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Harrison PW, Amode MR, Austine-Orimoloye O, Azov A, Barba M, Barnes I, Becker A, Bennett R, Berry A, Bhai J, Bhurji SK, Boddu S, Branco Lins PR, Brooks L, Ramaraju S, Campbell L, Martinez MC, Charkhchi M, Chougule K, Cockburn A, Davidson C, De Silva N, Dodiya K, Donaldson S, El Houdaigui B, Naboulsi T, Fatima R, Giron CG, Genez T, Grigoriadis D, Ghattaoraya G, Martinez JG, Gurbich T, Hardy M, Hollis Z, Hourlier T, Hunt T, Kay M, Kaykala V, Le T, Lemos D, Lodha D, Marques-Coelho D, Maslen G, Merino G, Mirabueno L, Mushtaq A, Hossain S, Ogeh D, Sakthivel MP, Parker A, Perry M, Piližota I, Poppleton D, Prosovetskaia I, Raj S, Pérez-Silva J, Salam A, Saraf S, Saraiva-Agostinho N, Sheppard D, Sinha S, Sipos B, Sitnik V, Stark W, Steed E, Suner MM, Surapaneni L, Sutinen K, Tricomi FF, Urbina-Gómez D, Veidenberg A, Walsh TA, Ware D, Wass E, Willhoft N, Allen J, Alvarez-Jarreta J, Chakiachvili M, Flint B, Giorgetti S, Haggerty L, Ilsley G, Keatley J, Loveland J, Moore B, Mudge J, Naamati G, Tate J, Trevanion S, Winterbottom A, Frankish A, Hunt SE, Cunningham F, Dyer S, Finn R, Martin F, Yates A. Ensembl 2024. Nucleic Acids Res 2024; 52:D891-D899. [PMID: 37953337 PMCID: PMC10767893 DOI: 10.1093/nar/gkad1049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 11/14/2023] Open
Abstract
Ensembl (https://www.ensembl.org) is a freely available genomic resource that has produced high-quality annotations, tools, and services for vertebrates and model organisms for more than two decades. In recent years, there has been a dramatic shift in the genomic landscape, with a large increase in the number and phylogenetic breadth of high-quality reference genomes, alongside major advances in the pan-genome representations of higher species. In order to support these efforts and accelerate downstream research, Ensembl continues to focus on scaling for the rapid annotation of new genome assemblies, developing new methods for comparative analysis, and expanding the depth and quality of our genome annotations. This year we have continued our expansion to support global biodiversity research, doubling the number of annotated genomes we support on our Rapid Release site to over 1700, driven by our close collaboration with biodiversity projects such as Darwin Tree of Life. We have also strengthened support for key agricultural species, including the first regulatory builds for farmed animals, and have updated key tools and resources that support the global scientific community, notably the Ensembl Variant Effect Predictor. Ensembl data, software, and tools are freely available.
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Affiliation(s)
- Peter W Harrison
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - M Ridwan Amode
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Olanrewaju Austine-Orimoloye
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Andrey G Azov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Matthieu Barba
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - If Barnes
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Arne Becker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Ruth Bennett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Andrew Berry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Jyothish Bhai
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Simarpreet Kaur Bhurji
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Sanjay Boddu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Paulo R Branco Lins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Lucy Brooks
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Shashank Budhanuru Ramaraju
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Lahcen I Campbell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Manuel Carbajo Martinez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Mehrnaz Charkhchi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Alexander Cockburn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Claire Davidson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Nishadi H De Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Kamalkumar Dodiya
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Sarah Donaldson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Bilal El Houdaigui
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Tamara El Naboulsi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Reham Fatima
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Carlos Garcia Giron
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Thiago Genez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Dionysios Grigoriadis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Gurpreet S Ghattaoraya
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Jose Gonzalez Martinez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Tatiana A Gurbich
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Matthew Hardy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Zoe Hollis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Mike Kay
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Vinay Kaykala
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Tuan Le
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Diana Lemos
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Disha Lodha
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Diego Marques-Coelho
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Gareth Maslen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Gabriela Alejandra Merino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Louisse Paola Mirabueno
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Aleena Mushtaq
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Syed Nakib Hossain
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Denye N Ogeh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Manoj Pandian Sakthivel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Anne Parker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Malcolm Perry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Ivana Piližota
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Daniel Poppleton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Irina Prosovetskaia
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Shriya Raj
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - José G Pérez-Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Ahamed Imran Abdul Salam
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Shradha Saraf
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Nuno Saraiva-Agostinho
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Dan Sheppard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Swati Sinha
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Botond Sipos
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Vasily Sitnik
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - William Stark
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Emily Steed
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Marie-Marthe Suner
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Likhitha Surapaneni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Kyösti Sutinen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Francesca Floriana Tricomi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - David Urbina-Gómez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Andres Veidenberg
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Thomas A Walsh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Doreen Ware
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
- USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853, USA
| | - Elizabeth Wass
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Natalie L Willhoft
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Jamie Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Jorge Alvarez-Jarreta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Marc Chakiachvili
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Bethany Flint
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Stefano Giorgetti
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Garth R Ilsley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Jon Keatley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Jane E Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Benjamin Moore
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Guy Naamati
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - John Tate
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Stephen J Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Andrea Winterbottom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Sarah Dyer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
| | - Andrew D Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK
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Contreras-Moreira B, Saraf S, Naamati G, Casas AM, Amberkar SS, Flicek P, Jones AR, Dyer S. GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation. Genome Biol 2023; 24:223. [PMID: 37798615 PMCID: PMC10552430 DOI: 10.1186/s13059-023-03071-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/21/2023] [Indexed: 10/07/2023] Open
Abstract
Crop pangenomes made from individual cultivar assemblies promise easy access to conserved genes, but genome content variability and inconsistent identifiers hamper their exploration. To address this, we define pangenes, which summarize a species coding potential and link back to original annotations. The protocol get_pangenes performs whole genome alignments (WGA) to call syntenic gene models based on coordinate overlaps. A benchmark with small and large plant genomes shows that pangenes recapitulate phylogeny-based orthologies and produce complete soft-core gene sets. Moreover, WGAs support lift-over and help confirm gene presence-absence variation. Source code and documentation: https://github.com/Ensembl/plant-scripts .
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Affiliation(s)
- Bruno Contreras-Moreira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
- Estación Experimental Aula Dei-CSIC, 50059, Zaragoza, Spain.
| | - Shradha Saraf
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Guy Naamati
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Ana M Casas
- Estación Experimental Aula Dei-CSIC, 50059, Zaragoza, Spain
| | - Sandeep S Amberkar
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Andrew R Jones
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Sarah Dyer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
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Chan ATC, Lee VHF, Hong RL, Ahn MJ, Chong WQ, Kim SB, Ho GF, Caguioa PB, Ngamphaiboon N, Ho C, Aziz MASA, Ng QS, Yen CJ, Soparattanapaisarn N, Ngan RKC, Kho SK, Tiambeng MLA, Yun T, Sriuranpong V, Algazi AP, Cheng A, Massarelli E, Swaby RF, Saraf S, Yuan J, Siu LL. Pembrolizumab monotherapy versus chemotherapy in platinum-pretreated, recurrent or metastatic nasopharyngeal cancer (KEYNOTE-122): an open-label, randomized, phase III trial. Ann Oncol 2023; 34:251-261. [PMID: 36535566 DOI: 10.1016/j.annonc.2022.12.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/22/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Pembrolizumab previously demonstrated robust antitumor activity and manageable safety in a phase Ib study of patients with heavily pretreated, programmed death ligand 1 (PD-L1)-positive, recurrent or metastatic nasopharyngeal carcinoma (NPC). The phase III KEYNOTE-122 study was conducted to further evaluate pembrolizumab versus chemotherapy in patients with platinum-pretreated, recurrent and/or metastatic NPC. Final analysis results are presented. PATIENTS AND METHODS KEYNOTE-122 was an open-label, randomized study conducted at 29 sites, globally. Participants with platinum-pretreated recurrent and/or metastatic NPC were randomly assigned (1 : 1) to pembrolizumab or chemotherapy with capecitabine, gemcitabine, or docetaxel. Randomization was stratified by liver metastasis (present versus absent). The primary endpoint was overall survival (OS), analyzed in the intention-to-treat population using the stratified log-rank test (superiority threshold, one-sided P = 0.0187). Safety was assessed in the as-treated population. RESULTS Between 5 May 2016 and 28 May 2018, 233 participants were randomly assigned to treatment (pembrolizumab, n = 117; chemotherapy, n = 116); Most participants (86.7%) received study treatment in the second-line or later setting. Median time from randomization to data cut-off (30 November 2020) was 45.1 months (interquartile range, 39.0-48.8 months). Median OS was 17.2 months [95% confidence interval (CI) 11.7-22.9 months] with pembrolizumab and 15.3 months (95% CI 10.9-18.1 months) with chemotherapy [hazard ratio, 0.90 (95% CI 0.67-1.19; P = 0.2262)]. Grade 3-5 treatment-related adverse events occurred in 12 of 116 participants (10.3%) with pembrolizumab and 49 of 112 participants (43.8%) with chemotherapy. Three treatment-related deaths occurred: 1 participant (0.9%) with pembrolizumab (pneumonitis) and 2 (1.8%) with chemotherapy (pneumonia, intracranial hemorrhage). CONCLUSION Pembrolizumab did not significantly improve OS compared with chemotherapy in participants with platinum-pretreated recurrent and/or metastatic NPC but did have manageable safety and a lower incidence of treatment-related adverse events.
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Affiliation(s)
- A T C Chan
- State Key Laboratory in Translational Oncology, Sir YK Pao Centre for Cancer, The Chinese University of Hong Kong, Hong Kong, China.
| | - V H F Lee
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong, China
| | - R-L Hong
- National Taiwan University Hospital, Taipei, Taiwan
| | - M-J Ahn
- Samsung Medical Centre, Seoul, South Korea
| | - W Q Chong
- National University Cancer Institute, Singapore, Singapore
| | - S-B Kim
- Asan Medical Centre, University of Ulsan College of Medicine, Seoul, South Korea
| | - G F Ho
- Clinical Oncology, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - P B Caguioa
- St. Luke's Medical Center, University of Santo Tomas Faculty of Medicine and Surgery, Manila, Philippines
| | - N Ngamphaiboon
- Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - C Ho
- BC Cancer, University of British Columbia, Vancouver, Canada
| | - M A S A Aziz
- Gleneagles Penang Clinical Research Center, Gleneagles Hospital Penang, Penang, Malaysia
| | - Q S Ng
- National Cancer Centre Singapore, Singapore, Singapore
| | - C-J Yen
- National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | | | - R K-C Ngan
- Queen Elizabeth Hospital, Kowloon, Hong Kong, China
| | - S K Kho
- Hospital Umum Sarawak, Kuching, Malaysia
| | - M L A Tiambeng
- Cardinal Santos Medical Center, San Juan City, Philippines
| | - T Yun
- National Cancer Center, Goyang-si, South Korea
| | - V Sriuranpong
- Chulalongkorn University and the King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | | | - A Cheng
- Princess Margaret Hospital, Hong Kong, China
| | - E Massarelli
- City of Hope Comprehensive Cancer Center, Duarte, USA
| | | | - S Saraf
- Merck & Co., Inc., Rahway, USA
| | - J Yuan
- Merck & Co., Inc., Rahway, USA
| | - L L Siu
- Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada
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Vishwanath D, Shanmugam A, Sundaresh M, Hariharan A, Saraf S, Bahadur U, Veeramachaneni V, Chandrasekhar N, Pillai V V, Bushan V, Shetty V, Subramaniam N, Kuriakose MA, Shivaprasad KS, Khadilkar K, Suresh A, Sum S, Lakhsmikantha A, Rekha PR, Zaidi SN, Gupta V, Kannan S. Development of a Low-cost NGS Test for the Evaluation of Thyroid Nodules. Indian J Surg Oncol 2022; 13:17-22. [PMID: 35462651 PMCID: PMC8986928 DOI: 10.1007/s13193-019-01000-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/25/2019] [Indexed: 10/25/2022] Open
Abstract
Ultrasound-guided fine needle aspiration cytology (FNAC) is the preferred method of identifying malignancy in palpable thyroid nodules using the Bethesda reporting system. However, in around 30-40% of FNACs (Bethesda categories III, IV, and V), the results are indeterminate and surgery is required to confirm malignancy. Out of those who undergo surgery, only 10-40% of patients in these categories are found to have malignancies, thus proving surgery to be unnecessary for some patients or to be incomplete in others. While molecular testing on thyroid FNAC material is part of the American Thyroid Association (ATA) guidelines in evaluating thyroid nodules, it is currently unavailable in India due to cost constraints. In this study, we prospectively collected FNAC samples from sixty-nine patients who presented with palpable thyroid nodules. We designed a cost-effective next-generation sequencing (NGS) test to query multiple variants in the DNA and RNA isolated from the fine needle aspirate. The identification of oncogenic variants was considered to be indicative of malignancy, and confirmed by surgical histopathology. The panel showed an overall sensitivity of 81.25% and a specificity of 100%, while in the case of Bethesda categories III, IV, and V, the sensitivity was higher (87.5%) and the specificity was established at 100%. The panel could thereby serve as a rule-in test for the diagnosis of thyroid cancer and therefore help identify patients who require surgery, especially in the indeterminate Bethesda categories III, IV, and V.
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Affiliation(s)
- Divya Vishwanath
- grid.465051.30000 0004 1799 1787Strand Life Sciences Pvt. Ltd., 5th Floor, Kirloskar Business Park, Bellary Road, Hebbal, Bangalore, 560024 India
| | - Ashwini Shanmugam
- grid.465051.30000 0004 1799 1787Strand Life Sciences Pvt. Ltd., 5th Floor, Kirloskar Business Park, Bellary Road, Hebbal, Bangalore, 560024 India
| | - Mahima Sundaresh
- grid.465051.30000 0004 1799 1787Strand Life Sciences Pvt. Ltd., 5th Floor, Kirloskar Business Park, Bellary Road, Hebbal, Bangalore, 560024 India
| | - Arun Hariharan
- grid.465051.30000 0004 1799 1787Strand Life Sciences Pvt. Ltd., 5th Floor, Kirloskar Business Park, Bellary Road, Hebbal, Bangalore, 560024 India
| | - Shradha Saraf
- grid.465051.30000 0004 1799 1787Strand Life Sciences Pvt. Ltd., 5th Floor, Kirloskar Business Park, Bellary Road, Hebbal, Bangalore, 560024 India
| | - Urvashi Bahadur
- grid.465051.30000 0004 1799 1787Strand Life Sciences Pvt. Ltd., 5th Floor, Kirloskar Business Park, Bellary Road, Hebbal, Bangalore, 560024 India
| | - Vamsi Veeramachaneni
- grid.465051.30000 0004 1799 1787Strand Life Sciences Pvt. Ltd., 5th Floor, Kirloskar Business Park, Bellary Road, Hebbal, Bangalore, 560024 India
| | - Naveen Chandrasekhar
- grid.416504.20000 0004 1796 819XDepartment of Head & Neck Surgical Oncology & Endocrinology, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Vijay Pillai V
- grid.416504.20000 0004 1796 819XDepartment of Head & Neck Surgical Oncology & Endocrinology, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Vidhya Bushan
- grid.416504.20000 0004 1796 819XDepartment of Head & Neck Surgical Oncology & Endocrinology, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Vivek Shetty
- grid.416504.20000 0004 1796 819XDepartment of Head & Neck Surgical Oncology & Endocrinology, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Narayana Subramaniam
- grid.416504.20000 0004 1796 819XDepartment of Head & Neck Surgical Oncology & Endocrinology, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Moni Abraham Kuriakose
- grid.416504.20000 0004 1796 819XDepartment of Head & Neck Surgical Oncology & Endocrinology, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - K. S. Shivaprasad
- grid.416504.20000 0004 1796 819XDepartment of Head & Neck Surgical Oncology & Endocrinology, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Kranti Khadilkar
- grid.416504.20000 0004 1796 819XDepartment of Head & Neck Surgical Oncology & Endocrinology, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Amritha Suresh
- grid.506019.bMazumdar Shaw Medical Foundation, 258/A, Hosur Road Anekal, Taluk, Bommasandra Industrial Area, Bangalore, Karnataka 560099 India
| | - Sum Sum
- grid.506019.bMazumdar Shaw Medical Foundation, 258/A, Hosur Road Anekal, Taluk, Bommasandra Industrial Area, Bangalore, Karnataka 560099 India
| | - Akhila Lakhsmikantha
- grid.416504.20000 0004 1796 819XDepartment of Pathology & Laboratory Services, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Pobbisetty Radhakrishnagupta Rekha
- grid.416504.20000 0004 1796 819XDepartment of Pathology & Laboratory Services, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Shaesta Naseem Zaidi
- grid.416504.20000 0004 1796 819XDepartment of Pathology & Laboratory Services, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
| | - Vaijayanti Gupta
- grid.465051.30000 0004 1799 1787Strand Life Sciences Pvt. Ltd., 5th Floor, Kirloskar Business Park, Bellary Road, Hebbal, Bangalore, 560024 India
| | - Subramanian Kannan
- grid.416504.20000 0004 1796 819XDepartment of Endocrinology, Narayana Health City, 258/A, Bommasandra Industrial Area Anekal Taluk, Hosur Rd, Bangalore, 560099 India
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5
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Halmos B, Cobb P, Johnson M, Jain L, Kim S, Saraf S, Lala M, Kurata T. 168TiP KEYNOTE-A86: Phase III, randomized, open-label study of first-line subcutaneous (SC) vs intravenous (IV) pembrolizumab with platinum doublet chemotherapy in metastatic squamous or nonsquamous non-small cell lung cancer (NSCLC). Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.10.187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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6
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Chan A, Lee H, Hong RL, Ahn MJ, Chong W, Kim SB, Fuang H, Caguioa P, Ngamphaiboon N, Ho C, Abdul Aziz M, Ng Q, Yen C, Soparattanapaisarn N, Ngan R, Kho S, Wang L, Swaby R, Saraf S, Siu L. 163P Health-related quality of life (HRQoL) with pembrolizumab (pembro) vs chemotherapy (chemo) in platinum-pretreated recurrent or metastatic (R/M) nasopharyngeal cancer (NPC): Phase III KEYNOTE-122 study. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.10.182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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7
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Chan A, Lee V, Hong RL, Ahn MJ, Chong W, Kim SB, Gwo Fuang H, Caguioa P, Ngamphaiboon N, Ho C, Abdul Aziz M, Ng Q, Yen CJ, Soparattanapaisarn N, Ngan K, Kho S, Swaby R, Saraf S, Ge J, Siu L. 858O Results of KEYNOTE-122: A phase III study of pembrolizumab (pembro) monotherapy vs chemotherapy (chemo) for platinum-pretreated, recurrent or metastatic (R/M) nasopharyngeal carcinoma (NPC). Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.1268] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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8
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Katragadda S, Hall TO, Bettadapura R, Dalton JC, Ganapathy A, Ghana P, Hariharan R, Janakiraman A, Kotha KBVSSP, Manjunath A, Mannan AU, Ms N, Saraf S, Tzeng KTH, Veeramachaneni V. Determining Cost-Optimal Next-Generation Sequencing Panels for Rare Disease and Pharmacogenomics Testing. Clin Chem 2021; 67:1122-1132. [PMID: 34120169 DOI: 10.1093/clinchem/hvab059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/25/2021] [Indexed: 12/23/2022]
Abstract
BACKGROUND Multi-gene panel sequencing using next-generation sequencing (NGS) methods is a key tool for genomic medicine. However, with an estimated 140 000 genomic tests available, current system inefficiencies result in high genetic-testing costs. Reduced testing costs are needed to expand the availability of genomic medicine. One solution to improve efficiency and lower costs is to calculate the most cost-effective set of panels for a typical pattern of test requests. METHODS We compiled rare diseases, associated genes, point prevalence, and test-order frequencies from a representative laboratory. We then modeled the costs of the relevant steps in the NGS process in detail. Using a simulated annealing-based optimization procedure, we determined panel sets that were more cost-optimal than whole exome sequencing (WES) or clinical exome sequencing (CES). Finally, we repeated this methodology to cost-optimize pharmacogenomics (PGx) testing. RESULTS For rare disease testing, we show that an optimal choice of 4-6 panels, uniquely covering genes that comprise 95% of the total prevalence of monogenic diseases, saves $257-304 per sample compared with WES, and $66-135 per sample compared with CES. For PGx, we show that the optimal multipanel solution saves $6-7 (27%-40%) over a single panel covering all relevant gene-drug associations. CONCLUSIONS Laboratories can reduce costs using the proposed method to obtain and run a cost-optimal set of panels for specific test requests. In addition, payers can use this method to inform reimbursement policy.
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9
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Awad M, Gadgeel S, Borghaei H, Patnaik A, Chih-Hsin Yang J, Powell S, Gentzler R, Martins R, Stevenson J, Altan M, Jalal S, Panwalkar A, Gubens M, Sequist L, Saraf S, Zhao B, Piperdi B, Langer C. OFP01.02 KEYNOTE-021 Cohort G Long-Term Follow-up: First-Line (1L) Pemetrexed and Carboplatin (PC) with or without Pembrolizumab for Advanced Nonsquamous NSCLC. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2020.10.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Koshy M, Son C, Spiotto M, Rondelli D, Saraf S. Prospective Evaluation of Total Body Radiation in the Conditioning Regimen of Patients Undergoing Allogeneic Stem Cell Transplantation for Sickle Cell Disease. Int J Radiat Oncol Biol Phys 2019. [DOI: 10.1016/j.ijrobp.2019.06.364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Grewal RK, Saraf S, Deb A, Kundu S. Differentially Expressed MicroRNAs Link Cellular Physiology to Phenotypic Changes in Rice Under Stress Conditions. Plant Cell Physiol 2018; 59:2143-2154. [PMID: 30010993 DOI: 10.1093/pcp/pcy136] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Indexed: 06/08/2023]
Abstract
Plant microRNAs (miRNAs) and their target genes have important functional roles in nutrition deficiency and stress response. However, the underlying mechanisms relating relative expression of miRNAs and target mRNAs to morphological adjustments are not well defined. By combining miRNA expression profiles, corresponding target genes and transcription factors that bind to computationally identified over-represented cis-regulatory elements (CREs) common in miRNAs and target gene promoters, we implement a strategy that identifies a set of differentially expressed regulatory interactions which, in turn, relate underlying cellular mechanisms to some of the phenotypic changes observed. Integration of experimentally reported individual interactions with identified regulatory interactions explains how (i) during mineral deficiency osa-miR167 inhibits shoot growth but activates adventitious root growth by influencing free auxin content; (ii) during sulfur deficiency osa-miR394 is involved in adventitious root growth inhibition, sulfur and iron homeostasis, and auxin-mediated regulation of sulfur homeostasis; (iii) osa-miR399 contributes to cross-talk between cytokinin and phosphorus deficiency signaling; and (iv) a feed-forward loop involving the osa-miR166, trihelix and HD-ZIP III transcription factors may regulate leaf senescence during drought. This strategy not only identifies various regulatory interactions connecting phenotypic changes with cellular or molecular events triggered by stress, but also provides a framework to deepen our understanding of stress cellular physiology.
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Affiliation(s)
- Rumdeep K Grewal
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
- Department of Botany, Bhairab Ganguly College, Kolkata, India
| | - Shradha Saraf
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| | - Arindam Deb
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| | - Sudip Kundu
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
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12
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Borghaei H, Langer C, Gadgeel S, Papadimitrakopoulou V, Patnaik A, Powell S, Gentzler R, Martins R, Stevenson J, Jalal S, Panwalkar A, Yang JH, Gubens M, Sequist L, Awad M, Fiore J, Saraf S, Raftopoulos H, Gandhi L. Updated results from KEYNOTE-021 cohort G: A randomized, phase 2 study of pemetrexed and carboplatin (PC) with or without pembrolizumab (pembro) as first-line therapy for advanced nonsquamous NSCLC. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx440.052] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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13
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Ahmad M, Brient CE, Egun PM, Grimes SM, Saraf S, Satyanarayana H. Charged-Particle Emission in Reactions of 9- and 11 -MeV Neutrons with63,65Cu. NUCL SCI ENG 2017. [DOI: 10.13182/nse95-296] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Munir Ahmad
- TRIUMF, 4004 Wesbrook Mall, Vancouver, British Columbia, Canada V6T 2A3
| | - C. E. Brient
- John E. Edwards Accelerator Laboratory, Ohio University, Athens, Ohio 45701
| | - P. M. Egun
- John E. Edwards Accelerator Laboratory, Ohio University, Athens, Ohio 45701
| | - S. M. Grimes
- John E. Edwards Accelerator Laboratory, Ohio University, Athens, Ohio 45701
| | - S. Saraf
- John E. Edwards Accelerator Laboratory, Ohio University, Athens, Ohio 45701
| | - H. Satyanarayana
- John E. Edwards Accelerator Laboratory, Ohio University, Athens, Ohio 45701
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14
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Ott PA, Piha-Paul SA, Munster P, Pishvaian MJ, van Brummelen EMJ, Cohen RB, Gomez-Roca C, Ejadi S, Stein M, Chan E, Simonelli M, Morosky A, Saraf S, Emancipator K, Koshiji M, Bennouna J. Safety and antitumor activity of the anti-PD-1 antibody pembrolizumab in patients with recurrent carcinoma of the anal canal. Ann Oncol 2017; 28:1036-1041. [PMID: 28453692 PMCID: PMC5406758 DOI: 10.1093/annonc/mdx029] [Citation(s) in RCA: 171] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background Safety and efficacy of pembrolizumab, a humanized programmed death 1 monoclonal antibody, was assessed in KEYNOTE-028, a multicohort, phase Ib trial for patients with programmed death ligand 1 (PD-L1)-positive advanced solid tumors. We report results for the cohort of patients with advanced anal carcinoma. Patients and methods Patients with PD-L1-positive tumors (≥1%) received intravenous pembrolizumab 10 mg/kg once every 2 weeks for up to 2 years or until confirmed progression or unacceptable toxicity. Response was assessed every 8 weeks for the first 6 months and every 12 weeks thereafter per Response Evaluation Criteria In Solid Tumors, version 1.1. Primary endpoints were safety and overall response rate per investigator review. Secondary endpoints included progression-free survival, overall survival, and response duration. Data cutoff date was 1 July 2015. Results Of the 43 patients with advanced anal carcinoma evaluable for PD-L1 expression, 32 (74%) had PD-L1-positive tumors as assessed with the 22C3 prototype assay, of whom 25 were enrolled between April and September 2014. Sixteen patients (64%) experienced treatment-related adverse events; the most common ones were diarrhea and fatigue in four patients (16%) each and nausea in three patients (12%). There were no treatment-related deaths or discontinuations as of the data cutoff date. Among the 24 patients with squamous cell carcinoma histology, four had confirmed partial response, for an overall response rate of 17% [95% confidence interval (CI), 5%-37%) and 10 (42%) had confirmed stable disease, for a disease control rate of 58%. One additional patient with non-squamous histology had confirmed stable disease. Conclusion In this population of patients with PD-L1-positive advanced squamous cell anal carcinoma, pembrolizumab demonstrated a manageable safety profile and encouraging antitumor activity. These data support further study of pembrolizumab for this patient population. ClinicalTrials.gov NCT02054806.
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MESH Headings
- Aged
- Aged, 80 and over
- Anal Canal/pathology
- Antibodies, Monoclonal, Humanized/adverse effects
- Antibodies, Monoclonal, Humanized/therapeutic use
- Antineoplastic Agents, Immunological/adverse effects
- Antineoplastic Agents, Immunological/therapeutic use
- Anus Neoplasms/drug therapy
- Anus Neoplasms/mortality
- Carcinoma, Squamous Cell/drug therapy
- Carcinoma, Squamous Cell/mortality
- Disease-Free Survival
- Female
- Humans
- Male
- Middle Aged
- Neoplasm Recurrence, Local/drug therapy
- Neoplasm Recurrence, Local/mortality
- Treatment Outcome
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Affiliation(s)
- P. A. Ott
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston
| | - S. A. Piha-Paul
- Department of Investigational Cancer Therapeutics, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston
| | - P. Munster
- Department of Medicine (Hematology/Oncology), Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco
| | - M. J. Pishvaian
- Department of Hematology/Oncology, Georgetown University, Washington DC, USA
| | - E. M. J. van Brummelen
- Department of Molecular Pathology & Clinical Pharmacology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - R. B. Cohen
- Department of Medicine, University of Pennsylvania, Philadelphia, USA
| | - C. Gomez-Roca
- Clinical Research Unit, Institut Claudius Regaud and Institut Universitaire du Cancer—Oncopole, Toulouse, France
| | - S. Ejadi
- Department of Medical Oncology, Virginia G. Piper Cancer Center, Scottsdale
| | - M. Stein
- Department of Medical Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick
| | - E. Chan
- Department of Medicine (Hematology/Oncology), Vanderbilt-Ingram Cancer Center, Nashville, USA
| | - M. Simonelli
- Department of Medical Oncology and Hematology, Humanitas Cancer Center, Rozzano, Italy
| | - A. Morosky
- Department of Clinical Oncology, Merck & Co, Inc., Kenilworth, USA
| | - S. Saraf
- Department of Clinical Oncology, Merck & Co, Inc., Kenilworth, USA
| | - K. Emancipator
- Department of Clinical Oncology, Merck & Co, Inc., Kenilworth, USA
| | - M. Koshiji
- Department of Clinical Oncology, Merck & Co, Inc., Kenilworth, USA
| | - J. Bennouna
- Department of Medical Oncology, Institut de Cancérologie de l’Ouest, Nantes, France
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15
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Chan A, Lee V, Ngan R, To K, Ahn MJ, Ng Q, Hong RL, Lin JC, Swaby R, Gause C, Saraf S, Spreafico A. 394TiP KEYNOTE-122: Phase 2 study of pembrolizumab versus standard-of-care chemotherapy in platinum-pretreated, recurrent or metastatic nasopharyngeal carcinoma. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw587.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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16
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Abstract
Trans-acting small interfering RNAs (ta-siRNAs) are a class of endogenous small RNA, associated with posttranscriptional gene silencing. Their biogenesis requires an initial microRNA (miRNA)-mediated cleavage of precursor RNA. Around 20 different ta-siRNA-producing loci (TASs), whose sequences are conserved, are reported in plants. In tomato, two TAS gene families have been identified, which are found to target auxin response factor gene and bacterial spot disease resistance protein Bs4 gene. Using high-throughput computational and experimental approach, we identified a new locus-producing ta-siRNA in tomato. We have also identified the putative miRNA regulating the production of ta-siRNA from this locus. The ta-siRNAs generated from TAS4 were up-regulated upon infection with a DNA virus. The potential targets of ta-siRNAs were predicted to be variety of proteins including MYB transcription factors and cell cycle regulators for some of the ta-siRNAs produced.
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Affiliation(s)
- Archana Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
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17
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Hansen A, Massard C, Ott P, Haas N, Lopez J, Ejadi S, Wallmark J, Keam B, Delord JP, Aggarwal R, Gould M, Qiu P, Saraf S, Keefe S, Piha-Paul S. Pembrolizumab for patients with advanced prostate adenocarcinoma: Preliminary results from the KEYNOTE-028 study. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw372.09] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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18
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Hsu C, Lee SH, Ejadi S, Even C, Cohen R, Le Tourneau C, Mehnert J, Algazi A, van Brummelen E, Saraf S, Thanigaimani P, Cheng J, Hansen A. 315O_PR Antitumor activity and safety of pembrolizumab in patients with PD-L1-positive nasopharyngeal carcinoma: Interim results from a phase 1b study. Ann Oncol 2015. [DOI: 10.1093/annonc/mdv527.02] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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19
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Saraf S, Shandra S, Saran R, Narain V, Dwivedi S, Sethi R, Pradhan A, Chaudhary G, Vishwakarma P. To detect occult coronary artery disease in global severe left ventricular hypokinesia. Indian Heart J 2015. [DOI: 10.1016/j.ihj.2015.10.253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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20
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Saraf S, Sanan-Mishra N, Gursanscky NR, Carroll BJ, Gupta D, Mukherjee SK. 3' and 5' microRNA-end post-biogenesis modifications in plant transcriptomes: Evidences from small RNA next generation sequencing data analysis. Biochem Biophys Res Commun 2015; 467:892-9. [PMID: 26471296 DOI: 10.1016/j.bbrc.2015.10.048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 10/08/2015] [Indexed: 11/29/2022]
Abstract
The processing of miRNA from its precursors is a precisely regulated process and after biogenesis, the miRNAs are amenable to different kinds of modifications by the addition or deletion of nucleotides at the terminal ends. However, the mechanism and functions of such modifications are not well studied in plants. In this study, we have specifically analysed the terminal end non-templated miRNA modifications, using NGS data of rice, tomato and Arabidopsis small RNA transcriptomes from different tissues and physiological conditions. Our analysis reveals template independent terminal end modifications in the mature as well as passenger strands of the miRNA duplex. Interestingly, it is also observed that miRNA sequences terminating with a cytosine (C) at the 3' end undergo a higher percentage of 5' end modifications. The terminal end modifications did not correlate with the miRNA abundances and are independent of tissue types, physiological conditions and plant species. Our analysis indicates that the addition of nucleotides at miRNA ends is not influenced by the absence of RNA dependent RNA polymerase 6. Moreover the terminal end modified miRNAs are also observed amongst AGO1 bound small RNAs and have potential to alter target, indicating its important functional role in repression of gene expression.
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Affiliation(s)
- Shradha Saraf
- Bioinformatics Laboratory, Structural and Computational Biology Group, ICGEB, New Delhi, India.
| | | | - Nial R Gursanscky
- School of Chemistry and Molecular Biosciences, The University of Queensland, Australia.
| | - Bernard J Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, Australia.
| | - Dinesh Gupta
- Bioinformatics Laboratory, Structural and Computational Biology Group, ICGEB, New Delhi, India.
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21
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Kaushik A, Saraf S, Mukherjee SK, Gupta D. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. PeerJ 2015; 3:e1332. [PMID: 26623179 PMCID: PMC4662591 DOI: 10.7717/peerj.1332] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/27/2015] [Indexed: 12/27/2022] Open
Abstract
In the past decade, the microRNAs (miRNAs) have emerged to be important regulators of gene expression across various species. Several studies have confirmed different types of post-transcriptional modifications at terminal ends of miRNAs. The reports indicate that miRNA modifications are conserved and functionally significant as it may affect miRNA stability and ability to bind mRNA targets, hence affecting target gene repression. Next Generation Sequencing (NGS) of the small RNA (sRNA) provides an efficient and reliable method to explore miRNA modifications. The need for dedicated software, especially for users with little knowledge of computers, to determine and analyze miRNA modifications in sRNA NGS data, motivated us to develop miRMOD. miRMOD is a user-friendly, Microsoft Windows and Graphical User Interface (GUI) based tool for identification and analysis of 5′ and 3′ miRNA modifications (non-templated nucleotide additions and trimming) in sRNA NGS data. In addition to identification of miRNA modifications, the tool also predicts and compares the targets of query and modified miRNAs. In order to compare binding affinities for the same target, miRMOD utilizes minimum free energies of the miRNA:target and modified-miRNA:target interactions. Comparisons of the binding energies may guide experimental exploration of miRNA post-transcriptional modifications. The tool is available as a stand-alone package to overcome large data transfer problems commonly faced in web-based high-throughput (HT) sequencing data analysis tools. miRMOD package is freely available at http://bioinfo.icgeb.res.in/miRMOD.
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Affiliation(s)
- Abhinav Kaushik
- Bioinformatics Laboratory, SCB Group, International Centre for Genetic Engineering & Biotechnology, New Delhi, India
| | - Shradha Saraf
- Bioinformatics Laboratory, SCB Group, International Centre for Genetic Engineering & Biotechnology, New Delhi, India
| | - Sunil K Mukherjee
- Department of Genetics, University of Delhi, South Campus, Delhi, India
| | - Dinesh Gupta
- Bioinformatics Laboratory, SCB Group, International Centre for Genetic Engineering & Biotechnology, New Delhi, India
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22
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Raveendran S, Kyprianou K, Zenonos K, Saraf S. A patient presenting with collapse and breathlessness. Acute Med 2015; 14:176-194. [PMID: 27119131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
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Prabakar C, Irani M, Julka N, Bhatt D, Homel P, Saraf S, Bral P. What Your Patient Does Not Know: A Survey of Patient Knowledge about Surgical Approaches in Gynecology. J Minim Invasive Gynecol 2014. [DOI: 10.1016/j.jmig.2014.08.431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Sherwin G, Akpinar P, Saraf S, Li X. Pricing and Market Access of Orphan Drugs in Asia: a Comparative Study Across Growth Markets. Value Health 2014; 17:A785. [PMID: 27202919 DOI: 10.1016/j.jval.2014.08.399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Affiliation(s)
- G Sherwin
- ICON Pricing and Market Access, London, UK
| | - P Akpinar
- ICON Pricing and Market Access, London, UK
| | - S Saraf
- ICON Pricing and Market Access, London, UK
| | - X Li
- ICON Commercialisation & Outcomes, London, UK
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Akpinar P, Saraf S, Severi Bruni D, Li X, Liu C, Sherwin G. Stakeholder Evidence Requirements and Price Expectations for Biosimilars in Three Asian Markets. Value Health 2014; 17:A775. [PMID: 27202867 DOI: 10.1016/j.jval.2014.08.339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Affiliation(s)
- P Akpinar
- ICON Pricing and Market Access, London, UK
| | - S Saraf
- ICON Pricing and Market Access, London, UK
| | | | - X Li
- ICON Commercialisation & Outcomes, London, UK
| | - C Liu
- ICON Pricing and Market Access, New York, NY, USA
| | - G Sherwin
- ICON Pricing and Market Access, London, UK
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Akpinar P, Saraf S, Severi Bruni D, Li X, Liu C, Sherwin G. Stakeholder Evidence Requirements and Price Expectations for Biosimilars in Three Asian Markets. Value Health 2014; 17:A775-A776. [PMID: 27202867 DOI: 10.1016/j.jval.2014.08.344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Affiliation(s)
- P Akpinar
- ICON Pricing and Market Access, London, UK
| | - S Saraf
- ICON Pricing and Market Access, London, UK
| | | | - X Li
- ICON Commercialisation & Outcomes, London, UK
| | - C Liu
- ICON Pricing and Market Access, New York, NY, USA
| | - G Sherwin
- ICON Pricing and Market Access, London, UK
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Sherwin G, Saraf S, Li X, Akpinar P. Provincial Hospital Tendering in China: Evaluating The Impact on Price. Value Health 2014; 17:A788. [PMID: 27202938 DOI: 10.1016/j.jval.2014.08.419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Affiliation(s)
- G Sherwin
- ICON Pricing and Market Access, London, UK
| | - S Saraf
- ICON Pricing and Market Access, London, UK
| | - X Li
- ICON Commercialisation & Outcomes, London, UK
| | - P Akpinar
- ICON Pricing and Market Access, London, UK
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Eaton KA, Suvan JE, Saraf S, Rist A. Introducing dental hygienists in general practice to research - an in-practice evaluation programme in the United Kingdom. Int J Dent Hyg 2014; 13:228-34. [PMID: 25318647 DOI: 10.1111/idh.12108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2014] [Indexed: 11/28/2022]
Abstract
AIM To introduce dental hygienists (DHs) in the UK to the principles of research through a practice-based product evaluation programme. METHODS The programme consisted of an initial training and orientation day with presentations on evidence-based practice, research methods and the structure of research papers. The programme and its aims were explained in detail, and participants were briefed on the methods to be used. Participants then recruited seven to ten patients from their practices (offices), carried out a baseline assessment of: plaque, gingival health, calculus and staining at anterior teeth, and gave the patients a questionnaire asking about their teeth and then provided a 3-month supply of a test toothpaste. About 10 weeks later, a follow-up assessment of the same variables was performed and the questionnaire was repeated. A second training day followed during which the DHs provided feedback of their experiences and received training in literature searching and critical appraisal of literature including interpretation of results. RESULTS Sixty-five DHs attended the first training day; 31 were able to recruit sufficient patients and attend the second training day. The DHs recruited 168 patients who received baseline and follow-up assessments. All the variables improved overall. Feedback from the DHs was very positive, and patients expressed delight with the care they had received. CONCLUSIONS Qualitative feedback for participating DHs suggests the programme met its aim and could be used in the future as a mechanism for helping DHs who want to increase their understanding of research methodology.
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Affiliation(s)
- K A Eaton
- Eastman and King's College London Dental Institutes, University College London, UK.,University of Kent, Ashford, UK
| | - J E Suvan
- Eastman Clinical Investigation Centre, University College London, London, UK
| | - S Saraf
- Oral-B, Procter & Gamble Western Europe, Geneva, Switzerland
| | - A Rist
- Oral-B, Procter & Gamble Western Europe, Geneva, Switzerland
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Pradhan B, Naqvi AR, Saraf S, Mukherjee SK, Dey N. Prediction and characterization of Tomato leaf curl New Delhi virus (ToLCNDV) responsive novel microRNAs in Solanum lycopersicum. Virus Res 2014; 195:183-95. [PMID: 25218481 DOI: 10.1016/j.virusres.2014.09.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 08/28/2014] [Accepted: 09/01/2014] [Indexed: 10/24/2022]
Abstract
Tomato leaf curl New Delhi virus (ToLCNDV) infects tomato (Solanum lycopersicum) plants and causes severe crop losses. As the microRNAs (miRNAs) are deregulated during stressful events, such as biotic stress, we wanted to study the effect of ToLCNDV infection on tomato miRNAs. We constructed two libraries, isolating small RNAs (sRNAs) from healthy (HT) and ToLCNDV infected (IT) tomato leaves, and sequenced the library-specific sRNAs using the next generation sequencing (NGS) approach. These data helped predict 112 mature miRNA sequences employing the miRDeep-P program. A substantial number (58) of the sequences were 24-mer in size, which was a bit surprising. Based on the calculation of precision values, 53 novel miRNAs were screened from the predicted sequences. Nineteen of these were chosen for expression analysis; a northern blot analysis showed 15 to be positive. Many of the predicted miRNAs were up-regulated following viral infection. The target genes of the miRNAs were also predicted and the expression analysis of selected transcripts showed a typical inverse relation between the accumulation of target transcripts and the abundance of corresponding miRNAs. Furthermore, the cleavage sites of the target transcripts for three novel miRNAs were mapped, confirming the correct annotation of the miRNA-targets. The sRNA deep sequencing clearly revealed that the virus modulated global miRNA expression in the host. The validated miRNAs (Tom_4; Tom_14; Tom_17; Tom_21; Tom_29; Tom_43) could be valuable tools for understanding the ToLCNDV-tomato interaction, ultimately leading to the development of a virus-resistant tomato plant.
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Affiliation(s)
- Bhubaneswar Pradhan
- Division of Gene Function and Regulation, Institute of Life Sciences, Nalco Square, Chandrasekharpur, Bhubaneswar 751023, Odisha, India.
| | - Afsar Raza Naqvi
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.
| | - Shradha Saraf
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.
| | - Sunil Kumar Mukherjee
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India; Department of Genetics, University of Delhi, South Campus, Benito Juarez Marg, New Delhi 110021, India.
| | - Nrisingha Dey
- Division of Gene Function and Regulation, Institute of Life Sciences, Nalco Square, Chandrasekharpur, Bhubaneswar 751023, Odisha, India.
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Wagner J, Saraf S, Fridman D. A Simplified Standardized Technique for LESS (Laparoendoscopic Single Site Surgery) Hysterectomy: Experience with over 300 Cases. J Minim Invasive Gynecol 2013. [DOI: 10.1016/j.jmig.2013.08.533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Abadie J, Abbott BP, Abbott R, Adhikari R, Ajith P, Allen B, Allen G, Amador Ceron E, Amin RS, Anderson SB, Anderson WG, Arain MA, Araya M, Aso Y, Aston S, Aufmuth P, Aulbert C, Babak S, Baker P, Ballmer S, Barker D, Barr B, Barriga P, Barsotti L, Barton MA, Bartos I, Bassiri R, Bastarrika M, Behnke B, Benacquista M, Bennett MF, Betzwieser J, Beyersdorf PT, Bilenko IA, Billingsley G, Biswas R, Black E, Blackburn JK, Blackburn L, Blair D, Bland B, Bock O, Bodiya TP, Bondarescu R, Bork R, Born M, Bose S, Brady PR, Braginsky VB, Brau JE, Breyer J, Bridges DO, Brinkmann M, Britzger M, Brooks AF, Brown DA, Bullington A, Buonanno A, Burmeister O, Byer RL, Cadonati L, Cain J, Camp JB, Cannizzo J, Cannon KC, Cao J, Capano C, Cardenas L, Caudill S, Cavaglià M, Cepeda C, Chalermsongsak T, Chalkley E, Charlton P, Chatterji S, Chelkowski S, Chen Y, Christensen N, Chua SSY, Chung CTY, Clark D, Clark J, Clayton JH, Conte R, Cook D, Corbitt TRC, Cornish N, Coward D, Coyne DC, Creighton JDE, Creighton TD, Cruise AM, Culter RM, Cumming A, Cunningham L, Dahl K, Danilishin SL, Danzmann K, Daudert B, Davies G, Daw EJ, Dayanga T, DeBra D, Degallaix J, Dergachev V, DeSalvo R, Dhurandhar S, Díaz M, Donovan F, Dooley KL, Doomes EE, Drever RWP, Driggers J, Dueck J, Duke I, Dumas JC, Dwyer S, Edgar M, Edwards M, Effler A, Ehrens P, Etzel T, Evans M, Evans T, Fairhurst S, Faltas Y, Fan Y, Fazi D, Fehrmann H, Finn LS, Flasch K, Foley S, Forrest C, Fotopoulos N, Frede M, Frei M, Frei Z, Freise A, Frey R, Fricke TT, Friedrich D, Fritschel P, Frolov VV, Fulda P, Fyffe M, Garofoli JA, Ghosh S, Giaime JA, Giampanis S, Giardina KD, Goetz E, Goggin LM, González G, Goßler S, Grant A, Gras S, Gray C, Greenhalgh RJS, Gretarsson AM, Grosso R, Grote H, Grunewald S, Gustafson EK, Gustafson R, Hage B, Hallam JM, Hammer D, Hammond GD, Hanna C, Hanson J, Harms J, Harry GM, Harry IW, Harstad ED, Haughian K, Hayama K, Hayler T, Heefner J, Heng IS, Heptonstall A, Hewitson M, Hild S, Hirose E, Hoak D, Hodge KA, Holt K, Hosken DJ, Hough J, Howell E, Hoyland D, Hughey B, Husa S, Huttner SH, Ingram DR, Isogai T, Ivanov A, Johnson WW, Jones DI, Jones G, Jones R, Ju L, Kalmus P, Kalogera V, Kandhasamy S, Kanner J, Katsavounidis E, Kawabe K, Kawamura S, Kawazoe F, Kells W, Keppel DG, Khalaidovski A, Khalili FY, Khan R, Khazanov E, Kim H, King PJ, Kissel JS, Klimenko S, Kokeyama K, Kondrashov V, Kopparapu R, Koranda S, Kozak D, Kringel V, Krishnan B, Kuehn G, Kullman J, Kumar R, Kwee P, Lam PK, Landry M, Lang M, Lantz B, Lastzka N, Lazzarini A, Leaci P, Lei M, Leindecker N, Leonor I, Lin H, Lindquist PE, Littenberg TB, Lockerbie NA, Lodhia D, Lormand M, Lu P, Lubinski M, Lucianetti A, Lück H, Lundgren A, Machenschalk B, MacInnis M, Mageswaran M, Mailand K, Mak C, Mandel I, Mandic V, Márka S, Márka Z, Markosyan A, Markowitz J, Maros E, Martin IW, Martin RM, Marx JN, Mason K, Matichard F, Matone L, Matzner RA, Mavalvala N, McCarthy R, McClelland DE, McGuire SC, McIntyre G, McKechan DJA, Mehmet M, Melatos A, Melissinos AC, Mendell G, Menéndez DF, Mercer RA, Merrill L, Meshkov S, Messenger C, Meyer MS, Miao H, Miller J, Mino Y, Mitra S, Mitrofanov VP, Mitselmakher G, Mittleman R, Miyakawa O, Moe B, Mohanty SD, Mohapatra SRP, Moreno G, Mors K, Mossavi K, MowLowry C, Mueller G, Müller-Ebhardt H, Mukherjee S, Mullavey A, Munch J, Murray PG, Nash T, Nawrodt R, Nelson J, Newton G, Nishida E, Nishizawa A, O’Dell J, O’Reilly B, O’Shaughnessy R, Ochsner E, Ogin GH, Oldenburg R, Ottaway DJ, Ottens RS, Overmier H, Owen BJ, Page A, Pan Y, Pankow C, Papa MA, Patel P, Pathak D, Pedraza M, Pekowsky L, Penn S, Peralta C, Perreca A, Pickenpack M, Pinto IM, Pitkin M, Pletsch HJ, Plissi MV, Postiglione F, Principe M, Prix R, Prokhorov L, Puncken O, Quetschke V, Raab FJ, Rabeling DS, Radkins H, Raffai P, Raics Z, Rakhmanov M, Raymond V, Reed CM, Reed T, Rehbein H, Reid S, Reitze DH, Riesen R, Riles K, Roberts P, Robertson NA, Robinson C, Robinson EL, Roddy S, Röver C, Rollins J, Romano JD, Romie JH, Rowan S, Rüdiger A, Ryan K, Sakata S, Sammut L, Sancho de la Jordana L, Sandberg V, Sannibale V, Santamaría L, Santostasi G, Saraf S, Sarin P, Sathyaprakash BS, Sato S, Satterthwaite M, Saulson PR, Savage R, Schilling R, Schnabel R, Schofield R, Schulz B, Schutz BF, Schwinberg P, Scott J, Scott SM, Searle AC, Seifert F, Sellers D, Sengupta AS, Sergeev A, Shapiro B, Shawhan P, Shoemaker DH, Sibley A, Siemens X, Sigg D, Sintes AM, Skelton G, Slagmolen BJJ, Slutsky J, Smith JR, Smith MR, Smith ND, Somiya K, Sorazu B, Speirits F, Stein AJ, Stein LC, Steplewski S, Stochino A, Stone R, Strain KA, Strigin S, Stroeer A, Stuver AL, Summerscales TZ, Sung M, Susmithan S, Sutton PJ, Szokoly GP, Talukder D, Tanner DB, Tarabrin SP, Taylor JR, Taylor R, Thorne KA, Thorne KS, Thüring A, Titsler C, Tokmakov KV, Torres C, Torrie CI, Traylor G, Trias M, Turner L, Ugolini D, Urbanek K, Vahlbruch H, Vallisneri M, Van Den Broeck C, van der Sluys MV, van Veggel AA, Vass S, Vaulin R, Vecchio A, Veitch J, Veitch PJ, Veltkamp C, Villar A, Vorvick C, Vyachanin SP, Waldman SJ, Wallace L, Wanner A, Ward RL, Wei P, Weinert M, Weinstein AJ, Weiss R, Wen L, Wen S, Wessels P, West M, Westphal T, Wette K, Whelan JT, Whitcomb SE, Whiting BF, Wilkinson C, Willems PA, Williams HR, Williams L, Willke B, Wilmut I, Winkelmann L, Winkler W, Wipf CC, Wiseman AG, Woan G, Wooley R, Worden J, Yakushin I, Yamamoto H, Yamamoto K, Yeaton-Massey D, Yoshida S, Zanolin M, Zhang L, Zhang Z, Zhao C, Zotov N, Zucker ME, Zweizig J, Buchner S. Publisher’s Note: Search for gravitational waves associated with the August 2006 timing glitch of the Vela pulsar [Phys. Rev. D83, 042001 (2011)]. Int J Clin Exp Med 2012. [DOI: 10.1103/physrevd.85.089902] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Abadie J, Abbott BP, Abbott R, Abernathy M, Accadia T, Acernese F, Adams C, Adhikari R, Ajith P, Allen B, Allen G, Amador Ceron E, Amin RS, Anderson SB, Anderson WG, Antonucci F, Arain MA, Araya M, Aronsson M, Arun KG, Aso Y, Aston S, Astone P, Atkinson DE, Aufmuth P, Aulbert C, Babak S, Baker P, Ballardin G, Ballinger T, Ballmer S, Barker D, Barnum S, Barone F, Barr B, Barriga P, Barsotti L, Barsuglia M, Barton MA, Bartos I, Bassiri R, Bastarrika M, Bauchrowitz J, Bauer TS, Behnke B, Beker MG, Belletoile A, Benacquista M, Bertolini A, Betzwieser J, Beveridge N, Beyersdorf PT, Bigotta S, Bilenko IA, Billingsley G, Birch J, Birindelli S, Biswas R, Bitossi M, Bizouard MA, Black E, Blackburn JK, Blackburn L, Blair D, Bland B, Blom M, Boccara C, Bock O, Bodiya TP, Bondarescu R, Bondu F, Bonelli L, Bonnand R, Bork R, Born M, Bose S, Bosi L, Bouhou B, Boyle M, Braccini S, Bradaschia C, Brady PR, Braginsky VB, Brau JE, Breyer J, Bridges DO, Brillet A, Brinkmann M, Brisson V, Britzger M, Brooks AF, Brown DA, Budzyński R, Bulik T, Bulten HJ, Buonanno A, Burguet-Castell J, Burmeister O, Buskulic D, Buy C, Byer RL, Cadonati L, Cagnoli G, Cain J, Calloni E, Camp JB, Campagna E, Campsie P, Cannizzo J, Cannon KC, Canuel B, Cao J, Capano C, Carbognani F, Caudill S, Cavaglià M, Cavalier F, Cavalieri R, Cella G, Cepeda C, Cesarini E, Chalermsongsak T, Chalkley E, Charlton P, Chassande-Mottin E, Chelkowski S, Chen Y, Chincarini A, Christensen N, Chua SSY, Chung CTY, Clark D, Clark J, Clayton JH, Cleva F, Coccia E, Colacino CN, Colas J, Colla A, Colombini M, Conte R, Cook D, Corbitt TR, Cornish N, Corsi A, Costa CA, Coulon JP, Coward D, Coyne DC, Creighton JDE, Creighton TD, Cruise AM, Culter RM, Cumming A, Cunningham L, Cuoco E, Dahl K, Danilishin SL, Dannenberg R, D’Antonio S, Danzmann K, Das K, Dattilo V, Daudert B, Davier M, Davies G, Davis A, Daw EJ, Day R, Dayanga T, De Rosa R, DeBra D, Degallaix J, del Prete M, Dergachev V, DeRosa R, DeSalvo R, Devanka P, Dhurandhar S, Di Fiore L, Di Lieto A, Di Palma I, Di Paolo Emilio M, Di Virgilio A, Díaz M, Dietz A, Donovan F, Dooley KL, Doomes EE, Dorsher S, Douglas ESD, Drago M, Drever RWP, Driggers JC, Dueck J, Dumas JC, Dwyer S, Eberle T, Edgar M, Edwards M, Effler A, Ehrens P, Ely G, Engel R, Etzel T, Evans M, Evans T, Fafone V, Fairhurst S, Fan Y, Farr BF, Fazi D, Fehrmann H, Feldbaum D, Ferrante I, Fidecaro F, Finn LS, Fiori I, Flaminio R, Flanigan M, Flasch K, Foley S, Forrest C, Forsi E, Fotopoulos N, Fournier JD, Franc J, Frasca S, Frasconi F, Frede M, Frei M, Frei Z, Freise A, Frey R, Fricke TT, Friedrich D, Fritschel P, Frolov VV, Fulda P, Fyffe M, Galimberti M, Gammaitoni L, Garofoli JA, Garufi F, Gemme G, Genin E, Gennai A, Ghosh S, Giaime JA, Giampanis S, Giardina KD, Giazotto A, Gill C, Goetz E, Goggin LM, González G, Goßler S, Gouaty R, Graef C, Granata M, Grant A, Gras S, Gray C, Greenhalgh RJS, Gretarsson AM, Greverie C, Grosso R, Grote H, Grunewald S, Guidi GM, Gustafson EK, Gustafson R, Hage B, Hall P, Hallam JM, Hammer D, Hammond G, Hanks J, Hanna C, Hanson J, Harms J, Harry GM, Harry IW, Harstad ED, Haughian K, Hayama K, Hayau JF, Hayler T, Heefner J, Heitmann H, Hello P, Heng IS, Heptonstall A, Hewitson M, Hild S, Hirose E, Hoak D, Hodge KA, Holt K, Hosken DJ, Hough J, Howell E, Hoyland D, Huet D, Hughey B, Husa S, Huttner SH, Huynh-Dinh T, Ingram DR, Inta R, Isogai T, Ivanov A, Jaranowski P, Johnson WW, Jones DI, Jones G, Jones R, Ju L, Kalmus P, Kalogera V, Kandhasamy S, Kanner J, Katsavounidis E, Kawabe K, Kawamura S, Kawazoe F, Kells W, Keppel DG, Khalaidovski A, Khalili FY, Khazanov EA, Kim H, King PJ, Kinzel DL, Kissel JS, Klimenko S, Kondrashov V, Kopparapu R, Koranda S, Kowalska I, Kozak D, Krause T, Kringel V, Krishnamurthy S, Krishnan B, Królak A, Kuehn G, Kullman J, Kumar R, Kwee P, Landry M, Lang M, Lantz B, Lastzka N, Lazzarini A, Leaci P, Leong J, Leonor I, Leroy N, Letendre N, Li J, Li TGF, Lin H, Lindquist PE, Lockerbie NA, Lodhia D, Lorenzini M, Loriette V, Lormand M, Losurdo G, Lu P, Luan J, Lubinski M, Lucianetti A, Lück H, Lundgren A, Machenschalk B, MacInnis M, Mageswaran M, Mailand K, Majorana E, Mak C, Maksimovic I, Man N, Mandel I, Mandic V, Mantovani M, Marchesoni F, Marion F, Márka S, Márka Z, Maros E, Marque J, Martelli F, Martin IW, Martin RM, Marx JN, Mason K, Masserot A, Matichard F, Matone L, Matzner RA, Mavalvala N, McCarthy R, McClelland DE, McGuire SC, McIntyre G, McIvor G, McKechan DJA, Meadors G, Mehmet M, Meier T, Melatos A, Melissinos AC, Mendell G, Menéndez DF, Mercer RA, Merill L, Meshkov S, Messenger C, Meyer MS, Miao H, Michel C, Milano L, Miller J, Minenkov Y, Mino Y, Mitra S, Mitrofanov VP, Mitselmakher G, Mittleman R, Moe B, Mohan M, Mohanty SD, Mohapatra SRP, Moraru D, Moreau J, Moreno G, Morgado N, Morgia A, Mors K, Mosca S, Moscatelli V, Mossavi K, Mours B, MowLowry C, Mueller G, Mukherjee S, Mullavey A, Müller-Ebhardt H, Munch J, Murray PG, Nash T, Nawrodt R, Nelson J, Neri I, Newton G, Nishida E, Nishizawa A, Nocera F, Nolting D, Ochsner E, O’Dell J, Ogin GH, Oldenburg RG, O’Reilly B, O’Shaughnessy R, Osthelder C, Ottaway DJ, Ottens RS, Overmier H, Owen BJ, Page A, Pagliaroli G, Palladino L, Palomba C, Pan Y, Pankow C, Paoletti F, Papa MA, Pardi S, Pareja M, Parisi M, Pasqualetti A, Passaquieti R, Passuello D, Patel P, Pathak D, Pedraza M, Pekowsky L, Penn S, Peralta C, Perreca A, Persichetti G, Pichot M, Pickenpack M, Piergiovanni F, Pietka M, Pinard L, Pinto IM, Pitkin M, Pletsch HJ, Plissi MV, Poggiani R, Postiglione F, Prato M, Predoi V, Price LR, Prijatelj M, Principe M, Prix R, Prodi GA, Prokhorov L, Puncken O, Punturo M, Puppo P, Quetschke V, Raab FJ, Rabeling DS, Radke T, Radkins H, Raffai P, Rakhmanov M, Rankins B, Rapagnani P, Raymond V, Re V, Reed CM, Reed T, Regimbau T, Reid S, Reitze DH, Ricci F, Riesen R, Riles K, Roberts P, Robertson NA, Robinet F, Robinson C, Robinson EL, Rocchi A, Roddy S, Röver C, Rolland L, Rollins J, Romano JD, Romano R, Romie JH, Rosińska D, Rowan S, Rüdiger A, Ruggi P, Ryan K, Sakata S, Sakosky M, Salemi F, Sammut L, Sancho de la Jordana L, Sandberg V, Sannibale V, Santamaría L, Santostasi G, Saraf S, Sassolas B, Sathyaprakash BS, Sato S, Satterthwaite M, Saulson PR, Savage R, Schilling R, Schnabel R, Schofield R, Schulz B, Schutz BF, Schwinberg P, Scott J, Scott SM, Searle AC, Seifert F, Sellers D, Sengupta AS, Sentenac D, Sergeev A, Shaddock D, Shapiro B, Shawhan P, Shoemaker DH, Sibley A, Siemens X, Sigg D, Singer A, Sintes AM, Skelton G, Slagmolen BJJ, Slutsky J, Smith JR, Smith MR, Smith ND, Somiya K, Sorazu B, Speirits FC, Sperandio L, Stein AJ, Stein LC, Steinlechner S, Steplewski S, Stochino A, Stone R, Strain KA, Strigin S, Stroeer A, Sturani R, Stuver AL, Summerscales TZ, Sung M, Susmithan S, Sutton PJ, Swinkels B, Talukder D, Tanner DB, Tarabrin SP, Taylor JR, Taylor R, Thomas P, Thorne KA, Thorne KS, Thrane E, Thüring A, Titsler C, Tokmakov KV, Toncelli A, Tonelli M, Torre O, Torres C, Torrie CI, Tournefier E, Travasso F, Traylor G, Trias M, Trummer J, Tseng K, Turner L, Ugolini D, Urbanek K, Vahlbruch H, Vaishnav B, Vajente G, Vallisneri M, van den Brand JFJ, Van Den Broeck C, van der Putten S, van der Sluys MV, van Veggel AA, Vass S, Vaulin R, Vavoulidis M, Vecchio A, Vedovato G, Veitch J, Veitch PJ, Veltkamp C, Verkindt D, Vetrano F, Viceré A, Villar A, Vinet JY, Vocca H, Vorvick C, Vyachanin SP, Waldman SJ, Wallace L, Wanner A, Ward RL, Was M, Wei P, Weinert M, Weinstein AJ, Weiss R, Wen L, Wen S, Wessels P, West M, Westphal T, Wette K, Whelan JT, Whitcomb SE, White DJ, Whiting BF, Wilkinson C, Willems PA, Williams L, Willke B, Winkelmann L, Winkler W, Wipf CC, Wiseman AG, Woan G, Wooley R, Worden J, Yakushin I, Yamamoto H, Yamamoto K, Yeaton-Massey D, Yoshida S, Yu PP, Yvert M, Zanolin M, Zhang L, Zhang Z, Zhao C, Zotov N, Zucker ME, Zweizig J. Publisher’s Note: Search for gravitational waves from compact binary coalescence in LIGO and Virgo data from S5 and VSR1 [Phys. Rev. D82, 102001 (2010)]. Int J Clin Exp Med 2012. [DOI: 10.1103/physrevd.85.089903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Saraf S, Patel P, Ozer H, Peace D, Quigley J, Mahmud N, Rondelli D. Improved Outcome of African American Multiple Myeloma Patients with Novel Agents and Autologous Stem Cell Transplant. Biol Blood Marrow Transplant 2012. [DOI: 10.1016/j.bbmt.2011.12.238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Abadie J, Abbott BP, Abbott R, Abernathy M, Accadia T, Acernese F, Adams C, Adhikari R, Ajith P, Allen B, Allen GS, Ceron EA, Amin RS, Anderson SB, Anderson WG, Antonucci F, Arain MA, Araya MC, Aronsson M, Arun KG, Aso Y, Aston SM, Astone P, Atkinson D, Aufmuth P, Aulbert C, Babak S, Baker P, Ballardin G, Ballmer S, Barker D, Barnum S, Barone F, Barr B, Barriga P, Barsotti L, Barsuglia M, Barton MA, Bartos I, Bassiri R, Bastarrika M, Bauchrowitz J, Bauer TS, Behnke B, Beker MG, Belletoile A, Benacquista M, Bertolini A, Betzwieser J, Beveridge N, Beyersdorf PT, Bigotta S, Bilenko IA, Billingsley G, Birch J, Birindelli S, Biswas R, Bitossi M, Bizouard MA, Black E, Blackburn JK, Blackburn L, Blair D, Bland B, Blom M, Boccara C, Bock O, Bodiya TP, Bondarescu R, Bondu F, Bonelli L, Bonnand R, Bork R, Born M, Bose S, Bosi L, Bouhou B, Boyle M, Braccini S, Bradaschia C, Brady PR, Braginsky VB, Brau JE, Breyer J, Bridges DO, Brillet A, Brinkmann M, Brisson V, Britzger M, Brooks AF, Brown DA, Budzyński R, Bulik T, Bulten HJ, Buonanno A, Burguet-Castell J, Burmeister O, Buskulic D, Buy C, Byer RL, Cadonati L, Cagnoli G, Cain J, Calloni E, Camp JB, Campagna E, Campsie P, Cannizzo J, Cannon K, Canuel B, Cao J, Capano C, Carbognani F, Caride S, Caudill S, Cavaglià M, Cavalier F, Cavalieri R, Cella G, Cepeda C, Cesarini E, Chalermsongsak T, Chalkley E, Charlton P, Chassande-Mottin E, Chelkowski S, Chen Y, Chincarini A, Christensen N, Chua SSY, Chung CTY, Clark D, Clark J, Clayton JH, Cleva F, Coccia E, Colacino CN, Colas J, Colla A, Colombini M, Conte R, Cook D, Corbitt TR, Cornish N, Corsi A, Costa CA, Coulon JP, Coward DM, Coyne DC, Creighton JDE, Creighton TD, Cruise AM, Culter RM, Cumming A, Cunningham L, Cuoco E, Dahl K, Danilishin SL, Dannenberg R, D'Antonio S, Danzmann K, Das K, Dattilo V, Daudert B, Davier M, Davies G, Davis A, Daw EJ, Day R, Dayanga T, De Rosa R, DeBra D, Degallaix J, del Prete M, Dergachev V, DeRosa R, DeSalvo R, Devanka P, Dhurandhar S, Di Fiore L, Di Lieto A, Di Palma I, Di Paolo Emilio M, Di Virgilio A, Díaz M, Dietz A, Donovan F, Dooley KL, Doomes EE, Dorsher S, Douglas ESD, Drago M, Drever RWP, Driggers JC, Dueck J, Dumas JC, Eberle T, Edgar M, Edwards M, Effler A, Ehrens P, Engel R, Etzel T, Evans M, Evans T, Fafone V, Fairhurst S, Fan Y, Farr BF, Fazi D, Fehrmann H, Feldbaum D, Ferrante I, Fidecaro F, Finn LS, Fiori I, Flaminio R, Flanigan M, Flasch K, Foley S, Forrest C, Forsi E, Fotopoulos N, Fournier JD, Franc J, Frasca S, Frasconi F, Frede M, Frei M, Frei Z, Freise A, Frey R, Fricke TT, Friedrich D, Fritschel P, Frolov VV, Fulda P, Fyffe M, Galimberti M, Gammaitoni L, Garofoli JA, Garufi F, Gemme G, Genin E, Gennai A, Gholami I, Ghosh S, Giaime JA, Giampanis S, Giardina KD, Giazotto A, Gill C, Goetz E, Goggin LM, González G, Gorodetsky ML, Gossler S, Gouaty R, Graef C, Granata M, Grant A, Gras S, Gray C, Greenhalgh RJS, Gretarsson AM, Greverie C, Grosso R, Grote H, Grunewald S, Guidi GM, Gustafson EK, Gustafson R, Hage B, Hall P, Hallam JM, Hammer D, Hammond G, Hanks J, Hanna C, Hanson J, Harms J, Harry GM, Harry IW, Harstad ED, Haughian K, Hayama K, Hayau JF, Hayler T, Heefner J, Heitmann H, Hello P, Heng IS, Heptonstall AW, Hewitson M, Hild S, Hirose E, Hoak D, Hodge KA, Holt K, Hosken DJ, Hough J, Howell EJ, Hoyland D, Huet D, Hughey B, Husa S, Huttner SH, Huynh-Dinh T, Ingram DR, Inta R, Isogai T, Ivanov A, Jaranowski P, Johnson WW, Jones DI, Jones G, Jones R, Ju L, Kalmus P, Kalogera V, Kandhasamy S, Kanner JB, Katsavounidis E, Kawabe K, Kawamura S, Kawazoe F, Kells W, Keppel DG, Khalaidovski A, Khalili FY, Khazanov EA, Kim H, King PJ, Kinzel DL, Kissel JS, Klimenko S, Kondrashov V, Kopparapu R, Koranda S, Kowalska I, Kozak D, Krause T, Kringel V, Krishnamurthy S, Krishnan B, Królak A, Kuehn G, Kullman J, Kumar R, Kwee P, Landry M, Lang M, Lantz B, Lastzka N, Lazzarini A, Leaci P, Leong J, Leonor I, Leroy N, Letendre N, Li J, Li TGF, Liguori N, Lin H, Lindquist PE, Lockerbie NA, Lodhia D, Lorenzini M, Loriette V, Lormand M, Losurdo G, Lu P, Luan J, Lubinski M, Lucianetti A, Lück H, Lundgren AD, Machenschalk B, MacInnis M, Mageswaran M, Mailand K, Majorana E, Mak C, Maksimovic I, Man N, Mandel I, Mandic V, Mantovani M, Marchesoni F, Marion F, Márka S, Márka Z, Maros E, Marque J, Martelli F, Martin IW, Martin RM, Marx JN, Mason K, Masserot A, Matichard F, Matone L, Matzner RA, Mavalvala N, McCarthy R, McClelland DE, McGuire SC, McIntyre G, McIvor G, McKechan DJA, Meadors G, Mehmet M, Meier T, Melatos A, Melissinos AC, Mendell G, Menéndez DF, Mercer RA, Merill L, Meshkov S, Messenger C, Meyer MS, Miao H, Michel C, Milano L, Miller J, Minenkov Y, Mino Y, Mitra S, Mitrofanov VP, Mitselmakher G, Mittleman R, Moe B, Mohan M, Mohanty SD, Mohapatra SRP, Moraru D, Moreau J, Moreno G, Morgado N, Morgia A, Morioka T, Mors K, Mosca S, Moscatelli V, Mossavi K, Mours B, Mow-Lowry CM, Mueller G, Mukherjee S, Mullavey A, Müller-Ebhardt H, Munch J, Murray PG, Nash T, Nawrodt R, Nelson J, Neri I, Newton G, Nishizawa A, Nocera F, Nolting D, Ochsner E, O'Dell J, Ogin GH, Oldenburg RG, O'Reilly B, O'Shaughnessy R, Osthelder C, Ottaway DJ, Ottens RS, Overmier H, Owen BJ, Page A, Pagliaroli G, Palladino L, Palomba C, Pan Y, Pankow C, Paoletti F, Papa MA, Pardi S, Pareja M, Parisi M, Pasqualetti A, Passaquieti R, Passuello D, Patel P, Pathak D, Pedraza M, Pekowsky L, Penn S, Peralta C, Perreca A, Persichetti G, Pichot M, Pickenpack M, Piergiovanni F, Pietka M, Pinard L, Pinto IM, Pitkin M, Pletsch HJ, Plissi MV, Poggiani R, Postiglione F, Prato M, Predoi V, Price LR, Prijatelj M, Principe M, Prix R, Prodi GA, Prokhorov L, Puncken O, Punturo M, Puppo P, Quetschke V, Raab FJ, Rabeling DS, Radke T, Radkins H, Raffai P, Rakhmanov M, Rankins B, Rapagnani P, Raymond V, Re V, Reed CM, Reed T, Regimbau T, Reid S, Reitze DH, Ricci F, Riesen R, Riles K, Roberts P, Robertson NA, Robinet F, Robinson C, Robinson EL, Rocchi A, Roddy S, Röver C, Rolland L, Rollins J, Romano JD, Romano R, Romie JH, Rosińska D, Rowan S, Rüdiger A, Ruggi P, Ryan K, Sakata S, Sakosky M, Salemi F, Sammut L, de la Jordana LS, Sandberg V, Sannibale V, Santamaría L, Santostasi G, Saraf S, Sassolas B, Sathyaprakash BS, Sato S, Satterthwaite M, Saulson PR, Savage R, Schilling R, Schnabel R, Schofield RMS, Schulz B, Schutz BF, Schwinberg P, Scott J, Scott SM, Searle AC, Seifert F, Sellers D, Sengupta AS, Sentenac D, Sergeev A, Shaddock DA, Shapiro B, Shawhan P, Shoemaker DH, Sibley A, Siemens X, Sigg D, Singer A, Sintes AM, Skelton G, Slagmolen BJJ, Slutsky J, Smith JR, Smith MR, Smith ND, Somiya K, Sorazu B, Speirits FC, Sperandio L, Stein AJ, Stein LC, Steinlechner S, Steplewski S, Stochino A, Stone R, Strain KA, Strigin S, Stroeer AS, Sturani R, Stuver AL, Summerscales TZ, Sung M, Susmithan S, Sutton PJ, Swinkels B, Szokoly GP, Talukder D, Tanner DB, Tarabrin SP, Taylor JR, Taylor R, Thomas P, Thorne KA, Thorne KS, Thrane E, Thüring A, Titsler C, Tokmakov KV, Toncelli A, Tonelli M, Torre O, Torres C, Torrie CI, Tournefier E, Travasso F, Traylor G, Trias M, Trummer J, Tseng K, Turner L, Ugolini D, Urbanek K, Vahlbruch H, Vaishnav B, Vajente G, Vallisneri M, van den Brand JFJ, Van Den Broeck C, van der Putten S, van der Sluys MV, van Veggel AA, Vass S, Vaulin R, Vavoulidis M, Vecchio A, Vedovato G, Veitch J, Veitch PJ, Veltkamp C, Verkindt D, Vetrano F, Viceré A, Villar AE, Vinet JY, Vocca H, Vorvick C, Vyachanin SP, Waldman SJ, Wallace L, Wanner A, Ward RL, Was M, Wei P, Weinert M, Weinstein AJ, Weiss R, Wen L, Wen S, Wessels P, West M, Westphal T, Wette K, Whelan JT, Whitcomb SE, White D, Whiting BF, Wilkinson C, Willems PA, Williams L, Willke B, Winkelmann L, Winkler W, Wipf CC, Wiseman AG, Woan G, Wooley R, Worden J, Yakushin I, Yamamoto H, Yamamoto K, Yeaton-Massey D, Yoshida S, Yu P, Yvert M, Zanolin M, Zhang L, Zhang Z, Zhao C, Zotov N, Zucker ME, Zweizig J. Directional limits on persistent gravitational waves using LIGO S5 science data. Phys Rev Lett 2011; 107:271102. [PMID: 22243300 DOI: 10.1103/physrevlett.107.271102] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2011] [Indexed: 05/31/2023]
Abstract
The gravitational-wave (GW) sky may include nearby pointlike sources as well as stochastic backgrounds. We perform two directional searches for persistent GWs using data from the LIGO S5 science run: one optimized for pointlike sources and one for arbitrary extended sources. Finding no evidence to support the detection of GWs, we present 90% confidence level (C.L.) upper-limit maps of GW strain power with typical values between 2-20×10(-50) strain(2) Hz(-1) and 5-35×10(-49) strain(2) Hz(-1) sr(-1) for pointlike and extended sources, respectively. The latter result is the first of its kind. We also set 90% C.L. limits on the narrow-band root-mean-square GW strain from interesting targets including Sco X-1, SN 1987A and the Galactic center as low as ≈7×10(-25) in the most sensitive frequency range near 160 Hz.
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Affiliation(s)
- J Abadie
- LIGO-California Institute of Technology, Pasadena, California 91125, USA
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Kenny C, Adhya S, Dworakowski R, Brickham B, Maccarthy P, Monaghan M, Guzzo A, Innocenti F, Vicidomini S, Lazzeretti D, Squarciotta S, De Villa E, Donnini C, Bulletti F, Guerrini E, Pini R, Bendjelid K, Viale J, Duperret S, Piriou V, Jacques D, Shahgaldi K, Silva C, Pedro F, Deister L, Brodin LA, Sahlen A, Manouras A, Winter R, Berjeb N, Cimadevilla C, Dreyfus J, Cueff C, Malanca M, Chiampan A, Vahanian A, Messika-Zeitoun D, Muraru D, Peluso D, Dal Bianco L, Beraldo M, Solda' E, Tuveri M, Cucchini U, Al Mamary A, Badano L, Iliceto S, Almuntaser I, King G, Norris S, Daly C, Ellis E, Murphy R, Erdei T, Denes M, Kardos A, Foldesi C, Temesvari A, Lengyel M, Bouzas Mosquera A, Broullon F, Alvarez-Garcia N, Peteiro J, Barge-Caballero G, Lopez-Perez M, Lopez-Sainz A, Castro-Beiras A, Luotolahti M, Luotolahti H, Kantola I, Viikari J, Andersen M, Ersboell M, Bro-Jeppesen J, Gustafsson F, Koeber L, Hassager C, Moller J, Coisne D, Diakov C, Vallet F, Lequeux B, Blouin P, Christiaens L, Esposito R, Santoro A, Schiano Lomoriello V, Raia R, Santoro C, De Simone G, Galderisi M, Sahlen A, Abdula G, Winter R, Kosmala W, Szczepanik-Osadnik H, Przewlocka-Kosmala M, Mysiak A, O' Moore-Sullivan T, Marwick T, Tan YT, Wenzelburger F, Leyva F, Sanderson J, Pichler P, Syeda B, Hoefer P, Zuckermann A, Binder T, Fijalkowski M, Koprowski A, Galaska R, Blaut K, Sworczak K, Rynkiewicz A, Lee S, Kim W, Jung L, Yun H, Song M, Ko J, Khalifa EA, Szymanski P, Lipczynska M, Klisieiwcz A, Hoffman P, Jorge C, Silva Marques J, Robalo Martins S, Calisto C, Mieiro M, Vieira S, Correia M, Carvalho De Sousa J, Almeida A, Nunes Diogo A, Park C, March K, Tillin T, Mayet J, Chaturvedi N, Hughes A, Di Bello V, Giannini C, Delle Donne M, De Sanctis F, Spontoni P, Cucco C, Corciu A, Grigoratos C, Bogazzi F, Balbarini A, Enescu O, Suran B, Florescu M, Cinteza M, Vinereanu D, Higuchi Y, Iwakura K, Okamura A, Date M, Fujii K, Jorge C, Cortez-Dias N, Silva D, Carrilho-Ferreira P, Silva Marques J, Magalhaes A, Ribeiro S, Goncalves S, Fiuza M, Pinto F, Jorge C, Cortez-Dias N, Silva D, Silva Marques J, Carrilho-Ferreira P, Placido R, Bordalo A, Goncalves S, Fiuza M, Pinto F, Grzywocz P, Mizia-Stec K, Chudek J, Gasior Z, Maceira Gonzalez AM, Cosin Sales J, Dalli E, Igual B, Diago J, Aguilar J, Ruvira J, Cimino S, Pedrizzetti G, Tonti G, Canali E, Petronilli V, Boccalini F, Mattatelli A, Hiramoto Y, Iacoboni C, Agati L, Trifunovic D, Ostojic M, Vujisic-Tesic B, Petrovic M, Nedeljkovic I, Banovic M, Boricic-Kostic M, Draganic G, Tesic M, Petrovic M, Gavina C, Lopes R, Lourenco A, Almeida J, Rodrigues J, Pinho P, Zamorano J, Leite-Moreira A, Rocha-Goncalves F, Clavel MA, Capoulade R, Dumesnil J, Mathieu P, Despres JP, Pibarot P, Bull S, Pitcher A, Augustine D, D'arcy J, Karamitsos T, Rai A, Prendergast B, Becher H, Neubauer S, Myerson S, Magne J, Donal E, Davin L, O'connor K, Pirlet C, Rosca M, Szymanski C, Cosyns B, Pierard L, Lancellotti P, Calin A, Rosca M, Popescu B, Beladan C, Enache R, Lupascu L, Sandu C, Lancellotti P, Pierard L, Ginghina C, Kamperidis V, Hadjimiltiadis S, Sianos G, Anastasiadis K, Grosomanidis V, Efthimiadis G, Karvounis H, Parharidis G, Styliadis I, Gonzalez Canovas C, Munoz-Esparza C, Bonaque Gonzalez J, Fernandez A, Salar Alcaraz M, Saura Espin D, Pinar Bermudez E, Oliva-Sandoval M, De La Morena Valenzuela G, Valdes Chavarri M, Dreyfus J, Brochet E, Lepage L, Attias D, Cueff C, Detaint D, Himbert D, Iung B, Vahanian A, Messika-Zeitoun D, Pirat B, Little S, Chang S, Tiller L, Kumar R, Zoghbi W, Lee APW, Hsiung M, Wan S, Wong R, Luo F, Fang F, Xie J, Underwood M, Sun J, Yu C, Jansen R, Tietge W, Sijbrandij K, Cramer M, De Heer L, Kluin J, Chamuleau SAJ, Oliveras Vila T, Ferrer Sistach E, Delgado Ramis L, Lopez Ayerbe J, Vallejo Camazon N, Gual Capllonch F, Garcia Alonso C, Teis Soley A, Ruyra Baliarda X, Bayes Genis A, Negrea S, Alexandrescu C, Bourlon F, Civaia F, Dreyfus G, Paetzold S, Luha O, Hoedl R, Stoschitzky G, Pfeiffer K, Zweiker D, Pieske B, Maier R, Sevilla T, Revilla A, Lopez J, Vilacosta I, Arnold R, Gomez I, San Roman J, Nikcevic G, Djordjevic Dikic A, Djordjevic S, Raspopovic S, Jovanovic V, Kircanski B, Pavlovic S, Milasinovic G, Ruiz-Zamora I, Cabrera Bueno F, Molina M, Fernandez-Pastor J, Pena J, Linde A, Barrera A, Alzueta J, Bremont C, Bensaid A, Alonso H, Zaghden O, Nahum J, Dubois-Rande J, Gueret P, Lim P, Lee SP, Park K, Kim HR, Lee JH, Ahn HS, Kim JH, Kim HK, Kim YJ, Sohn DW, Niemann M, Herrmann S, Hu K, Liu D, Beer M, Ertl G, Wanner C, Takenaka T, Tei C, Weidemann F, Silva D, Madeira H, Mendes Pedro M, Nunes Diogo A, Brito D, Schiano Lomoriello V, Ippolito R, Santoro A, Esposito R, Raia R, De Palma D, Galderisi M, Gati S, Oxborough D, Reed M, Zaidi A, Ghani S, Sheikh N, Papadakis M, Sharma S, Chow V, Ng A, Pasqualon T, Zhao W, Hanzek D, Chung T, Yeoh T, Kritharides L, Florescu M, Magda L, Enescu O, Mihalcea D, Suran B, Jinga D, Mincu R, Cinteza M, Vinereanu D, Ferrazzi E, Segato G, Folino F, Famoso G, Senzolo M, Bellu R, Corbetti F, Iliceto S, Tona F, Azevedo O, Quelhas I, Guardado J, Fernandes M, Pereira V, Medeiros R, Lourenco A, Sousa P, Santos W, Pereira S, Marques N, Mimoso J, Marques V, Jesus I, Rustad L, Nytroen K, Gullestad L, Amundsen B, Aakhus S, Linhartova K, Sterbakova G, Necas J, Kovalova S, Cerbak R, Nelassov N, Korotkijan N, Shishkina A, Gagieva B, Nagaplev M, Eroshenko O, Morgunov M, Parmon S, Velthuis S, Van Gent M, Post M, Westermann C, Mager J, Snijder R, Koyalakonda SP, Anderson M, Burgess M, Bergenzaun L, Chew M, Ohlin H, Gjerdalen GF, Hisdal J, Solberg E, Andersen T, Radunovic Z, Steine K, Rutz T, Kuehn A, Petzuch K, Pekala M, Elmenhorst J, Fratz S, Mueller J, Hager A, Hess J, Vogt M, Van Der Linde D, Van De Laar I, Wessels M, Bekkers J, Moelker A, Tanghe H, Van Kooten F, Oldenburg R, Bertoli-Avella A, Roos-Hesselink J, Cresti A, Fontani L, Calabria P, Capati E, Severi S, Lynch M, Saraf S, Sandler B, Yoon S, Kim S, Ko C, Ryu S, Byun Y, Seo H, Ciampi Q, Rigo F, Pratali L, Gherardi S, Villari B, Picano E, Sicari R, Celutkiene J, Zakarkaite D, Skorniakov V, Zvironaite V, Grabauskiene V, Sinicyna J, Gruodyte G, Janonyte K, Laucevicius A, O'driscoll J, Schmid K, Marciniak A, Saha A, Gupta S, Smith R, Sharma R, Bouzas Mosquera A, Alvarez Garcia N, Peteiro J, Broullon F, Prada O, Rodriguez Vilela A, Barge Caballero G, Lopez Perez M, Lopez Sainz A, Castro Beiras A, Kochanowski J, Scislo P, Piatkowski R, Grabowski M, Marchel M, Roik M, Kosior D, Opolski G, Van De Heyning CM, Magne J, O'connor K, Mahjoub H, Pibarot P, Pirlet C, Pierard L, Lancellotti P, Clausen H, Basaggianis C, Newton J, Del Pasqua A, Carotti A, Di Carlo D, Cetrano E, Toscano A, Iacobelli R, Esposito C, Chinali M, Pongiglione G, Rinelli G, Larsson M, Larsson M, Bjallmark A, Winter R, Caidahl K, Brodin L, Velthuis S, Van Gent M, Mager J, Westermann C, Snijder R, Post M, Gao H, Coisne D, Lugiez M, Guivier C, Rieu R, D'hooge J, Lugiez M, Hang G, D'hooge J, Guerin C, Christiaens L, Menard M, Voigt JU, Coisne D, Dungu J, Campos G, Jaffarulla R, Gomes-Pereira S, Sutaria N, Baker C, Nihoyannopoulos P, Bellamy M, Adhya S, Harries D, Walker N, Pearson P, Reiken J, Batteson J, Kamdar R, Murgatroyd F, Monaghan M, D'andrea A, Riegler L, Scarafile R, Pezzullo E, Salerno G, Bossone E, Limongelli G, Russo M, Pacileo G, Calabro' R, Kang Y, Cui J, Chen H, Pan C, Shu X, Kiotsekoglou A, Saha S, Toole R, Govind S, Gopal A, Crispi F, Bijnens B, Sepulveda-Swatson E, Rojas-Benavente J, Dominguez J, Illa M, Eixarch E, Sitges M, Gratacos E, Prinz C, Faludi R, Walker A, Amzulescu M, Gao H, Uejima T, Fraser A, Voigt J, Esmaeilzadeh M, Maleki M, Amin A, Vakilian F, Noohi F, Ojaghi Haghighi Z, Nakhostin Davari P, Bakhshandeh Abkenar H, Rimbas R, Dulgheru R, Margulescu A, Florescu M, Vinereanu D, Toscano A, Chinali M, D' Asaro M, Iacobelli R, Del Pasqua A, Esposito C, Mizzon C, Parisi F, Pongiglione G, Rinelli G, Jung BC, Lee BY, Kang HJ, Kim S, Kim M, Kim Y, Cho D, Park S, Hong S, Lim D, Shim W, Bellsham-Revell H, Tibby S, Bell AJ, Miller OI, Greil G, Simpson JM, Providencia RA, Trigo J, Botelho A, Gomes P, Seca L, Barra S, Faustino A, Costa G, Quintal N, Leitao-Marques A, Nestaas E, Stoylen A, Fugelseth D, Mornos C, Ionac A, Petrescu L, Cozma D, Dragulescu D, Mornos A, Pescariu S, Fontana A, Abbate M, Cazzaniga M, Giannattasio C, Trocino G, Laser K, Faber L, Fischer M, Koerperich H, Kececioglu D, Elnoamany MF, Dawood A, Elhabashy M, Khalil Y, Fontana A, Abbate M, Cazzaniga M, Giannattasio C, Trocino G, Piriou N, Warin-Fresse K, Caza M, Fau G, Crochet D, Xhabija N, Allajbeu I, Petrela E, Heba M, Barreiro Perez M, Martin Fernandez M, Renilla Gonzalez A, Florez Munoz J, Fernandez Cimadevilla O, Alvarez Pichel I, Velasco Alonso E, Leon Duran D, Benito Martin E, Secades Gonzalez S, Gargani L, Pang P, Davis E, Schumacher A, Sicari R, Picano E, Silva Ferreira A, Bettencourt N, Matos P, Oliveira L, Almeida A, Maceira Gonzalez AM, Cosin-Sales J, Igual B, Lopez Lereu M, Monmeneu J, Estornell J, Tsverava M, Tsverava D, Varela A, Salagianni M, Galani I, Andreakos E, Davos C, Ikonomidis I, Lekakis J, Tritakis V, Kadoglou N, Papadakis J, Trivilou P, Tzortzis S, Koukoulis C, Paraskevaidis I, Anastasiou-Nana M, Kim G, Youn H, Park C, Ibrahimi P, Bajraktari G, Jashari F, Ahmeti A, Poniku A, Haliti E, Henein M, Pezo Nikolic B, Jurin H, Lovric D, Baricevic Z, Ivanac Vranesic I, Lovric Bencic M, Ernst A, Separovic Hanzevacki J. Poster Session 3: Friday 9 December 2011, 08:30-12:30 * Location: Poster Area. European Journal of Echocardiography 2011. [DOI: 10.1093/ejechocard/jer214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Saraf S, Fridman D, Wagner J. Single-Incision Laparoscopic Gynecological Surgeries: 1 Year Experience. J Minim Invasive Gynecol 2011. [DOI: 10.1016/j.jmig.2011.08.555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Fridman D, Saraf S, Wagner J. Single-Incision Laparoscopy as the Primary Approach to Benign Hysterectomy: One Year Experience. J Minim Invasive Gynecol 2011. [DOI: 10.1016/j.jmig.2011.08.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Anand A, Pundir R, Pandian CS, Saraf S, Gupta H. Cefoperazone sodium impregnated polycaprolactone composite implant for osteomyelitis. Indian J Pharm Sci 2011; 71:377-81. [PMID: 20502542 PMCID: PMC2865808 DOI: 10.4103/0250-474x.57285] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2008] [Revised: 07/03/2009] [Accepted: 07/04/2009] [Indexed: 11/05/2022] Open
Abstract
The use of local antibiotics from a biodegradable implant for chronic osteomyelitis is an attractive alternative. The implant delivers high antibiotic concentration at tissue levels, obliterates dead space, aids bone repair and does not need to be removed. The purpose of this paper is to develop and evaluate a calcium sulphate and polycaprolactone based composite biodegradable implantable delivery system of cefoperazone sodium. Implants were prepared by modified fabrication technique to avoid solvent use. Interaction studies were carried out to check any incompatibility between ingredients. Prepared implants were evaluated for various in vitro parameters like dimensions, hardness, tensile strength, drug release profile and sterility. Morphological changes in pellet before and after drug release were evaluated by scanning electron microscopy. The pellet were also tested for microbiological efficacy and compared with plain drug solution in different concentrations. Developed pellets are regular in shape and size with good tensile strength. The release profile displayed drug levels above MIC continuously up to 2 months. Wide zone of inhibition by pellet against Staph. aureus as compared to drug solution proves its efficacy in treatment of osteomyelitis.
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Affiliation(s)
- A Anand
- Babu Banarasi Das National Institute of Technology & Management, Lucknow-226 007, India
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Saraf S, Singh K. P162. Unusual case report of a malignant soft tissue tumor with review on emerging newer trends in histopathological diagnosis. Oral Oncol 2011. [DOI: 10.1016/j.oraloncology.2011.06.405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Saraf S, Kharbanda J. O67. A rare case report of an adenomatoid odontogenic tumor arising in the wall of an odontogenic keratocyst. Oral Oncol 2011. [DOI: 10.1016/j.oraloncology.2011.06.178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Ramachandran S, Saraf S, Shetty C, Capps N, Bailey C. Paradoxical decrease in HDL-cholesterol and apolipoprotein A1 with simvastatin and atorvastatin in a patient with type 2 diabetes. Ann Clin Biochem 2010; 48:75-8. [PMID: 21115572 DOI: 10.1258/acb.2010.010081] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Statins are agents widely used to lower LDL-cholesterol (LDL-C) in primary and secondary prevention of coronary heart disease. The five statins available in the UK (simvastatin, pravastatin, fluvastatin, atorvastatin and rosuvastatin) differ in many of their pharmacologic properties. In addition to lowering LDL-C, statins also increase HDL-cholesterol (HDL-C) moderately. There have been rare reports of significant HDL-C decreases in patients commenced on fibrates and when thiazolidinediones are added to fibrates. This is known as a 'paradoxical HDL-C decrease' as both groups of agents usually increase HDL-C. This phenomenon has never been clearly documented following statin therapy. We now describe a patient with type 2 diabetes who showed this paradoxical fall in HDL-C (baseline HDL-C: 1.8 mmol/L; on simvastatin 40 mg HDL-C 0.6 mmol/L; on atorvastatin 20 mg HDL-C 0.9 mmol/L) with a similar decrease in apolipoprotein A1. No similar decrease was observed with pravastatin and rosuvastatin therapy. This phenomenon appeared to be associated with statin treatment and not a statin/fibrate combination. Our patient clearly demonstrated a paradoxical HDL-C fall with simvastatin and atorvastatin, but not pravastatin or rosuvastatin. Simvastatin and atorvastatin share many pharmacokinetic properties such as lipophilicity while pravastatin and rosuvastatin are relatively hydrophilic and are not metabolized by cytochrome P450 3A4. However, these characteristics do not explain the dramatic reductions in HDL-C observed.
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Affiliation(s)
- S Ramachandran
- Department of Clinical Biochemistry, Good Hope Hospital, Heart of England Foundation Trust, Sutton Coldfield, West Midlands, UK.
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Singh D, Rawat Singh M, Saraf S, Dixit V, Saraf S. Formulation Optimization of Metronidazole Loaded Chitosan Microspheres for Wound Management by 3-Factor, 3-Level Box-Behnken Design. ACTA ACUST UNITED AC 2010. [DOI: 10.2174/1876402911002020070] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Ajazuddin, Saraf S. Applications of novel drug delivery system for herbal formulations. Fitoterapia 2010; 81:680-9. [PMID: 20471457 DOI: 10.1016/j.fitote.2010.05.001] [Citation(s) in RCA: 240] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 04/28/2010] [Accepted: 05/04/2010] [Indexed: 10/19/2022]
Abstract
Over the past several years, great advances have been made on development of novel drug delivery systems (NDDS) for plant actives and extracts. The variety of novel herbal formulations like polymeric nanoparticles, nanocapsules, liposomes, phytosomes, nanoemulsions, microsphere, transferosomes, and ethosomes has been reported using bioactive and plant extracts. The novel formulations are reported to have remarkable advantages over conventional formulations of plant actives and extracts which include enhancement of solubility, bioavailability, protection from toxicity, enhancement of pharmacological activity, enhancement of stability, improved tissue macrophages distribution, sustained delivery, and protection from physical and chemical degradation. The present review highlights the current status of the development of novel herbal formulations and summarizes their method of preparation, type of active ingredients, size, entrapment efficiency, route of administration, biological activity and applications of novel formulations.
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Affiliation(s)
- Ajazuddin
- University Institute of Pharmacy, Pt. Ravi Shankar Shukla University, Raipur, C.G., 492010, India
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Fanaras N, Saraf S, Majumdar A. P81 Surgically assisted rapid maxillary expansion with transpalatal distractors – initial surgical results. Br J Oral Maxillofac Surg 2010. [DOI: 10.1016/s0266-4356(10)60172-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abstract
Phytoconstituents are gaining popularity as ingredients in cosmetic formulations as they can protect the skin against exogenous and endogenous harmful agents and can help remedy many skin conditions. Exposure of skin to sunlight and other atmospheric conditions causes the production of reactive oxygen species, which can react with DNA, proteins, and fatty acids, causing oxidative damage and impairment of antioxidant system. Such injuries damage regulation pathways of skin and lead to photoaging and skin cancer development. The effects of aging include wrinkles, roughness, appearance of fine lines, lack of elasticity, and de- or hyperpigmentation marks. Herbal extracts act on these areas and produce healing, softening, rejuvenating, and sunscreen effects. We have selected a few photoprotective phytoconstituents, such as curcumin, resveratrol, tea polyphenols, silymarin, quercetin and ascorbic acid, and have discussed the considerations to be undertaken for the development of herbal cosmetic formulations that could reduce the occurrence of skin cancer and delay the process of photoaging. This article is aimed at providing specific and compiled knowledge for the successful preparation of photoprotective herbal cosmetic formulations.
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Affiliation(s)
- S. Saraf
- University Institute of Pharmacy, Pt. Ravishankar Shukla University, Raipur (C.G.) - 492 010, India
| | - C. D. Kaur
- University Institute of Pharmacy, Pt. Ravishankar Shukla University, Raipur (C.G.) - 492 010, India
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Abstract
Aspirin and clopidogrel are the most commonly used antiplatelet agents in patients with coronary artery disease. The existence of resistance to these agents has been a controversial issue and new drugs are being developed to overcome this problem. Laboratory tests, which can identify resistance and correlate this with clinical outcome, are being studied in order to identify patients at risk of future thrombotic events. We discuss the evidence for the existence of antiplatelet resistance—both in the laboratory and in the clinical setting. So far, platelet aggregometry has been considered the gold standard test, but is very operator dependant, time consuming, and has shown little correlation with other available tests of antiplatelet resistance. We discuss the available tests of platelet function, their limitations, and evidence for their use. A simple, rapid, near-patient test, which is affordable and useful in the clinical (not just laboratory) setting, could allow risk stratification of patients and individualization of antiplatelet medication to improve outcome.
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Affiliation(s)
- S. Saraf
- Cardiology Department, East and North Hertfordshire NHS Trust, UK
| | - I. Bensalha
- Cardiology Department, East and North Hertfordshire NHS Trust, UK
| | - D.A. Gorog
- Cardiology Department, East and North Hertfordshire NHS Trust, UK
- Imperial College, London, UK
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Saraf S, Bensalha I, Gorog D. Antiplatelet Resistance-Does it Exist and How to Measure it? Clin Med Cardiol 2009; 3:77-91. [PMID: 20508768 PMCID: PMC2872576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Aspirin and clopidogrel are the most commonly used antiplatelet agents in patients with coronary artery disease. The existence of resistance to these agents has been a controversial issue and new drugs are being developed to overcome this problem. Laboratory tests, which can identify resistance and correlate this with clinical outcome, are being studied in order to identify patients at risk of future thrombotic events. We discuss the evidence for the existence of antiplatelet resistance-both in the laboratory and in the clinical setting. So far, platelet aggregometry has been considered the gold standard test, but is very operator dependant, time consuming, and has shown little correlation with other available tests of antiplatelet resistance. We discuss the available tests of platelet function, their limitations, and evidence for their use. A simple, rapid, near-patient test, which is affordable and useful in the clinical (not just laboratory) setting, could allow risk stratification of patients and individualization of antiplatelet medication to improve outcome.
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Affiliation(s)
- S. Saraf
- Cardiology Department, East and North Hertfordshire NHS Trust, UK
| | - I. Bensalha
- Cardiology Department, East and North Hertfordshire NHS Trust, UK
| | - D.A. Gorog
- Cardiology Department, East and North Hertfordshire NHS Trust, UK.,Imperial College, London, UK.,
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Saraf S, Wellsted D, Sharma S, Gorog DA. Shear-induced global thrombosis test of native blood: pivotal role of ADP allows monitoring of P2Y12 antagonist therapy. Thromb Res 2009; 124:447-51. [PMID: 19476973 DOI: 10.1016/j.thromres.2009.04.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Revised: 04/20/2009] [Accepted: 04/26/2009] [Indexed: 10/20/2022]
Abstract
BACKGROUND It is claimed that in shear-induced platelet function tests, shear-stress is the sole agonist causing platelet activation and resultant thrombosis. However, the fact that red blood cells (RBC) are essential to achieve platelet aggregation in these tests supports recent evidence that ADP makes an important contribution to shear-induced platelet reaction. AIM To establish the role of ADP in shear-induced thrombosis, and investigate whether a shear-induced thrombosis test can assess ADP-receptor (P2Y12) antagonist medication. METHODS Blood from healthy volunteers was tested using the Global Thrombosis Test (GTT), before and after clopidogrel. To investigate the importance of contact of blood with plastic, the reactive part of the tube was primed with saline. We also investigated the effect of priming the tube with water, to cause localised haemolysis and ADP release. RESULTS Saline-priming prolonged occlusion times (OT) by 25% (p<0.01) confirming ADP release from platelets and RBC as a result of contact. Water-priming shortened OT, accelerating the thrombotic reaction (accelerated GTT; aGTT) (OT 379 vs. 177s, p<0.01). Clopidogrel increased OT (379 vs. 477s, p<0.01), preventing the shortening of aGTT-OT (177 vs. 362s, pre- and post-clopidogrel; p<0.01). CONCLUSION In addition to thrombin formation, ADP released from platelets and RBC in native blood subjected to high shear-stress makes an important contribution to the resultant thrombotic occlusion. The described aGTT sensitively detected the effect of clopidogrel and thus seems suitable for monitoring and individualizing ADP-receptor antagonist therapy. Parallel measurement of GTT and aGTT would allow assessment of both global thrombotic status and response to P2Y12 antagonist therapy.
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Affiliation(s)
- S Saraf
- Cardiology Department, East & North Hertfordshire NHS Trust, Welwyn Garden City, Hertfordshire, United Kingdom
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Abbott BP, Abbott R, Adhikari R, Ajith P, Allen B, Allen G, Amin RS, Anderson SB, Anderson WG, Arain MA, Araya M, Armandula H, Armor P, Aso Y, Aston S, Aufmuth P, Aulbert C, Babak S, Baker P, Ballmer S, Bantilan H, Barish BC, Barker C, Barker D, Barr B, Barriga P, Barsotti L, Barton MA, Bartos I, Bassiri R, Bastarrika M, Behnke B, Benacquista M, Betzwieser J, Beyersdorf PT, Bilenko IA, Billingsley G, Biswas R, Black E, Blackburn JK, Blackburn L, Blair D, Bland B, Bodiya TP, Bogue L, Bork R, Boschi V, Bose S, Brady PR, Braginsky VB, Brau JE, Brinkmann M, Brooks AF, Brown DA, Brunet G, Bullington A, Buonanno A, Burmeister O, Byer RL, Cadonati L, Cagnoli G, Camp JB, Cannizzo J, Cannon KC, Cao J, Cardenas L, Cardoso V, Caride S, Casebolt T, Castaldi G, Caudill S, Cavaglià M, Cepeda C, Chalkley E, Charlton P, Chatterji S, Chelkowski S, Chen Y, Christensen N, Clark D, Clark J, Clayton JH, Cokelaer T, Conte R, Cook D, Corbitt TRC, Cornish N, Coyne DC, Creighton JDE, Creighton TD, Cruise AM, 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Schnabel R, Schofield R, Schutz BF, Schwinberg P, Scott J, Scott SM, Searle AC, Sears B, Seifert F, Sellers D, Sengupta AS, Sergeev A, Shapiro B, Shawhan P, Shoemaker DH, Sibley A, Siemens X, Sigg D, Sinha S, Sintes AM, Slagmolen BJJ, Slutsky J, Smith JR, Smith MR, Smith ND, Somiya K, Sorazu B, Stein LC, Strain KA, Stuver A, Summerscales TZ, Sun KX, Sung M, Sutton PJ, Takahashi H, Tanner DB, Taylor R, Taylor R, Thacker J, Thorne KA, Thorne KS, Thüring A, Tokmakov KV, Torres C, Torrie C, Traylor G, Trias M, Ugolini D, Urbanek K, Vahlbruch H, Van Den Broeck C, van der Sluys MV, van Veggel AA, Vass S, Vaulin R, Vecchio A, Veitch JD, Veitch P, Villar A, Vorvick C, Vyachanin SP, Waldman SJ, Wallace L, Ward H, Ward RL, Weinert M, Weinstein AJ, Weiss R, Wen L, Wen S, Wette K, Whelan JT, Whitcomb SE, Whiting BF, Wilkinson C, Willems PA, Williams HR, Williams L, Willke B, Wilmut I, Winkler W, Wipf CC, Wiseman AG, Woan G, Wooley R, Worden J, Wu W, Yakushin I, Yamamoto H, Yan Z, Yoshida S, Zanolin M, Zhang J, Zhang L, Zhao C, Zotov N, Zucker ME, Zur Mühlen H, Zweizig J. All-sky LIGO search for periodic gravitational waves in the early fifth-science-run data. Phys Rev Lett 2009; 102:111102. [PMID: 19392186 DOI: 10.1103/physrevlett.102.111102] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2008] [Indexed: 05/11/2023]
Abstract
We report on an all-sky search with the LIGO detectors for periodic gravitational waves in the frequency range 50-1100 Hz and with the frequency's time derivative in the range -5 x 10{-9}-0 Hz s{-1}. Data from the first eight months of the fifth LIGO science run (S5) have been used in this search, which is based on a semicoherent method (PowerFlux) of summing strain power. Observing no evidence of periodic gravitational radiation, we report 95% confidence-level upper limits on radiation emitted by any unknown isolated rotating neutron stars within the search range. Strain limits below 10{-24} are obtained over a 200-Hz band, and the sensitivity improvement over previous searches increases the spatial volume sampled by an average factor of about 100 over the entire search band. For a neutron star with nominal equatorial ellipticity of 10{-6}, the search is sensitive to distances as great as 500 pc.
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Affiliation(s)
- B P Abbott
- LIGO-California Institute of Technology, Pasadena, California 91125, USA
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