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1. Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases.

Author

Garrison, McKinzie, Jang, Yeongjun, Bae, Taejeong, Cherskov, Adriana, Emery, Sarah, Fasching, Liana, Jones, Attila, Moldovan, John, Molitor, Cindy, Pochareddy, Sirisha, Peters, Mette, Shin, Joo, Wang, Yifan, Yang, Xiaoxu, Akbarian, Schahram, Chess, Andrew, Gage, Fred, Gleeson, Joseph, Kidd, Jeffrey, McConnell, Michael, Mills, Ryan, Moran, John, Park, Peter, Sestan, Nenad, Urban, Alexander, Vaccarino, Flora, Walsh, Christopher, Weinberger, Daniel, Wheelan, Sarah, and Abyzov, Alexej

Subjects
Humans, Autism Spectrum Disorder, Mosaicism, Genome, Brain, Genomics
Abstract

Somatic mosaicism is defined as an occurrence of two or more populations of cells having genomic sequences differing at given loci in an individual who is derived from a single zygote. It is a characteristic of multicellular organisms that plays a crucial role in normal development and disease. To study the nature and extent of somatic mosaicism in autism spectrum disorder, bipolar disorder, focal cortical dysplasia, schizophrenia, and Tourette syndrome, a multi-institutional consortium called the Brain Somatic Mosaicism Network (BSMN) was formed through the National Institute of Mental Health (NIMH). In addition to genomic data of affected and neurotypical brains, the BSMN also developed and validated a best practices somatic single nucleotide variant calling workflow through the analysis of reference brain tissue. These resources, which include >400 terabytes of data from 1087 subjects, are now available to the research community via the NIMH Data Archive (NDA) and are described here.

Published
2023

4. Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability

Author

Bae, Taejeong, Fasching, Liana, Wang, Yifan, Shin, Joo Heon, Suvakov, Milovan, Jang, Yeongjun, Norton, Scott, Dias, Caroline, Mariani, Jessica, Jourdon, Alexandre, Wu, Feinan, Panda, Arijit, Pattni, Reenal, Chahine, Yasmine, Yeh, Rebecca, Roberts, Rosalinda C, Huttner, Anita, Kleinman, Joel E, Hyde, Thomas M, Straub, Richard E, Walsh, Christopher A, Urban, Alexander E, Leckman, James F, Weinberger, Daniel R, Vaccarino, Flora M, Abyzov, Alexej, Park, Peter J, Sestan, Nenad, Weinberger, Daniel, Moran, John V, Gage, Fred H, Gleeson, Joseph, Mathern, Gary, Courchesne, Eric, Roy, Subhojit, Chess, Andrew J, Akbarian, Schahram, Bizzotto, Sara, Coulter, Michael, D’Gama, Alissa, Ganz, Javier, Hill, Robert, Huang, August Yue, Khoshkhoo, Sattar, Kim, Sonia, Lee, Alice, Lodato, Michael, Maury, Eduardo A, Miller, Michael, Borges-Monroy, Rebeca, Rodin, Rachel, Zhou, Zinan, Bohrson, Craig, Chu, Chong, Cortes-Ciriano, Isidro, Dou, Yanmei, Galor, Alon, Gulhan, Doga, Kwon, Minseok, Luquette, Joe, Sherman, Maxwell, Viswanadham, Vinay, Jones, Attila, Rosenbluh, Chaggai, Cho, Sean, Langmead, Ben, Thorpe, Jeremy, Erwin, Jennifer, Jaffe, Andrew, McConnell, Michael, Narurkar, Rujuta, Paquola, Apua, Shin, Jooheon, Straub, Richard, Molitor, Cindy, Peters, Mette, Linker, Sara, Reed, Patrick, Wang, Meiyan, Urban, Alexander, Zhou, Bo, Zhu, Xiaowei, Serres Amero, Aitor, Juan, David, Lobon, Irene, Marques-Bonet, Tomas, Solis Moruno, Manuel, Garcia Perez, Raquel, Povolotskaya, Inna, Soriano, Eduardo, Antaki, Danny, and Averbuj, Dan

Subjects
Biotechnology, Brain Disorders, Intellectual and Developmental Disabilities (IDD), Genetics, Autism, Pediatric, Mental Health, Human Genome, Underpinning research, 2.1 Biological and endogenous factors, Aetiology, 1.1 Normal biological development and functioning, Mental health, Aging, Autistic Disorder, Brain, Enhancer Elements, Genetic, Gene Expression Regulation, Humans, Mutagenesis, Mutation, Protein Binding, Transcription Factors, Whole Genome Sequencing, Brain Somatic Mosaicism Network§, General Science & Technology
Abstract

We analyzed 131 human brains (44 neurotypical, 19 with Tourette syndrome, 9 with schizophrenia, and 59 with autism) for somatic mutations after whole genome sequencing to a depth of more than 200×. Typically, brains had 20 to 60 detectable single-nucleotide mutations, but ~6% of brains harbored hundreds of somatic mutations. Hypermutability was associated with age and damaging mutations in genes implicated in cancers and, in some brains, reflected in vivo clonal expansions. Somatic duplications, likely arising during development, were found in ~5% of normal and diseased brains, reflecting background mutagenesis. Brains with autism were associated with mutations creating putative transcription factor binding motifs in enhancer-like regions in the developing brain. The top-ranked affected motifs corresponded to MEIS (myeloid ectopic viral integration site) transcription factors, suggesting a potential link between their involvement in gene regulation and autism.

Published
2022

7. A collaborative and near-comprehensive North Pacific humpback whale photo-ID dataset

Author

Cheeseman, Ted, Southerland, Ken, Acebes, Jo Marie, Audley, Katherina, Barlow, Jay, Bejder, Lars, Birdsall, Caitlin, Bradford, Amanda L., Byington, Josie K., Calambokidis, John, Cartwright, Rachel, Cedarleaf, Jen, Chavez, Andrea Jacqueline García, Currie, Jens J., De Weerdt, Joëlle, Doe, Nicole, Doniol-Valcroze, Thomas, Dracott, Karina, Filatova, Olga, Finn, Rachel, Flynn, Kiirsten, Ford, John K. B., Frisch-Jordán, Astrid, Gabriele, Christine M., Goodwin, Beth, Hayslip, Craig, Hildering, Jackie, Hill, Marie C., Jacobsen, Jeff K., Jiménez-López, M. Esther, Jones, Meagan, Kobayashi, Nozomi, Lyman, Edward, Malleson, Mark, Mamaev, Evgeny, Martínez Loustalot, Pamela, Masterman, Annie, Matkin, Craig, McMillan, Christie J., Moore, Jeff E., Moran, John R., Neilson, Janet L., Newell, Hayley, Okabe, Haruna, Olio, Marilia, Pack, Adam A., Palacios, Daniel M., Pearson, Heidi C., Quintana-Rizzo, Ester, Ramírez Barragán, Raul Fernando, Ransome, Nicola, Rosales-Nanduca, Hiram, Sharpe, Fred, Shaw, Tasli, Stack, Stephanie H., Staniland, Iain, Straley, Jan, Szabo, Andrew, Teerlink, Suzie, Titova, Olga, Urban R., Jorge, van Aswegen, Martin, de Morais, Marcel Vinicius, von Ziegesar, Olga, Witteveen, Briana, Wray, Janie, Yano, Kymberly M., Zwiefelhofer, Denny, and Clapham, Phil

Published
2023
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10. Comprehensive identification of somatic nucleotide variants in human brain tissue

Author

Wang, Yifan, Bae, Taejeong, Thorpe, Jeremy, Sherman, Maxwell A, Jones, Attila G, Cho, Sean, Daily, Kenneth, Dou, Yanmei, Ganz, Javier, Galor, Alon, Lobon, Irene, Pattni, Reenal, Rosenbluh, Chaggai, Tomasi, Simone, Tomasini, Livia, Yang, Xiaoxu, Zhou, Bo, Akbarian, Schahram, Ball, Laurel L, Bizzotto, Sara, Emery, Sarah B, Doan, Ryan, Fasching, Liana, Jang, Yeongjun, Juan, David, Lizano, Esther, Luquette, Lovelace J, Moldovan, John B, Narurkar, Rujuta, Oetjens, Matthew T, Rodin, Rachel E, Sekar, Shobana, Shin, Joo Heon, Soriano, Eduardo, Straub, Richard E, Zhou, Weichen, Chess, Andrew, Gleeson, Joseph G, Marquès-Bonet, Tomas, Park, Peter J, Peters, Mette A, Pevsner, Jonathan, Walsh, Christopher A, Weinberger, Daniel R, Vaccarino, Flora M, Moran, John V, Urban, Alexander E, Kidd, Jeffrey M, Mills, Ryan E, and Abyzov, Alexej

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Neurosciences, Human Genome, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Alleles, Brain, Chromosome Mapping, Computational Biology, Genetic Association Studies, Genetic Variation, Genomics, Germ Cells, High-Throughput Nucleotide Sequencing, Humans, Organ Specificity, Polymorphism, Single Nucleotide, Brain Somatic Mosaicism Network, Environmental Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundPost-zygotic mutations incurred during DNA replication, DNA repair, and other cellular processes lead to somatic mosaicism. Somatic mosaicism is an established cause of various diseases, including cancers. However, detecting mosaic variants in DNA from non-cancerous somatic tissues poses significant challenges, particularly if the variants only are present in a small fraction of cells.ResultsHere, the Brain Somatic Mosaicism Network conducts a coordinated, multi-institutional study to examine the ability of existing methods to detect simulated somatic single-nucleotide variants (SNVs) in DNA mixing experiments, generate multiple replicates of whole-genome sequencing data from the dorsolateral prefrontal cortex, other brain regions, dura mater, and dural fibroblasts of a single neurotypical individual, devise strategies to discover somatic SNVs, and apply various approaches to validate somatic SNVs. These efforts lead to the identification of 43 bona fide somatic SNVs that range in variant allele fractions from ~ 0.005 to ~ 0.28. Guided by these results, we devise best practices for calling mosaic SNVs from 250× whole-genome sequencing data in the accessible portion of the human genome that achieve 90% specificity and sensitivity. Finally, we demonstrate that analysis of multiple bulk DNA samples from a single individual allows the reconstruction of early developmental cell lineage trees.ConclusionsThis study provides a unified set of best practices to detect somatic SNVs in non-cancerous tissues. The data and methods are freely available to the scientific community and should serve as a guide to assess the contributions of somatic SNVs to neuropsychiatric diseases.

Published
2021

11. Federal Circuit Focuses On POV Camera Technology In Latest Patent Eligibility Opinion

Author

Moran, John P.

Subjects
United States. Court of Appeals for the Federal Circuit -- Cases, GoPro Inc. -- Intellectual property -- Cases, Summary judgments -- Cases, Patentability -- Cases, Video equipment industry -- Cases -- Intellectual property, Recall of judicial decisions -- Cases, Company legal issue, Business, international
Abstract

In Contour IP Holding LLC v. GoPro, Inc., the U.S. Court of Appeals for the Federal Circuit reversed a summary judgment in which the asserted patents were directed to an [...]

Published
2024

12. Author Correction: Machine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia

Author

Zhu, Xiaowei, Zhou, Bo, Pattni, Reenal, Gleason, Kelly, Tan, Chunfeng, Kalinowski, Agnieszka, Sloan, Steven, Fiston-Lavier, Anna-Sophie, Mariani, Jessica, Petrov, Dmitri, Barres, Ben A., Duncan, Laramie, Abyzov, Alexej, Vogel, Hannes, Moran, John V., Vaccarino, Flora M., Tamminga, Carol A., Levinson, Douglas F., and Urban, Alexander E.

Published
2023
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14. Ecosystem response persists after a prolonged marine heatwave

Author

Suryan, Robert M., Arimitsu, Mayumi L., Coletti, Heather A., Hopcroft, Russell R., Lindeberg, Mandy R., Barbeaux, Steven J., Batten, Sonia D., Burt, William J., Bishop, Mary A., Bodkin, James L., Brenner, Richard, Campbell, Robert W., Cushing, Daniel A., Danielson, Seth L., Dorn, Martin W., Drummond, Brie, Esler, Daniel, Gelatt, Thomas, Hanselman, Dana H., Hatch, Scott A., Haught, Stormy, Holderied, Kris, Iken, Katrin, Irons, David B., Kettle, Arthur B., Kimmel, David G., Konar, Brenda, Kuletz, Kathy J., Laurel, Benjamin J., Maniscalco, John M., Matkin, Craig, McKinstry, Caitlin A. E., Monson, Daniel H., Moran, John R., Olsen, Dan, Palsson, Wayne A., Pegau, W. Scott, Piatt, John F., Rogers, Lauren A., Rojek, Nora A., Schaefer, Anne, Spies, Ingrid B., Straley, Janice M., Strom, Suzanne L., Sweeney, Kathryn L., Szymkowiak, Marysia, Weitzman, Benjamin P., Yasumiishi, Ellen M., and Zador, Stephani G.

Published
2021
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17. Evaluating Tandem Language Learning by E-Mail: Report on a Bilateral Project. CLCS Occasional Paper No. 55.

Author

Trinity Coll., Dublin (Ireland). Centre for Language and Communication Studies., Little, David, Ushioda, Ema, Appel, Marie Christine, Moran, John, O'Rourke, Breffni, and Schwienhorst, Klaus

Abstract

The report details the Irish portion of an experiment in tandem language learning by electronic mail (e-mail). The partners were Trinity College, Dublin (Ireland) and Ruhr University, Bochum (Germany), funded by the European Union within the International E-Mail Tandem Network as part of a two-year project. Tandem language learning is a form of open learning in which two individuals with different native languages work together to learn each other's language, in this case, English and German; success depends on adherence to the principles of reciprocity and learner autonomy. The report describes the network and the principles of tandem language learning by e-mail, the organization of this part of the study, including pedagogical design and considerations, the process of affective and linguistic data collection, and data analysis. The linguistic data analysis focused on bilingual skills, language register, discourse fillers, punctuation, explicit coordination between partners, error correction and generalizations made, thematic content, control and critical detachment, use of metalanguage, and accuracy of corrections. Implications for future work in this area are discussed briefly. Contains 10 references. (MSE)

Published
1999

18. PD First: Peritoneal Dialysis as the Default Transition to Dialysis Therapy

Author

Ghaffari, Arshia, Kalantar‐Zadeh, Kamyar, Lee, Joseph, Maddux, Franklin, Moran, John, and Nissenson, Allen

Subjects
Clinical Research, Neurodegenerative, Kidney Disease, Brain Disorders, Health Services, Renal and urogenital, Health Policy, Health Services Accessibility, Humans, Kidney Failure, Chronic, Patient Education as Topic, Patient Selection, Peritoneal Dialysis, Practice Patterns, Physicians', Quality of Life, Time Factors, Treatment Outcome, Clinical Sciences, Urology & Nephrology
Abstract

Peritoneal dialysis (PD) and in-center hemodialysis (HD) are accepted as clinically equivalent dialysis modalities, yet in-center HD is the predominant renal replacement therapy (RRT) modality offered to new end-stage renal disease (ESRD) patients in the United States and most other industrialized nations. This predominance has little to do with clinical outcomes, patient choice, cost, or quality of life. It has been driven by ease of HD initiation, physician experience and training, inadequate pre-ESRD patient education, ample in-center HD capacity, and lack of adequate infrastructure for PD-related care. As compared with in-center HD, PD is a widely applicable, yet underutilized modality of RRT that provides comparable clinical outcomes, superior quality of life measures, significant cost savings, and many other unmeasured advantages. A "PD First" approach not only has advantages for patients but also physicians, healthcare systems, and society. In this review, we will summarize evidence demonstrating that PD should be the default modality when new ESRD patients are transitioning to dialysis therapy when preemptive transplantation is not an option and highlight the essential infrastructural requirements to allow for a "PD First" model.

Published
2013

19. Serum Albumin as a Predictor of Mortality in Peritoneal Dialysis: Comparisons With Hemodialysis

Author

Mehrotra, Rajnish, Duong, Uyen, Jiwakanon, Sirin, Kovesdy, Csaba P, Moran, John, Kopple, Joel D, and Kalantar-Zadeh, Kamyar

Subjects
Clinical Research, Neurodegenerative, Cardiovascular, Kidney Disease, Good Health and Well Being, Adult, Aged, Cardiovascular Diseases, Female, Humans, Male, Middle Aged, Peritoneal Dialysis, Predictive Value of Tests, Protein-Energy Malnutrition, Renal Dialysis, Serum Albumin, Survival Analysis, Peritoneal dialysis, hemodialysis, albumin, protein-energy wasting, mortality, Clinical Sciences, Public Health and Health Services, Urology & Nephrology
Abstract

BackgroundSerum albumin level predicts mortality in dialysis patients and is used to assess their health status and the quality of delivered care. Whether the threshold level of serum albumin at which mortality risk increases in peritoneal dialysis (PD) patients is the same as for hemodialysis (HD) patients has not been studied.Study designObservational cohort study of dialysis patients undertaken to determine the survival-predictability of serum albumin level in PD patients and compare it with that in HD patients.Setting & participants130,052 dialysis patients (PD, 12,171; HD, 117,851) who received treatment in any of the 580 dialysis units owned by DaVita Inc between July 1, 2001, through June 30, 2006, followed up through June 30, 2007.PredictorBaseline and time-averaged serum albumin level (assayed using bromcresol green) and change in serum albumin level over 6 months.Outcome measuresAll-cause, cardiovascular, and infection-related mortality.ResultsPD patients with baseline serum albumin level

Published
2011

20. African-American Parent Perspectives on Special Education

Author

Moran, John Gerard

Abstract

The purpose of this study was to explore how some parents of AA students in SPED in a large, urban school district in California view SPED, their child's placement into SPED, and their involvement with their children's education. A mixed methods approach was employed via six parent interviews and a survey of twenty-three parents. Major findings: (1) AA parents perceive their child's SPED placement process negatively but SPED placement as appropriate; (2) AA parents are not sure if SPED is a track to academic success; (3) AA parental attitudes about SPED may impact their efforts to achieve placement; and (4) AA parents involvement with their children's education has no influence on their child's initial placement into SPED. Implications for practice: (1) Improve communication with AA parents; (2) Consider upgrades to SPED programs; and (3) Foster increased AA Parental involvement with their children in SPED. Future research: (1) What are the reasons behind poor communication?; (2) How can SPED professionals help AA parents be more involved with their children's education?; (3) Conduct broader research studies on how AA parents view race as a factor in disproportionality; and (4) Repeat this study with a larger sample. Conclusions: (1) AA parents do not advocate for their children to be placed into SPED more than any other group; (2) Poor relations and communication between AA parents and Special Educators remain a barrier to equity; and (3) Racism is still the most likely cause of disproportional SPED placement. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]

Published
2016

23. MEG Coherence and DTI Connectivity in mTLE

Author

Nazem-Zadeh, Mohammad-Reza, Bowyer, Susan M., Moran, John E., Davoodi-Bojd, Esmaeil, Zillgitt, Andrew, Weiland, Barbara J., Bagher-Ebadian, Hassan, Mahmoudi, Fariborz, Elisevich, Kost, and Soltanian-Zadeh, Hamid

Published
2016
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25. Income and the Use of Prescription Drugs by the Elderly: Evidence from the Notch Cohorts

Author

Moran, John R. and Simon, Kosali Ilayperuma

Abstract

We use exogenous variation in Social Security payments created by the Social Security benefits notch to estimate how retirees' use of prescription medications responds to changes in their incomes. Using data from the 1993 Wave of the AHEAD, we obtain instrumental variables estimates of the income elasticity of prescription drug use that are uniformly above one, with a middle estimate of 1.32. Simulations based on our estimates suggest that reductions in Social Security benefits similar to those incorporated in recent reform proposals would significantly reduce prescription drug use among the elderly.

Published
2006

26. Managing Organizational Priorities.

Author

Brightman, Baird K. and Moran, John W.

Abstract

Suggests that individuals can compile an action plan for professional and organizational change that aligns personal and organizational priorities by considering leadership, coaching, corporate citizenship, change management, efficiency, teamwork, customer focus, and decision making. Presents models and assessment instruments for personal development plans. (Author/JOW)

Published
2001

27. U.S. District Judge: Method Of Determining Webpage Visitor Intent Is Abstract

Author

Moran, John P.

Subjects
United States. District Court. Western District of Texas -- Cases -- Powers and duties, Patentability -- Laws, regulations and rules, Web sites -- Forecasts and trends, Government regulation, Company Web site/Web page, Market trend/market analysis, Business, international
Abstract

In USC IP Partnership, L.P. v. Facebook, Inc., 2021 WL 6690275, U.S. District Judge Alan Albright of the U.S. District Court for the Western District of Texas found U.S. Patent [...]

Published
2022

29. Federal Circuit: Characterization Of An Invention Must Reflect The Claimed Invention

Author

Moran, John P.

Subjects
United States. Court of Appeals for the Federal Circuit -- Powers and duties, Patent infringement -- Cases, Company legal issue, Business, international
Abstract

In Mentone Solutions LLC v. Digi International Inc., 2021 WL 5291802 (Fed. Cir. Nov. 15, 2021) the U.S. Court of Appeals for the Federal Circuit reversed the U.S. District Court [...]

Published
2022

50. Hospital‐acquired complications: the relative importance of hospital‐ and patient‐related factors.

Author

Duke, Graeme J, Moran, John L, Bersten, Andrew D, Bihari, Shailesh, Roodenburg, Owen, Karnon, Jonathan, Hirth, Steven, Hakendorf, Paul, and Santamaria, John D

Abstract

Objective: To quantify the prevalence of hospital‐acquired complications; to determine the relative influence of patient‐ and hospital‐related factors on complication rates. Design, participants: Retrospective analysis of administrative data (Integrated South Australian Activity Collection; Victorian Admitted Episodes Dataset) for multiple‐day acute care episodes for adults in public hospitals. Setting: Thirty‐eight major public hospitals in South Australia and Victoria, 2015–2018. Main outcome measures: Hospital‐acquired complication rates, overall and by complication class, by hospital and hospital type (tertiary referral, major metropolitan service, major regional service); variance in rates (intra‐class correlation coefficient, ICC) at the patient, hospital, and hospital type levels as surrogate measures of their influence on rates. Results: Of 1 558 978 public hospital episodes (10 029 918 bed‐days), 151 486 included a total of 214 286 hospital‐acquired complications (9.72 [95% CI, 9.67–9.77] events per 100 episodes; 2.14 [95% CI, 2.13–2.15] events per 100 bed‐days). Complication rates were highest in tertiary referral hospitals (12.7 [95% CI, 12.6–12.8] events per 100 episodes) and for episodes including intensive care components (37.1 [95% CI, 36.7–37.4] events per 100 episodes). For all complication classes, inter‐hospital variation was determined more by patient factors (overall ICC, 0.55; 95% CI, 0.53–0.57) than by hospital factors (ICC, 0.04; 95% CI, 0.02–0.07) or hospital type (ICC, 0.01; 95% CI, 0.001–0.03). Conclusions: Hospital‐acquired complications were recorded for 9.7% of hospital episodes, but patient‐related factors played a greater role in determining their prevalence than the treating hospital. [ABSTRACT FROM AUTHOR]

Published
2022
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