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Reiner J, Chung Y, Misha SH, Lehner C, Moehle C, Poulos D, Monir S, Charde KJ, Macha P, Kranz L, Thorvaldson I, Thorgrimsson B, Keith D, Hsueh YL, Rahman R, Gorman SK, Keizer JG, Simmons MY. High-fidelity initialization and control of electron and nuclear spins in a four-qubit register. Nat Nanotechnol 2024:10.1038/s41565-023-01596-9. [PMID: 38326467 DOI: 10.1038/s41565-023-01596-9] [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] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 12/20/2023] [Indexed: 02/09/2024]
Abstract
Single electron spins bound to multi-phosphorus nuclear spin registers in silicon have demonstrated fast (0.8 ns) two-qubit [Formula: see text] gates and long spin relaxation times (~30 s). In these spin registers, when the donors are ionized, the nuclear spins remain weakly coupled to their environment, allowing exceptionally long coherence times. When the electron is present, the hyperfine interaction allows coupling of the spin and charge degrees of freedom for fast qubit operation and control. Here we demonstrate the use of the hyperfine interaction to enact electric dipole spin resonance to realize high-fidelity ([Formula: see text]%) initialization of all the nuclear spins within a four-qubit nuclear spin register. By controllably initializing the nuclear spins to [Formula: see text], we achieve single-electron qubit gate fidelities of F = 99.78 ± 0.07% (Clifford gate fidelities of 99.58 ± 0.14%), above the fault-tolerant threshold for the surface code with a coherence time of [Formula: see text].
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Affiliation(s)
- J Reiner
- Centre of Excellence for Quantum Computation and Communication Technology, School of Physics, University of New South Wales, Sydney, New South Wales, Australia
- Silicon Quantum Computing Pty Ltd., University of New South Wales, Sydney, New South Wales, Australia
| | - Y Chung
- Centre of Excellence for Quantum Computation and Communication Technology, School of Physics, University of New South Wales, Sydney, New South Wales, Australia
- Silicon Quantum Computing Pty Ltd., University of New South Wales, Sydney, New South Wales, Australia
| | - S H Misha
- Centre of Excellence for Quantum Computation and Communication Technology, School of Physics, University of New South Wales, Sydney, New South Wales, Australia
- Silicon Quantum Computing Pty Ltd., University of New South Wales, Sydney, New South Wales, Australia
| | - C Lehner
- Centre of Excellence for Quantum Computation and Communication Technology, School of Physics, University of New South Wales, Sydney, New South Wales, Australia
- Silicon Quantum Computing Pty Ltd., University of New South Wales, Sydney, New South Wales, Australia
| | - C Moehle
- Centre of Excellence for Quantum Computation and Communication Technology, School of Physics, University of New South Wales, Sydney, New South Wales, Australia
- Silicon Quantum Computing Pty Ltd., University of New South Wales, Sydney, New South Wales, Australia
| | - D Poulos
- Centre of Excellence for Quantum Computation and Communication Technology, School of Physics, University of New South Wales, Sydney, New South Wales, Australia
- Silicon Quantum Computing Pty Ltd., University of New South Wales, Sydney, New South Wales, Australia
| | - S Monir
- Silicon Quantum Computing Pty Ltd., University of New South Wales, Sydney, New South Wales, Australia
- School of Physics, University of New South Wales, Sydney, New South Wales, Australia
| | - K J Charde
- Centre of Excellence for Quantum Computation and Communication Technology, School of Physics, University of New South Wales, Sydney, New South Wales, Australia
- Silicon Quantum Computing Pty Ltd., University of New South Wales, Sydney, New South Wales, Australia
| | - P Macha
- Centre of Excellence for Quantum Computation and Communication Technology, School of Physics, University of New South Wales, Sydney, New South Wales, Australia
- Silicon Quantum Computing Pty Ltd., University of New South Wales, Sydney, New South Wales, Australia
| | - L Kranz
- Centre of Excellence for Quantum Computation and Communication Technology, School of Physics, University of New South Wales, Sydney, New South Wales, Australia
- Silicon Quantum Computing Pty Ltd., University of New South Wales, Sydney, New South Wales, Australia
| | - I Thorvaldson
- Centre of Excellence for Quantum Computation and Communication Technology, School of Physics, University of New South Wales, Sydney, New South Wales, Australia
- Silicon Quantum Computing Pty Ltd., University of New South Wales, Sydney, New South Wales, Australia
| | - B Thorgrimsson
- Centre of Excellence for Quantum Computation and Communication Technology, School of Physics, University of New South Wales, Sydney, New South Wales, Australia
- Silicon Quantum Computing Pty Ltd., University of New South Wales, Sydney, New South Wales, Australia
| | - D Keith
- Centre of Excellence for Quantum Computation and Communication Technology, School of Physics, University of New South Wales, Sydney, New South Wales, Australia
- Silicon Quantum Computing Pty Ltd., University of New South Wales, Sydney, New South Wales, Australia
| | - Y L Hsueh
- Silicon Quantum Computing Pty Ltd., University of New South Wales, Sydney, New South Wales, Australia
- School of Physics, University of New South Wales, Sydney, New South Wales, Australia
| | - R Rahman
- Silicon Quantum Computing Pty Ltd., University of New South Wales, Sydney, New South Wales, Australia
- School of Physics, University of New South Wales, Sydney, New South Wales, Australia
| | - S K Gorman
- Centre of Excellence for Quantum Computation and Communication Technology, School of Physics, University of New South Wales, Sydney, New South Wales, Australia
- Silicon Quantum Computing Pty Ltd., University of New South Wales, Sydney, New South Wales, Australia
| | - J G Keizer
- Centre of Excellence for Quantum Computation and Communication Technology, School of Physics, University of New South Wales, Sydney, New South Wales, Australia
- Silicon Quantum Computing Pty Ltd., University of New South Wales, Sydney, New South Wales, Australia
| | - M Y Simmons
- Centre of Excellence for Quantum Computation and Communication Technology, School of Physics, University of New South Wales, Sydney, New South Wales, Australia.
- Silicon Quantum Computing Pty Ltd., University of New South Wales, Sydney, New South Wales, Australia.
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Ali S, Athar M, Rahman R, Rehman F. Ceftriaxone-induced Kounis syndrome: A case report and review of the literature. Rev Esp Anestesiol Reanim (Engl Ed) 2024; 71:129-133. [PMID: 37683977 DOI: 10.1016/j.redare.2023.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 01/22/2023] [Indexed: 09/10/2023]
Abstract
Kounis syndrome is defined as cardiovascular symptoms that occur secondary to allergic or hypersensitivity insults, and is also called allergic angina and allergic myocardial infarction. We report a case of pre-operative ceftriaxone-induced Kounis syndrome with no evident dermatological manifestation, and describe our diagnostic dilemma. The patient was symptomatically managed and discharged in stable condition with a warning against future use of ceftriaxone.
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Affiliation(s)
- S Ali
- Department of Anaesthesiology and Critical Care, J.N. Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - M Athar
- Department of Anaesthesiology and Critical Care, J.N. Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India.
| | - R Rahman
- Department of Anaesthesiology and Critical Care, J.N. Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - F Rehman
- Department of Anaesthesiology and Critical Care, J.N. Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
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Rahman R, Siddique T, Nipa FA, Sultana S, Devi P, Islam F, Nainu F, Obaidullah AJ, Emran TB, Khatun MR. Bark extract of Chaetocarpus castanocarpus (Roxb.) exhibits potent sedative, anxiolytic, and antidepressant effects through an in vivo approach in Swiss albino mice. Eur Rev Med Pharmacol Sci 2024; 28:1202-1212. [PMID: 38375725 DOI: 10.26355/eurrev_202402_35359] [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: 02/21/2024]
Abstract
OBJECTIVE Standard phytochemical investigations were performed to identify the secondary metabolites in the methanol extract of Chaetocarpus castanocarpus bark (MECC) and investigate the neuropharmacological potential of MECC in Swiss albino mice. MATERIALS AND METHODS Swiss albino mice were used in the forced swimming test (FST) and tail suspension test (TST) to evaluate the antidepressant effect of MECC. Also, the hole board test (HBT) and elevated plus maze (EPM) were conducted to examine anxiolytic activities. In contrast, the open field test (OFT) and hole cross test (HCT) were employed to evaluate sleeping disorders. RESULTS Alkaloids, glycosides, flavonoids, terpenoids, coumarins, and tannins are only a few secondary metabolites identified in MECC by qualitative and quantitative phytochemical investigations. The oral administration of MECC considerably shortened the immobility duration during FST and TST. Encouraging dose-dependent anxiolytic effects were also observed in all relevant experiments compared to the control. Additionally, during the OFT and HCT assessment, a noteworthy decline in the locomotor activities of the experimental animals was observed. CONCLUSIONS The results of this investigation suggest that the Chaetocarpus castanocarpus bark is a possible source of therapeutic candidates for treating neurological disorders.
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Affiliation(s)
- R Rahman
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, Bangladesh.
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Amirah N, Rahman R. Mental Health Status during COVID-19 Pandemic and its Relationship with Economic Hardship and Financial Threat among Rural Population in Sarawak, Malaysia. Kathmandu Univ Med J (KUMJ) 2023; 21:149-155. [PMID: 38628007] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Background During the COVID-19 pandemic, job and income loss, social isolation may aggravate mental health, particularly among the most vulnerable groups. Objective To assess the current mental health situation among the rural population in Samarahan district and determine the relationship between economic hardships, financial threats, and mental health status. Method This study was a cross-sectional study conducted among the 530 households in the Samarahan district. A multistage cluster sampling technique was used to select the participants in this study. Data were collected by face-to-face interview using a structured questionnaire. The mental health status was assessed by using a validated and translated DASS-21 scale. Data analysis was done by SPSS version 27.0. A p-value of ≤ .05 was considered statistically significant. Result Analysis showed that two-thirds of the respondents (66.6%) had no mental health problem. Meanwhile, 22.4% had anxiety, 1% had depression, and 0.19% had stress. Anxiety and depression accounted for 5.8% and stress and anxiety 1.3%. However, 2.64% had stress, anxiety, and depression. In bivariate analysis, age, monthly income, type of job, economic hardship, and expenditure difference appeared to be significant predictors of mental health problems (p < .05). Conclusion Depression, anxiety, and stress pose a significant threat to the rural population's health. Therefore, public health practitioners and policymakers need to address this to minimise the pandemic's impact on mental health and provide psychological support, particularly among the most affected group.
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Affiliation(s)
- N Amirah
- Department of Community Medicine and Public Health, Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
| | - R Rahman
- Department of Community Medicine and Public Health Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
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MAHJABIN S, Rahman R, Haque E, Islam N. WCN23-0544 CLINICAL PROFILE, IMMUNOSUPPRESSIVE MANAGMENT AND OUTCOME IN ADULT RENAL ALLOGRAFT RECIPIENTS WITH COVID-19 INFECTION: A CASE SERIES FROM SINGLE CENTRE IN BANGLADESH. Kidney Int Rep 2023. [PMCID: PMC10025673 DOI: 10.1016/j.ekir.2023.02.1007] [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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Yousuf S, Mahmood S, Rahman R, Khatun R, Tanzin F, Arzoo S, Ferdous NE. Efficacy and Safety of Repeated Use of Ulipristal Acetate in Uterine Fibroids. Mymensingh Med J 2023; 32:168-176. [PMID: 36594317] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Uterine fibroids are benign tumor of the uterus that often appear during child bearing ages. Medical treatments are considered the first-line treatment to preserve fertility, avoid or delaying surgery. This randomized control study was carried out in OPD of Obstetrics and Gynecology Department of BSMMU, Dhaka, Bangladesh from May 2018 to March 2019 to evaluate the efficacy and safety of ulipristal acetate (5mg) once daily in reproductive women with three months treatment courses. Total 52 samples with symptomatic uterine fibroids for treatment course-1, among them 36 were needed for treatment course-2 which was slow or non-responding in treatment course-1. Main outcome measures were amenorrhea, controlled bleeding, fibroid volume, anaemia, quality of life. Sixty one percent (61.0%) of patients were achieved amenorrheic during both treatment courses. Ninety percent (90.0%) patients were control of bleeding during both treatment courses. In treatment course-1, reductions from baseline in fibroid volume were 62.70%, whereas in course-2, reductions in fibroid volume were 75.33%. Five percent (5.0%) of patients were discontinuing Ulipristal acetate due to adverse effects. Renal and liver function tests were performed before and after each course of treatment. The level of creatinine, SGPT in the blood for both treatment courses had no statistically significant effects. Ulipristal acetate may be an alternative to surgical treatment, the safety profiles and prolong effects with improvement of symptoms, quality of life after cessation of drugs. Repeated use of drugs reduces the size and also improves the patient's condition.
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Affiliation(s)
- S Yousuf
- Dr Shereen Yousuf, Medical Officer, Department of Obstetrics and Gynaecology, BSMMU, Dhaka, Bangladesh; E-mail:
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Elhalawani H, Hammoudeh L, Cagney D, Qian J, Martin A, Zgrabik J, Meyers J, Pataki K, Martin K, Khouj Y, Verry C, Bi W, Arnaout O, Christ S, Alexander B, Tanguturi S, Rahman R, Haas-Kogan D, Aizer A. Leveraging Serial MRI Radiomics and Machine Learning to Predict Risk of Radiation Necrosis in Patients with Brain Metastases Managed with Stereotactic Radiation and Immunotherapy. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.954] [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: 10/31/2022]
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Woon E, Rahman R, Ibeto L, MacLaran K, Norman-Taylor J, Nikolaou D. P-703 Developing individualized treatment strategies using detailed subgroup analysis to optimise pregnancy outcomes for women 40 and above. Hum Reprod 2022. [DOI: 10.1093/humrep/deac107.652] [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: 11/13/2022] Open
Abstract
Abstract
Study question
What are the prognostic factors and treatment strategies for women 40 and above within different ovarian reserve subgroups?
Summary answer
Women in each ovarian reserve subgroup have different prognostic factors of pregnancy success and specific treatment strategies are needed for each subgroup.
What is known already
The number of women 40 and above seeking subfertility treatment is increasing and many are willing to undergo treatment despite extremely poor prognosis. POSEIDON criteria suggested the usage of ovarian reserve and female age as a basis for the study of the management of women in different prognostic categories. However, this classification may not be detailed enough to lead to specific recommendations for individualised management in women 40 and above, as there is rapid decline of oocyte quality and quantity. Large observational studies may lack finer detail due to challenges in recruiting women within different ovarian reserve subgroups.
Study design, size, duration
We carried out a detailed retrospective analysis of 382 IVF/ICSI cycles for 253 women from January 2019 to December 2021 in a special clinical and academic program for reproductive ageing and fertility. Inclusion criteria were all women who had IVF/ICSI cycles aged 40 and over. Analysis was done for all fresh cycles including cancelled cycles, failed fertilization, no eggs collected and embryo arrest. Cycles resulting in freezing of all embryos were excluded in analysis.
Participants/materials, setting, methods
The participants were divided into three main subroups: Group A, “normal ovarian reserve” (AMH 2.5-29.9pmol/l, n = 271 cycles); Group B, “extremely poor ovarian reserve” (AMH <2.5pmol/l, n = 85 cycles); and Group C “extremely high ovarian reserve” (PCOS or AMH ≥30.0pmol/l, n = 26 cycles). Chi-square and Mann-Whitney U tests were used to compare pregnant and non-pregnant groups for nominal and continuous data respectively. Multi-variate logistic regression was performed when indicated. All descriptive statistics are stated in median and percentages.
Main results and the role of chance
In Group A, univariate analysis showed that pregnancies were associated with lower female (41 vs 42) and male age (40 vs 43.5), administering long agonist versus antagonist protocol (73% vs 27%), the absence of androgen pretreatment (12% vs 88%), higher oestradiol level (7681pmol/l vs 6114pmol/l), higher number of oocytes retrieved (8 vs 4) and normally fertilized (4 vs 3), and embryo transfer on day 3 compared to 2 or 5 (all p < 0.05). The use of combined FSH/LH vs FSH only for ovarian stimulation given for 12 days at 300IU daily, higher endometrial thickness (11.3mm vs 10.6mm), IVF versus ICSI (65% vs 35%), and addition of subcutaneous progesterone for luteal support versus vaginal progesterone only (51% vs 43%) were trending towards but were not significant (p > 0.05). Multivariate logistic regression analysis revealed lower female and male age, less number of IVF cycles, and higher number of embryos transferred as independent factors contributing to pregnancy. In Group B, significant predictors of pregnancy included younger female age, higher gravidity, previous successful IVF and higher number of eggs fertilized (p < 0.05). In Group C, factors that contributed to positive pregnancy outcome included antagonist cycles versus agonist and usage of FSH and LH versus FSH alone (p > 0.05).
Limitations, reasons for caution
The retrospective nature of the study design limits control of potential confounding variables. Although there were clear trends, in a few sub-categories there were insufficient numbers to reach statistical significance. Continuing data collection is necessary to achieve adequate power for smaller groups especially Group B and C.
Wider implications of the findings
This detailed analysis will allow us to better understand the prognostic factors in women 40 and above, especially for women with extremes of ovarian reserve, who may benefit substantially from individualised care. We recommend standardisation of data collection and development of artificial intelligence algorithms to streamline management in the future.
Trial registration number
N/A
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Affiliation(s)
- E.V Woon
- Chelsea and Westminster Hospital NHS Foundation Trust, Assisted Conception Unit , London, United Kingdom
- Imperial College London, Department of Metabolism- Digestion and Reproduction , London, United Kingdom
| | - R Rahman
- Chelsea and Westminster Hospital NHS Foundation Trust, Assisted Conception Unit , London, United Kingdom
| | - L Ibeto
- Chelsea and Westminster Hospital NHS Foundation Trust, Assisted Conception Unit , London, United Kingdom
| | - K MacLaran
- Chelsea and Westminster Hospital NHS Foundation Trust, Assisted Conception Unit , London, United Kingdom
| | - J Norman-Taylor
- Chelsea and Westminster Hospital NHS Foundation Trust, Assisted Conception Unit , London, United Kingdom
| | - D Nikolaou
- Chelsea and Westminster Hospital NHS Foundation Trust, Assisted Conception Unit , London, United Kingdom
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Yang N, Srivastav SP, Rahman R, Ma Q, Dayama G, Li S, Chinen M, Lei EP, Rosbash M, Lau NC. Transposable element landscapes in aging Drosophila. PLoS Genet 2022; 18:e1010024. [PMID: 35239675 PMCID: PMC8893327 DOI: 10.1371/journal.pgen.1010024] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/10/2022] [Indexed: 11/28/2022] Open
Abstract
Genetic mechanisms that repress transposable elements (TEs) in young animals decline during aging, as reflected by increased TE expression in aged animals. Does increased TE expression during aging lead to more genomic TE copies in older animals? To address this question, we quantified TE Landscapes (TLs) via whole genome sequencing of young and aged Drosophila strains of wild-type and mutant backgrounds. We quantified TLs in whole flies and dissected brains and validated the feasibility of our approach in detecting new TE insertions in aging Drosophila genomes when small RNA and RNA interference (RNAi) pathways are compromised. We also describe improved sequencing methods to quantify extra-chromosomal DNA circles (eccDNAs) in Drosophila as an additional source of TE copies that accumulate during aging. Lastly, to combat the natural progression of aging-associated TE expression, we show that knocking down PAF1, a conserved transcription elongation factor that antagonizes RNAi pathways, may bolster suppression of TEs during aging and extend lifespan. Our study suggests that in addition to a possible influence by different genetic backgrounds, small RNA and RNAi mechanisms may mitigate genomic TL expansion despite the increase in TE transcripts during aging. Transposable elements, also called transposons, are genetic parasites found in all animal genomes. Normally, transposons are compacted away in silent chromatin in young animals. But, as animals age and transposon-silencing defense mechanisms break down, transposon RNAs accumulate to significant levels in old animals like fruit flies. An open question is whether the increased levels of transposon RNAs in older animals also correspond to increased genomic copies of transposons. This study approached this question by sequencing the whole genomes of young and old wild-type and mutant flies lacking a functional RNA interference (RNAi) pathway, which naturally silences transposon RNAs. Although the wild-type flies with intact RNAi activity had little new accumulation of transposon copies, the sequencing approach was able to detect several transposon accumulation occurrences in some RNAi mutants. In addition, we found that some fly transposon families can also accumulate as extra-chromosomal circular DNA copies. Lastly, we showed that genetically augmenting the expression of RNAi factors can counteract the rising transposon RNA levels in aging and promote longevity. This study improves our understanding of the animal host genome relationship with transposons during natural aging processes.
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Affiliation(s)
- Nachen Yang
- Boston University School of Medicine, Department of Biochemistry, Boston, Massachusetts, United States of America
| | - Satyam P. Srivastav
- Boston University School of Medicine, Department of Biochemistry, Boston, Massachusetts, United States of America
| | - Reazur Rahman
- Brandeis University, Department of Biology and Howard Hughes Medical Institute, Waltham, Massachusetts, United States of America
| | - Qicheng Ma
- Boston University School of Medicine, Department of Biochemistry, Boston, Massachusetts, United States of America
| | - Gargi Dayama
- Boston University School of Medicine, Department of Biochemistry, Boston, Massachusetts, United States of America
| | - Sizheng Li
- Boston University School of Medicine, Department of Biochemistry, Boston, Massachusetts, United States of America
| | - Madoka Chinen
- Nuclear Organization and Gene Expression Section, NIDDK, NIH, Bethesda, Maryland, United States of America
| | - Elissa P. Lei
- Nuclear Organization and Gene Expression Section, NIDDK, NIH, Bethesda, Maryland, United States of America
| | - Michael Rosbash
- Brandeis University, Department of Biology and Howard Hughes Medical Institute, Waltham, Massachusetts, United States of America
| | - Nelson C. Lau
- Boston University School of Medicine, Department of Biochemistry, Boston, Massachusetts, United States of America
- Boston University Genome Science Institute, Boston, Massachusetts, United States of America
- * E-mail:
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Arora S, Singh GK, Das P, Rahman R, Bellad P, Shrivastav R, Bahuguna A, Sapra D, Gupta A. A study of COVID‐19 vaccine (Covishield) induced dermatological adverse effects from India. J Eur Acad Dermatol Venereol 2022; 36:e402-e404. [DOI: 10.1111/jdv.17951] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/25/2021] [Accepted: 01/19/2022] [Indexed: 11/26/2022]
Affiliation(s)
- S Arora
- Department of Dermatology Base Hospital Delhi Cantt & Army College of Medical Sciences New Delhi India
| | - G K Singh
- Department of Dermatology Base Hospital Delhi Cantt & Army College of Medical Sciences New Delhi India
| | - P Das
- Department of Dermatology Base Hospital Delhi Cantt & Army College of Medical Sciences New Delhi India
| | - R Rahman
- Department of Physiology Base Hospital Delhi Cantt & Army College of Medical Sciences New Delhi India
| | - P Bellad
- Department of Dermatology Base Hospital Delhi Cantt & Army College of Medical Sciences New Delhi India
| | | | - Amit Bahuguna
- Department of Dermatology Base Hospital Delhi Cantt & Army College of Medical Sciences New Delhi India
| | - Devyani Sapra
- Department of Dermatology Base Hospital Delhi Cantt & Army College of Medical Sciences New Delhi India
| | - Akanksha Gupta
- Department of Dermatology Base Hospital Delhi Cantt & Army College of Medical Sciences New Delhi India
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Payne A, Alfa-Wali M, Rahman R, Bullingham R, Vamadeva S. 596 Redeployment of Surgical Trainees to Intensive Care During the COVID-19 Pandemic: Evaluation of the Impact on Training and Wellbeing. Br J Surg 2021. [PMCID: PMC8524572 DOI: 10.1093/bjs/znab259.860] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Aim The aim of this study was to evaluate the impact of redeployment of surgical trainees to intensive care units (ICUs) during the COVID-19 pandemic in terms of transferrable technical and nontechnical skills and wellbeing. Method This was a survey study consisting of a 23-point questionnaire. The study involved senior house officer level surgical trainees that had been redeployed to the (ICU) across all hospitals in London during the COVID-19 pandemic. The survey was sent to 90 surgical trainees. Thirty-two trainees responded to the questionnaire and were included in the study results. Results All respondents spent between 4 and 8 weeks working in ICU. Prior to redeployment, 78% of participants had previous experience of ICU or an affiliated specialty, and >90% had attended at least 1 educational course with relevance to ICU. There were statistically significant increases in confidence performing central venous cannulation and peripheral arterial catheterisation (p < 0.05). With regards to clinical skills, respondents reported feeling more confident managing ventilated patients, patients on noninvasive ventilation, dialysis, and circulatory failure patients after working in ICU. Respondents (97%) felt that the experience would be beneficial to their future careers but 53% felt the redeployment had a negative impact on their mental health. Conclusions Redeployment of surgical trainees to ICU led to increased confidence in a number of technical and nontechnical skills. However, proactive interventions are needed for training surgeons with regard to their psychological wellbeing in these extraordinary circumstances and to improve workforce planning for future pandemics.
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Affiliation(s)
- A Payne
- Barts Health NHS Trust, London, United Kingdom
| | - M Alfa-Wali
- Imperial Health NHS Trust, London, United Kingdom
| | - R Rahman
- Barts Health NHS Trust, London, United Kingdom
| | | | - S Vamadeva
- Guy's and St Thomas' NHS Trust, London, United Kingdom
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Ortega Franco A, Adamson-Raieste A, Rahman R, Pihlak R, Peters N, Scott JA, Aruketty S, Thomson C, Dransfield S, Henshaw A, Ward A, Cutts T, Carter L, Thistlethwaite F, Cook N, Graham D, Stevenson J, Krebs M. 44P Value of comprehensive genomic profiling in pre-screening patients for NTRK fusion in STARTRK2 trial: Single centre experience. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.2040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Banerjee S, Grochot R, Shinde R, Lima J, Krebs M, Rahman R, Little M, Tunariu N, Curcean A, Badham H, Mahmud M, Turner A, Parmar M, Yap C, Minchom A, Lopez J, de Bono J, Banerji U. 725MO Phase I study of the combination of the dual RAF/MEK inhibitor VS-6766 and the FAK inhibitor defactinib: Results of efficacy in low grade serous ovarian cancer. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.1168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Billy Graham Mariam N, Rahman R, Mistry H, Aruketty S, Adamson-Raieste A, Church M, Scott JA, Carter L, Thistlethwaite F, Krebs M, Cook N, Graham D. 1849P Ethnicity and socioeconomic deprivation in early phase clinical trials in a UK tertiary referral centre. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.737] [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: 10/20/2022] Open
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15
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Abstract
Targets of RNA-binding proteins discovered by editing (TRIBE) determines RNA-proteins interactions and nuclear organization with minimal false positives. We detail necessary steps for performing mammalian cell RBP-TRIBE to determine the targets of RNA-binding proteins and MS2-TRIBE to determine RNA-RNA interactions within the nucleus. Necessary steps for performing a TRIBE experiment are detailed, starting with plasmid/cell line generation, cellular transfection, and RNA sequencing library preparation and concluding with bioinformatics analysis of RNA editing sites and identification of target RNAs. For complete details on the use and execution of this protocol, please refer to Biswas et al. (2020).
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Affiliation(s)
- Jeetayu Biswas
- Department of Anatomy and Structural Biology, Bronx, NY 10461, USA
| | - Michael Rosbash
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02451, USA
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Bronx, NY 10461, USA.,Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA.,Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - Reazur Rahman
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02451, USA
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16
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Browne I, Chew S, Fennelly D, Crown J, Murray H, Rahman R, McCaffrey J, Kelly C, Osman N. 57P The efficacy and safety of pembrolizumab in advanced cervical cancer: A real-world treatment study. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.10.544] [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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17
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Abstract
BACKGROUND Biomarkers that predict treatment response are the foundation of precision medicine in clinical decision-making and have the potential to significantly improve the efficiency of clinical trials. Such biomarkers may be identified before clinical testing but many trials enroll unselected populations. We hypothesized that time-varying treatment effects in unselected trials may result from identifiable responder subpopulations that may have associated biomarkers. MATERIALS AND METHODS We first simulated scenarios of clinical trials with biomarker populations of varying prevalence and prognostic and predictive associations to illustrate the impact of subgroup-specific effects on overall population estimates. To show a real-world example of time-dependent treatment effects resulting from a prognostic and predictive biomarker, we re-analyzed data from a published clinical trial (RTOG, Radiation Therapy Oncology Group, 9402). We then demonstrated a quantitative framework to fit survival data from clinical trials using statistical models incorporating known estimates of biomarker prevalence and prognostic value to prioritize predictive biomarker hypotheses. RESULTS Our simulation studies demonstrate how biomarker subgroups that are both predictive and prognostic can manifest as time-dependent treatment effects in overall populations. RTOG 9402 provides a representative example where 1p/19q co-deletion and IDH mutation biomarker-specific effects led to time-varying treatment effects and a considerable deviation from proportional hazards in the overall trial population. Finally, using biomarker data from The Cancer Genome Atlas, we were able to generate statistical models that correctly identified and prioritized a commonly used biomarker through retrospective analysis of published clinical trial data. CONCLUSIONS Biomarkers that are both predictive and prognostic can result in characteristic changes in survival results. Retrospectively analyzing survival data from clinical trials may highlight potential indications for which an underlying predictive biomarker may be found.
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Affiliation(s)
- R Rahman
- Department of Radiation Oncology, Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston; Department of Radiation Oncology, Harvard Medical School, Boston
| | - S Ventz
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston
| | - G Fell
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston
| | - A M Vanderbeek
- Department of Biostatistics, Columbia University Mailman School of Public Health, New York, USA
| | - L Trippa
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston
| | - B M Alexander
- Department of Radiation Oncology, Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston; Department of Radiation Oncology, Harvard Medical School, Boston.
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18
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Jin H, Xu W, Rahman R, Na D, Fieldsend A, Song W, Liu S, Li C, Rosbash M. TRIBE editing reveals specific mRNA targets of eIF4E-BP in Drosophila and in mammals. Sci Adv 2020; 6:eabb8771. [PMID: 32851185 PMCID: PMC7423359 DOI: 10.1126/sciadv.abb8771] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/30/2020] [Indexed: 05/04/2023]
Abstract
4E-BP (eIF4E-BP) represses translation initiation by binding to the 5' cap-binding protein eIF4E and inhibiting its activity. Although 4E-BP has been shown to be important in growth control, stress response, cancer, neuronal activity, and mammalian circadian rhythms, it is not understood how it preferentially represses a subset of mRNAs. We successfully used HyperTRIBE (targets of RNA binding proteins identified by editing) to identify in vivo 4E-BP mRNA targets in both Drosophila and mammals under conditions known to activate 4E-BP. The protein associates with specific mRNAs, and ribosome profiling data show that mTOR inhibition changes the translational efficiency of 4E-BP TRIBE targets more substantially compared to nontargets. In both systems, these targets have specific motifs and are enriched in translation-related pathways, which correlate well with the known activity of 4E-BP and suggest that it modulates the binding specificity of eIF4E and contributes to mTOR translational specificity.
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Affiliation(s)
- Hua Jin
- Department of Biology, Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02453, USA
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, People's Republic of China
| | - Weijin Xu
- Department of Biology, Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02453, USA
| | - Reazur Rahman
- Department of Biology, Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02453, USA
| | - Daxiang Na
- Department of Biology, Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02453, USA
| | - Allegra Fieldsend
- Department of Biology, Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02453, USA
| | - Wei Song
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, People's Republic of China
| | - Shaobo Liu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, People's Republic of China
| | - Chong Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, People's Republic of China
| | - Michael Rosbash
- Department of Biology, Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02453, USA
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19
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Biswas J, Rahman R, Gupta V, Rosbash M, Singer RH. MS2-TRIBE Evaluates Both Protein-RNA Interactions and Nuclear Organization of Transcription by RNA Editing. iScience 2020; 23:101318. [PMID: 32674054 PMCID: PMC7363692 DOI: 10.1016/j.isci.2020.101318] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 04/13/2020] [Accepted: 06/25/2020] [Indexed: 12/27/2022] Open
Abstract
Both UV-cross-linking and immunoprecipitation (CLIP) and RNA editing (TRIBE) can identify the targets of RNA-binding proteins. To evaluate false-positives of CLIP and TRIBE, endogenous β-actin mRNA was tagged with MS2 stem loops, making it the only bona fide target mRNA for the MS2 capsid protein (MCP). CLIP and TRIBE detected β-actin, albeit with false-positives. False-positive CLIP signals were attributed to nonspecific antibody interactions. In contrast, putative false-positive TRIBE targets were genes spatially proximal to the β-actin gene. MCP-ADAR edited nearby nascent transcripts consistent with interchromosomal contacts observed in Hi-C. The identification of nascent contacts implies RNA regulatory proteins (e.g., splicing factors) associated with multiple nascent transcripts, forming domains of post-transcriptional activity. Repeating these results with an integrated inducible MS2 reporter indicated that MS2-TRIBE can be applied to a broad array of cells and transcripts to study spatial organization and nuclear RNA regulation.
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Affiliation(s)
- Jeetayu Biswas
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Reazur Rahman
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02453, USA
| | - Varun Gupta
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Michael Rosbash
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02453, USA
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA.
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20
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Herzog JJ, Xu W, Deshpande M, Rahman R, Suib H, Rodal AA, Rosbash M, Paradis S. TDP-43 dysfunction restricts dendritic complexity by inhibiting CREB activation and altering gene expression. Proc Natl Acad Sci U S A 2020; 117:11760-11769. [PMID: 32393629 PMCID: PMC7260973 DOI: 10.1073/pnas.1917038117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are two related neurodegenerative diseases that present with similar TDP-43 pathology in patient tissue. TDP-43 is an RNA-binding protein which forms aggregates in neurons of ALS and FTD patients as well as in a subset of patients diagnosed with other neurodegenerative diseases. Despite our understanding that TDP-43 is essential for many aspects of RNA metabolism, it remains obscure how TDP-43 dysfunction contributes to neurodegeneration. Interestingly, altered neuronal dendritic morphology is a common theme among several neurological disorders and is thought to precede neurodegeneration. We previously found that both TDP-43 overexpression (OE) and knockdown (KD) result in reduced dendritic branching of cortical neurons. In this study, we used TRIBE (targets of RNA-binding proteins identified by editing) as an approach to identify signaling pathways that regulate dendritic branching downstream of TDP-43. We found that TDP-43 RNA targets are enriched for pathways that signal to the CREB transcription factor. We further found that TDP-43 dysfunction inhibits CREB activation and CREB transcriptional output, and restoring CREB signaling rescues defects in dendritic branching. Finally, we demonstrate, using RNA sequencing, that TDP-43 OE and KD cause similar changes in the abundance of specific messenger RNAs, consistent with their ability to produce similar morphological defects. Our data therefore provide a mechanism by which TDP-43 dysfunction interferes with dendritic branching, and may define pathways for therapeutic intervention in neurodegenerative diseases.
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Affiliation(s)
- Josiah J Herzog
- Department of Biology, Brandeis University, Waltham, MA 02453
- Volen Center for Complex Systems, Brandeis University, Waltham, MA 02453
| | - Weijin Xu
- Department of Biology, Brandeis University, Waltham, MA 02453
- Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02453
| | - Mugdha Deshpande
- Department of Biology, Brandeis University, Waltham, MA 02453
- Volen Center for Complex Systems, Brandeis University, Waltham, MA 02453
| | - Reazur Rahman
- Department of Biology, Brandeis University, Waltham, MA 02453
- Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02453
| | - Hannah Suib
- Department of Biology, Brandeis University, Waltham, MA 02453
- Volen Center for Complex Systems, Brandeis University, Waltham, MA 02453
| | - Avital A Rodal
- Department of Biology, Brandeis University, Waltham, MA 02453
| | - Michael Rosbash
- Department of Biology, Brandeis University, Waltham, MA 02453;
- Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02453
| | - Suzanne Paradis
- Department of Biology, Brandeis University, Waltham, MA 02453;
- Volen Center for Complex Systems, Brandeis University, Waltham, MA 02453
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21
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Uddin MJ, Rahman AF, Rahman S, Momenuzzaman NM, Rahman A, Majumder AS, Mohibullah AM, Chowdhury AH, Malik FN, Ahsan SA, Mohsin K, Haq MM, Chowdhury AW, Sohrabuzzaman AM, Rahman M, Chakraborty B, Rahman R, Khan SR, Khan KN, Reza AM, Hussain KS, Rashid M, Choudhury AK, Karmakar KK, Ali Z, Alam N, Rahman Z, Kabir CS, Banik D, Dutta A, Badiuzzaman M, Islam AW, Sium AH, Hossain MD, Ahmed N, Jahan J, Islam MS, Arefin MM, Cader FA, Banerjee SK, Hoque H, Shofiuddin M, Selim A, Das PK, Ahmed M, Dutto B, Alam S, Paul GK, Paul SK, Azam MG. National Clinical Guidance for the Management of Cardiovascular Intervention in the COVID-19 Pandemic: From Bangladesh Society of Cardiovascular Interventions (BSCI). Mymensingh Med J 2020; 29:488-494. [PMID: 32506111] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Since the first recorded case of SARS-CoV-2 in Bangladesh on 8th March 2020, COVID-19 has spread widely through different regions of the country, resulting in a necessity to re-evaluate the delivery of cardiovascular services, particularly procedures pertaining to interventional cardiology in resource-limited settings. Given its robust capacity for human-to-human transmission and potential of being a nosocomial source of infection, the disease has specific implications on healthcare systems and health care professionals faced with performing essential cardiac procedures in patients with a suspected or confirmed diagnosis of COVID-19. The limited resources in terms of cardiac catheterization laboratories that can be designated to treat only COVID positive patients are further compounded by the additional challenges of unavailability of widespread rapid testing on-site at tertiary cardiac hospitals in Bangladesh. This document prepared for our nation by the Bangladesh Society of Cardiovascular Interventions (BSCI) is intended to serve as a clinical practice guideline for cardiovascular health care professionals, with a focus on modifying standard practice of care during the COVID-19 pandemic, in order to ensure continuation of adequate and timely treatment of cardiovascular emergencies avoiding hospital-based transmission of SARS-COV-2 among healthcare professionals and the patients. This is an evolving document based on currently available global data and is tailored to healthcare systems in Bangladesh with particular focus on, but not limited to, invasive cardiology facilities (cardiac catheterization, electrophysiology & pacing labs). This guideline is limited to the provision of cardiovascular care, and it is expected that specific targeted pharmaco-therapeutics against SARS-CoV-2 be prescribed as stipulated by the National Guidelines on Clinical Management of Corona virus Disease 2019 (COVID-19) published by the Director General of Health Services, Ministry of Health and Family Welfare of Bangladesh.
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Affiliation(s)
- M J Uddin
- Professor MG Azam, National Institute of Cardiovascular Diseases, Dhaka, Bangladesh; E-mail:
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22
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Srivastav SP, Rahman R, Ma Q, Pierre J, Bandyopadhyay S, Lau NC. Har-P, a short P-element variant, weaponizes P-transposase to severely impair Drosophila development. eLife 2019; 8:49948. [PMID: 31845649 PMCID: PMC6917496 DOI: 10.7554/elife.49948] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/16/2019] [Indexed: 12/20/2022] Open
Abstract
Without transposon-silencing Piwi-interacting RNAs (piRNAs), transposition causes an ovarian atrophy syndrome in Drosophila called gonadal dysgenesis (GD). Harwich (Har) strains with P-elements cause severe GD in F1 daughters when Har fathers mate with mothers lacking P-element-piRNAs (i.e. ISO1 strain). To address the mystery of why Har induces severe GD, we bred hybrid Drosophila with Har genomic fragments into the ISO1 background to create HISR-D or HISR-N lines that still cause Dysgenesis or are Non-dysgenic, respectively. In these lines, we discovered a highly truncated P-element variant we named ‘Har-P’ as the most frequent de novo insertion. Although HISR-D lines still contain full-length P-elements, HISR-N lines lost functional P-transposase but retained Har-P’s that when crossed back to P-transposase restores GD induction. Finally, we uncovered P-element-piRNA-directed repression on Har-P’s transmitted paternally to suppress somatic transposition. The Drosophila short Har-P’s and full-length P-elements relationship parallels the MITEs/DNA-transposase in plants and SINEs/LINEs in mammals. DNA provides the instructions needed for life, a role that relies on it being a very stable and organized molecule. However, some sections of DNA are able to move from one place in the genome to another. When these “mobile genetic elements” move they may disrupt other genes and cause disease. For example, a mobile section of DNA known as the P-element causes a condition called gonadal dysgenesis in female fruit flies, leading to infertility. Only certain strains of fruit flies carry P-elements and the severity of gonadal dysgenesis in their daughters varies. For example, when male fruit flies of a strain known as Harwich (or Har for short) is crossed with female fruit flies that do not contain P-elements, all of their daughters develop severe gonadal dysgenesis and are infertile. However, if the cross is done the other way around, and female Har flies mate with males that do not contain P-elements, the daughters are fertile because the Har mothers provide their daughters with protective molecules that silence the P-elements. But it was a mystery as to why the P-elements from the Har fathers always caused such severe gonadal dysgenesis in all the daughters. Here, Srivastav et al. bred fruit flies to create offspring that had different pieces of Har DNA in a genetic background that was normally free from P-elements; they then analyzed the ‘hybrid’ offspring to identify which pieces of the Har genome caused gonadal dysgenesis in the daughter flies. These experiments showed that Har flies possess a very short variant of the P-element (named “Har-P”) that is more mobile than other variants. However, the Har-P variants still depended on an enzyme known as P-transposase encoded by the full-length P-elements to move around the genome. Further experiments showed that other strains of fruit flies that cause severe gonadal dysgenesis also had very short P-element variants that were almost identical to Har-P. These findings may explain why Har and some other strains of fruit flies drive severe gonadal dysgenesis. In the future, it may be possible to transfer P-transposase and Har-P into mosquitoes, ticks and other biting insects to make them infertile and help reduce the spread of certain diseases in humans.
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Affiliation(s)
- Satyam P Srivastav
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, United States
| | - Reazur Rahman
- Department of Biology, Brandeis University, Waltham, United States
| | - Qicheng Ma
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, United States
| | - Jasmine Pierre
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, United States
| | - Saptaparni Bandyopadhyay
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, United States
| | - Nelson C Lau
- Department of Biochemistry, Boston University School of Medicine, Boston University, Boston, United States.,Department of Biology, Brandeis University, Waltham, United States.,Genome Science Institute, Boston University School of Medicine, Boston, United States
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23
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Keihani S, Kluever V, Mandad S, Bansal V, Rahman R, Fritsch E, Gomes LC, Gärtner A, Kügler S, Urlaub H, Wren JD, Bonn S, Rizzoli SO, Fornasiero EF. The long noncoding RNA neuroLNC regulates presynaptic activity by interacting with the neurodegeneration-associated protein TDP-43. Sci Adv 2019; 5:eaay2670. [PMID: 31897430 PMCID: PMC6920028 DOI: 10.1126/sciadv.aay2670] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 10/23/2019] [Indexed: 05/26/2023]
Abstract
The cellular and the molecular mechanisms by which long noncoding RNAs (lncRNAs) may regulate presynaptic function and neuronal activity are largely unexplored. Here, we established an integrated screening strategy to discover lncRNAs implicated in neurotransmitter and synaptic vesicle release. With this approach, we identified neuroLNC, a neuron-specific nuclear lncRNA conserved from rodents to humans. NeuroLNC is tuned by synaptic activity and influences several other essential aspects of neuronal development including calcium influx, neuritogenesis, and neuronal migration in vivo. We defined the molecular interactors of neuroLNC in detail using chromatin isolation by RNA purification, RNA interactome analysis, and protein mass spectrometry. We found that the effects of neuroLNC on synaptic vesicle release require interaction with the RNA-binding protein TDP-43 (TAR DNA binding protein-43) and the selective stabilization of mRNAs encoding for presynaptic proteins. These results provide the first proof of an lncRNA that orchestrates neuronal excitability by influencing presynaptic function.
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Affiliation(s)
- S. Keihani
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Excellence Cluster Multiscale Bioimaging, 37073 Göttingen, Germany
| | - V. Kluever
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Excellence Cluster Multiscale Bioimaging, 37073 Göttingen, Germany
| | - S. Mandad
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Excellence Cluster Multiscale Bioimaging, 37073 Göttingen, Germany
- Department of Clinical Chemistry, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - V. Bansal
- Institute of Medical Systems Biology, Center for Molecular Neurobiology (ZMNH), UKE, 20246 Hamburg, Germany
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
| | - R. Rahman
- Institute of Medical Systems Biology, Center for Molecular Neurobiology (ZMNH), UKE, 20246 Hamburg, Germany
| | - E. Fritsch
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Excellence Cluster Multiscale Bioimaging, 37073 Göttingen, Germany
| | - L. Caldi Gomes
- Department of Neurology, University Medical Center Göttingen, 37073 Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), 37075 Göttingen, Germany
| | - A. Gärtner
- VIB Center for the Biology of Disease and Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - S. Kügler
- Department of Neurology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - H. Urlaub
- Department of Clinical Chemistry, University Medical Center Göttingen, 37077 Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max Planck Institute of Biophysical Chemistry, 37077 Göttingen, Germany
| | - J. D. Wren
- Department of Genes and Human Disease, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - S. Bonn
- Institute of Medical Systems Biology, Center for Molecular Neurobiology (ZMNH), UKE, 20246 Hamburg, Germany
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
| | - S. O. Rizzoli
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Excellence Cluster Multiscale Bioimaging, 37073 Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), 37075 Göttingen, Germany
| | - E. F. Fornasiero
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Excellence Cluster Multiscale Bioimaging, 37073 Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), 37075 Göttingen, Germany
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24
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Smith S, Serra R, Rowlinson J, Gorelick N, Veal G, Shakesheff K, Brem H, Grundy R, Tyler B, Rahman R. P11.60 Neurosurgical delivery of the poly ADP ribose polymerase-1 inhibitor olaparib from a thermo-responsive biodegradable paste potentiates radiotherapy and prolongs survival. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz126.206] [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: 11/14/2022] Open
Abstract
Abstract
BACKGROUND
There has been considerable interest in repurposing the poly ADP ribose polymerase inhibitor and purported radiosensitiser olaparib (Lynparza), with a recent dose escalation study of olaparib plus temozolomide in recurrent GBM showing good tolerance. Due to systemic therapy-associated caveats such as dose-limiting toxicities and blood-brain-barrier penetration, here we assess localised post-surgical delivery of olaparib from our previously developed PLGA/PEG thermo-sensitive biodegradable paste.
MATERIAL AND METHODS
Metabolic and clonogenic assays were used to assess effects on proliferation and clonal growth upon in vitro glioma exposure to olaparib. Flow cytometry and Annexin V/Propidium iodide were used to determine apoptosis. The 9L high-grade glioma orthotopic allograft model was utilised to assess survival upon intra-cavity olaparib delivery.
RESULTS
Metabolic and clonogenic assays revealed impaired proliferation and clonal growth respectively, upon acute exposure of high-grade glioma cells to olaparib (3–5µM), an effect dramatically potentiated with 3Gy radiation. Flow cytometry of Annexin V+/Propidium iodide+ rodent and human high-grade glioma cells, revealed a significant cell proportion increase at late stage apoptosis when exposed to 2–3µM olaparib and 3Gy radiation (relative to untreated, olaparib alone or radiation alone). A high-grade glioma orthotopic allograft study revealed a significant overall survival benefit of locally-delivered 10% and 20% w/w (drug:polymer ratio) olaparib via PLGA/PEG paste post-surgery with adjuvant radiotherapy, compared to surgery/oral temozolomide/radiotherapy (GBM standard-of-care) and surgery/systemic olaparib (95 vs. 44 vs. 30 days respectively). A more pronounced survival benefit, as measured by number of animals surviving long-term, was observed with combined PLGA/PEG/olaparib/temozolomide/radiotherapy or PLGA/PEG/olaparib/etoposide/radiotherapy, relative to standard-of-care (95 vs. 44 days). Clinical correlation was determined using RNAseq data from 10 GBM patients, showing significantly elevated levels of apoptosis-inducing factor-1 in 5-aminolevulinic acid (5ALA)+ fluorescence-activated cell sorted populations (i.e. purified tumour cells from the invasive margin), relative to 5ALA- cells, confirming PARP-1 activity in infiltrative tumour cells.
CONCLUSION
Collectively our data supports a clinical rationale for localised olaparib delivery with adjuvant radiotherapy.
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Affiliation(s)
- S Smith
- University of Nottingham, Nottingham, United Kingdom
| | - R Serra
- Johns Hopkins University, Baltimore, MD, United States
| | - J Rowlinson
- University of Nottingham, Nottingham, United Kingdom
| | - N Gorelick
- Johns Hopkins University, Baltimore, MD, United States
| | - G Veal
- Newcastle University, Newcastle, United Kingdom
| | - K Shakesheff
- University of Nottingham, Nottingham, United Kingdom
| | - H Brem
- Johns Hopkins University, Baltimore, MD, United States
| | - R Grundy
- University of Nottingham, Nottingham, United Kingdom
| | - B Tyler
- Johns Hopkins University, Baltimore, MD, United States
| | - R Rahman
- University of Nottingham, Nottingham, United Kingdom
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Rowlinson J, McCrorie P, Smith S, Barrett D, Kim D, Grundy R, Scurr D, Rahman R. P11.62 Brain distribution models to select polymer-delivered drugs for the intra-cavity treatment of malignant glioma. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz126.208] [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: 11/13/2022] Open
Abstract
Abstract
BACKGROUND
Conventional oral or intravenous chemotherapy distributes drugs to the whole body whereby systemic toxicity to healthy parts of the body (e.g. bone marrow failure) limits the maximum dose that can be achieved in the brain. This presents a particular concern for CNS tumours where the blood-brain-barrier (BBB) restricts drug influx from the circulation. The ability to deliver chemotherapy locally at the tumour site offers the opportunity to target residual cancer cells post-surgery whilst minimising systemic toxicity. We have developed a poly(lactic-co-glycolic acid)/poly(ethylene glycol) (PLGA/PEG) polymer matrix that forms a porous paste at room temperature when mixed with chemotherapy-containing saline, solidifying only at body temperature, with close apposition to the irregular surgical cavity. It is important that we can observe whether the drugs released from PLGA/PEG can penetrate brain parenchyma beyond the surgical resection margin at therapeutic doses. Currently the only way to measure the distribution of drugs in the body is to inject radioactive drugs into an animal. We aim to establish drug distribution parameters using label-free mass spectrometry imaging methods, prior to selection of drug formulations for clinically-relevant in vivo models. Drugs that penetrate the brain the furthest will be identified as good candidates for localised brain cancer drug delivery using PLGA/PEG paste.
MATERIAL AND METHODS
Diffusion rates were measured by examining the proportion of olaparib, dasatnib, carboplatin, etoposide, paclitaxel and gemcitabine at 2mg/ml concentration, which passes through 1mm slices of rat brain tissue within Franz cell chambers over a 6 hour period. The spatio-temporal distribution of label-free olaparib and dasatinib within mouse brain homogenate was quantitatively measured using innovative 3D OrbiSIMS, a hybrid time-of-flight / OrbitrapTM secondary ion mass spectrometer.
RESULTS
Within the Franz cell model, carboplatin and gemcitabine showed the highest diffusion rate diffusion at 16.4 and 6.53 µg/cm2/h respectively whereas olaparib, etoposide and paclitaxel were relatively poorly diffused at 1.87, 3.82 and 2.27 µg/cm2/h respectively. The minimum threshold of OrbiSIMS detection for label-free olaparib and dasatinib ions was 0.025 mg/ml and 0.2 mg/ml respectively throughout brain homogenate.
CONCLUSION
This study demonstrates different diffusion rates through brain tissue, between label-free chemotherapy drugs of distinct chemistries, with highest diffusion rates observed for carboplatin and gemcitabine. We also demonstrate label-free detection of olaparib and dasatinib using the innovative 3D OrbiSIMS method. These models will facilitate the rapid identification of agents most amenable for localised biomaterial-based chemotherapy delivery with high brain penetrance.
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Affiliation(s)
- J Rowlinson
- University of Nottingham, UK, Nottingham, United Kingdom
| | - P McCrorie
- University of Nottingham, UK, Nottingham, United Kingdom
| | - S Smith
- University of Nottingham, UK, Nottingham, United Kingdom
| | - D Barrett
- University of Nottingham, UK, Nottingham, United Kingdom
| | - D Kim
- University of Nottingham, UK, Nottingham, United Kingdom
| | - R Grundy
- University of Nottingham, UK, Nottingham, United Kingdom
| | - D Scurr
- University of Nottingham, UK, Nottingham, United Kingdom
| | - R Rahman
- University of Nottingham, UK, Nottingham, United Kingdom
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Rahman R, Clark MD, Collins Z, Traore F, Dioukhane EM, Thiam H, Ndiaye Y, De Jesus EL, Danfakha N, Peters KE, Komarek T, Linn AM, Linn PE, Wallner KE, Charles M, Hasnain M, Peterson CE, Dykens JA. Cervical cancer screening decentralized policy adaptation: an African rural-context-specific systematic literature review. Glob Health Action 2019; 12:1587894. [PMID: 30938248 PMCID: PMC6450494 DOI: 10.1080/16549716.2019.1587894] [Citation(s) in RCA: 20] [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] [Indexed: 01/27/2023] Open
Abstract
Background: Worldwide, nearly 570,000 women are diagnosed with cervical cancer each year, with 85% of new cases in low- and middle-income countries. The African continent is home to 35 of 40 countries with the highest cervical cancer mortality rates. In 2014, a partnership involving a rural region of Senegal, West Africa, was facing cervical cancer screening service sustainability barriers and began adapting regional-level policy to address implementation challenges. Objective: This manuscript reports the findings of a systematic literature review describing the implementation of decentralized cervical cancer prevention services in Africa, relevant in context to the Senegal partnership. We report barriers and policy-relevant recommendations through Levesque’s Patient-Centered Access to Healthcare Framework and discuss the impact of this information on the partnership’s approach to shaping Senegal’s regional cervical cancer screening policy. Methods: The systematic review search strategy comprised two complementary sub-searches. We conducted an initial search identifying 4272 articles, then applied inclusion criteria, and ultimately 19 studies were included. Data abstraction focused on implementation barriers categorized with the Levesque framework and by policy relevance. Results: Our findings identified specific demand-side (clients and community) and supply-side (health service-level) barriers to implementation of cervical cancer screening services. We identify the most commonly reported demand- and supply-side barriers and summarize salient policy recommendations discussed within the reviewed literature. Conclusions: Overall, there is a paucity of published literature regarding barriers to and best practices in implementation of cervical cancer screening services in rural Africa. Many articles in this literature review did describe findings with notable policy implications. The Senegal partnership has consulted this literature when faced with various similar barriers and has developed two principal initiatives to address contextual challenges. Other initiatives implementing cervical cancer visual screening services in decentralized areas may find this contextual reporting of a literature review helpful as a construct for identifying evidence for the purpose of guiding ongoing health service policy adaptation.
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Affiliation(s)
- R Rahman
- a University of Toledo College of Medicine and Life Sciences , Toledo , OH , USA
| | - M D Clark
- b Library of the Health Sciences , University Library, University of Illinois at Chicago , Chicago , IL , USA.,c Department of Medical Education, College of Medicine , University of Illinois at Chicago , Chicago , IL , USA
| | - Z Collins
- d Department of Family Medicine, Institute for Health Research and Policy , University of Illinois at Chicago (UIC) , Chicago , IL , USA
| | - F Traore
- e Region medical de Kedougou , Bureau de la santé de la reproduction, prevention transmission mere enfant du VIH-SIDA , Kedougou , Senegal
| | | | - H Thiam
- g Region medical de Kedougou , Bureau régional de la formation, de la supervision et de la recherche , Kedougou , Senegal
| | - Y Ndiaye
- h Département de Recherche , Sénégal Ministère de la Santé et l'Action Sociale , Dakar , Sénégal
| | - E L De Jesus
- i School of Public Health (SPH) , University of Illinois at Chicago (UIC) , Chicago , IL , USA
| | | | - K E Peters
- k School of Public Health, Division of Community Health Sciences, Illinois Prevention Research Center, Institute for Health Research and Policy , University of Illinois at Chicago (UIC) , Chicago , IL , USA
| | - T Komarek
- l Uniformed Services University , Bethesda , MD , USA
| | - A M Linn
- m School of Public Health, Center for Communications Programs , Johns Hopkins University , Baltimore , MD , USA
| | - P E Linn
- n Logistics Management Institute , Tysons , VA , USA
| | - K E Wallner
- o Elizabeth Glaser Pediatric AIDS Foundation , Washington , DC , USA
| | - M Charles
- p Department of Internal Medicine , University of Illinois at Chicago , Chicago , IL , USA
| | - M Hasnain
- q Department of Family Medicine , University of Illinois at Chicago College of Medicine , Chicago , IL , USA
| | - C E Peterson
- r School of Public Health, Division of Epidemiology & Biostatistics, UI Cancer Center , University of Illinois at Chicago (UIC) , Chicago , IL , USA
| | - J A Dykens
- s Department of Family Medicine, Center for Global Health, Institute for Health Research and Policy, Cancer Center , University of Illinois at Chicago (UIC) , Chicago , IL , USA
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Tabrizi S, Rahman R, Cagney D, Aizer A, Tanguturi S, Arvold N, Reardon D, Lee E, Nayak L, Rinne M, Ligon K, Wen P, Alexander B. Impact of Delay in Initiation of Radiation Therapy in Newly Diagnosed Glioblastoma Patients after Gross Total Resection. Int J Radiat Oncol Biol Phys 2019. [DOI: 10.1016/j.ijrobp.2019.06.2314] [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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Abstract
RNA-binding proteins (RBPs) accompany RNA from birth to death, affecting RNA biogenesis and functions. Identifying RBP-RNA interactions is essential to understanding their complex roles in different cellular processes. However, detecting in vivo RNA targets of RBPs, especially in a small number of discrete cells, has been a technically challenging task. We previously developed a novel technique called TRIBE (targets of RNA-binding proteins identified by editing) to overcome this problem. TRIBE expresses a fusion protein consisting of a queried RBP and the catalytic domain of the RNA-editing enzyme ADAR (adenosine deaminase acting on RNA) (ADARcd), which marks target RNA transcripts by converting adenosine to inosine near the RBP binding sites. These marks can be subsequently identified via high-throughput sequencing. In spite of its usefulness, TRIBE is constrained by a low editing efficiency and editing-sequence bias from the ADARcd. Therefore, we developed HyperTRIBE by incorporating a previously characterized hyperactive mutation, E488Q, into the ADARcd. This strategy increases the editing efficiency and reduces sequence bias, which markedly increases the sensitivity of this technique without sacrificing specificity. HyperTRIBE provides a more powerful strategy for identifying RNA targets of RBPs with an easy experimental and computational protocol at low cost, that can be performed not only in flies, but also in mammals. The HyperTRIBE experimental protocol described below can be carried out in cultured Drosophila S2 cells in 1 week, using tools available in a common molecular biology laboratory; the computational analysis requires 3 more days.
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Affiliation(s)
- Reazur Rahman
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA, USA
| | - Weijin Xu
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA, USA
| | - Hua Jin
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA, USA
| | - Michael Rosbash
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA, USA.
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Khan KN, Khan MH, Rahman R. TCTAP A-006 Primary Angioplasty for the Treatment of Acute ST Elevated Myocardial Infarction: Single Centre Experience of Three and Half Years. J Am Coll Cardiol 2019. [DOI: 10.1016/j.jacc.2019.03.032] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Nazrul Islam MM, Khan MH, Khan KN, Rahman R. TCTAP A-007 Correlation of Left Ventricular Ejection Fraction with In-hospital Outcomes After First Attack of Non-ST Segment Elevation Myocardial Infarction. J Am Coll Cardiol 2019. [DOI: 10.1016/j.jacc.2019.03.033] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Rahman R, Sridharan V, Hanna G, Chau N, Lorch J, Kass J, Annino D, Goguen L, Uppaluri R, Haddad R, Tishler R, Margalit D, Schoenfeld J, Huang R. Predicting PD-L1 Expression using Radiomics in Oropharyngeal Cancer Patients Treated with Definitive Radiation. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.07.1054] [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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Golbek A, Reafsnyder S, Rancourt D, Kelly P, Rahman R, Weiss E. Peppermint Oil Fails to Improve Exercise Performance. J Acad Nutr Diet 2018. [DOI: 10.1016/j.jand.2018.06.177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Weiss E, Wroble K, Trott M, Schweitzer G, Rahman R, Kelly P. Low-carbohydrate, Ketogenic Diet Impairs Anaerobic Exercise Performance. J Acad Nutr Diet 2018. [DOI: 10.1016/j.jand.2018.06.176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Jaaks P, Vis D, Barthorpe A, Aben N, Van der Meer D, Lightfoot H, Michaut M, Rahman R, Wessels L, Garnett M. PO-023 A multi-step framework to analyse high-throughput drug combination screens. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.558] [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: 11/03/2022] Open
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35
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Nasreen S, Nessa A, Islam F, Khanam A, Sultana R, Rahman R, Hossain M. Changes of Peak Expiratory Flow Rate in Adult Asthmatic Patient. Mymensingh Med J 2018; 27:245-250. [PMID: 29769485] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Asthma is a common pulmonary disorder characterizerized by airway inflammation, airway- hyper reactivity, and reversible airflow obstruction. The classic triad of symptoms is wheezing, chronic episodic dyspnea and chronic cough. The prevalence of asthma increased steadily over the latter part of the last century, first in the developed and then in the developing world. The number of people with asthma in the world may be as high as 334 million. Asthma in Bangladesh appears to be a substantial public health problem: an estimated 11.6 million people including 4.1 million children suffer from asthma-related symptoms. A cross sectional study was conducted from January 1999 to August 1999 on 5642 Bangladeshi people and another same study carried out from November 2009 to April 2010 on 8088 subjects. In 1999 the prevalence of asthma was 6.9% whereas in 2010 it is 6.96%. Airway resistance is always increased during the asthmatic attack. Airways obstruction, such as that caused by asthma, results in a reduced and variable Peak Expiratory Flow Rate (PEFR). PEFR is classically reduced in asthma. Recent asthma guidelines recommended the assessment of severity levels based on the most severe symptoms and peak expiratory flow rate. This descriptive type of cross-sectional study was done to find the changes of Peak expiratory flow rate in adult asthmatic patients and carried out in the Department of Physiology, Mymensingh Medical College, Mymensingh, Bangladesh from July 2014 to January 2016. Fifty (50) male and 50 (fifty) female adult asthmatic patients aged 18-60 years were included in the study group. They are enrolled from the Department of Medicine, Mymensingh Medical College, Mymensingh, Bangladesh and also from locality. For comparison age matched 50 male and 50 female apparently healthy persons were also studied as control. PEFR was estimated by Wright's Peak flow meter. For statistical analysis unpaired student's 't' test was used. Mean PEFR were significantly decreased in study group in comparison to control group and the result was statistically significant (p<0.001). From this study, it may be concluded that peak expiratory flow rate was decreased in asthmatic patient and there was a significant relation of decline lung function.
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Affiliation(s)
- S Nasreen
- Dr Shamima Nasreen, Assistant Professor, Department of Physiology, TMSS Medical College, Bogra, Bangladesh; E-mail:
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Xu W, Rahman R, Rosbash M. Mechanistic implications of enhanced editing by a HyperTRIBE RNA-binding protein. RNA 2018; 24:173-182. [PMID: 29127211 PMCID: PMC5769745 DOI: 10.1261/rna.064691.117] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 11/10/2017] [Indexed: 05/21/2023]
Abstract
We previously developed TRIBE, a method for the identification of cell-specific RNA-binding protein targets. TRIBE expresses an RBP of interest fused to the catalytic domain (cd) of the RNA-editing enzyme ADAR and performs adenosine-to-inosine editing on RNA targets of the RBP. However, target identification is limited by the low editing efficiency of the ADARcd. Here we describe HyperTRIBE, which carries a previously characterized hyperactive mutation (E488Q) of the ADARcd. HyperTRIBE identifies dramatically more editing sites, many of which are also edited by TRIBE but at a much lower editing frequency. HyperTRIBE therefore more faithfully recapitulates the known binding specificity of its RBP than TRIBE. In addition, separating RNA binding from the enhanced editing activity of the HyperTRIBE ADAR catalytic domain sheds light on the mechanism of ADARcd editing as well as the enhanced activity of the HyperADARcd.
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Affiliation(s)
- Weijin Xu
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Reazur Rahman
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Michael Rosbash
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts 02453, USA
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Arora R, Rahman R, Joe W, Bakhshi S, Dhawan D, Radhakrishnan V, Kalra M, Chinnaswamy G, Das A, Mudaliar S, Sangareddi S, Sharma S, Seth R, Singh A, De S, Scott J, Uppuluri R, Borker A, Sankaran H, Bagai P. Families Of Children Newly Diagnosed With Cancer Incur Significant Out-Of-Pocket Expenditure For Treatment – Report Of A Multi-Site Prospective Longitudinal Study From India (INPOG-ACC-16-01). Pediatric Hematology Oncology Journal 2018. [DOI: 10.1016/j.phoj.2018.11.038] [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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38
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Nasreen S, Nessa A, Islam F, Khanam A, Sultana R, Alam K, Naznin R, Tajkia T, Rahman R, Hossain M, Sultana MA, Kamal ST. Interaction between Hypertension and Asthma in Adult. Mymensingh Med J 2018; 27:34-40. [PMID: 29459589] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Asthma has been defined as a chronic inflammatory disorder of the airways that is associated with recruitment of inflammatory cells and the clinical development of wheezing, shortness of breath, chest tightness, and cough. The prevalence of asthma increased steadily over the latter part of the last century, first in the developed and then in the developing world. Current estimates suggest that asthma affects 300 million people worldwide, with a predicted additional 100 million people affected by 2025. This cross sectional study was conducted from January 1999 to August 1999 on 5642 Bangladeshi people and another same study carried out from November 2009 to April 2010 on 8088 subjects. In 1999 the prevalence of asthma was 6.9% whereas in 2010 it is 6.96%. Both asthma and hypertension are spastic disorders of smooth muscle, there is the similarities between these two diseases may predispose the individuals with one disease to the other. This descriptive type of cross-sectional study was done to find the Interaction between hypertension and asthma in adult and carried out in the Department of Physiology, Mymensingh Medical College, Mymensingh, Bangladesh from July 2014 to January 2016. Fifty (50) male and fifty (50) female adult asthmatic patients aged 18-60 years were included in the study group. They are enrolled from the Department of Medicine, Mymensingh Medical College, Mymensingh and also from locality. For comparison age matched 50 male and 50 female apparently healthy persons were also studied as control. Blood pressure was estimated by auscultatory method by sphygmomanometer. For statistical analysis unpaired student's 't' test was used. Mean blood pressure were significantly increased in study group in comparison to control group and the result was statistically significant (p<0.001). The study findings showed a high prevalence of hypertension among asthmatic patients than non asthmatic healthy persons. From this study, it may be concluded that hypertension and asthma are closely connected.
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Affiliation(s)
- S Nasreen
- Dr Shamima Nasreen, Assistant Professor, Department of Physiology, TMSS Medical College, Bogra, Bangladesh; E-mail:
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Al-Emran M, Rahman R, Miah MI, Shahjahan M. Effects of stocking density on growth and production in monoculture of Thai sharpunti (Barbonymus gonionotus). Progress Agric 2017; 28:249-252. [DOI: 10.3329/pa.v28i3.34662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
An experiment was carried out to study the density dependent growth of Thai sharpunti (Barbonymusgonionotus) for two months period. Three stocking densities such as 50/decimal, 100/decimal and 150/decimal representing treatment one (T1), treatment two (T2) and treatment three (T3), respectively were tested in three replications. A commercial diet (25% crude protein) was supplied twice daily throughout the study period up to satiation level. The total production of sharpunti was found 14.67 ± 2.05, 27.06 ± 3.09 and 36.87 ± 2.16 kg/decimal in T1, T2 and T3, respectively and they were significantly different (p<0.05) from each other. A higher net benefit of BDT 1079.50 was obtained from T2 where the stocking density was 100/decimal. The present study indicated that the growth and production of Thai sharpunti was density dependent in monoculture systems.Progressive Agriculture 28 (3): 249-252, 2017
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Rahman R, Cortes A, Oh K, Flaherty K, Lawrence D, Sullivan R, Shih H. The Impact of Timing of Immunotherapy with Cranial Irradiation on Early Distant Brain Progression and Overall Survival in Patients with Melanoma Brain Metastases. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.06.833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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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41
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Khan MH, Islam MN, Aditya GP, Islam MZ, Bhuiyan AS, Saha B, Bhowmick K, Hassan M, Paul PK, Chowdhury S, Rahman R. Correlation of Troponin-I Level with Left Ventricular Ejection Fraction and In-hospital outcomes after First Attack of Non-ST Segment Elevation Myocardial Infarction. Mymensingh Med J 2017; 26:721-731. [PMID: 29208858] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Coronary heart disease (CHD) is the most common cause of heart disease and is the single most important cause of premature death in developed world. Recognizing a patient with ACS is important because the diagnosis triggers both triage and management. cTnI is 100% tissue-specific for the myocardium and it has been shown to be a very sensitive and specific marker for acute myocardial infarction (AMI). Ventricular function is the best predictor of death after an acute coronary syndrome. It serves as a marker of myocardial damage, provides information on systolic function as well as diagnosis and prognosis. The study aimed at investigating the impact of elevated Troponin-I level on LV ejection fraction and in-hospital outcomes in patients with first attack of Non ST-segment Elevation Myocardial Infarction (NSTEMI). This prospective analytical study was conducted in the Department of Cardiology in Mymensingh Medical College Hospital from December 2015 to November 2016. Total 130 first attack of NSTEMI patients were included considering inclusion and exclusion criteria. The sample population was divided into two groups: Group I - Patients with first attack of NSTEMI with good LV function (LVEF: ≥55%). Group II - Patients with first attack of NSTEMI with LV systolic dysfunction (LVEF: <55%). Then Troponin-I and LVEF levels were correlated using Pearson's correlation coefficient test. In this study mean Troponin-I of Group I and Group II were 5.53±7.43 and 16.46±15.79ng/ml respectively. It was statistically significant (p<0.05). Echocardiography showed that patients with high Troponin-I level had low ejection fraction (LVEF) and patients with low Troponin-I level had preserved ejection fraction (LVEF). Analysis showed that patients with severe left ventricular systolic dysfunction (LVEF <35%) had the highest level of Troponin-I with worse in-hospital outcomes and vice versa-the patients with the preserved systolic function (LVEF ≥55%) had the lowest levels of Troponin-I with better in-hospital outcomes. In our study, it also showed that the levels of Troponin-I had negative correlation with LV ejection fraction levels, with medium strength of association (r= -0.5394, p=0.001). The study enabled us to conclude that, the higher was the Troponin-I level, the lower was the LV ejection fraction level and thus worse in-hospital outcomes in first attack of NSTEMI patients.
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Affiliation(s)
- M H Khan
- Dr Mahmood Hasan Khan, MD (Thesis) Student, Department of Cardiology, Mymensingh Medical College (MMC), Mymensingh, Bangladesh
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Clark JP, Rahman R, Yang N, Yang LH, Lau NC. Drosophila PAF1 Modulates PIWI/piRNA Silencing Capacity. Curr Biol 2017; 27:2718-2726.e4. [PMID: 28844648 DOI: 10.1016/j.cub.2017.07.052] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 04/14/2017] [Revised: 06/06/2017] [Accepted: 07/24/2017] [Indexed: 01/09/2023]
Abstract
To test the directness of factors in initiating PIWI-directed gene silencing, we employed a Piwi-interacting RNA (piRNA)-targeted reporter assay in Drosophila ovary somatic sheet (OSS) cells [1]. This assay confirmed direct silencing roles for piRNA biogenesis factors and PIWI-associated factors [2-12] but suggested that chromatin-modifying proteins may act downstream of the initial silencing event. Our data also revealed that RNA-polymerase-II-associated proteins like PAF1 and RTF1 antagonize PIWI-directed silencing. PAF1 knockdown enhances PIWI silencing of reporters when piRNAs target the transcript region proximal to the promoter. Loss of PAF1 suppresses endogenous transposable element (TE) transcript maturation, whereas a subset of gene transcripts and long-non-coding RNAs adjacent to TE insertions are affected by PAF1 knockdown in a similar fashion to piRNA-targeted reporters. Additionally, transcription activation at specific TEs and TE-adjacent loci during PIWI knockdown is suppressed when PIWI and PAF1 levels are both reduced. Our study suggests a mechanistic conservation between fission yeast PAF1 repressing AGO1/small interfering RNA (siRNA)-directed silencing [13, 14] and Drosophila PAF1 opposing PIWI/piRNA-directed silencing.
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Affiliation(s)
- Josef P Clark
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA, USA
| | - Reazur Rahman
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA, USA
| | - Nachen Yang
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA, USA
| | - Linda H Yang
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA, USA
| | - Nelson C Lau
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, MA, USA.
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Khan KN, Khan MH, Rahman R, Rashid MA, Haque SZ, Zakia Z. Primary Angioplasty for the Treatment of Acute ST Elevated Myocardial Infarction: Single Centre Experience. Mymensingh Med J 2017; 26:351-355. [PMID: 28588172] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Worldwide primary angioplasty is a recommended strategy of reperfusion in patient with acute myocardial infarction as because it ensures reperfusion of the infarct-related vessels more than 90% whereas, with thrombolytics it is only 60-70%. This retrospective observational study includes all patients treated with primary angioplasty at United Hospital from Between March 2007 to January 2011. Total 114 consecutive patients with acute myocardial infarction were treated with primary angioplasty included. Those presented beyond 12 hours of onset of chest pain, in cardiogenic shock, resuscitate and intubated before the procedure were excluded from the study. Majority (89%) of the patient were male, age was minimum 30 years and maximum 90 years, 41.5% were diabetics, 58.4% were hypertensive, 43.5% were dyslipidaemic, 17% were smoker, 29.3% with positive family history. Fifty seven percent patients presented with anterior MI , 42 % with inferior MI and 1% with lateral MI. Left anterior descending (LAD) is the most common vessel involved (57%), followed by Right coronary artery (RCA) 31%, Left circumflex artery (LCX) 8 %, Ramus 1.3% and Graft vessel 2.7%. Our door to balloon time was minimum 23 min, maximum 184 min. We used drug eluting stents for most of the patients, GP IIb- IIIa receptor blockers used in 50% cases and thrombus suction device were used when indicated. We faced complications like arrhythmias in 24%, hypotension in18%, no flow or slow flow in 45%, cardiac arrest in 3% and coronary perforation in 1%. Our overall survival was 97.9%. Primary angioplasty is an emerging area in context of our country. Many of the new centers start this novel strategy which helps to save many lives Primary angioplasty is feasible and safe method of reperfusion in patient with acute myocardial infarction in our center. With the help of our initial experience we can perform PAMI with confidence to those who can afford and who need most.
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Affiliation(s)
- K N Khan
- Dr Kaisar Nasrullah Khan, Department of Cardiology, United Hospital Limited (UHL), Gulshan, Dhaka, Banglaldesh
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Movafagh S, Raj D, Sanaei-Ardekani M, Bhatia D, Vo K, Mahmoudieh M, Rahman R, Kim EH, Harralson AF. Hypoxia Inducible Factor 1: A Urinary Biomarker of Kidney Disease. Clin Transl Sci 2017; 10:201-207. [PMID: 28181420 PMCID: PMC5421733 DOI: 10.1111/cts.12445] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 01/03/2017] [Indexed: 01/22/2023] Open
Abstract
Identifying noninvasive biomarkers of kidney disease is valuable for diagnostic and therapeutic purposes. Hypoxia inducible factor 1 (HIF-1) expression is known to be elevated in the kidneys in several renal disease pathologies. We hypothesized that the urinary HIF-1a mRNA level may be a suitable biomarker for expression of this protein in chronic kidney disease (CKD). We compared HIF-1a mRNA levels from urine pellets of CKD and healthy subjects. To ensure that urinary HIF-1a mRNA is of kidney origin, we examined colocalization of HIF-1a mRNA with two kidney specific markers in urine cells. We found that HIF-1a mRNA is readily quantifiable in urine pellets and its expression was significantly higher in CKD patients compared with healthy adults. We also showed that the urinary HIF-1a mRNA comes primarily from cells of renal origin. Our data suggest that urinary HIF-1a mRNA is a potential biomarker in CKD and can be noninvasively assessed in patients.
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Affiliation(s)
- S Movafagh
- Department of Pharmacogenomics, Bernard J. Dunn School of Pharmacy, Shenandoah University, Ashburn, Virginia, USA
| | - D Raj
- Department of Nephrology, George Washington University Division of Kidney Diseases and Hypertension, Washington, DC, USA
| | | | - D Bhatia
- Department of Pharmacogenomics, Bernard J. Dunn School of Pharmacy, Shenandoah University, Ashburn, Virginia, USA
| | - K Vo
- Bernard J. Dunn School of Pharmacy, Shenandoah University, Ashburn, Virginia, USA
| | - M Mahmoudieh
- Bernard J. Dunn School of Pharmacy, Shenandoah University, Ashburn, Virginia, USA
| | - R Rahman
- Kidney and Hypertension Specialists, Manassas, Virginia, USA
| | - E H Kim
- Kidney and Hypertension Specialists, Manassas, Virginia, USA
| | - A F Harralson
- Department of Pharmacogenomics, Bernard J. Dunn School of Pharmacy, Shenandoah University, Ashburn, Virginia, USA
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Abruzzi KC, Zadina A, Luo W, Wiyanto E, Rahman R, Guo F, Shafer O, Rosbash M. RNA-seq analysis of Drosophila clock and non-clock neurons reveals neuron-specific cycling and novel candidate neuropeptides. PLoS Genet 2017; 13:e1006613. [PMID: 28182648 PMCID: PMC5325595 DOI: 10.1371/journal.pgen.1006613] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 02/24/2017] [Accepted: 02/01/2017] [Indexed: 12/21/2022] Open
Abstract
Locomotor activity rhythms are controlled by a network of ~150 circadian neurons within the adult Drosophila brain. They are subdivided based on their anatomical locations and properties. We profiled transcripts “around the clock” from three key groups of circadian neurons with different functions. We also profiled a non-circadian outgroup, dopaminergic (TH) neurons. They have cycling transcripts but fewer than clock neurons as well as low expression and poor cycling of clock gene transcripts. This suggests that TH neurons do not have a canonical circadian clock and that their gene expression cycling is driven by brain systemic cues. The three circadian groups are surprisingly diverse in their cycling transcripts and overall gene expression patterns, which include known and putative novel neuropeptides. Even the overall phase distributions of cycling transcripts are distinct, indicating that different regulatory principles govern transcript oscillations. This surprising cell-type diversity parallels the functional heterogeneity of the different neurons. Organisms ranging from bacteria to humans contain circadian clocks. They keep internal time and also integrate environmental cues such as light to provide external time information for entrainment. In the fruit fly Drosophila melanogaster, ~150 brain neurons contain the circadian machinery and are critical for controlling behavior. Several subgroups of these clock neurons have been identified by their anatomical locations and specific functions. Our work aims to profile these neurons and to characterize their molecular contents: what to they contain and how do they differ? To this end, we have purified 3 important subgroups of clock neurons and identified their expressed genes at different times of day. Some are expressed at all times, whereas others are “cycling,” i.e., expressed more strongly at a particular time of day like the morning. Interestingly, each circadian subgroup is quite different. The data provide hints about what functions each group of neurons carries out and how they may work together to keep time. In addition, even a non-circadian group of neurons has cycling genes and has implications for the extent to which all cells have or do not have a functional circadian clock.
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Affiliation(s)
- Katharine C. Abruzzi
- Howard Hughes Medical Institute and National Center for Behavioral Genomics,Department of Biology, Brandeis University, Waltham, United States of America
| | - Abigail Zadina
- Howard Hughes Medical Institute and National Center for Behavioral Genomics,Department of Biology, Brandeis University, Waltham, United States of America
| | - Weifei Luo
- Howard Hughes Medical Institute and National Center for Behavioral Genomics,Department of Biology, Brandeis University, Waltham, United States of America
| | - Evelyn Wiyanto
- Howard Hughes Medical Institute and National Center for Behavioral Genomics,Department of Biology, Brandeis University, Waltham, United States of America
| | - Reazur Rahman
- Howard Hughes Medical Institute and National Center for Behavioral Genomics,Department of Biology, Brandeis University, Waltham, United States of America
| | - Fang Guo
- Howard Hughes Medical Institute and National Center for Behavioral Genomics,Department of Biology, Brandeis University, Waltham, United States of America
| | - Orie Shafer
- Howard Hughes Medical Institute and National Center for Behavioral Genomics,Department of Biology, Brandeis University, Waltham, United States of America
| | - Michael Rosbash
- Howard Hughes Medical Institute and National Center for Behavioral Genomics,Department of Biology, Brandeis University, Waltham, United States of America
- * E-mail:
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Abstract
Activity-regulated genes (ARGs) are important for neuronal functions like long-term memory and are well-characterized in mammals but poorly studied in other model organisms like Drosophila. Here we stimulated fly neurons with different paradigms and identified ARGs using high-throughput sequencing from brains as well as from sorted neurons: they included a narrow set of circadian neurons as well as dopaminergic neurons. Surprisingly, many ARGs are specific to the stimulation paradigm and very specific to neuron type. In addition and unlike mammalian immediate early genes (IEGs), fly ARGs do not have short gene lengths and are less enriched for transcription factor function. Chromatin assays using ATAC-sequencing show that the transcription start sites (TSS) of ARGs do not change with neural firing but are already accessible prior to stimulation. Lastly based on binding site enrichment in ARGs, we identified transcription factor mediators of firing and created neuronal activity reporters. DOI:http://dx.doi.org/10.7554/eLife.19942.001
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Affiliation(s)
- Xiao Chen
- Howard Hughes Medical Institute, Brandeis University, Waltham, United States.,National Center for Behavioral Genomics, Department of Biology, Brandeis University, Waltham, United States
| | - Reazur Rahman
- Howard Hughes Medical Institute, Brandeis University, Waltham, United States.,National Center for Behavioral Genomics, Department of Biology, Brandeis University, Waltham, United States
| | - Fang Guo
- Howard Hughes Medical Institute, Brandeis University, Waltham, United States.,National Center for Behavioral Genomics, Department of Biology, Brandeis University, Waltham, United States
| | - Michael Rosbash
- Howard Hughes Medical Institute, Brandeis University, Waltham, United States.,National Center for Behavioral Genomics, Department of Biology, Brandeis University, Waltham, United States
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Rayjada P, Vaghela N, Rahman R, Bhatnagar M, Ranjan M, Chauhan N, Sircar A, Manocha L, Raole P. Er 2 O 3 coating by reactive magnetron sputtering: Effect of oxygen supply and erbium pre-layer deposition. Nuclear Materials and Energy 2016. [DOI: 10.1016/j.nme.2016.05.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Wood J, Kim D, Alqahtani S, Smith S, Barrett D, Grundy R, Rahman R. P01.04 Adult and paediatric GBM cells show differential phenotypic responses to external lipoprotein deprivation. Neuro Oncol 2016. [DOI: 10.1093/neuonc/now188.061] [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: 11/13/2022] Open
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Wood J, Kim D, Smith S, Lourdusamy A, Ward J, Barrett D, Grundy R, Rahman R. P08.18 LC-MS-based genome-wide profiling of glioblastoma multiforme reveals distinct metabolism within the invasive region. Neuro Oncol 2016. [DOI: 10.1093/neuonc/now188.151] [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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Ayodele O, Ali I, Konenko A, Duggan L, O'Mara N, Rahman R, Ged Y, Calvert P, Horgan A, O'Connor M. Menopausal status on tumour biology in early breast cancer. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw364.18] [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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