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4. Neptune: an environment for the delivery of genomic medicine

Author

Venner Eric, Victoria Yi, David Murdock, Sara E. Kalla, Tsung-Jung Wu, Aniko Sabo, Shoudong Li, Qingchang Meng, Xia Tian, Mullai Murugan, Michelle Cohen, Christie Kovar, Wei-Qi Wei, Wendy K. Chung, Chunhua Weng, Georgia L. Wiesner, Gail P. Jarvik, Donna Muzny, Richard A. Gibbs, Debra Abrams, Samuel E. Adunyah, Ladia Albertson-Junkans, Berta Almoguera, Darren C. Ames, Paul Appelbaum, Samuel Aronson, Sharon Aufox, Lawrence J. Babb, Adithya Balasubramanian, Hana Bangash, Melissa Basford, Lisa Bastarache, Samantha Baxter, Meckenzie Behr, Barbara Benoit, Elizabeth Bhoj, Suzette J. Bielinski, Sarah T. Bland, Carrie Blout, Kenneth Borthwick, Erwin P. Bottinger, Mark Bowser, Harrison Brand, Murray Brilliant, Wendy Brodeur, Pedro Caraballo, David Carrell, Andrew Carroll, Lisa Castillo, Victor Castro, Gauthami Chandanavelli, Theodore Chiang, Rex L. Chisholm, Kurt D. Christensen, Wendy Chung, Christopher G. Chute, Brittany City, Beth L. Cobb, John J. Connolly, Paul Crane, Katherine Crew, David R. Crosslin, Jyoti Dayal, Mariza De Andrade, Jessica De la Cruz, Josh C. Denny, Shawn Denson, Tim DeSmet, Ozan Dikilitas, Michael J. Dinsmore, Sheila Dodge, Phil Dunlea, Todd L. Edwards, Christine M. Eng, David Fasel, Alex Fedotov, Qiping Feng, Mark Fleharty, Andrea Foster, Robert Freimuth, Christopher Friedrich, Stephanie M. Fullerton, Birgit Funke, Stacey Gabriel, Vivian Gainer, Ali Gharavi, Andrew M. Glazer, Joseph T. Glessner, Jessica Goehringer, Adam S. Gordon, Chet Graham, Robert C. Green, Justin H. Gundelach, Heather S. Hain, Hakon Hakonarson, Maegan V. Harden, John Harley, Margaret Harr, Andrea Hartzler, M. Geoffrey Hayes, Scott Hebbring, Nora Henrikson, Andrew Hershey, Christin Hoell, Ingrid Holm, Kayla M. Howell, George Hripcsak, Jianhong Hu, Elizabeth Duffy Hynes, Joy C. Jayaseelan, Yunyun Jiang, Yoonjung Yoonie Joo, Sheethal Jose, Navya Shilpa Josyula, Anne E. Justice, Divya Kalra, Elizabeth W. Karlson, Brendan J. Keating, Melissa A. Kelly, Eimear E. Kenny, Dustin Key, Krzysztof Kiryluk, Terrie Kitchner, Barbara Klanderman, Eric Klee, David C. Kochan, Viktoriya Korchina, Leah Kottyan, Emily Kudalkar, Alanna Kulchak Rahm, Iftikhar J. Kullo, Philip Lammers, Eric B. Larson, Matthew S. Lebo, Magalie Leduc, Ming Ta (Michael) Lee, Niall J. Lennon, Kathleen A. Leppig, Nancy D. Leslie, Rongling Li, Wayne H. Liang, Chiao-Feng Lin, Jodell E. Linder, Noralane M. Lindor, Todd Lingren, James G. Linneman, Cong Liu, Wen Liu, Xiuping Liu, John Lynch, Hayley Lyon, Alyssa Macbeth, Harshad Mahadeshwar, Lisa Mahanta, Bradley Malin, Teri Manolio, Maddalena Marasa, Keith Marsolo, Michelle L. McGowan, Elizabeth McNally, Jim Meldrim, Frank Mentch, Hila Milo Rasouly, Jonathan Mosley, Shubhabrata Mukherjee, Thomas E. Mullen, Jesse Muniz, David R. Murdock, Shawn Murphy, Melanie F. Myers, Bahram Namjou, Yizhao Ni, Robert C. Onofrio, Aniwaa Owusu Obeng, Thomas N. Person, Josh F. Peterson, Lynn Petukhova, Cassandra J. Pisieczko, Siddharth Pratap, Cynthia A. Prows, Megan J. Puckelwartz, Ritika Raj, James D. Ralston, Arvind Ramaprasan, Andrea Ramirez, Luke Rasmussen, Laura Rasmussen-Torvik, Soumya Raychaudhuri, Heidi L. Rehm, Marylyn D. Ritchie, Catherine Rives, Beenish Riza, Dan M. Roden, Elisabeth A. Rosenthal, Avni Santani, Schaid Dan, Steven Scherer, Stuart Scott, Aaron Scrol, Soumitra Sengupta, Ning Shang, Himanshu Sharma, Richard R. Sharp, Rajbir Singh, Patrick M.A. Sleiman, Kara Slowik, Joshua C. Smith, Maureen E. Smith, Duane T. Smoot, Jordan W. Smoller, Sunghwan Sohn, Ian B. Stanaway, Justin Starren, Mary Stroud, Jessica Su, Casey Overby Taylor, Kasia Tolwinski, Sara L. Van Driest, Sean M. Vargas, Matthew Varugheese, David Veenstra, Eric Venner, Miguel Verbitsky, Gina Vicente, Michael Wagner, Kimberly Walker, Theresa Walunas, Liwen Wang, Qiaoyan Wang, Scott T. Weiss, Quinn S. Wells, Peter S. White, Ken L. Wiley, Janet L. Williams, Marc S. Williams, Michael W. Wilson, Leora Witkowski, Laura Allison Woods, Betty Woolf, Julia Wynn, Yaping Yang, Ge Zhang, Lan Zhang, and Hana Zouk

Subjects
Computer science, business.industry, Process (engineering), MEDLINE, High-Throughput Nucleotide Sequencing, Genomics, Data science, Article, Personalization, Variety (cybernetics), Workflow, Neptune, Pharmacogenomics, Health care, Electronic Health Records, Humans, business, Software, Genetics (clinical)
Abstract

Genomic medicine holds great promise for improving health care, but integrating searchable and actionable genetic data into electronic health records (EHRs) remains a challenge. Here we describe Neptune, a system for managing the interaction between a clinical laboratory and an EHR system during the clinical reporting process. We developed Neptune and applied it to two clinical sequencing projects that required report customization, variant reanalysis, and EHR integration. Neptune has been applied for the generation and delivery of over 15,000 clinical genomic reports. This work spans two clinical tests based on targeted gene panels that contain 68 and 153 genes respectively. These projects demanded customizable clinical reports that contained a variety of genetic data types including single-nucleotide variants (SNVs), copy-number variants (CNVs), pharmacogenomics, and polygenic risk scores. Two variant reanalysis activities were also supported, highlighting this important workflow. Methods are needed for delivering structured genetic data to EHRs. This need extends beyond developing data formats to providing infrastructure that manages the reporting process itself. Neptune was successfully applied on two high-throughput clinical sequencing projects to build and deliver clinical reports to EHR systems. The software is open source and available at https://gitlab.com/bcm-hgsc/neptune .

Published
2021
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6. Implementation of preemptive DNA sequence-based pharmacogenomics testing across a large academic medical center: The Mayo-Baylor RIGHT 10K Study

Author

Liewei Wang, Steven E. Scherer, Suzette J. Bielinski, Donna M. Muzny, Leila A. Jones, John Logan Black, Ann M. Moyer, Jyothsna Giri, Richard R. Sharp, Eric T. Matey, Jessica A. Wright, Lance J. Oyen, Wayne T. Nicholson, Mathieu Wiepert, Terri Sullard, Timothy B. Curry, Carolyn R. Rohrer Vitek, Tammy M. McAllister, Jennifer L. St. Sauver, Pedro J. Caraballo, Konstantinos N. Lazaridis, Eric Venner, Xiang Qin, Jianhong Hu, Christie L. Kovar, Viktoriya Korchina, Kimberly Walker, HarshaVardhan Doddapaneni, Tsung-Jung Wu, Ritika Raj, Shawn Denson, Wen Liu, Gauthami Chandanavelli, Lan Zhang, Qiaoyan Wang, Divya Kalra, Mary Beth Karow, Kimberley J. Harris, Hugues Sicotte, Sandra E. Peterson, Amy E. Barthel, Brenda E. Moore, Jennifer M. Skierka, Michelle L. Kluge, Katrina E. Kotzer, Karen Kloke, Jessica M. Vander Pol, Heather Marker, Joseph A. Sutton, Adrijana Kekic, Ashley Ebenhoh, Dennis M. Bierle, Michael J. Schuh, Christopher Grilli, Sara Erickson, Audrey Umbreit, Leah Ward, Sheena Crosby, Eric A. Nelson, Sharon Levey, Michelle Elliott, Steve G. Peters, Naveen Pereira, Mark Frye, Fadi Shamoun, Matthew P. Goetz, Iftikhar J. Kullo, Robert Wermers, Jan A. Anderson, Christine M. Formea, Razan M. El Melik, John D. Zeuli, Joseph R. Herges, Carrie A. Krieger, Robert W. Hoel, Jodi L. Taraba, Scott R. St. Thomas, Imad Absah, Matthew E. Bernard, Stephanie R. Fink, Andrea Gossard, Pamela L. Grubbs, Therese M. Jacobson, Paul Takahashi, Sharon C. Zehe, Susan Buckles, Michelle Bumgardner, Colette Gallagher, Kelliann Fee-Schroeder, Nichole R. Nicholas, Melody L. Powers, Ahmed K. Ragab, Darcy M. Richardson, Anthony Stai, Jaymi Wilson, Joel E. Pacyna, Janet E. Olson, Erica J. Sutton, Annika T. Beck, Caroline Horrow, Krishna R. Kalari, Nicholas B. Larson, Hongfang Liu, Liwei Wang, Guilherme S. Lopes, Bijan J. Borah, Robert R. Freimuth, Ye Zhu, Debra J. Jacobson, Matthew A. Hathcock, Sebastian M. Armasu, Michaela E. McGree, Ruoxiang Jiang, Tyler H. Koep, Jason L. Ross, Matthew G. Hilden, Kathleen Bosse, Bronwyn Ramey, Isabelle Searcy, Eric Boerwinkle, Richard A. Gibbs, and Richard M. Weinshilboum

Subjects
Academic Medical Centers, Base Sequence, Cytochrome P-450 CYP2D6, Genotype, Pharmacogenetics, Humans, Genetics (clinical), Article
Abstract

PURPOSE: The Mayo-Baylor RIGHT 10K Study enabled preemptive, sequence-based pharmacogenomics (PGx)-driven drug prescribing practices in routine clinical care within a large cohort. We also generated the tools and resources necessary for clinical PGx implementation and identified challenges to be overcome. Furthermore, we measured the frequency of both common genetic variation for which clinical guidelines already exist and that of rare variation that could be detected by DNA sequencing, rather than genotyping. METHODS: Targeted oligonucleotide-capture sequencing of 77 “pharmacogenes” was performed using DNA from 10,077 consented Mayo Clinic Biobank volunteers. The resulting predicted drug response related phenotypes for 13 genes, including CYP2D6 and HLA, affecting 21 drug-gene pairs, were deposited preemptively in the Mayo electronic health record (EHR). RESULTS: For the 13 pharmacogenes of interest, the genomes of 79% of participants carried clinically actionable variants in 3 or more genes and DNA sequencing identified an average of 3.3 additional conservatively predicted deleterious variants that would not have been evident using genotyping. CONCLUSIONS: Implementation of preemptive rather than reactive, sequence-based rather than genotype-based PGx prescribing revealed nearly universal patient applicability and required integrated institution-wide resources to fully realize individualized drug therapy and to demonstrate more efficient use of health care resources.

Published
2021

7. Harmonizing Clinical Sequencing and Interpretation for the eMERGE III Network

Author

Ian B. Stanaway, Dan M. Roden, Divya Kalra, Dustin Key, Debra J. Abrams, David Fasel, Victor Castro, Brad Malin, Berta Almoguera, Beenish Riza, Meckenzie A. Behr, Eric Venner, Christine M. Eng, Joy Jayaseelan, Scott J. Hebbring, Michelle L. McGowan, Steven E. Scherer, Theresa L. Walunas, Mark Bowser, James D. Ralston, Wei-Qi Wei, Liwen Wang, David R. Murdock, Wayne H. Liang, Julia Wynn, Nancy D. Leslie, Laura J. Rasmussen-Torvik, Ming Ta (Michael) Lee, Frank D. Mentch, Lan Zhang, Alanna Kulchak Rahm, Josh F. Peterson, Jodell E. Linder, Joshua C. Smith, Soumitra Sengupta, Brendan J. Keating, Gina Vicente, Andrew Carroll, Nora B. Henrikson, Anne E. Justice, Heather S. Hain, Wen Liu, Andrea H. Ramirez, Matthew S. Lebo, Hana Zouk, Georgia L. Wiesner, Andrea L. Hartzler, Cassandra J. Pisieczko, Catherine M. Rives, Jessica Goehringer, Maegan V. Harden, John Lynch, Chiao-Feng Lin, Peter White, Phil Dunlea, Shawn N. Murphy, Mullai Murugan, Harshad Mahadeshwar, Mark Fleharty, Andrea Foster, Arvind Ramaprasan, Christopher A. Friedrich, Justin H. Gundelach, Hayley Lyon, Niall J. Lennon, Eric W. Klee, David R. Crosslin, Ge Zhang, Rongling Li, Ozan Dikilitas, Xiuping Liu, Christin Hoell, Aniwaa Owusu Obeng, Katherine D. Crew, Lisa M. Castillo, Justin Starren, Jonathan D. Mosley, Carrie L. Blout, Himanshu Sharma, Elizabeth M. McNally, Sarah T. Bland, Megan J. Puckelwartz, Matthew Varugheese, Keith Marsolo, Betty Woolf, Sharon Aufox, Janet L. Williams, Kimberly Walker, Murray H. Brilliant, Birgit Funke, Laura Allison Woods, Marylyn D. Ritchie, Brittany City, Todd Lingren, Hila Milo Rasouly, Lawrence J. Babb, Alex Fedotov, Robert C. Onofrio, Margaret Harr, Suzette J. Bielinski, Michael W. Wilson, Shubhabrata Mukherjee, Robert R. Freimuth, Chet Graham, Todd L. Edwards, Quinn S. Wells, Marc S. Williams, Jordan W. Smoller, Wendy K. Chung, Avni Santani, Paul K. Crane, George Hripcsak, QiPing Feng, Ali G. Gharavi, Yizhao Ni, Iftikhar J. Kullo, Michael Wagner, Philip E. Lammers, Michael J. Dinsmore, Thomas N. Person, Victoria Yi, Samuel E. Adunyah, Tim DeSmet, Eric B. Larson, Elizabeth Hynes, David C. Kochan, Eimear E. Kenny, Magalie S. Leduc, Lisa Mahanta, David Carrell, Paul S. Appelbaum, Viktoriya Korchina, Beth L. Cobb, Lynn Petukhova, Jessica De la Cruz, Patrick M. A. Sleiman, Stuart A. Scott, Tsung-Jung Wu, Gail P. Jarvik, Erwin P. Bottinger, Ken Wiley, Josh C. Denny, Melissa A. Basford, Samuel J. Aronson, David L. Veenstra, Yaping Yang, Kayla Marie Howell, John J. Connolly, Jessica Su, Yoonjung Yoonie Joo, Miguel Verbitsky, Sean M. Vargas, Cong Liu, Barbara Benoit, Andrew Hershey, Richard A. Gibbs, Cynthia A. Prows, Hana Bangash, Wendy Brodeur, Gauthami Chandanavelli, Sara L. Van Driest, Kurt D. Christensen, Elizabeth J. Bhoj, Vivian S. Gainer, Adam S. Gordon, Robert C. Green, Hakon Hakonarson, Krzysztof Kiryluk, Elisabeth A. Rosenthal, Rajbir Singh, James G. Linneman, Harrison Brand, Theodore Chiang, Sheila Dodge, Ingrid A. Holm, M. Geoffrey Hayes, Yunyun Jiang, Ning Shang, Samantha Baxter, Noralane M. Lindor, Kathleen A. Leppig, Teri A. Manolio, Sara E. Kalla, Pedro J. Caraballo, Ritika Raj, Aaron Scrol, Jyoti G. Dayal, Richard R. Sharp, Christie Kovar, Soumya Raychaudhuri, Sunghwan Sohn, Emily Kudalkar, Maddalena Marasa, Stacey Gabriel, Dan Schaid, Ladia Albertson-Junkans, Rex L. Chisholm, Maureen E. Smith, Donna M. Muzny, Casey Overby Taylor, Jianhong Hu, Elizabeth W. Karlson, Lisa Bastarache, Darren C. Ames, Joseph T. Glessner, Leora Witkowski, Siddharth Pratap, Qiaoyan Wang, Melissa A. Kelly, Adithya Balasubramanian, Kara Slowik, Terrie Kitchner, Barbara J. Klanderman, Shawn Denson, Mary Stroud, Alyssa Macbeth, Melanie F. Myers, Jesse Muniz, Kasia Tolwinski, Scott T. Weiss, Chunhua Weng, Stephanie M. Fullerton, John B. Harley, Christopher G. Chute, Heidi L. Rehm, Sheethal Jose, Andrew M. Glazer, Navya Shilpa Josyula, Kenneth M. Borthwick, Thomas E. Mullen, Mariza de Andrade, Leah C. Kottyan, Luke V. Rasmussen, James Meldrim, and Bahram Namjou

Subjects
0301 basic medicine, Standardization, Test data generation, business.industry, Computer science, Sequence Analysis, DNA, 030105 genetics & heredity, Precision medicine, Data science, Clinical decision support system, Biobank, Article, 3. Good health, Data sharing, 03 medical and health sciences, 030104 developmental biology, Genetics, Humans, Genetic Testing, Prospective Studies, Sample collection, Personalized medicine, Precision Medicine, business, Genetics (clinical)
Abstract

The advancement of precision medicine requires new methods to coordinate and deliver genetic data from heterogeneous sources to physicians and patients. The eMERGE III Network enrolled >25,000 participants from biobank and prospective cohorts of predominantly healthy individuals for clinical genetic testing to determine clinically actionable findings. The network developed protocols linking together the 11 participant collection sites and 2 clinical genetic testing laboratories. DNA capture panels targeting 109 genes were used for testing of DNA and sample collection, data generation, interpretation, reporting, delivery, and storage were each harmonized. A compliant and secure network enabled ongoing review and reconciliation of clinical interpretations, while maintaining communication and data sharing between clinicians and investigators. A total of 202 individuals had positive diagnostic findings relevant to the indication for testing and 1,294 had additional/secondary findings of medical significance deemed to be returnable, establishing data return rates for other testing endeavors. This study accomplished integration of structured genomic results into multiple electronic health record (EHR) systems, setting the stage for clinical decision support to enable genomic medicine. Further, the established processes enable different sequencing sites to harmonize technical and interpretive aspects of sequencing tests, a critical achievement toward global standardization of genomic testing. The eMERGE protocols and tools are available for widespread dissemination.

Published
2019
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9. Abstract 2079: Prediction of DDR and other mutation signatures using targeted panels for FFPE samples

Author

Rushikesh Kanap, Ajithavalli Chellappan, Chintan Vora, Shilpa Nair, Ritika Raj, Jagannath Patro, and Fiona Hyland

Subjects
Genetics, Cancer Research, Oncology, Mutation (genetic algorithm), Biology
Abstract

Mutational processes can cause driver mutations and are considered the primary cause of tumorigenesis. Cosmic signatures classify environmental or intrinsic mutational processes. Identification of signatures including DNA Damage Response (DDR) signatures enables research into the origin of cancer mutagenesis and into treatment optimization. Typically, Mutation signatures are identified using Whole Genome Sequencing or Whole Exome Sequencing. We demonstrate signature prediction of mutation signatures with two amplification-based targeted panels, which have a high sequencing success rate for FFPE samples. ~2000 FFPE Samples from a pan-solid tumor cohort were sequenced with either of two AmpliSeq panels (OCAplus and OTMLA), sizes 1.4 Mb and 1.7 Mb, to optimize a method to identify mutation signatures. First, we identified somatic SNVs by filtering out likely population germline mutations, and used these to construct the single base change substitution (SBS) matrix. The COSMIC cancer signatures use properties of the whole genome: we normalized to extend signature detection to targeted panel data. We adjusted the mutation frequencies observed using the ratio of trinucleotide counts in the genome and the ratio in the panel. Next, we measured the cosine similarity between the normalized sample and the COSMIC signatures. We selected the signatures with a strong match (>0.7) to the normalized sample. We further impute the signatures using a reduced candidate set, to assess the signature fit in the sample and reduce false positives. These steps provide the optimized signatures. We detected optimized signatures in 33% of the samples. A single signature was detected in 9% of the samples, 2 signatures in 6%, and >2 signatures in 17% of the samples. ~3% of samples showed at least one MMR signatures (SBS6, SBS14, SBS15, SBS20, SBS21, SBS26 and SBS44). In all 10 OCAPlus samples with MMR signatures, we also detected mutation(s) in an MMR gene. APOBEC signatures, SBS2 and SBS13, were observed in 3% of samples sequenced with OCAPlus panel and TML panel. We found 3 samples showing HRR signature SBS3. We successfully identified the putative causal DDR mutation in a number of samples. For example, of 62 samples with NTHL1 mutations, 60 had NTHL1 related signature SBS30. A sample with MUTYH mutations was assigned the SBS36 signature. We sequenced matched Tumor/Normal pairs; in most cases, the tumor sample showed a stronger mutational signature, with their corresponding normal sample showing either no signature or a weaker matching signature. We assessed reproducibility of the mutational signature. Looking at duplicate and triplicate replicates, we found that replicates consistently displayed the same mutational signatures. We show identification of mutation signatures using targeted panels designed for FFPE samples. Citation Format: Fiona Hyland, Ajithavalli Chellappan, Chintan Vora, Shilpa Nair, Jagannath Patro, Ritika Raj, Rushikesh Kanap. Prediction of DDR and other mutation signatures using targeted panels for FFPE samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2079.

Published
2021
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10. Evaluation of usage of immunity boosters among the citizens of Pune district during the COVID-19 pandemic

Author

Manjusha Sajith, Ritika Rajendra Danole, Jilu Treasa Shaji, and Ansee Kuruvila

Subjects
covid-19, immune supplements, immunity boosters, side effects, Public aspects of medicine, RA1-1270
Abstract

Introduction: Post the coronavirus disease (COVID-19 pandemic), there was a spike in demand for immunity boosters, leading to the irrational use of supplements. To assess the usage of immunity boosters among the citizens of Pune City and correlate the side effects associated with supplements. Material and Methods: A cross-sectional study was conducted from September 2020 to May 2021 in Pune. Data, such as demographic, supplement intake (allopathic, homeopathic, and ayurvedic/home remedies), duration, frequency of supplements, and side effects associated with supplements, were collected through a personal interview and e-form circulation. The correlation of the immunity boosters with the side effects was done using Karl Pearson's Correlation test in SPSS software version 22.0. Results: Out of 1006, the ayurvedic supplements/home remedies were preferred by 906 (98%) allopathic supplements by 599 (65%) and homeopathic supplements by 256 (28%) participants. The commonly reported side effects were acidity (37%), headache (29.6%), nausea (9%), loss of appetite (8.8%), diarrhea (7%), stomach ache (6%), cough (5.6%), and constipation (4.1%). These side effects had a weak positive linear proportionality with ayurvedic supplements such as amla (r = 0.162), Giloy Vati (r = 0.139), turmeric (r = 0.108), and Kadha (r = 0.102); also, Eupatorium perfoliatum, Vitamin C, and Vitamin D showed a linear proportionality with loss of appetite (r = 0.15), headache (r = 0.12), and cough (r = 0.12), respectively. A higher incidence of side effects such as nausea (r = 0.267), diarrhea (r = 0.243), headache (r = 0.164), and acidity (r = 0.113) was observed when supplements were taken for 6 months. Conclusion: Most participants were on immunity boosters during the COVID-19 pandemic. The study concluded that using immunity boosters in excess or for more than 6 months causes side effects, the most recurrent ones being acidity, headache, nausea, and lack of appetite.

Published
2023
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11. DEVELOPMENT OF SCADA LIKE APPLICATION USING ARDUINO WITH .NET INTERFACE

Author

RITIKA RAJ and S.A ANNADATE

Subjects
ComputerApplications_COMPUTERSINOTHERSYSTEMS
Abstract

Nowadays SCADA systems are used for Home automation, Greenhouse automation, E-agriculture etc. Basically these SCADA applications include Level Monitoring, Light & Climate Control, Security & Surveillance, control and manage spatially separated utility sites and Control of Shutters & Doors and so on. With the arrival of new hardware and software technologies here a system is proposed which can perform the similar SCADA applications at lower cost and lower maintenances. This paper proposes a viable solution for SCADA like applications which include Water level monitoring, Oil level monitoring & Displacement control by using a microcontroller board and .NET interfacing. This system can not only perform these industrial applications but also proposes fine web based solution to access all these acquired data and equipments. Here a remote based application is used which will allow the user to access the data/equipments in industries via internet, it also overcome the problem of weak encryption used by the SCADA. In future this system using .NET platform may replace these SCADA solutions.

Published
2014
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12. Cohort Profile: The Right Drug, Right Dose, Right Time: Using Genomic Data to Individualize Treatment Protocol (RIGHT Protocol)

Author

Liwei Wang, Jason L. Ross, Donna M. Muzny, Eric Boerwinkle, John L. Black, Richard R. Sharp, Jyothsna Giri, Pedro J. Caraballo, Viktoriya Korchina, Christie Kovar, Ritika Raj, Steven E. Scherer, Leila A. Jones, Lance J. Oyen, Richard A. Gibbs, Sandra L. Lee, Christine M. Formea, Tammy M. McAllister, Jianhong Hu, Suzette J. Bielinski, Bijan J. Borah, Timothy B. Curry, Tsung-Jung Wu, Michaela E. McGree, Véronique L. Roger, Liewei Wang, Richard M. Weinshilboum, Eric T. Matey, Hongfang Liu, Kimberly Walker, Robert R. Freimuth, Qiaoyan Wang, Harshavardhan Doddapaneni, Tyler H. Koep, Eric Venner, Jennifer L. St. Sauver, Janet E. Olson, Xiang Qin, Wayne T. Nicholson, Nicholas B. Larson, Paul Y. Takahashi, Ann M. Moyer, Matthew A. Hathcock, Sara E. Kalla, Jessica A. Wright, Matthew E. Bernard, Debra J. Jacobson, and Carolyn R. Rohrer Vitek

Subjects
Male, Drug, Protocol (science), Epidemiology, business.industry, media_common.quotation_subject, Genomics, General Medicine, Bioinformatics, Biobank, Genome, Clinical decision support system, Cohort Studies, Text mining, Clinical Protocols, Pharmacogenetics, Pharmacogenomics, Cohort, Humans, Medicine, Female, Precision Medicine, business, Cohort Profiles, media_common
Published
2019
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13. Molecular Analysis, Based on 28s rDNA Dctylogyroides Species, Parasitizing Puntius Species

Author

M. K. Upadhyay, Nirupama Agrawal, and Ritika Raj Shrivastava

Subjects
Puntius, biology, Phylogenetic tree, Zoology, General Medicine, Ribosomal RNA, biology.organism_classification, chemistry.chemical_compound, chemistry, Genus, Cypriniformes, Molecular marker, Molecular phylogenetics, Ribosomal DNA
Abstract

The interrelationship of the helminthes have attracted attention from both phylogeneticists restricting their attention to morphological characters and those relying solely on molecular data. The phylogenic relationships exsisting among four monogenoideans belonging to genus Dactylogyroides found on two species of freshwater cypriniformes Puntius as P.sophore and P.chola in the River Gomti, India. These relationships were investigated via the use of the partial 28S ribosomal DNA (rDNA). characters for the differentiation of closely related genera or species group are usually selected based on practical purposes, taking no account of the evolutionary values of the characters. It is really difficult to establish a criterion for genus erection for the diversified monogenoideans. Analyses of 28S region in this study revealed that this gene is a very good molecular marker for inferring a relationship between closely related species. The aim of this paper is to describe the phylogenetic relationships between the monogenoidean parasites (genus Dactylogyroides) infesting genus Puntius, using DNA sequence data from nuclear ribosomal clusters.

Published
2013
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14. Diversity, host specificity, speciation and ecological equivalence in some dactylogyrid monogenoideans of freshwater fish

Author

Nirupama Agrawa, Amrin Ali, and Ritika Raj Shrivastava

Subjects
Gill, Habitat, Sympatric speciation, Ecology, Fauna, Freshwater fish, Taxonomy (biology), Taxonomic rank, Biology, biology.organism_classification, Biochemistry, Genetics and Molecular Biology (miscellaneous), Host specificity
Abstract

Objective To observe their specificity, speciation and ecological equivalence by using previous and present records, from freshwater fish from Tanakpur to Sultanpur areas, during 2009 & 2010. Methods Data is gathered from the published records to compare it with the present records and entered into a computer database. The taxonomy of monogenoideans follows and those of fish follows. The worms were gently scrapped from the gills of fish and counted manually. They were studied mostly live, under a phase contrast microscope (Olympus CX 41 U-DA 4E 03365 Japan) or fixed in 3% formalin, after being relaxed in lukewarm water. Results These monogenoids have perfect ecological equivalence, as their macro habitat is geologically connected. They exhibit specificity at different taxonomic levels of the parasites and the hosts. Sympatric speciation of parasites and their host is evident in the present study. Conclusions The monogenoidean fauna, in this region, has its species integrity in the past sixty to sixty five years. From this important body of study, it seems likely that host specificity among monogenoids from the fresh water fish is more widely spread than previously thought. Seasonal variations, probable controlling factor of infection, determine the intensity.

Published
2012
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15. MCM3 proliferative index is worthier over Ki-67 in the characterization of salivary gland tumors

Author

Ritika Raja, Devi Charan Shetty, Chandrakanta, Saurabh Juneja, Ankita Tandon, and Nikita Gulati

Subjects
mcm3, neoplasms, ki-67, salivary gland, Pathology, RB1-214, Microbiology, QR1-502
Abstract

Background: Salivary gland tumors bear uncanny characteristics of being different based on their morphological aspects rather than the presence of clear demarcation. This ambiguity in the spectrum from benign to malignant salivary gland neoplasms while categorizing the neoplasm is having inherent pitfalls. The present study was, therefore, designed to characterize benign and malignant salivary gland tumors based on their proliferative indices. Materials and Method: Study samples comprised of 97 cases of histopathologically confirmed benign and malignant salivary gland tumors. The cases were immunohistochemically assessed for MCM3 and Ki-67 expressions and the molecular characterization was performed based on the findings. Results: The majority of benign and malignant salivary gland tumors were from the parotid gland, (51.2%) and (42.4%), respectively. Overall mean labeling index of MCM3 was higher i.e., (5.60 ± 3.99) in comparison to Ki-67 i.e., (2.82 ± 3.14) with P = 0.05 using paired t-test. Besides, malignant salivary gland neoplasms represented a higher mean score of MCM3 and Ki-67 than benign neoplasms. Conclusion: The requirement of a novel marker has led to the use of MCM3 which has a characteristic role in the entire spectrum of the cell cycle. The present study highlighted the extrapolation of MCM3 over Ki-67 for diagnosis and for true characterization of biologic behavior of salivary gland pathologies which may, in turn, influence the treatment modality employed for such lesions.

Published
2021
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16. Traumatic ulcerative granuloma with stromal eosinophilia

Author

Aashka Sethi, Akanksha Banga, Ritika Raja, and Reema Raina

Subjects
cd15, eosinophils, traumatic ulcerative granuloma with stromal eosinophilia (tugse), ulcer, Dentistry, RK1-715
Abstract

Oral ulcers constitute one of the most common chief complaints of patients attending any dental practice. The cause of oral mucosal ulceration is generally attributed to acute or chronic trauma from local factors. However, oral lesions may be the initial manifestation of many systemic conditions. Moreover, a group of oral ulcerative lesions have been reported to exhibit vast numbers of eosinophils and known as Traumatic Ulcerative Granuloma with Stromal Eosinophilia (TUGSE). We present two cases of oral ulcers which on microscopic examination exhibited numerous eosinophils from ulcerated epithelium to deep into the submucosa and an exuberant lymphoid proliferation. CD15 immunohistochemical marker was used in these cases to ease the identification of the eosinophils. We also highlight the differential diagnosis of TUGSE that may manifest as oral lesions, as an important diagnostic guide for clinicians in contemporary practice.

Published
2020
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18. Nutrition in Disguise: Effects of Food Neophobia, Healthy Eating Interests and Provision of Health Information on Liking and Perceptions of Nutrient-Dense Foods in Older Adults

Author

Olivia C. Romaniw, Ritika Rajpal, Alison M. Duncan, Heather H. Keller, and Lisa M. Duizer

Subjects
older adults, nutrient-enhanced foods, food neophobia, healthy eating, health information, liking, Chemical technology, TP1-1185
Abstract

Older adults (60+ years) are at higher risk of malnutrition. Improving the nutrient-density of their diets is important but presents challenges due to the introduction of new ingredients, liking implications and heterogeneity of older consumers. Ten nutrient-enhanced foods were evaluated for liking (9-point hedonic scale) and sensory perception (check-all-that-apply) by 71 older adults. Three foods were re-evaluated after participants were provided with information about their healthy ingredients and benefits. Participants were also segmented based on their degrees of food neophobia and interests in healthy eating, using questionnaires. The results showed that eight foods had adequate sensory appeal (overall hedonic score of ≥6) to be pursued for residential care menus. Segmentation based on food neophobia and healthy eating interests did not yield any meaningful differences between groups. The effect of health information on liking for the overall sample and subgroups was product-specific: liking scores only increased for the raspberry banana smoothie in the overall test population and higher healthy eating interest subgroup. Health information may lead to the experience of more positive attributes in some foods. Overall, eight foods that were tested could be accepted by a wide range of consumers and providing them with health information may further improve acceptance.

Published
2020
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