additional, Mendez, Donna, additional, Petrack, Emory M., additional, Rice, Lauren, additional, Rose, Emily A., additional, Ruttan, Timothy, additional, Saidinejad, Mohsen, additional, Santillanes, Genevieve, additional, Simpson, Joelle N., additional, Sivasankar, Shyam M., additional, Slubowski, Daniel, additional, Sorrentino, Annalise, additional, Stoner, Michael J., additional, Sulton, Carmen D., additional, Valente, Jonathan H., additional, Vora, Samreen, additional, Wall, Jessica J., additional, Wallin, Dina, additional, Walls, Theresa A., additional, Waseem, Muhammad, additional, Woolridge, Dale P., additional, Brandt, Cam, additional, Kult, Krisi M., additional, Milici, Justin J., additional, Nelson, Nicholas A., additional, Redlo, Michele A., additional, Curtis Cooper, Maureen R., additional, Redlo, Michele, additional, Kult, Krisi, additional, Logee, Katherine, additional, Bryant, Dixie Elizabeth, additional, Cooper, Maureen Curtis, additional, and Cline, Kristen, additional

Published
2021
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108. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

Author

Rozowsky, Joel, primary, Drenkow, Jorg, additional, Yang, Yucheng T, additional, Gursoy, Gamze, additional, Galeev, Timur, additional, Borsari, Beatrice, additional, Epstein, Charles B, additional, Xiong, Kun, additional, Xu, Jinrui, additional, Gao, Jiahao, additional, Yu, Keyang, additional, Berthel, Ana, additional, Chen, Zhanlin, additional, Navarro, Fabio, additional, Liu, Jason, additional, Sun, Maxwell S, additional, Wright, James, additional, Chang, Justin, additional, Cameron, Christopher JF, additional, Shoresh, Noam, additional, Gaskell, Elizabeth, additional, Adrian, Jessika, additional, Aganezov, Sergey, additional, Aguet, François, additional, Balderrama-Gutierrez, Gabriela, additional, Banskota, Samridhi, additional, Corona, Guillermo Barreto, additional, Chee, Sora, additional, Chhetri, Surya B, additional, Cortez Martins, Gabriel Conte, additional, Danyko, Cassidy, additional, Davis, Carrie A, additional, Farid, Daniel, additional, Farrell, Nina P, additional, Gabdank, Idan, additional, Gofin, Yoel, additional, Gorkin, David U, additional, Gu, Mengting, additional, Hecht, Vivian, additional, Hitz, Benjamin C, additional, Issner, Robbyn, additional, Kirsche, Melanie, additional, Kong, Xiangmeng, additional, Lam, Bonita R, additional, Li, Shantao, additional, Li, Bian, additional, Li, Tianxiao, additional, Li, Xiqi, additional, Lin, Khine Zin, additional, Luo, Ruibang, additional, Mackiewicz, Mark, additional, Moore, Jill E, additional, Mudge, Jonathan, additional, Nelson, Nicholas, additional, Nusbaum, Chad, additional, Popov, Ioann, additional, Pratt, Henry E, additional, Qiu, Yunjiang, additional, Ramakrishnan, Srividya, additional, Raymond, Joe, additional, Salichos, Leonidas, additional, Scavelli, Alexandra, additional, Schreiber, Jacob M, additional, Sedlazeck, Fritz J, additional, See, Lei Hoon, additional, Sherman, Rachel M, additional, Shi, Xu, additional, Shi, Minyi, additional, Sloan, Cricket Alicia, additional, Strattan, J Seth, additional, Tan, Zhen, additional, Tanaka, Forrest Y, additional, Vlasova, Anna, additional, Wang, Jun, additional, Werner, Jonathan, additional, Williams, Brian, additional, Xu, Min, additional, Yan, Chengfei, additional, Yu, Lu, additional, Zaleski, Christopher, additional, Zhang, Jing, additional, Ardlie, Kristin, additional, Cherry, J Michael, additional, Mendenhall, Eric M, additional, Noble, William S, additional, Weng, Zhiping, additional, Levine, Morgan E, additional, Dobin, Alexander, additional, Wold, Barbara, additional, Mortazavi, Ali, additional, Ren, Bing, additional, Gillis, Jesse, additional, Myers, Richard M, additional, Snyder, Michael P, additional, Choudhary, Jyoti, additional, Milosavljevic, Aleksandar, additional, Schatz, Michael C, additional, Guigó, Roderic, additional, Bernstein, Bradley E, additional, Gingeras, Thomas R, additional, and Gerstein, Mark, additional

Published
2021
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110. Development and validation of the Dynamic Collimation Monte Carlo simulation package for pencil beam scanning proton therapy

Author

Nelson, Nicholas P., primary, Culberson, Wesley S., additional, Hyer, Daniel E., additional, Geoghegan, Theodore J., additional, Patwardhan, Kaustubh A., additional, Smith, Blake R., additional, Flynn, Ryan T., additional, Yu, Jen, additional, Rana, Suresh, additional, Gutiérrez, Alonso N., additional, and Hill, Patrick M., additional

Published
2021
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113. A textual approach to harmonizing Sherbert and Smith on free exercise accomodations.

Author

Nelson, Nicholas J.

Subjects
Freedom of religion -- Laws, regulations and rules, Religious discrimination -- Laws, regulations and rules, Sherbert v. Verner (374 U.S. 398 (1963)), Employment Division, Department of Human Resources v. Smith (494 U.S. 872 (1990)), Government regulation, United States Constitution (U.S. Const. amend. 1)
Published
2008

115. Acute acalculous cholecystitis in an infant after gastroschisis closure.

Author

Shehzad, Irfan, Nelson, Nicholas, Vora, Niraj, Wills, Hale, Birkemeier, Krista, and Govande, Vinayak

Abstract

Gastroschisis is a common type of congenital anterior abdominal wall defect with intraabdominal organs exposed outside the abdominal cavity. With modern neonatology and surgical practices, the overall prognosis for infants with gastroschisis is excellent. However, a subset of infants with gastroschisis will develop complications, requiring repeat surgical interventions. We present a case of a female infant with complicated gastroschisis who developed acute perforated acalculous cholecystitis, which was accurately diagnosed with abdominal ultrasound and successfully treated with medical management and a percutaneous cholecystostomy tube. [ABSTRACT FROM AUTHOR]

Published
2023
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116. Lament Scenes in Xenophon of Ephesus: A Study in Self-Fashioning

Author

Nelson, Nicholas Paul and Nelson, Nicholas Paul

Abstract

Scholars often exclude Xenophon’s Ephesiaca from consideration with texts of the so-called Second Sophistic due to its style. Recent scholarship, especially by Whitmarsh (2001, 2005, 2011), sees a concern with identity to be an important characteristic of Imperial Greek literature. This thesis analyzes the protagonists’ lament scenes of Xenophon’s Ephesiaca in order to see how Anthia and Habrocomes define their identities and interrogate different facets of their identities. Aelius Theon (Prog. 115–6) provides a useful discussion of different character types which delineates different social antitheses: old men and young men, men and women, slaves and freed people, and people in love and those who have sophrosyne. Habrocomes and Anthia interrogate where they stands in relation to these different strands throughout the novel. Habrocomes defines himself in relation to these various character types frequently in his lament scenes. At 1.4. 1–3, he views himself as being in a military contest with Eros and views his loss in this metaphorical battle as a loss of masculinity, thus defining himself with respect to Aelius Theon’s category of men and women. At 1.4. 4–5 he defines scorning Eros as sophrosyne, thus showing himself to prefer a definition of sophrosyne that is closer to Hippolytus’ than is usually seen in the Greek novel. Throughout the rest of Book 1, where Habrocomes defines sophrosyne on his wedding night and in the oath scene, his definition of sophrosyne becomes gradually closer to the one usually seen in the Greek novel. At 2.1.2–4 he argues that if he were to submit to Corymbus he would be a “whore instead of a man,” which further defines his sophrosyne as an integral part of his masculinity. At 2.4.3–5 Habrocomes defines himself in terms of being a slave vs. a freed person and states that although his body is enslaved, his soul is free. After he is freed, for the rest of the novel, he does not truly view himself as free until he is reunited with Anthia. A

Published
2020

119. Endogenous estrogen mediates a higher threshold for endotoxin-induced myocardial protection in females

Author

Pitcher, Jeffrey M., Wang, Meijing, Tsai, Ben M., Kher, Ajay, Nelson, Nicholas T., and Meldrum, Daniel R.

Subjects
Acute disease -- Research, Rats as laboratory animals -- Research, Cardiomyopathy -- Research, Heart diseases -- Research, Biological sciences
Abstract

Myocardial endotoxin tolerance may be induced in both males and females; however, it remains unknown whether there are mechanistic and threshold differences between the sexes. We hypothesized that endogenous estrogen mediates a higher threshold for endotoxin (ETX)-induced protection in females. Adult proestrus and ovariectomized (OVX) female rats were preconditioned (PC) with intraperitoneal injections of 125 (PC+125) or 500 (PC+500) [micro]g/kg Salmonella typhimurium LPS (ETX) or normal saline (PC-). Twenty-four hours later, injury dose ETX (500 [micro]g/kg) was injected. After 6 h, myocardial function was measured via Langendorff. p38 MAPK and JNK activation and TNF-[alpha], IL-1, and IL-6 expression were evaluated. ETX injury significantly decreased left ventricular developed pressure in PC- groups vs. controls. PC+500 regimen protected against ETX injury, resulting in normal cardiac function. PC+125 regimen protected OVX but not proestrus females, which had diminished myocardial function. Activated JNK and TNF-[alpha] increased in PC- but were diminished in PC+500 animals. Importantly, activated JNK and TNF increased in PC+125 proestrus females, whereas PC+125 OVX females displayed decreases in these molecules. There were no differences in p38 MAPK activation or expression of IL-1 or IL-6. These results demonstrate that proestrus females require a higher stimulus (PC+500) to achieve myocardial protection against ETX injury. Removal of endogenous estrogen (OVX) lowered the preconditioning threshold (PC+125), resulting in protection after lesser injury. Additionally, myocardial JNK and TNF expression was decreased in OVX PC+125 females, which correlated with myocardial function differences. Therefore, we conclude that endogenous estrogen mediates a higher threshold for ETX tolerance in female myocardium. tolerance; gender; acute injury

Published
2006

123. Scaling the Security Staircase

Author

Carr, Stuart C., primary, Hopner, Veronica, additional, Hakim, Moh. Abdul, additional, Hodgetts, Darrin J., additional, Chamberlain, Kerry, additional, Nelson, Nicholas, additional, Ball, Rhys, additional, and Jones, Harvey, additional

Published
2020
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131. A tale from the trenches

Author

Chattopadhyay, Souti, primary, Nelson, Nicholas, additional, Au, Audrey, additional, Morales, Natalia, additional, Sanchez, Christopher, additional, Pandita, Rahul, additional, and Sarma, Anita, additional

Published
2020
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137. Structural Competency: Curriculum for Medical Students, Residents, and Interprofessional Teams on the Structural Factors That Produce Health Disparities

Author

Neff, Joshua, primary, Holmes, Seth M., additional, Knight, Kelly R., additional, Strong, Shirley, additional, Thompson-Lastad, Ariana, additional, McGuinness, Cara, additional, Duncan, Laura, additional, Saxena, Nimish, additional, Harvey, Michael J., additional, Langford, Alice, additional, Carey-Simms, Katiana L., additional, Minahan, Sara N., additional, Satterwhite, Shannon, additional, Ruppel, Caitlin, additional, Lee, Sonia, additional, Walkover, Lillian, additional, De Avila, Jorge, additional, Lewis, Brett, additional, Matthews, Jenifer, additional, and Nelson, Nicholas, additional

Published
2020
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142. Scaling the Security Staircase.

Author

Carr, Stuart C., Hopner, Veronica, Hakim, Moh. Abdul, Hodgetts, Darrin J., Chamberlain, Kerry, Nelson, Nicholas, Ball, Rhys, and Jones, Harvey

Subjects
STAIRCASES, HUMAN security, NATIONAL security, FOOD security, SECURITY management, SECURITY (Psychology)
Abstract

Building on the U.N. human security taxonomy of 1994, this article aims to explore the constructability of a reliable, valid, parsimonious, useful measure of human security that is relevant to contemporary environments and situations? A seminal 1994 U.N. report, Human Security in Theory and Practice, outlined seven types of human security (personal, health, food, community, economic, environmental, political). A quarter‐century on, we added two more, cyber and national security, and tested if a single measure could capture all nine security concerns. A national sample of N = 1033 New Zealanders completed a brief online measure in which participants reported yes or no to experiencing each type of security and basic demographics. Guttman scaling placed these needs in an ascending order of difficulty. Analogous to a staircase, security may be scaled from personal up to political security (coefficient of reproducibility =.88), with three distinct but interrelated flights: (1) proximal (personal, health, food security); (2) social (cyber, community, economic, environmental); and (3) distal (national, political). We confirmed this nine‐step, three‐flight measure in our sample (Χ2 = 81.72; df = 24; RMSEA =.048, 90%CI [.037,.06]; CFI =.976; TLI =.964; SRMR =.028). The measure showed configural, metric, scalar, and factorial invariances (across random‐split subgroups). Ethnic groups and the precariously employed scored significantly differently, in coherent ways, on the security staircase scale. [ABSTRACT FROM AUTHOR]

Published
2021
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143. A Tale from the Trenches: Cognitive Biases and Software Development.

Author

Chattopadhyay, Souti, Nelson, Nicholas, Au, Audrey, Morales, Natalia, Sanchez, Christopher, Pandita, Rahul, and Sarma, Anita

Subjects
COGNITIVE bias, MACHINE learning, COMPUTER software development, INTERVIEWING, COGNITION
Abstract

Cognitive biases are hard-wired behaviors that influence developer actions and can set them on an incorrect course of action, necessitating backtracking. While researchers have found that cognitive biases occur in development tasks in controlled lab studies, we still don't know how these biases affect developers' everyday behavior. Without such an understanding, development tools and practices remain inadequate. To close this gap, we conducted a 2-part field study to examine the extent to which cognitive biases occur, the consequences of these biases on developer behavior, and the practices and tools that developers use to deal with these biases. About 70% of observed actions that were reversed were associated with at least one cognitive bias. Further, even though developers recognized that biases frequently occur, they routinely are forced to deal with such issues with ad hoc processes and sub-optimal tool support. As one participant (IP12) lamented: There is no salvation! [ABSTRACT FROM AUTHOR]

Published
2020
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144. Design of a Modular, Partially Disposable Robot for Minimally Invasive Surgery

Author

Nelson Nicholas and Carl A. Nelson

Subjects
Computer science, business.industry, Invasive surgery, Degrees of freedom, Robot, Control engineering, Instrumentation (computer programming), Modular design, business
Abstract

Most robots for minimally invasive surgery (MIS) are large, bulky devices which mimic the paradigm of manual MIS by manipulating long, rigid instruments from outside the body [1]. Some of these incorporate “wristed” instruments to place some local dexterity at or near the tool tip [2]. In contrast, a small number of MIS robot designs place all of the degrees of freedom inside the patient’s body in order to increase the local dexterity [3].

Published
2018

145. Vancomycin Pharmacokinetics in Neurocritically Ill Patients with Traumatic Brain Injury

Author

Nelson, Nicholas

Abstract

Background Traumatic brain injury (TBI) is associated with secondary complications, especially infection, and often exhibit augmented renal clearance (ARC). This phenomenon has been associated with subtherapeutic levels of renally cleared drugs such as vancomycin, which is dosed based on body weight and creatinine clearance (CrCl). Many clinicians, however, cap CrCl at 120 mL/min/1.73m2 when calculating vancomycin dosing regimens. We hypothesize that capping patient CrCl, as opposed to utilizing the actual CrCl, when determining vancomycin dosing schemes results in subtherapeutic serum trough concentrations, and possibly therapeutic failure. Methods This was a retrospective study of adult patients with TBI admitted between April 2014 and December 2015 who received vancomycin. Population based pharmacokinetic parameters using actual calculated CrCl and capped CrCl were compared with patient specific pharmacokinetic parameters based on serum trough concentrations. Results Thirty-two patients with TBI were included in the study. ARC was demonstrated by 24 (75%) patients with a median CrCl at serum trough concentration of 167.3 (127.7-197.7) mL/min. The mean dosing regimen was 17.1 (13.2-19.2) mg/kg every 8 (8-8) h. There was no difference between the median measured trough concentration and predicted value using actual CrCl [10.4 (7.1- 15.0) vs. 11.5 (7.8-13.7) mcg/mL; p=0.7986]. The median measured trough concentration was significantly lower than the predicted trough concentration based on capping CrCl [16.3 (15.3-22.0) vs. 11.5 (7.8-13.7) mcg/mL; p

Published
2018
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