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Ashktorab H, Oskrochi G, Challa SR, Chirumamilla LG, Saroya S, Dusmatova S, Shayegh N, Nair V, Senthilvelan K, Byer D, Morrison N, Grossi B, Barclay A, Smith T, Watson K, Rashid M, Rashid R, Deverapalli M, Latella G, Carethers JM, Youssef A, Brim H. Age, Gender, and Liver Enzyme Impact Hospital Stay in COVID-19 Minority Patient with Cancer in the USA: Does Race Matters in the Pandemic? Ann Clin Med Case Rep 2024; 13:7. [PMID: 38633403 PMCID: PMC11022387] [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] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Patients with cancer are known to have a poor prognosis when infected with SARS-CoV-2 infection. We aimed in this study to assess health outcomes in COVID-19 patients with different cancers in comparison to non-cancer COVID-19 patients from different centers in the United States (US). We evaluated medical records of 1,943 COVID-19 Cancer patients from 3 hospitals admitted between December 2019 to October 2021 and compared them with non-cancer COVID-19 patients. Among 1,943 hospitalized COVID-19 patients, 18.7% (n=364) have an active or previous history of cancer. Among these 364 cancer patients, 222 were African Americans (61.7%) and 121 were Caucasians (33.2%). Cancer patients had significantly longer hospitalization compared to controls (8.24 vs 6.7 days). Overall, Lung cancer is associated with high mortality. Patients with a previous history of cancer were more prone to death (p=0.04) than active cancer patients. In univariate and multivariate analyses, predictors of death among cancer patients were male sex, older age, presence of dyspnea, elevated troponin, elevated AST (0.001) and ALT (0.05), low albumin (p=0.04) and mechanical ventilation (p=0.001). Patients with a previous history of cancer were more prone to death when compared to active cancer COVID-19 patients. Early recognition of cancer COVID-19 patients' death-associated risk factors can help determine appropriate treatment and management plans for better prognosis and outcome.
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Affiliation(s)
- H Ashktorab
- Department of Medicine, GI Division, Cancer Center, Howard University Hospital, Washington DC, USA
| | - G Oskrochi
- College of Engineering and Technology, American University of the Middle East, Kuwait
| | - S R Challa
- Department of Medicine, GI Division, Cancer Center, Howard University Hospital, Washington DC, USA
| | - L G Chirumamilla
- Department of Medicine, GI Division, Cancer Center, Howard University Hospital, Washington DC, USA
| | - S Saroya
- Department of Medicine, GI Division, Cancer Center, Howard University Hospital, Washington DC, USA
| | - S Dusmatova
- Department of Medicine, GI Division, Cancer Center, Howard University Hospital, Washington DC, USA
| | - N Shayegh
- Department of Medicine, GI Division, Cancer Center, Howard University Hospital, Washington DC, USA
| | - V Nair
- Department of Medicine, GI Division, Cancer Center, Howard University Hospital, Washington DC, USA
| | - K Senthilvelan
- Department of Medicine, GI Division, Cancer Center, Howard University Hospital, Washington DC, USA
| | - D Byer
- Department of Medicine, GI Division, Cancer Center, Howard University Hospital, Washington DC, USA
| | - N Morrison
- Department of Medicine, GI Division, Cancer Center, Howard University Hospital, Washington DC, USA
| | - B Grossi
- Department of Medicine, GI Division, Cancer Center, Howard University Hospital, Washington DC, USA
| | - A Barclay
- Department of Medicine, GI Division, Cancer Center, Howard University Hospital, Washington DC, USA
| | - T Smith
- Department of Medicine, GI Division, Cancer Center, Howard University Hospital, Washington DC, USA
| | - K Watson
- Department of Medicine, GI Division, Cancer Center, Howard University Hospital, Washington DC, USA
| | - M Rashid
- Department of Medicine, GI Division, Cancer Center, Howard University Hospital, Washington DC, USA
| | - R Rashid
- Department of Medicine, GI Division, Cancer Center, Howard University Hospital, Washington DC, USA
| | - M Deverapalli
- Department of Medicine, GI Division, Cancer Center, Howard University Hospital, Washington DC, USA
| | - G Latella
- Gastroenterology Unit, Division of Gastroenterology, Hepatology, and Nutrition, Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - J M Carethers
- Division of Gastroenterology & Hepatology, Department of Medicine and Moores Cancer Center, UC San Diego, USA
| | - A Youssef
- Division of Gastroenterology and Hepatology, Department of Internal Medicine; Department of Human Genetics and Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - H Brim
- Department of Pathology and Cancer Center, Department of Biochemistry & Molecular Biology, Howard University College of Medicine, Washington DC, USA
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Tesolin D, Nair V. Conventionally Fractionated vs. Hypofractionated Radiotherapy for Treatment of Unresectable Pancreatic Cancer: Local Control and Survival Outcomes in a Retrospective Single-Institutional Analysis. Int J Radiat Oncol Biol Phys 2023; 117:e344. [PMID: 37785199 DOI: 10.1016/j.ijrobp.2023.06.2410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Unresectable pancreatic cancer (UPC) is associated with dismal survival outcomes, with a reported median survival of 8-12 months. The role of radiotherapy (RT) and the choice of optimal fractionation remains unclear. Our objective was analyzing the outcomes associated with local radiotherapy as well as determine the best radiotherapeutic approach to treat these patients. MATERIALS/METHODS From a database of 209 radiation plans of patients treated for pancreatic cancer in a single institution between August 2007 to August 2021, patients with UPC were selected for this REB approved retrospective study. RESULTS From the 209 plans, 136 unique patients were identified who had RT for UPC. The mean age of the cohort was 67.6 years, 10% were >80 years and 37% were female. Median follow-up was 9.3 months. 54 patients had distant metastases at the time of RT and were analyzed separately. Outcomes where analyzed based on whether patients received Conventionally fractionated RT (CFRT) (defined as >15 fractions) (n = 23 (17%)), Hypofractionated RT (HypoRT) (defined as ≤15 fractions and EQD2<40Gy for α/β = 3) (n = 40 (29%)) and those treated with Stereotactic Body RT (SBRT) (defined as ≤5 fractions and EQD2≥40Gy for α/β = 3) (n = 19 (14%)). The mean overall survival (OS) and freedom from progression (FFP) in the SBRT cohort was 17.2 and 7.4 months respectively, in the CFRT cohort was 22.6 and 9.9 months respectively and in the HypoRT cohort was 11.4 and 4.9 months respectively. All CFRT patients received chemotherapy. Mean OS was drastically lower in SBRT and HypoRT patients who did not receive any chemotherapy (11.9 and 3.4 months respectively). Patients with metastatic disease at presentation and receiving HypoRT had mean OS of 13.4 months. The average EQD2 for the cohorts were 45.4 Gy, 49.2 Gy and 30.3 Gy for CFRT, SBRT and HypoRT respectively. CONCLUSION Our study demonstrates that CFRT with concurrent chemotherapy offers better therapeutic outcomes in patients with UPC compared to HypoRT. The role of dose escalated SBRT needs to be explored as an equal alternative.
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Affiliation(s)
- D Tesolin
- Ottawa Hospital Cancer Centre, Ottawa, ON, Canada
| | - V Nair
- The Ottawa Hospital Cancer Centre, Ottawa, ON, Canada
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Kappelman MD, Lewis JD, Zhang X, Lin FC, Weisbein L, Chen W, Burris J, Dorand JE, Parlett LE, Haynes K, Nair V, Kaul AF, Dobes A, Long MD. Comparing Patient-Reported Outcomes Among Anti-TNF-Experienced Patients with Crohn's Disease Initiating Vedolizumab Versus Ustekinumab. Dig Dis Sci 2023:10.1007/s10620-023-07942-0. [PMID: 37115362 DOI: 10.1007/s10620-023-07942-0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/30/2023] [Indexed: 04/29/2023]
Abstract
BACKGROUND Primary and secondary non-response to anti-tumor necrosis factor (TNF) therapy is common in patients with Crohn's disease (CD), yet limited research has compared the effectiveness of subsequent biological therapy. OBJECTIVE We sought to compare the effectiveness of vedolizumab and ustekinumab in anti-TNF-experienced patients with CD, focusing on patient-prioritized patient-reported outcomes (PROs). METHODS We conducted a prospective, internet-based cohort study nested within IBD Partners. We identified anti-TNF-experienced patients initiating with CD vedolizumab or ustekinumab and analyzed PROs reported approximately 6 months later (minimum 4 months, maximum 10 months). Co-primary outcomes were Patient-Reported Outcome Measurement Information System (PROMIS) domains of Fatigue and Pain Interference. Secondary outcomes included patient-reported short Crohn's disease activity index (sCDAI), treatment persistence, and corticosteroid use. Inverse probability of treatment weighting (IPTW) was used to control for a number of potential confounders and incorporated into linear and logistic regression models for continuous and categorical outcomes, respectively. RESULTS Overall, 141 vedolizumab and 219 ustekinumab initiators were included in our analysis. After adjustment, we found no differences between treatment groups in our primary outcomes of Pain Interference or Fatigue or the secondary outcome of sCDAI. However, vedolizumab was associated with lower treatment persistence (OR 0.4, 95% CI 0.2-0.6) and higher corticosteroid use at follow-up assessment (OR 1.7, 95% CI 1.1-2.6). DISCUSSION Among anti-TNF experienced patients with CD, Pain Interference or Fatigue was not significantly different 4-10 months after starting ustekinumab or vedolizumab. However, reduced steroid use and increased persistence suggest superiority of ustekinumab for non-PRO outcomes.
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Affiliation(s)
- Michael D Kappelman
- University of North Carolina at Chapel Hill, Bioinformatics Building, 130 Mason Farm Rd., Campus Box 7229, Chapel Hill, NC, 27599-7555, USA.
| | - J D Lewis
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - X Zhang
- University of North Carolina at Chapel Hill, Bioinformatics Building, 130 Mason Farm Rd., Campus Box 7229, Chapel Hill, NC, 27599-7555, USA
| | - F C Lin
- University of North Carolina at Chapel Hill, Bioinformatics Building, 130 Mason Farm Rd., Campus Box 7229, Chapel Hill, NC, 27599-7555, USA
| | - L Weisbein
- University of North Carolina at Chapel Hill, Bioinformatics Building, 130 Mason Farm Rd., Campus Box 7229, Chapel Hill, NC, 27599-7555, USA
| | - W Chen
- University of North Carolina at Chapel Hill, Bioinformatics Building, 130 Mason Farm Rd., Campus Box 7229, Chapel Hill, NC, 27599-7555, USA
| | - J Burris
- Yale School of Medicine, New Haven, CT, USA
| | - J E Dorand
- Crohn's & Colitis Foundation, New York, NY, USA
| | | | | | - V Nair
- Medical Outcomes Management and the Practice Research Network (PRACNET), Sharon, MA, USA
| | - A F Kaul
- Medical Outcomes Management and the Practice Research Network (PRACNET), Sharon, MA, USA
| | - A Dobes
- Crohn's & Colitis Foundation, New York, NY, USA
| | - M D Long
- University of North Carolina at Chapel Hill, Bioinformatics Building, 130 Mason Farm Rd., Campus Box 7229, Chapel Hill, NC, 27599-7555, USA
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Chih S, Tavoosi A, Nair V, Chong A, Džavík V, Aleksova N, So D, Amara I, Wells G, Bernick J, Overgaard C, Mielniczuk L, Stadnick E, Ross H, Beanlands R. Cardiac Pet Flow Quantification Assessment of Early Cardiac Allograft Vasculopathy. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.059] [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: 04/05/2023] Open
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ALAKWAA F, McCown P, Naik A, Schaub J, Menon R, Otto E, Nair V, Eddy S, Pyle L, Hartman J, Hodgin J, Nelson R, Brosius Division F, Kretzler M, Bjornstad P. WCN23-0471 THE ENHANCEMENT OF METALLOTHIONEIN BIND METAL PATHWAY WITH SGLT2 INHIBITORS IN KIDNEY PROXIMAL TUBULES OF ADOLESCENTS WITH TYPE 2 DIABETES USING SINGLE CELL RNA-SEQ DATA. Kidney Int Rep 2023. [DOI: 10.1016/j.ekir.2023.02.432] [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: 03/22/2023] Open
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Pitcher T, Kammer M, Nair V. PP01.35 Validation of a High-Specificity Blood-Based Autoantibody Test to Detect Lung Cancer in Pulmonary Nodules. J Thorac Oncol 2023. [DOI: 10.1016/j.jtho.2022.09.061] [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: 01/30/2023]
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Tseng D, Chiou SH, Nair V, Martins RG, Santana-Davila R, Lee S, Eaton KD, Baik CS, Houghton AM. Peripheral blood T-cell receptor repertoire profiling of advanced non-small cell lung cancer patients receiving PD-1/PD-L1 treatment. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.e21004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e21004 Background: Whether peripheral blood T cell receptor (TCR) repertoire profiling can serve as a biomarker to predict clinical benefit from anti-PD-1/PD-L1 checkpoint immunotherapy is not well understood. Moreover, it is not known which methods for TCR repertoire analysis are most clinically meaningful. To address this, we have performed TCR repertoire analysis of patients with advanced/metastatic non-small cell lung cancer (NSCLC) receiving PD-1/PD-L1 treatment. Methods: We analyzed 29 patients receiving PD-1/PD-L1 monotherapy or combination therapy in any line of treatment, excluding patients with EGFR mutations or Alk alterations. Genomic DNA was extracted from peripheral blood examples, and CDR3 regions of the rearranged TCR beta genes were amplified and sequenced using the immunoSEQ platform (Adaptive Biotechnologies, Seattle, WA). Libraries were sequenced using Illumina HiSeq 2500. TCR clonality, diversity, evenness, and the percentage of high-frequency clones (> 0.1% of the repertoire) were calculated at pre-treatment and post-treatment (1 – 3 months) timepoints. Morisita’s overlap index was calculated for 25 paired pre- and post-treatment samples. Metrics were compared in patients with and without durable clinical response at 6 months using the Mann-Whitney test. Results: There were no statistically significant differences in TCR repertoire clonality, diversity, evenness, or high-frequency clones between patients with and without durable clinical benefit, either at pre-treatment or post-treatment time points (p > 0.05). Conclusions: TCR repertoire metrics including clonality, diversity, evenness, percentage of high-frequency clones, and Morisita’s overlap index do not predict immunotherapy responses in this cohort of advanced/metastatic NSCLC patients receiving PD-1/PD-L1 monotherapy or combination therapy. Limitations of this study include sample size and heterogeneity of the patient cohort. This highlights the need for advanced TCR repertoire metrics, for example, considering shared TCR specificities and clonal identity. In ongoing work, we are defining TCR specificity groups and TCR clones in NSCLC as biomarkers of immunotherapy responsiveness.
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Affiliation(s)
| | | | - Viswam Nair
- Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | - Sylvia Lee
- University of Washington School of Medicine, Seattle, WA
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Sampathkumar G, Valiyaparambil PP, Kumar H, Bhavani N, Nair V, Menon U, Menon A, Abraham N, Chapla A, Thomas N. Low genetic confirmation rate in South Indian subjects with a clinical diagnosis of maturity-onset diabetes of the young (MODY) who underwent targeted next-generation sequencing for 13 genes. J Endocrinol Invest 2022; 45:607-615. [PMID: 34741762 DOI: 10.1007/s40618-021-01698-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 10/29/2021] [Indexed: 12/29/2022]
Abstract
PURPOSE To screen for maturity-onset diabetes of the young (MODY) variants in subjects with an early age of onset and positive family history of diabetes mellitus. METHODS 60 subjects with onset of diabetes between 3 and 30 years of age and parental history (onset < 35 years) of diabetes were recruited after excluding autoimmune, pancreatic and syndromic forms of diabetes. Detailed pedigree chart and clinical data were recorded. MODY genetic testing (MODY 1-13) was performed and variant classification was done adhering to the ACMG guidelines. RESULTS Baseline characteristics of subjects were as follows: mean age of onset of diabetes 19.9 ± 7 years, mean duration of diabetes 6.3 ± 6.8 years, BMI 23.3 ± 3 kg/m2 and C-peptide 1.56 ± 1.06 nmol/l. Four out of sixty (6.6%) were positive for variants classifiable as pathogenic/likely pathogenic: one patient with HNF4Ac.691C > T, (p.Arg231Trp), two with HNF 1A c.746C > A(p.Ser249Ter) and c.1340C > T(p.Pro447Leu), and one with ABCC8 c.4544C > T (p.Thr1515Met). MODY 1 and MODY 3 variants were documented in the paediatric age group (< 18 years). CONCLUSION A genetic diagnosis of MODY could be confirmed in only 6.6% (4/60) of patients clinically classifiable as MODY. This is less than that reported in clinically diagnosed MODY subjects of European descent. Newly published population data and more stringent criteria for assessment of pathogenicity and younger age of onset of type 2 diabetes in Indians could have contributed to the lower genetic confirmation rate. Apart from variants in the classical genes (HNF1A, HNF4A), a likely pathogenic variant in a non-classical gene (ABCC8) was noted in this study.
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Affiliation(s)
- G Sampathkumar
- Department of Endocrinology, Amrita Institute of Medical Sciences, Amrita University, Ponnekara P.O, Cochin, 682041, Kerala, India
| | - P P Valiyaparambil
- Department of Endocrinology, Amrita Institute of Medical Sciences, Amrita University, Ponnekara P.O, Cochin, 682041, Kerala, India.
| | - H Kumar
- Department of Endocrinology, Amrita Institute of Medical Sciences, Amrita University, Ponnekara P.O, Cochin, 682041, Kerala, India
| | - N Bhavani
- Department of Endocrinology, Amrita Institute of Medical Sciences, Amrita University, Ponnekara P.O, Cochin, 682041, Kerala, India
| | - V Nair
- Department of Endocrinology, Amrita Institute of Medical Sciences, Amrita University, Ponnekara P.O, Cochin, 682041, Kerala, India
| | - U Menon
- Department of Endocrinology, Amrita Institute of Medical Sciences, Amrita University, Ponnekara P.O, Cochin, 682041, Kerala, India
| | - A Menon
- Department of Endocrinology, Amrita Institute of Medical Sciences, Amrita University, Ponnekara P.O, Cochin, 682041, Kerala, India
| | - N Abraham
- Department of Endocrinology, Amrita Institute of Medical Sciences, Amrita University, Ponnekara P.O, Cochin, 682041, Kerala, India
| | - A Chapla
- Department of Endocrinology, Christian Medical College, Vellore, Tamil Nadu, India
| | - N Thomas
- Department of Endocrinology, Christian Medical College, Vellore, Tamil Nadu, India
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MATUROSTRAKUL B, Bhaskaran M, Jang H, Nair V, Nair G, Abate M, Teperman L, Grodstein E. POS-781 THROMBOTIC MICROANGIOPATHY IN RENAL TRANSPLANT RECIPIENT WITH NPHS 2 GENE MUTATION. Kidney Int Rep 2022. [DOI: 10.1016/j.ekir.2022.01.817] [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] Open
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Molouki A, Ghalyanchilangeroudi A, Abdoshah M, Shoushtari A, Abtin A, Eshtartabadi F, Mahmoudzadeh Akhijahani M, Ziafatikafi Z, Babaeimarzango SS, Allahyari E, Ahmadzadeh L, Fallah Mehrabadi MH, Lim SHE, Rouhani K, Hosseini H, Nair V. Report of a new meq gene size: The first study on genetic characterisation of Marek's disease viruses circulating in Iranian commercial layer and backyard chicken. Br Poult Sci 2021; 63:142-149. [PMID: 34423692 DOI: 10.1080/00071668.2021.1963677] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
1. In recent months, several outbreaks with clinical signs of MDV-1 were reported in Iranian parent and laying hen farms, in addition to backyard chickens. Several meq gene sequences from these outbreaks were amplified and molecularly characterised.2. The meq protein sequences revealed three different sizes, namely the standard 339 aa, a shorter form of 338 aa lacking a proline residue at position 191, and a very short (vs) size of 265 aa. Based on sequence and size, the 265 aa meq has never been reported from international research groups before. The protein has only one PPPP repeat motif suggesting it belongs to a highly virulent strain.3. The standard meq sequences showed 100% BLAST identity to the vv+ isolate Polen5. However, the 338 aa form clustered to the clade usually reported from North America.4. This is the first report on genetic analysis of MDV-1 from Iran, but further study is required to obtain a better picture of the diversity and prevalence of different MDV-1 strains circulating in the country's farms, backyard poultry and other bird species.
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Affiliation(s)
- A Molouki
- Department of Avian Diseases Research and Diagnostics, Razi Vaccine and Serum Research, Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - A Ghalyanchilangeroudi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - M Abdoshah
- Department of Avian Diseases Research and Diagnostics, Razi Vaccine and Serum Research, Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - A Shoushtari
- Department of Avian Diseases Research and Diagnostics, Razi Vaccine and Serum Research, Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - A Abtin
- Department of Avian Diseases Research and Diagnostics, Razi Vaccine and Serum Research, Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - F Eshtartabadi
- Department of Avian Diseases Research and Diagnostics, Razi Vaccine and Serum Research, Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - M Mahmoudzadeh Akhijahani
- Department of Avian Diseases Research and Diagnostics, Razi Vaccine and Serum Research, Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Z Ziafatikafi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | | | - E Allahyari
- Faculty of Veterinary Medicine, Urmia University, Urmia, Iran
| | - L Ahmadzadeh
- Faculty of Veterinary Medicine, Urmia University, Urmia, Iran
| | - M H Fallah Mehrabadi
- Department of Avian Diseases Research and Diagnostics, Razi Vaccine and Serum Research, Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - S H E Lim
- Health Sciences Division, Abu Dhabi Women's College, Higher Colleges of Technology, Abu Dhabi, United Arab Emirates
| | - K Rouhani
- Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - H Hosseini
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Islamic Azad University, Karaj, Iran
| | - V Nair
- Viral Oncogenesis Group & OIE Marek's Disease Virus Reference Laboratory, Pirbright Institute, Surrey, UK
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Volpini M, Jooya A, La Russa D, Sutherland J, Samant R, Nair V. PO-1730 Feasibility of Virtual Reality-based target volume delineation for craniospinal irradiation. Radiother Oncol 2021. [DOI: 10.1016/s0167-8140(21)08181-0] [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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Gorsi U, Agarwal V, Nair V, Kang M, Kalra N, Sreedhara BC, Gupta R, Rana SS, Dutta U, Sandhu MS. Corrigendum to: "Re: endovascular and percutaneous trans abdominal embolisation of pseudoaneurysms in pancreatitis: an experience from a tertiary care referral centre" [76 (4) e17-e23]. Clin Radiol 2021; 76:629.e19. [PMID: 34045069 DOI: 10.1016/j.crad.2021.04.008] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- U Gorsi
- Department of Radiodiagnosis, PGIMER, Chandigarh, India.
| | - V Agarwal
- Department of Radiodiagnosis, PGIMER, Chandigarh, India
| | - V Nair
- Department of Radiodiagnosis, PGIMER, Chandigarh, India
| | - M Kang
- Department of Radiodiagnosis, PGIMER, Chandigarh, India
| | - N Kalra
- Department of Radiodiagnosis, PGIMER, Chandigarh, India
| | - B C Sreedhara
- Department of Radiodiagnosis, PGIMER, Chandigarh, India
| | - R Gupta
- Department of Surgery, PGIMER, Chandigarh, India
| | - S S Rana
- Department of Gastroenterology, PGIMER, Chandigarh, India
| | - U Dutta
- Department of Gastroenterology, PGIMER, Chandigarh, India
| | - M S Sandhu
- Department of Radiodiagnosis, PGIMER, Chandigarh, India
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Smyth LJ, Kilner J, Nair V, Liu H, Brennan E, Kerr K, Sandholm N, Cole J, Dahlström E, Syreeni A, Salem RM, Nelson RG, Looker HC, Wooster C, Anderson K, McKay GJ, Kee F, Young I, Andrews D, Forsblom C, Hirschhorn JN, Godson C, Groop PH, Maxwell AP, Susztak K, Kretzler M, Florez JC, McKnight AJ. Assessment of differentially methylated loci in individuals with end-stage kidney disease attributed to diabetic kidney disease: an exploratory study. Clin Epigenetics 2021; 13:99. [PMID: 33933144 PMCID: PMC8088646 DOI: 10.1186/s13148-021-01081-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 12/08/2020] [Accepted: 04/15/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND A subset of individuals with type 1 diabetes mellitus (T1DM) are predisposed to developing diabetic kidney disease (DKD), the most common cause globally of end-stage kidney disease (ESKD). Emerging evidence suggests epigenetic changes in DNA methylation may have a causal role in both T1DM and DKD. The aim of this exploratory investigation was to assess differences in blood-derived DNA methylation patterns between individuals with T1DM-ESKD and individuals with long-duration T1DM but no evidence of kidney disease upon repeated testing to identify potential blood-based biomarkers. Blood-derived DNA from individuals (107 cases, 253 controls and 14 experimental controls) were bisulphite treated before DNA methylation patterns from both groups were generated and analysed using Illumina's Infinium MethylationEPIC BeadChip arrays (n = 862,927 sites). Differentially methylated CpG sites (dmCpGs) were identified (false discovery rate adjusted p ≤ × 10-8 and fold change ± 2) by comparing methylation levels between ESKD cases and T1DM controls at single site resolution. Gene annotation and functionality was investigated to enrich and rank methylated regions associated with ESKD in T1DM. RESULTS Top-ranked genes within which several dmCpGs were located and supported by functional data with methylation look-ups in other cohorts include: AFF3, ARID5B, CUX1, ELMO1, FKBP5, HDAC4, ITGAL, LY9, PIM1, RUNX3, SEPTIN9 and UPF3A. Top-ranked enrichment pathways included pathways in cancer, TGF-β signalling and Th17 cell differentiation. CONCLUSIONS Epigenetic alterations provide a dynamic link between an individual's genetic background and their environmental exposures. This robust evaluation of DNA methylation in carefully phenotyped individuals has identified biomarkers associated with ESKD, revealing several genes and implicated key pathways associated with ESKD in individuals with T1DM.
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Affiliation(s)
- L J Smyth
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK.
| | - J Kilner
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - V Nair
- Internal Medicine, Department of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - H Liu
- Department of Department of Medicine/ Nephrology, Department of Genetics, Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - E Brennan
- Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - K Kerr
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - N Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - J Cole
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA.,Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - E Dahlström
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - A Syreeni
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - R M Salem
- Department of Family Medicine and Public Health, UC San Diego, San Diego, CA, USA
| | - R G Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - H C Looker
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ, USA
| | - C Wooster
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - K Anderson
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - G J McKay
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - F Kee
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - I Young
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - D Andrews
- Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - C Forsblom
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - J N Hirschhorn
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - C Godson
- Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - P H Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - A P Maxwell
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK.,Regional Nephrology Unit, Belfast City Hospital, Belfast, Northern Ireland, UK
| | - K Susztak
- Department of Department of Medicine/ Nephrology, Department of Genetics, Institute of Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - M Kretzler
- Internal Medicine, Department of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - J C Florez
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - A J McKnight
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University Belfast, Belfast, UK
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14
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Gorsi U, Agarwal V, Nair V, Kang M, Kalra N, Sreedhara BC, Gupta R, Rana SS, Dutta U, Sandhu MS. Endovascular and percutaneous transabdominal embolisation of pseudoaneurysms in pancreatitis: an experience from a tertiary-care referral centre. Clin Radiol 2021; 76:314.e17-314.e23. [PMID: 33526255 DOI: 10.1016/j.crad.2020.12.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/24/2020] [Indexed: 12/31/2022]
Abstract
AIM To analyse the technical challenges, clinical success, and associated complications of endovascular and percutaneous embolisation of pancreatitis-related pseudoaneurysms. MATERIALS AND METHODS A retrospective study of patients referred for embolisation of pancreatitis-related pseudoaneurysms between January 2014 and March 2019 was conducted. Computed tomography angiography (CTA) was performed to assess the morphology of the aneurysms prior to any intervention. Percutaneous or endovascular embolisation was performed. Details of CTA and methods of embolisation were recorded. Technical success, clinical success, and complications were reported. RESULTS A total of 80 patients (mean age, 40.69 ± 13.41 years, 73 male) underwent embolisation during the study period. Pseudoaneurysms were related to chronic pancreatitis (CP) in 44 (55%) patients and acute pancreatitis (AP) in 36 (45%) patients. Pseudoaneurysms were detected in 65 (81.2%) patients on CTA. The most common site of pseudoaneurysms was gastroduodenal artery (GDA) followed by splenic artery. Seven patients were treated with percutaneous thrombin injection and five were treated with percutaneous glue injection under ultrasound/fluoroscopy guidance. The remaining patients (n=68) underwent catheter angiography with endovascular embolisation. Technical success was achieved in 4/7 (57%) percutaneous thrombin cases and in all the cases (5/5, 100%) with percutaneous glue or endovascular (68/68,100%) embolisation. CONCLUSION Endovascular or percutaneous embolisation of pseudoaneurysms has high technical success with an excellent safety profile.
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Affiliation(s)
- U Gorsi
- Department of Radiodiagnosis, PGIMER, Chandigarh, India.
| | - V Agarwal
- Department of Radiodiagnosis, PGIMER, Chandigarh, India
| | - V Nair
- Department of Radiodiagnosis, PGIMER, Chandigarh, India
| | - M Kang
- Department of Radiodiagnosis, PGIMER, Chandigarh, India
| | - N Kalra
- Department of Radiodiagnosis, PGIMER, Chandigarh, India
| | - B C Sreedhara
- Department of Radiodiagnosis, PGIMER, Chandigarh, India
| | - R Gupta
- Department of Surgery, PGIMER, Chandigarh, India
| | - S S Rana
- Department of Gastroenterology, PGIMER, Chandigarh, India
| | - U Dutta
- Department of Gastroenterology, PGIMER, Chandigarh, India
| | - M S Sandhu
- Department of Radiodiagnosis, PGIMER, Chandigarh, India
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15
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Yilmaz A, Turan N, Bayraktar E, Tali HE, Aydin O, Umar S, Cakan B, Sadeyen JR, Baigent S, Iqbal M, Nair V, Yilmaz H. Molecular characterisation and phylogenetic analysis of Marek's disease virus in Turkish layer chickens. Br Poult Sci 2020; 61:523-530. [PMID: 32316760 DOI: 10.1080/00071668.2020.1758301] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
1. There is no current data about the genotypes of Marek's disease virus (MDV) in Turkish poultry flocks; hence, this study was performed to analyse CVI988/Rispens, turkey herpesvirus (HVT) vaccine viruses and MDV field viruses as well as to perform phylogenetic analysis of MDV in Turkish layer chickens. 2. In 2017 and 2018, a total of 602 spleen samples from 49 layer flocks were collected from the Marmara, West Black Sea and Aegean regions. DNA was extracted from the spleen samples and the samples were analysed by real-time PCR probe assay to detect CVI988/Rispens and HVT vaccine viruses and MDV field strains. Samples found positive for MDV by real-time PCR were subjected to PCR using the Meq gene primers for phylogenetic analysis. 3. Amongst 49 flocks, virulent MDV was detected in nine flocks. CVI988/Rispens and HVT vaccine strains were detected in 47 flocks and HVT in all 49 flocks. Splenomegaly, hepatomegaly and tumours in the oviduct were observed in chickens of affected flocks. Virulent MDV was detected in 120 out of 602 spleen samples. Sequencing and phylogenetic analyses showed that MDVs detected in this study were closely related to MDV strains from Italy, Poland, Saudi Arabia, Iraq, India and China but showed diversity with MDV strains from Egypt and Hungary. Multiple sequence analysis of the Meq protein revealed several point mutations in deduced amino acid sequences. Interestingly, CVI988/Rispens vaccine virus from China (AF493555) showed mutations at position 66 (G66R) and 71 (S66A) along with two other vaccine strains from China (GU354326.1) and Russia (EU032468.1), in comparison with the other vaccine strain CVI988/Rispens (DQ534538). The molecular analyses of the Meq gene suggested that Turkish field strains of MDV are in the class of virulent or very virulent pathotypes. 4. The results have shown that MDV still affects poultry health, and the phylogenetic and amino acid variation data obtained will help in vaccination and control strategies.
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Affiliation(s)
- A Yilmaz
- Department of Virology, Istanbul University-Cerrahpasa, Veterinary Faculty , Istanbul, Turkey
| | - N Turan
- Department of Virology, Istanbul University-Cerrahpasa, Veterinary Faculty , Istanbul, Turkey
| | - E Bayraktar
- Poultry Division, CEVA Animal Health , Maslak, Turkey
| | - H E Tali
- Department of Virology, Istanbul University-Cerrahpasa, Veterinary Faculty , Istanbul, Turkey
| | - O Aydin
- Department of Virology, Istanbul University-Cerrahpasa, Veterinary Faculty , Istanbul, Turkey
| | - S Umar
- Department of Virology, Istanbul University-Cerrahpasa, Veterinary Faculty , Istanbul, Turkey
| | - B Cakan
- Poultry Division, CEVA Animal Health , Maslak, Turkey
| | - J-R Sadeyen
- Avian Influenza Group, The Pirbright Institute , Woking, UK
| | - S Baigent
- Avian Influenza Group, The Pirbright Institute , Woking, UK
| | - M Iqbal
- Avian Influenza Group, The Pirbright Institute , Woking, UK
| | - V Nair
- Avian Influenza Group, The Pirbright Institute , Woking, UK
| | - H Yilmaz
- Department of Virology, Istanbul University-Cerrahpasa, Veterinary Faculty , Istanbul, Turkey
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16
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López-Osorio S, Villar D, Piedrahita D, Ramírez-Nieto G, Nair V, Baigent S, Chaparro-Gutiérrez J. Molecular detection of Marek's disease virus in feather and blood samples from young laying hens in Colombia. Acta Virol 2019; 63:380-391. [PMID: 31802681 DOI: 10.4149/av_2019_402] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Marek's disease virus (MDV) is an immunosuppressive pathogen that can cause low production efficiency and high mortality rates in chickens. There is no current information on the MDV serotypes and pathotypes circulating in vaccinated commercial farms in Colombia where the birds are vaccinated in the incubator with Gallid herpesvirus (GaHV-2) and Meleagrid herpesvirus 1 (MeHV-1). Based on that, the main focus of this study was to understand the MDV's infection dynamics for the three known serotypes and to detect wild-virus pathogenic strains in 4-layer poultry farms in Antioquia. Samples of blood, feathers and spleens were collected from three randomly chosen animals according to age category: 1, 15, 30, 60, 90, and 120 days. Quantitative real-time PCR (qPCR) that differentiates between the three serotypes of MDV was used to assess viral loads over time, and phylogenetic analysis of the Meq oncogene was done to compare the strains of MDV with those of known pathogenicity. Meleagrid herpesvirus 1 (MeHV-1) was detected in all blood and feather follicle samples with an average number of genome copies (per 10,000 cells) of 31.44 in blood as expected as a result of vaccination. GaHV-2 was also detected in almost 100% of the blood and feather follicle samples throughout all defined age categories, with an average of 10.65 genome copies in blood samples. Gallid herpesvirus 3 (GaHV-3) was detected in 72% of blood and 84.61% of feather samples, with less than 1 copy per 10,000 cells. Based on the number of 132 bp repeats of the BamHI-H and BamHI-D regions in pooled feather samples, there were 70% (8/25) of attenuated MDV and 30% (17/25) of virulent MDV strains circulating in the farms. Virus isolation was performed successfully from every farm. In conclusion, different strains of MDV are circulating for up to 120 days in layers in Antioquia-Colombia and could be of major impact in poultry health. Keywords: Marek's disease virus (MDV); Antioquia-Colombia; qPCR; PCR; Meq gene phylogeny.
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17
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Nair V, Bik-Yu Hui A, Chabon J, Esfahani M, Stehr H, Nabet B, Benson J, Chaudhuri A, Zhou L, Ayers K, Bedi H, Ramsey M, Van Wert R, Sung A, Lui N, Backhus L, Berry M, Massion P, Shrager J, Alizadeh A, Diehn M. P2.05-01 Broad Genomic Profiling of Bronchoalveolar Lavage Fluid in Lung Cancer. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.1600] [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: 10/25/2022]
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18
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Song J, Belec J, Caudrelier J, Lacasse P, Aldosary G, Nair V. Dose-Sparing Effect of Deep Inspiration Breath Hold Technique (DIBH) on Coronary Artery Segments. Int J Radiat Oncol Biol Phys 2019. [DOI: 10.1016/j.ijrobp.2019.06.878] [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: 10/26/2022]
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19
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Zheng J, Hinduja R, Pantarotto J, Cook G, Nair V, MacRae R. Outcome Differences Between Early Stage Adenocarcinoma and Squamous Cell Carcinoma Lung Cancers Treated with Stereotactic Body Radiation Therapy: Results of a Large Canadian Single Center Retrospective Analysis. Int J Radiat Oncol Biol Phys 2019. [DOI: 10.1016/j.ijrobp.2019.06.1268] [Citation(s) in RCA: 1] [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: 10/26/2022]
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20
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Antic S, Osterman T, Balar A, Lakhani D, Nguyen R, Block S, Fileds K, Winston B, Muterspaugh A, Huo Y, Gao R, Leader J, Wilson D, Nair V, Gillies R, Schabath M, Shah C, Landman B, Massion P. Abstract 3317: Development of a lung nodule cohort with integrated clinical, molecular and imaging biomarkers. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: We are facing an epidemic of indeterminate pulmonary nodules (IPN). Current diagnostic strategies lack accuracy such that the management of IPNs 6-30 mm leads to an unacceptable rate of invasive biopsies and of missed opportunities for cure. Based on the critical need of evaluating candidate biomarkers across heterogeneous populations, we intended to assemble a large cohort of fully annotated IPNs from five collaborative institutions.
Methods: Standard operating procedures (SOPs) were developed to capture subject demographics and assign consistent identifiers across clinical, bio-specimens, and imaging data. REDCap database was created for clinical, imaging and biospecimen data capture. Sample collection, processing, storage and shipping SOPs were created and shared among institutions to assure for consistency and quality accuracy. DICOM files, demographic and clinical data, blood and tissue samples were collected prospectively through IRB approved studies at each institution (VUMC, Nashville VAMC, Moffitt Cancer Center, and UPMC). Imaging studies and specimens were de-identified locally using custom JavaScript program in a secure web browser and assigned as specific identifier. De-identified thin slice, non-contrast chest CT studies were tested for quality control and transmitted to an imaging repository (eXtensible Neuroimaging Repository-XNAT) that can be mined by all collaborators.
Results: To date, a cohort of 845 subjects, 507 (60%) males and 338 (40%) females, with lung nodules was assembled. 36 % are current smokers, 56 % former smokers and 8% never smokers, with an average of 46 pack year smoking history. Clinical data including risk prediction models such as the Mayo and PLCO m2012 are reported. Pathological confirmation of nodules is available for 322 benign and 444 malignant nodules. The cohort 283 lung adenocarcinomas, 71 squamous cell carcinomas, 53 small cell carcinoma, 17 non-small cell lung cancer, 9 carcinoid, and 79 subjects considered benign based on CT follow without growth. Serum, plasma and peripheral blood monocyte related DNA is available on all. All diagnostic chest CT are available in our thoracic imaging repository (XNAT) in a de-identified format.
Conclusions: We assembled a unique cohort of incidental and screening detected lung nodules prospectively enrolled at four institutions for which full clinical data capture, chest CT DICOM files and blood specimens were collected. This repository allows the derivation and independent validation of candidate molecular and imaging biomarkers for the management of IPNs. This work is supported by UO1 152662, UO1CA186145 and UO1CA196405
Citation Format: Sanja Antic, Travis Osterman, Aneri Balar, Dhairya Lakhani, Rina Nguyen, Sara Block, Kimberly Fileds, Brandon Winston, Anel Muterspaugh, Yuankai Huo, Riqiang Gao, Joseph Leader, David Wilson, Viswam Nair, Robert Gillies, Matthew Schabath, Chirayu Shah, Bennett Landman, Pierre Massion. Development of a lung nodule cohort with integrated clinical, molecular and imaging biomarkers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3317.
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21
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Ascani H, Tomilo M, Nair V, Eichinger F, Eddy S, Ju W, Hodgin J, Steck R, Grega D, Kretzler M. MON-332 ADVANCING SYSTEMS-BIOLOGY FOCUSED, GLOMERULAR DISEASE RESEARCH THROUGH PUBLIC-PRIVATE PARTNERSHIPS. Kidney Int Rep 2019. [DOI: 10.1016/j.ekir.2019.05.1152] [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: 10/26/2022] Open
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22
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Song J, Samant R, Fan X, Jay M, Chaudry H, MacDonald D, Bence-Bruckler I, Nair V. EP-1221 Palliative cranial irradiation improves survival in PCNSL patients ineligible for systemic therapy. Radiother Oncol 2019. [DOI: 10.1016/s0167-8140(19)31641-x] [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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23
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Dermime S, Inchakalody V, Nair V, El-Ashi A, Taleb S, Fernandes Q, Al-Zaidan L, Iskandarani A, Sivaraman S, Sahir F, Krishnankutty R, Therachiyil L, Merhi M, Raza A, Uddin S, Elkord E, Knuth A. Enhancing NY-ESO-1 antigen expression in lung cancer cells through gene hypomethylation using 5-Aza-2′-deoxycytidine. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy487.034] [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: 11/13/2022] Open
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24
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Nair V, Nazri D, Hashim R, Lau A, Muniasamy M. Bridging Barriers, Building Partners: Success of a Multistakeholder Collaborative Effort in Building and Implementing a Free Mammography Programme for Underprivileged Malaysian Women. J Glob Oncol 2018. [DOI: 10.1200/jgo.18.66700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background and context: Research has revealed two large problems in the Malaysian breast cancer control context. First, a large disparity existed in diagnostic stages of Malaysian patients during first presentation; with a large percentage of patients presenting in Stage 3 or 4. Second, patients presenting in later stages of disease were revealed to be of lower socioeconomic backgrounds. Shortcomings are thus thought to exist in the capability of women from lower socioeconomic groups to access breast cancer screening. To address these gaps, the National Cancer Society of Malaysia conceptualized and put together a multistakeholder collaborative project. Aim: The aim of this project was to build, finance and implement a free mammography program for underprivileged Malaysian women. Strategy/Tactics: To ensure geographic equity in provision of this program, 14 individual private hospitals in 10 different states in peninsular Malaysia were negotiated with and agreed to provide the mammogram at highly competitive prices. To address transport and other costs which may have acted as a barrier for patients to attend their screening, transportation costs for groups going for their screening was also subsidized. Additional stakeholders' engaged were nongovernmental organizations (NGOs) especially those working with the economically underprivileged such as religious and other community NGOs. They were roped in as partners to spread the message, identify eligible participants and schedule visits. Some NGOs carried this out as part of their own outreach activities; reserving specific days at the screening centers for themselves. Program/Policy process: The program consisted of a free mammogram provided to Malaysian women above 40 years of age who were determined to be underprivileged; defined for this program as those having a monthly household income below the poverty line (RM5000). If the mammogram was found to be suspicious, a confirmatory breast ultrasound was also performed sans payment. Once conceptualized, the program was successfully pitched by NCSM to ETIQA Insurance, a large Malaysian insurer, who agreed to fund this project as part of their sustainable corporate social responsibility (CSR) initiative. In total, the program funded mammograms for 5000 women over a period of 1 year from July 2017 to July 2018. NCSM advertised the program through various channels; including traditional media, social media, and at various outreach programs and events. Outcomes/What was learned: The program has run for 8 months and has already screened 3550 women nationwide. The multistakeholder collaborative effort has been highly successful at creating awareness on breast cancer screening and providing accurate breast cancer screening for a large number of underprivileged women, some for the first time in their lives.
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Affiliation(s)
- V. Nair
- National Cancer Society Malaysia, Kuala Lumpur, Malaysia
| | - D. Nazri
- National Cancer Society Malaysia, Kuala Lumpur, Malaysia
| | - R. Hashim
- National Cancer Society Malaysia, Kuala Lumpur, Malaysia
| | - A. Lau
- National Cancer Society Malaysia, Kuala Lumpur, Malaysia
| | - M. Muniasamy
- National Cancer Society Malaysia, Kuala Lumpur, Malaysia
- Chulalongkorn University, College of Public Health Sciences, Bangkok, Thailand
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Harjani Hinduja R, Seely J, Gupta A, Nair V, Cook G, Macrae R. P2.16-19 Feasibility and Outcomes of Radiofrequency Ablation as Salvage Modality After Hypofractionated Radiation/SBRT for Early NSCLC. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.1494] [Citation(s) in RCA: 1] [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: 11/30/2022]
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26
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Zhang S, Harris J, Boyle T, Williams C, Antonia S, Chiappori A, Gray J, Tanvetyanon T, Creelan B, Haura E, Shafique M, Fontaine J, Cox J, Kaszuba F, Keenan R, Nair V, Toloza E. P09 Comparison of Liquid Biopsy and Histopathologic Results with Clinical Outcomes in Non–Small Cell Lung Cancer Patients. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.07.048] [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: 10/28/2022]
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27
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Lee EH, Zhou M, Gamboa N, Brennan K, Itakura H, Nair V, Napel S, Wong S, Gevaert O. Abstract 3048: Deep learning to predict survival prognosis for patients with non-small cell lung cancer using images and clinical data. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Goal
We present a deep learning framework to predict survival prognosis of patients with non-small cell lung cancer using CT images and clinical data developed and validated in multi-institutional cohorts.
Methods
We developed 3D convolutional neural networks (CNNs) using CT images, tumor nodule segmentation, clinical data (i.e. age, sex, histology, and stage) and survival times as input to predict survival of non-small cell lung cancer. Both the CT images and the segmentations were used as inputs for the CNN, the latter to localize the volumes-of-interests (VOIs) in the CT scans. We used three cohorts to evaluate our framework: Moffitt (n=186), Maastro (n=311), and Stanford (n=130). We investigated pre-training with the LIDC-IDRI dataset (n=1010) and compared deep learning performance with 1674 manually-curated radiomics features and clinical data. We used two ways to evaluate the models. First, we split the three cohorts into training and test sets by selecting two of the cohorts for training and the remaining for testing. Secondly, we combined all cohorts and performed a 10-fold stratified cross-validation. We used the Concordance Index (CI) to estimate model performance. Next, we evaluated priming whereby we use 10% of the validation cohort during training and test on the remaining patients in the test cohort. To ensure that the test set was identical for both priming and non-priming experiments, we discarded these samples for the non-priming tests.
Results
Table 1 shows the results of the two evaluation strategies. We observed consistently high CIs for all three cohorts. LIDC pretraining and priming yielded the highest CIs as compared to radiomic and clinical-only pipelines. For the 10-fold cross-validation experiment, our pipeline achieved an average CI=0.64.
Conclusion
Our study highlights the promising results of our pipeline to predict survival prognosis across three cohorts without the need to define radiomics features.
Train on two cohorts, test on 3rd cohortpretrain on LIDC-IDRItest w/o primingtest w/ primingtest w/o priming (only radiomics features / clinical)test w/ priming (only radiomics features / clinical)train on Moffitt + Maastro, test on Stanfordyes0.620.630.52 (radiomics only)0.53 (radiomics only)train on Moffitt + Maastro, test on Stanfordno0.610.620.57 (clinical only)0.57 (clinical only)train on Moffitt + Stanford, test on Maastroyes0.60.60.55 (radiomics only)0.55 (radiomics only)train on Moffitt + Stanford, test on Maastrono0.580.60.56 (clinical only)0.56 (clinical only)train on Stanford + Maastro, test on Moffittyes0.580.60.53 (radiomics only)0.53 (radiomics only)train on Stanford + Maastro, test on Moffittno0.60.570.56 (clinical only)0.56 (clinical only)
Citation Format: Edward H. Lee, Mu Zhou, Noah Gamboa, Kevin Brennan, Haruka Itakura, Viswam Nair, Sandy Napel, Simon Wong, Olivier Gevaert. Deep learning to predict survival prognosis for patients with non-small cell lung cancer using images and clinical data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3048.
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Affiliation(s)
| | - Mu Zhou
- Stanford University, Stanford, CA
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Abdel-Rahman W, Nair V, Al-khayyal N. PO-206 Calponin 3 (CNN3) promotes epithelial to mesenchymal transition and drug resistance of colon cancer cells. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.241] [Citation(s) in RCA: 1] [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: 11/04/2022] Open
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Zhang W, Bouchard G, Yu A, Shafiq M, Jamali M, Shrager JB, Ayers K, Bakr S, Gentles AJ, Diehn M, Quon A, West RB, Nair V, van de Rijn M, Napel S, Plevritis SK. GFPT2-Expressing Cancer-Associated Fibroblasts Mediate Metabolic Reprogramming in Human Lung Adenocarcinoma. Cancer Res 2018; 78:3445-3457. [PMID: 29760045 DOI: 10.1158/0008-5472.can-17-2928] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 02/16/2018] [Accepted: 05/09/2018] [Indexed: 01/03/2023]
Abstract
Metabolic reprogramming of the tumor microenvironment is recognized as a cancer hallmark. To identify new molecular processes associated with tumor metabolism, we analyzed the transcriptome of bulk and flow-sorted human primary non-small cell lung cancer (NSCLC) together with 18FDG-PET scans, which provide a clinical measure of glucose uptake. Tumors with higher glucose uptake were functionally enriched for molecular processes associated with invasion in adenocarcinoma and cell growth in squamous cell carcinoma (SCC). Next, we identified genes correlated to glucose uptake that were predominately overexpressed in a single cell-type comprising the tumor microenvironment. For SCC, most of these genes were expressed by malignant cells, whereas in adenocarcinoma, they were predominately expressed by stromal cells, particularly cancer-associated fibroblasts (CAF). Among these adenocarcinoma genes correlated to glucose uptake, we focused on glutamine-fructose-6-phosphate transaminase 2 (GFPT2), which codes for the glutamine-fructose-6-phosphate aminotransferase 2 (GFAT2), a rate-limiting enzyme of the hexosamine biosynthesis pathway (HBP), which is responsible for glycosylation. GFPT2 was predictive of glucose uptake independent of GLUT1, the primary glucose transporter, and was prognostically significant at both gene and protein level. We confirmed that normal fibroblasts transformed to CAF-like cells, following TGFβ treatment, upregulated HBP genes, including GFPT2, with less change in genes driving glycolysis, pentose phosphate pathway, and TCA cycle. Our work provides new evidence of histology-specific tumor stromal properties associated with glucose uptake in NSCLC and identifies GFPT2 as a critical regulator of tumor metabolic reprogramming in adenocarcinoma.Significance: These findings implicate the hexosamine biosynthesis pathway as a potential new therapeutic target in lung adenocarcinoma. Cancer Res; 78(13); 3445-57. ©2018 AACR.
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Affiliation(s)
- Weiruo Zhang
- Department of Radiology, Stanford University School of Medicine, Stanford, California
| | - Gina Bouchard
- Department of Radiology, Stanford University School of Medicine, Stanford, California
| | - Alice Yu
- Department of Radiology, Stanford University School of Medicine, Stanford, California
| | - Majid Shafiq
- Department of Radiology, Stanford University School of Medicine, Stanford, California
| | - Mehran Jamali
- Department of Radiology, Stanford University School of Medicine, Stanford, California
| | - Joseph B Shrager
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, California.,Veterans Affairs Palo Alto Health Care System, Palo Alto, California
| | - Kelsey Ayers
- Department of Radiology, Stanford University School of Medicine, Stanford, California
| | - Shaimaa Bakr
- Department of Electrical Engineering, Stanford University, Stanford, California
| | - Andrew J Gentles
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California
| | - Andrew Quon
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Robert B West
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Viswam Nair
- Canary Center at Stanford for Cancer Early Detection, Palo Alto, California
| | - Matt van de Rijn
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Sandy Napel
- Department of Radiology, Stanford University School of Medicine, Stanford, California
| | - Sylvia K Plevritis
- Department of Radiology, Stanford University School of Medicine, Stanford, California. .,Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California
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Chabon J, Chaudhuri A, Azad T, Kurtz D, Stehr H, Liu C, Martin JS, Merriott D, Carter J, Ayers K, Mansfield A, Jen J, Ren H, West R, Nair V, Shrager J, Neal J, Wakelee H, Loo B, Alizadeh A, Diehn M. MA 13.01 Clinical and Pathological Variables Influencing Noninvasive Detection of Early Stage Lung Cancer Using Circulating Tumor DNA. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2017.09.560] [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: 10/18/2022]
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31
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Samant R, Sabloff M, Atkins H, Altouri S, Kekre N, Bredeson C, Huebsch L, Ramsay T, Allan D, Fulcher J, Nair V. High Dose Total Body Irradiation for Refractory Acute Myeloid Leukemia. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.06.450] [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: 10/18/2022]
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Moradzadeh N, Hwang G, Nair V, Guo HH. Methyl Methacrylate Mimicking a Retained Guide Wire. J Vasc Interv Radiol 2017; 27:1906. [PMID: 27886956 DOI: 10.1016/j.jvir.2016.07.020] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 07/21/2016] [Accepted: 07/21/2016] [Indexed: 10/20/2022] Open
Affiliation(s)
- Nathaniel Moradzadeh
- Department of Radiology, Stanford University School of Medicine, 300 Pasteur Dr., H3630, Stanford, CA 94305-5642.
| | - Gloria Hwang
- Divisions of Interventional Radiology, Stanford University School of Medicine, 300 Pasteur Dr., H3630, Stanford, CA 94305-5642
| | - Viswam Nair
- Pulmonary and Critical Care Medicine, Stanford University School of Medicine, 300 Pasteur Dr., H3630, Stanford, CA 94305-5642
| | - Haiwei Henry Guo
- (d)Thoracic Radiology, Stanford University School of Medicine, 300 Pasteur Dr., H3630, Stanford, CA 94305-5642
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Nagandran Y, Dimond S, Nair V. 124FACTORS AFFECTING 30 DAY READMISSION OF HIP FRACTURE PATIENTS DISCHARGED FROM ORTHOGERIATRIC UNIT. Age Ageing 2017. [DOI: 10.1093/ageing/afx072.124] [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: 11/12/2022] Open
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Affiliation(s)
- V. Nair
- Department of Pharmacology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - R. Kumar
- Department of Pharmacology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - S. Singh
- Department of Pharmacology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Y.K. Gupta
- Department of Pharmacology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
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35
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Hameed S, Nair V. 37P Expression pattern of cyclooxygenase-2 in carcinoma of cervix. Ann Oncol 2016. [DOI: 10.1016/s0923-7534(21)00197-6] [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: 11/24/2022] Open
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36
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Echegaray S, Nair V, Kadoch M, Leung A, Rubin D, Gevaert O, Napel S. A Rapid Segmentation-Insensitive "Digital Biopsy" Method for Radiomic Feature Extraction: Method and Pilot Study Using CT Images of Non-Small Cell Lung Cancer. ACTA ACUST UNITED AC 2016; 2:283-294. [PMID: 28612050 PMCID: PMC5466872 DOI: 10.18383/j.tom.2016.00163] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [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] [Indexed: 12/25/2022]
Abstract
Quantitative imaging approaches compute features within images' regions of interest. Segmentation is rarely completely automatic, requiring time-consuming editing by experts. We propose a new paradigm, called “digital biopsy,” that allows for the collection of intensity- and texture-based features from these regions at least 1 order of magnitude faster than the current manual or semiautomated methods. A radiologist reviewed automated segmentations of lung nodules from 100 preoperative volume computed tomography scans of patients with non–small cell lung cancer, and manually adjusted the nodule boundaries in each section, to be used as a reference standard, requiring up to 45 minutes per nodule. We also asked a different expert to generate a digital biopsy for each patient using a paintbrush tool to paint a contiguous region of each tumor over multiple cross-sections, a procedure that required an average of <3 minutes per nodule. We simulated additional digital biopsies using morphological procedures. Finally, we compared the features extracted from these digital biopsies with our reference standard using intraclass correlation coefficient (ICC) to characterize robustness. Comparing the reference standard segmentations to our digital biopsies, we found that 84/94 features had an ICC >0.7; comparing erosions and dilations, using a sphere of 1.5-mm radius, of our digital biopsies to the reference standard segmentations resulted in 41/94 and 53/94 features, respectively, with ICCs >0.7. We conclude that many intensity- and texture-based features remain consistent between the reference standard and our method while substantially reducing the amount of operator time required.
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Affiliation(s)
- Sebastian Echegaray
- Department of Electrical Engineering, Stanford University, Stanford, California
| | - Viswam Nair
- Department of Radiology, Stanford University School of Medicine, Stanford, California.,Department of Medicine, Stanford University School of Medicine, Stanford, California.,Canary Center for Cancer Early Detection, Stanford University, Stanford, California
| | - Michael Kadoch
- Department of Radiology, Stanford University School of Medicine, Stanford, California
| | - Ann Leung
- Department of Radiology, Stanford University School of Medicine, Stanford, California
| | - Daniel Rubin
- Department of Radiology, Stanford University School of Medicine, Stanford, California.,Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Olivier Gevaert
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Sandy Napel
- Department of Radiology, Stanford University School of Medicine, Stanford, California
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Ebcioglu Z, Liu C, Shapiro R, Rana M, Salem F, Florman S, Huprikar S, Nair V. Belatacept Conversion in an HIV-Positive Kidney Transplant Recipient With Prolonged Delayed Graft Function. Am J Transplant 2016; 16:3278-3281. [PMID: 27328903 DOI: 10.1111/ajt.13923] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [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: 01/28/2016] [Revised: 05/15/2016] [Accepted: 06/12/2016] [Indexed: 01/25/2023]
Abstract
We report an HIV-positive renal transplant recipient with delayed graft function who was converted from tacrolimus to belatacept in an attempt to improve renal function. The patient had kidney biopsies at 4 and 8 weeks posttransplant that revealed acute tubular necrosis and mild fibrosis. After 14 weeks of delayed function, belatacept was initiated and tacrolimus was weaned off. Shortly after discontinuing tacrolimus, renal function began to improve. The patient was able to discontinue dialysis 21 weeks posttransplant. HIV viral load was undetectable at last follow-up. To our knowledge, this is the first report of belatacept use in a patient with HIV.
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Affiliation(s)
- Z Ebcioglu
- Recanati/Miller Transplantation Institute, The Mount Sinai Medical Center, New York, NY.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - C Liu
- Recanati/Miller Transplantation Institute, The Mount Sinai Medical Center, New York, NY
| | - R Shapiro
- Recanati/Miller Transplantation Institute, The Mount Sinai Medical Center, New York, NY
| | - M Rana
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - F Salem
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - S Florman
- Recanati/Miller Transplantation Institute, The Mount Sinai Medical Center, New York, NY
| | - S Huprikar
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - V Nair
- Recanati/Miller Transplantation Institute, The Mount Sinai Medical Center, New York, NY. .,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY.
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Nair V, Madan H, Sofat S, Ganguli P, Jacob MJ, Datta R, Bharadwaj P, Sarkar RS, Pandit AJ, Nityanand S, Goel PK, Garg N, Gambhir S, George PV, Chandy S, Mathews V, George OK, Talwar KK, Bahl A, Marwah N, Bhatacharya A, Bhargava B, Airan B, Mohanty S, Patel CD, Sharma A, Bhatnagar S, Mondal A, Jose J, Srivastava A. Authors' response. Indian J Med Res 2016; 143:833. [PMID: 27748312 PMCID: PMC5094127 DOI: 10.4103/0971-5916.192081] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- V Nair
- Army Hospital (Research & Referral), New Delhi, India
| | - H Madan
- Army Hospital (Research & Referral), New Delhi, India
| | - S Sofat
- Army Hospital (Research & Referral), New Delhi, India
| | - P Ganguli
- Army Hospital (Research & Referral), New Delhi, India
| | - M J Jacob
- Army Hospital (Research & Referral), New Delhi, India
| | - R Datta
- Military Hospital, Cardio Thoracic Centre, Pune, India
| | - P Bharadwaj
- Military Hospital, Cardio Thoracic Centre, Pune, India
| | - R S Sarkar
- Military Hospital, Cardio Thoracic Centre, Pune, India
| | - A J Pandit
- Military Hospital, Cardio Thoracic Centre, Pune, India
| | - S Nityanand
- Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - P K Goel
- Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - N Garg
- Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - S Gambhir
- Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - P V George
- Christian Medical College, Vellore, India
| | - S Chandy
- Christian Medical College, Vellore, India
| | - V Mathews
- Christian Medical College, Vellore, India
| | - O K George
- Christian Medical College, Vellore, India
| | - K K Talwar
- Postgraduate Institute of Medical Education & Research, Chandhigarh, India
| | - A Bahl
- Postgraduate Institute of Medical Education & Research, Chandhigarh, India
| | - N Marwah
- Postgraduate Institute of Medical Education & Research, Chandhigarh, India
| | - A Bhatacharya
- Postgraduate Institute of Medical Education & Research, Chandhigarh, India
| | - B Bhargava
- All India Institute of Medical Sciences, New Delhi, India
| | - B Airan
- All India Institute of Medical Sciences, New Delhi, India
| | - S Mohanty
- All India Institute of Medical Sciences, New Delhi, India
| | - C D Patel
- All India Institute of Medical Sciences, New Delhi, India
| | - A Sharma
- Department of Biotechnology, Government of India, New Delhi, India
| | - S Bhatnagar
- All India Institute of Medical Sciences, New Delhi, India
| | - A Mondal
- Institute of Nuclear Medicine & Allied Sciences, Delhi, India
| | - J Jose
- Christian Medical College, Vellore, India
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Lin G, Tripathi P, Naemi H, Nair V. The Performance of Two Commercial, Diagnostic Blood Tests to Evaluate the Incidentally Detected, Indeterminate Pulmonary Nodule. Chest 2016. [DOI: 10.1016/j.chest.2016.08.828] [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] Open
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Abstract
Previous studies showing circadian variation in pharmacologic response to drugs in man and experimental animals have been reviewed. The chronobiologic response is discussed in terms of the pharmacologic factors that determine drug action. The importance of internal markers in chronopharmacologic studies is emphasized and is illustrated by our studies with the antihypersive drugs. Identification of chronobiologic variations in the therapeutic and toxic response to drugs, when present, along with an understanding of their mechanisms, would permit the design of optimal therapeutic regimens for these drugs.
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Affiliation(s)
- V. Nair
- Depts. of Pharmacology and Pathology University of Health Sciences, The Chicago Medical School North Chicago, Illinois 60064
| | - A. Chedid
- Depts. of Pharmacology and Pathology University of Health Sciences, The Chicago Medical School North Chicago, Illinois 60064
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Nandi S, Whyte J, Taylor L, Sherman A, Nair V, Kaiser P, McGrew MJ. Cryopreservation of specialized chicken lines using cultured primordial germ cells. Poult Sci 2016; 95:1905-11. [PMID: 27099306 PMCID: PMC4988548 DOI: 10.3382/ps/pew133] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [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] [Accepted: 02/22/2016] [Indexed: 01/03/2023] Open
Abstract
Biosecurity and sustainability in poultry production requires reliable germplasm conservation. Germplasm conservation in poultry is more challenging in comparison to other livestock species. Embryo cryopreservation is not feasible for egg-laying animals, and chicken semen conservation has variable success for different chicken breeds. A potential solution is the cryopreservation of the committed diploid stem cell precursors to the gametes, the primordial germ cells ( PGCS: ). Primordial germ cells are the lineage-restricted cells found at early embryonic stages in birds and form the sperm and eggs. We demonstrate here, using flocks of partially inbred, lower-fertility, major histocompatibility complex- ( MHC-: ) restricted lines of chicken, that we can easily derive and cryopreserve a sufficient number of independent lines of male and female PGCs that would be sufficient to reconstitute a poultry breed. We demonstrate that germ-line transmission can be attained from these PGCs using a commercial layer line of chickens as a surrogate host. This research is a major step in developing and demonstrating that cryopreserved PGCs could be used for the biobanking of specialized flocks of birds used in research settings. The prospective application of this technology to poultry production will further increase sustainability to meet current and future production needs.
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Affiliation(s)
- S Nandi
- The Roslin Institute and Royal Dick School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - J Whyte
- The Roslin Institute and Royal Dick School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - L Taylor
- The Roslin Institute and Royal Dick School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - A Sherman
- The Roslin Institute and Royal Dick School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - V Nair
- Avian Oncogenic Virus Group, The Pirbright Institute, Ash Road, Woking, Guildford, Surrey, GU24 0NF, UK
| | - P Kaiser
- The Roslin Institute and Royal Dick School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - M J McGrew
- The Roslin Institute and Royal Dick School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
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Sutherland J, Pantarotto J, Nair V, Cook G, Plourde M, Vandervoort E. WE-AB-303-05: Breathing Motion of Liver Segments From Fiducial Tracking During Robotic Radiosurgery and Comparison with 4D-CT-Derived Fiducial Motion. Med Phys 2015. [DOI: 10.1118/1.4925870] [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: 11/07/2022] Open
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Nair V, Soraisham A, Yee W, Singhal N. 5: Impact of Open Lung Strategy on the Neonatal Outcomes in Preterm Infants. Paediatr Child Health 2014. [DOI: 10.1093/pch/19.6.e35-5] [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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Nair V, Loganahan P, Soriasham A. 70: Macrolides for Prevention of Bronchopulmonary Dysplasia: Systematic Review and Meta-Analysis. Paediatr Child Health 2014. [DOI: 10.1093/pch/19.6.e35-68] [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: 11/12/2022] Open
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Nair V, Hasan SU, Yusuf K. 96: Serum Levels of Soluble FAS and Soluble FAS Ligand in Pregnant Women Who Smoke. Paediatr Child Health 2014. [DOI: 10.1093/pch/19.6.e35-94] [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: 11/13/2022] Open
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Yusuf K, Nair V, Alshaikh B, Hasan SU, Lodha A, Silva OD, Alvaro RE, Lee SK, Shah PS. 95: Neonatal Outcomes in Infants <29 Weeks Gestation in Relation to Maternal Hypertension and Smoking Status. Paediatr Child Health 2014. [DOI: 10.1093/pch/19.6.e35-93] [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: 11/13/2022] Open
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Ahmed I, Biswas A, Krishnamurthy S, Julka P, Rath G, Back M, Huang D, Gzell C, Chen J, Kastelan M, Gaur P, Wheeler H, Badiyan SN, Robinson CG, Simpson JR, Tran DD, Rich KM, Dowling JL, Chicoine MR, Leuthardt EC, Kim AH, Huang J, Michaelsen SR, Christensen IJ, Grunnet K, Stockhausen MT, Broholm H, Kosteljanetz M, Poulsen HS, Tieu M, Lovblom E, Macnamara M, Mason W, Rodin D, Tai E, Ubhi K, Laperriere N, Millar BA, Menard C, Perkins B, Chung C, Clarke J, Molinaro A, Phillips J, Butowski N, Chang S, Perry A, Costello J, DeSilva A, Rabbitt J, Prados M, Cohen AL, Anker C, Shrieve D, Hall B, Salzman K, Jensen R, Colman H, Farber O, Weinberg U, Palti Y, Fisher B, Chen H, Macdonald D, Lesser G, Coons S, Brachman D, Ryu S, Werner-Wasik M, Bahary JP, Chakravarti A, Mehta M, Gupta T, Nair V, Epari S, Godasastri J, Moiyadi A, Shetty P, Juvekar S, Jalali R, Herrlinger U, Schafer N, Steinbach J, Weyerbrock A, Hau P, Goldbrunner R, Kohnen R, Urbach H, Stummer W, Glas M, Houillier C, Ghesquieres H, Chabrot C, Soussain C, Ahle G, Choquet S, Faurie P, Bay JO, Vargaftig J, Gaultier C, Nicolas-Virelizier E, Hoang-Xuan K, Iskanderani O, Izar F, Benouaich-Amiel A, Filleron T, Moyal E, Iweha C, Jain S, Melian E, Sethi A, Albain K, Shafer D, Emami B, Kong XT, Green S, Filka E, Green R, Yong W, Nghiemphu P, Cloughesy T, Lai A, Mallick S, Biswas A, Roy S, Purkait S, Gupta S, Julka PK, Rath GK, Marosi C, Thaler J, Ay C, Kaider A, Reitter EM, Haselbock J, Preusser M, Flechl B, Zielinski C, Pabinger I, Miyatake SI, Furuse M, Miyata T, Yoritsune E, Kawabata S, Kuroiwa T, Muragaki Y, Maruyama T, Iseki H, Akimoto J, Ikuta S, Nitta M, Maebayashi K, Saito T, Okada Y, Kaneko S, Matsumura A, Kuroiwa T, Karasawa K, Nakazato Y, Kayama T, Nabors LB, Fink KL, Mikkelsen T, Grujicic D, Tarnawski R, Nam DH, Mazurkiewicz M, Salacz M, Ashby L, Thurzo L, Zagonel V, Depenni R, Perry JR, Henslee-Downey J, Picard M, Reardon DA, Nambudiri N, Nayak L, LaFrankie D, Wen P, Ney D, Carlson J, Damek D, Blatchford P, Gaspar L, Kavanagh B, Waziri A, Lillehei K, Reddy K, Chen C, Rashed I, Melian E, Sethi A, Barton K, Anderson D, Prabhu V, Rusch R, Belongia M, Maheshwari M, Firat S, Schiff D, Desjardins A, Cloughesy T, Mikkelsen T, Glantz M, Chamberlain M, Reardon DA, Wen P, Shapiro W, Gopal S, Judy K, Patel S, Mahapatra A, Shan J, Gupta D, Shih K, Bacha JA, Brown D, Garner WJ, Steino A, Schwart R, Kanekal S, Li M, Lopez L, Burris HA, Soderberg-Naucler C, Rahbar A, Stragliotto G, Song AJ, Kumar AMS, Murphy ES, Tekautz T, Suh JH, Recinos V, Chao ST, Spoor J, Korami K, Kloezeman J, Balvers R, Dirven C, Lamfers M, Leenstra S, Sumrall A, Haggstrom D, Crimaldi A, Symanowski J, Giglio P, Asher A, Burri S, Sunkersett G, Khatib Z, Prajapati CM, Magalona EE, Mariano M, Sih IM, Torcuator R, Taal W, Oosterkamp H, Walenkamp A, Beerenpoot L, Hanse M, Buter J, Honkoop A, Boerman D, de Vos F, Jansen R, van der Berkmortel F, Brandsma D, Enting R, Kros J, Bromberg J, van Heuvel I, Smits M, van der Holt R, Vernhout R, van den Bent M, Weinberg U, Farber O, Palti Y, Wick W, Suarez C, Rodon J, Desjardins A, Forsyth P, Gueorguieva I, Cleverly A, Burkholder T, Desaiah D, Lahn M, Zach L, Guez D, Last D, Daniels D, Nissim O, Grober Y, Hoffmann C, Nass D, Talianski A, Spiegelmann R, Cohen Z, Mardor Y. MEDICAL RADIATION THERAPIES. Neuro Oncol 2013; 15:iii75-iii84. [PMCID: PMC3823894 DOI: 10.1093/neuonc/not179] [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: 09/21/2023] Open
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Nair V, Sinu C, Padmaja D, Jini P, Lakshmi K. NHC-Catalyzed Annulation of Enals to 2,4-Dien-1-ones: Efficient Diastereoselective Synthesis of 1,3-Diaryl-4-styrenyl Cyclopentenes. Synlett 2013. [DOI: 10.1055/s-0033-1339308] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Gu B, Burt BM, Merritt RE, Stephanie S, Nair V, Hoang CD, Shrager JB. A dominant adenocarcinoma with multifocal ground glass lesions does not behave as advanced disease. Ann Thorac Surg 2013; 96:411-8. [PMID: 23806231 DOI: 10.1016/j.athoracsur.2013.04.048] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 04/12/2013] [Accepted: 04/15/2013] [Indexed: 10/26/2022]
Abstract
BACKGROUND Invasive lung adenocarcinomas increasingly present with synchronous, multifocal, in situ lesions that appear as ground glass opacities (GGOs). The optimal approach in this circumstance (often nonsmokers) remains unclear. We evaluated a general strategy of anatomic resection of the dominant tumor (DT) and wedge resection of accessible ipsilateral GGOs. METHODS This is a retrospective review of 39 patients with suspected multifocal in situ adenocarcinomas and 1 DT in a predominantly Caucasian population. Mean follow-up is 30.7 months. RESULTS Forty-nine percent of patients had no or minimal smoking history; 21% were Asian. The resected DT was pathologically "bronchioloalveolar carcinoma" (26%), minimally invasive adenocarcinoma (5%), adenocarcinoma with bronchioloalveolar features (41%), or moderate well-differentiated adenocarcinoma (28%). The p stage of the DT was IA in 20, IB in 15, and IIA in 4, with mean diameter of 2.6 cm. Thirty-two patients (82%) underwent anatomic resection of the DT; 7 (18%) underwent wedge resection. The mean number of GGOs present initially was 2.7 (range, 1 to 7) with a 5.2-mm mean diameter. An unresected nodule increased in size during follow-up in only 9 patients (23%). The mean diameter growth among these was 3.2 mm, with mean doubling time of 49 months. New GGOs (range, 1 to 8) developed in 16 patients (41%), all of which remained at 7 mm or less. Distant metastasis developed in 2 patients (5.2%); only 1 patient has required intervention for progression of a GGO. The overall survival is 100%. CONCLUSIONS Patients with limited, multifocal, in situ adenocarcinomas and a clinical N0 DT enjoy prolonged survival with generally anatomic resection of the DT and wedge resection of accessible GGOs. These patients should not be considered to harbor T4 or M1a disease.
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Affiliation(s)
- Bo Gu
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, California, USA
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Nair V, Sharma A, DAS S, Sharma S, Grover N, Kaur J. Allogeneic haematopoietic stem cell transplantation: the Army hospital experience. Natl Med J India 2013; 26:6-11. [PMID: 24066986] [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] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
BACKGROUND We analysed the results of allogeneic haematopoietic stem cell transplantation (HSCT) in various genetic disorders, bone marrow failures and haematological malignancies done from 2002 to 2010 at the Army Hospital, Research and Referral, Delhi. METHODS A total of 119 matched-related allogeneic- HSCTs (allo-HSCTs) were done in 114 patients (men 76, women 38) aged between 2 and 60 years. Peripheral blood stem cells (n=75) and bone marrow (n=43) were used as the source of stem cells. RESULTS The overall survival was 62.3% (71/114) at a median follow-up of 34 months. Graft versus host disease (GVHD) was seen in 42 (36.8%) patients; grade III/IV acute GVHD in 17 (15%) and chronic GVHD in 24 (21%) patients. There were 4 (3.5%) graft rejections and one nonengraftment. The overall mortality was 37.7% (n=43) and the main causes of death were GVHD (32%), infections (26%), relapse (23%) and regimen-related toxicity (11%). CONCLUSION Our results are comparable to published data in most disease conditions. With improvements in GVHD prophylaxis and better supportive care, we need to further reduce our mortality and morbidity.
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Affiliation(s)
- V Nair
- Armed Forces Medical College, Pune 411040, Maharashtra, India. Department of Medicine and Clinical Haematology
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