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273 results on '"Munshi, S."'

1. Ionospheric contributions to the excess power in high-redshift 21-cm power-spectrum observations with LOFAR

Author: Brackenhoff, S. A., Mevius, M., Koopmans, L. V. E., Offringa, A., Ceccotti, E., Chege, J. K., Gehlot, B. K., Ghosh, S., Höfer, C., Mertens, F. G., Munshi, S., and Zaroubi, S.
Subjects: Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics
Abstract: The turbulent ionosphere causes phase shifts to incoming radio waves on a broad range of temporal and spatial scales. When an interferometer is not sufficiently calibrated for the direction-dependent ionospheric effects, the time-varying phase shifts can cause the signal to decorrelate. The ionosphere's influence over various spatiotemporal scales introduces a baseline-dependent effect on the interferometric array. We study the impact of baseline-dependent decorrelation on high-redshift observations with the Low Frequency Array (LOFAR). Datasets with a range of ionospheric corruptions are simulated using a thin-screen ionosphere model, and calibrated using the state-of-the-art LOFAR Epoch of Reionisation pipeline. For the first time ever, we show the ionospheric impact on various stages of the calibration process including an analysis of the transfer of gain errors from longer to shorter baselines using realistic end-to-end simulations. We find that direction-dependent calibration for source subtraction leaves excess power of up to two orders of magnitude above the thermal noise at the largest spectral scales in the cylindrically averaged auto-power spectrum under normal ionospheric conditions. However, we demonstrate that this excess power can be removed through Gaussian process regression, leaving no excess power above the ten per cent level for a $5~$km diffractive scale. We conclude that ionospheric errors, in the absence of interactions with other aggravating effects, do not constitute a dominant component in the excess power observed in LOFAR Epoch of Reionisation observations of the North Celestial Pole. Future work should therefore focus on less spectrally smooth effects, such as beam modelling errors., Comment: 22 pages, 20 figures. Accepted for publication in Monthly Notices of the Royal Astronomical Society (MNRAS)
Published: 2024
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2. The impact of lossy data compression on the power spectrum of the high redshift 21-cm signal with LOFAR

Author: Chege, J. K., Koopmans, L. V. E., Offringa, A. R., Gehlot, B. K., Brackenhoff, S. A., Ceccotti, E., Ghosh, S., Höfer, C., Mertens, F. G., Mevius, M., and Munshi, S.
Subjects: Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics
Abstract: Current radio interferometers output multi-petabyte-scale volumes of data per year making the storage, transfer, and processing of this data a sizeable challenge. This challenge is expected to grow with the next-generation telescopes such as the Square Kilometre Array. Lossy compression of interferometric data post-correlation can abate this challenge. However, since high-redshift 21-cm studies impose strict precision requirements, the impact of such lossy data compression on the 21-cm signal power spectrum statistic should be understood. We apply Dysco visibility compression, a technique to normalize and quantize specifically designed for radio interferometric data. We establish the level of the compression noise in the power spectrum in comparison to the thermal noise as well as its coherency behavior. Finally, for optimal compression results, we compare the compression noise obtained from different compression settings to a nominal 21-cm signal power. From a single night of observation, we find that the noise introduced due to the compression is more than five orders of magnitude lower than the thermal noise level in the power spectrum. The noise does not affect calibration. The compression noise shows no correlation with the sky signal and has no measurable coherent component. The level of compression error in the power spectrum ultimately depends on the compression settings. Dysco visibility compression is found to be of insignificant concern for 21-cm power spectrum studies. Hence, data volumes can be safely reduced by factors of $\sim 4$ and with insignificant bias to the final power spectrum. Data from SKA-low will likely be compressible by the same factor as LOFAR, owing to the similarities of the two instruments. The same technique can be used to compress data from other telescopes, but a small adjustment of the compression parameters might be required., Comment: 12 pages, 9 figures, and 3 tables; submitted to Astronomy and Astrophysics (A&A)
Published: 2024

3. Beyond the horizon: Quantifying the full sky foreground wedge in the cylindrical power spectrum

Author: Munshi, S., Mertens, F. G., Koopmans, L. V. E., Offringa, A. R., Ceccotti, E., Brackenhoff, S. A., Chege, J. K., Gehlot, B. K., Ghosh, S., Höfer, C., and Mevius, M.
Subjects: Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics
Abstract: One of the main obstacles preventing the detection of the redshifted 21-cm signal from neutral hydrogen in the early Universe is the astrophysical foreground emission, which is several orders of magnitude brighter than the signal. The foregrounds, due to their smooth spectra, are expected to predominantly occupy a region in the cylindrical power spectrum known as the foreground wedge. However, the conventional equations describing the extent of the foreground wedge are derived under a flat-sky approximation. This assumption breaks down for tracking wide-field instruments, thus rendering these equations inapplicable in these situations. In this paper, we derive equations for the full sky foreground wedge and show that the foregrounds can potentially extend far beyond what the conventional equations suggest. We also derive the equations that describe a specific bright source in the cylindrical power spectrum space. The validity of both sets of equations is tested against numerical simulations. Many current and upcoming interferometers (e.g., LOFAR, NenuFAR, MWA, SKA) are wide-field phase-tracking instruments. These equations give us new insights into the nature of foreground contamination in the cylindrical power spectra estimated using wide-field instruments. Additionally, they allow us to accurately associate features in the power spectrum to foregrounds or instrumental effects. The equations are also important for correctly selecting the "EoR window" for foreground avoidance analyses, and for planning 21-cm observations. In future analyses, it is recommended to use these updated horizon lines to indicate the foreground wedge in the cylindrical power spectrum accurately. The new equations for generating the updated wedge lines are made available in a Python library, pslines., Comment: 21 pages, 13 figures, and 2 tables; submitted to Astronomy and Astrophysics (A&A)
Published: 2024

4. First upper limits on the 21 cm signal power spectrum from cosmic dawn from one night of observations with NenuFAR

Author: Munshi, S., Mertens, F. G., Koopmans, L. V. E., Offringa, A. R., Semelin, B., Aubert, D., Barkana, R., Bracco, A., Brackenhoff, S. A., Cecconi, B., Ceccotti, E., Corbel, S., Fialkov, A., Gehlot, B. K., Ghara, R., Girard, J. N., Grießmeier, J. M., Höfer, C., Hothi, I., Mériot, R., Mevius, M., Ocvirk, P., Shaw, A. K., Theureau, G., Yatawatta, S., Zarka, P., and Zaroubi, S.
Subjects: Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics
Abstract: The redshifted 21 cm signal from neutral hydrogen is a direct probe of the physics of the early universe and has been an important science driver of many present and upcoming radio interferometers. In this study we use a single night of observations with the New Extension in Nan\c{c}ay Upgrading LOFAR (NenuFAR) to place upper limits on the 21 cm power spectrum from cosmic dawn at a redshift of $z$ = 20.3. NenuFAR is a new low-frequency radio interferometer, operating in the 10-85 MHz frequency range, currently under construction at the Nan\c{c}ay Radio Observatory in France. It is a phased array instrument with a very dense uv coverage at short baselines, making it one of the most sensitive instruments for 21 cm cosmology analyses at these frequencies. Our analysis adopts the foreground subtraction approach, in which sky sources are modeled and subtracted through calibration and residual foregrounds are subsequently removed using Gaussian process regression. The final power spectra are constructed from the gridded residual data cubes in the uv plane. Signal injection tests are performed at each step of the analysis pipeline, the relevant pipeline settings are optimized to ensure minimal signal loss, and any signal suppression is accounted for through a bias correction on our final upper limits. We obtain a best 2$\sigma$ upper limit of $2.4\times 10^7$ $\text{mK}^{2}$ at $z$ = 20.3 and $k$ = 0.041 $h\,\text{cMpc}^{-1}$. We see a strong excess power in the data, making our upper limits two orders of magnitude higher than the thermal noise limit. We investigate the origin and nature of this excess power and discuss further improvements to the analysis pipeline that can potentially mitigate it and consequently allow us to reach thermal noise sensitivity when multiple nights of observations are processed in the future., Comment: 27 pages, 21 figures, and 6 tables; accepted for publication in Astronomy and Astrophysics (A&A); language edits implemented; typos corrected
Published: 2023
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5. Transient RFI environment of LOFAR-LBA at 72-75 MHz: Impact on ultra-widefield AARTFAAC Cosmic Explorer observations of the redshifted 21-cm signal

Author: Gehlot, B. K., Koopmans, L. V. E., Brackenhoff, S. A., Ceccotti, E., Ghosh, S., Höfer, C., Mertens, F. G., Mevius, M., Munshi, S., Offringa, A. R., Pandey, V. N., Rowlinson, A., Shulevski, A., Wijers, R. A. M. J., Yatawatta, S., and Zaroubi, S.
Subjects: Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics
Abstract: Measurement of the redshifted 21-cm signal of neutral hydrogen from the Cosmic Dawn (CD) and Epoch of Reionisation (EoR) promises to unveil a wealth of information about the astrophysical processes during the first billion years of evolution of the universe. The AARTFAAC Cosmic Explorer (ACE) utilises the AARTFAAC wide-field imager of LOFAR to measure the power spectrum of the intensity fluctuations of the redshifted 21-cm signal from the CD at z~18. The RFI from various sources contaminates the observed data and it is crucial to exclude the RFI-affected data in the analysis for reliable detection. In this work, we investigate the impact of non-ground-based transient RFI using cross-power spectra and cross-coherence metrics to assess the correlation of RFI over time and investigate the level of impact of transient RFI on the ACE 21-cm power spectrum estimation. We detected moving sky-based transient RFI sources that cross the field of view within a few minutes and appear to be mainly from aeroplane communication beacons at the location of the LOFAR core in the 72-75 MHz band, by inspecting filtered images. This transient RFI is mostly uncorrelated over time and is only expected to dominate over the thermal noise for an extremely deep integration time of 3000 hours or more with a hypothetical instrument that is sky temperature dominated at 75 MHz. We find no visible correlation over different k-modes in Fourier space in the presence of noise for realistic thermal noise scenarios. We conclude that the sky-based transient RFI from aeroplanes, satellites and meteorites at present does not pose a significant concern for the ACE analyses at the current level of sensitivity and after integrating over the available 500 hours of observed data. However, it is crucial to mitigate or filter such transient RFI for more sensitive experiments aiming for significantly deeper integration., Comment: 13 pages, 9 figures, and 3 tables; accepted for publication in Astronomy and Astrophysics (A&A)
Published: 2023
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6. A novel radio imaging method for physical spectral index modelling

Author: Ceccotti, E., Offringa, A. R., Koopmans, L. V. E., Timmerman, R., Brackenhoff, S. A., Gehlot, B. K., Mertens, F. G., Munshi, S., Pandey, V. N., van Weeren, R. J., Yatawatta, S., and Zaroubi, S.
Subjects: Astrophysics - Instrumentation and Methods for Astrophysics
Abstract: We present a new method, called "forced-spectrum fitting", for physically-based spectral modelling of radio sources during deconvolution. This improves upon current common deconvolution fitting methods, which often produce inaccurate spectra. Our method uses any pre-existing spectral index map to assign spectral indices to each model component cleaned during the multi-frequency deconvolution of WSClean, where the pre-determined spectrum is fitted. The component magnitude is evaluated by performing a modified weighted linear least-squares fit. We test this method on a simulated LOFAR-HBA observation of the 3C196 QSO and a real LOFAR-HBA observation of the 4C+55.16 FRI galaxy. We compare the results from the forced-spectrum fitting with traditional joined-channel deconvolution using polynomial fitting. Because no prior spectral information was available for 4C+55.16, we demonstrate a method for extracting spectral indices in the observed frequency band using "clustering". The models generated by the forced-spectrum fitting are used to improve the calibration of the datasets. The final residuals are comparable to existing multi-frequency deconvolution methods, but the output model agrees with the provided spectral index map, embedding correct spectral information. While forced-spectrum fitting does not solve the determination of the spectral information itself, it enables the construction of accurate multi-frequency models that can be used for wide-band calibration and subtraction., Comment: 17 pages, 9 figures, 5 tables. Accepted for publication in MNRAS
Published: 2023
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7. Assessing the impact of two independent direction-dependent calibration algorithms on the LOFAR 21-cm signal power spectrum

Author: Gan, H., Mertens, F. G., Koopmans, L. V. E., Offringa, A. R., Mevius, M., Pandey, V. N., Brackenhoff, S. A., Ceccotti, E., Ciardi, B., Gehlot, B. K., Ghara, R., Giri, S. K., Iliev, I. T., and Munshi, S.
Subjects: Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics
Abstract: Detecting the 21-cm signal from the Epoch of Reionisation (EoR) is challenging due to the strong astrophysical foregrounds, ionospheric effects, radio frequency interference and instrumental effects. Understanding and calibrating these effects are crucial for the detection. In this work, we introduce a newly developed direction-dependent (DD) calibration algorithm DDECAL and compare its performance with an existing algorithm, SAGECAL, in the context of the LOFAR-EoR 21-cm power spectrum experiment. In our data set, the North Celestial Pole (NCP) and its flanking fields were observed simultaneously. We analyse the NCP and one of its flanking fields. The NCP field is calibrated by the standard pipeline, using SAGECAL with an extensive sky model and 122 directions, and the flanking field is calibrated by DDECAL and SAGECAL with a simpler sky model and 22 directions. Additionally, two strategies are used for subtracting Cassiopeia A and Cygnus A. The results show that DDECAL performs better at subtracting sources in the primary beam region due to the application of a beam model, while SAGECAL performs better at subtracting Cassiopeia A and Cygnus A. This indicates that including a beam model during DD calibration significantly improves the performance. The benefit is obvious in the primary beam region. We also compare the 21-cm power spectra on two different fields. The results show that the flanking field produces better upper limits compared to the NCP in this particular observation. Despite the minor differences between DDECAL and SAGECAL due to the beam application, we find that the two algorithms yield comparable 21-cm power spectra on the LOFAR-EoR data after foreground removal. Hence, the current LOFAR-EoR 21-cm power spectrum limits are not likely to depend on the DD calibration method., Comment: 28 pages, 14 figures, accepted for publication in A&A; a few equations in section 3 were corrected in this version
Published: 2022
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8. Improving integrated care for (future) parents facing vulnerable circumstances in the early life course of their (future) child: An action research protocol.

Author: Munshi, S. C., Weggelaar-Jansen, A. M., van den Berg-Bakker, A., Blanchette, L. M. G., Harmsen van der Vliet-Torij, H. W., Hodes, M. W., van 't Hof, M., Lambregtse-van den Berg, M. P., van der Meer, L., Ernst-Smelt, H. E., and Bijma, H. H.
Subjects: *CONTINUUM of care, *RESEARCH protocols, *CHILDREN'S health, *FOSTER home care, *ACTION research
Abstract: Introduction: Suboptimal circumstances during the early life course, ranging from 100 days before conception to 1000 days following birth, significantly impact a child's future health and well-being. To optimize these circumstances, collaboration is needed which includes professionals working in medical, social and public domains, as well as parents. This action research protocol aims to improve care for (future) parents facing suboptimal circumstances during the early life course by enhancing inter-professional, cross-domain collaboration and (future) parents-professional collaboration. By employing iterative action research cycles, we seek to foster integrated care pathways and improve continuity of care across the medical, social and public domains. The research will be conducted in Rotterdam, the Netherlands. Methods and analysis: Four action research cycles incorporating descriptive qualitative and quantitative studies, including focus groups, questionnaires and observations with (future) parents facing suboptimal circumstances, professionals and policymakers. This intervention study will not only foster improved, integrated care around identification of the need of additional support, referral and care, but also foster the necessary conditions for a self-supporting neighbourhood care learning network of (future) parents, professionals and policymakers to encourage bidirectional feedback and enable reflection beyond a single organisation. These interventions will also be evaluated. Dissemination: The results will be disseminated through peer-reviewed publications, layman summaries, regional and national knowledge platforms and presentations and factsheets relevant to all involved actors. [ABSTRACT FROM AUTHOR]
Published: 2024
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9. Ionospheric contributions to the excess power in high-redshift 21-cm power-spectrum observations with LOFAR.

Author: Brackenhoff, S A, Mevius, M, Koopmans, L V E, Offringa, A, Ceccotti, E, Chege, J K, Gehlot, B K, Ghosh, S, Höfer, C, Mertens, F G, Munshi, S, and Zaroubi, S
Subjects: KRIGING, THERMAL noise, IONOSPHERE, AGE of stars, MIDDLE Ages
Abstract: The turbulent ionosphere causes phase shifts to incoming radio waves on a broad range of temporal and spatial scales. When an interferometer is not sufficiently calibrated for the direction-dependent ionospheric effects, the time-varying phase shifts can cause the signal to decorrelate. The ionosphere's influence over various spatiotemporal scales introduces a baseline-dependent effect on the interferometric array. We study the impact of baseline-dependent decorrelation on high-redshift observations with the Low Frequency Array (LOFAR). Data sets with a range of ionospheric corruptions are simulated using a thin-screen ionosphere model, and calibrated using the state-of-the-art LOFAR epoch of reionization pipeline. For the first time ever, we show the ionospheric impact on various stages of the calibration process including an analysis of the transfer of gain errors from longer to shorter baselines using realistic end-to-end simulations. We find that direction-dependent calibration for source subtraction leaves excess power of up to two orders of magnitude above the thermal noise at the largest spectral scales in the cylindrically averaged autopower spectrum under normal ionospheric conditions. However, we demonstrate that this excess power can be removed through Gaussian process regression, leaving no excess power above the 10 per cent level for a |$5~$| km diffractive scale. We conclude that ionospheric errors, in the absence of interactions with other aggravating effects, do not constitute a dominant component in the excess power observed in LOFAR epoch of reionization observations of the North Celestial Pole. Future work should therefore focus on less spectrally smooth effects, such as beam modelling errors. [ABSTRACT FROM AUTHOR]
Published: 2024
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10. Opportunistic infections and AIDS malignancies early after initiating combination antiretroviral therapy in high-income countries.

Author: Lodi, S, Del Amo, J, Moreno, S, Bucher, HC, Furrer, H, Logan, R, Sterne, J, Pérez-Hoyos, S, Jarrín, I, Phillips, A, Olson, A, Van Sighem, A, Reiss, P, Sabin, C, Jose, S, Justice, A, Goulet, J, Miró, JM, Ferrer, E, Meyer, L, Seng, R, Vourli, G, Antoniadou, A, Dabis, F, Vandenhede, MA, Costagliola, D, Abgrall, S, Hernán, MA, Hernan, M, Bansi, L, Hill, T, Dunn, D, Porter, K, Glabay, A, Orkin, C, Thomas, R, Jones, K, Fisher, M, Perry, N, Pullin, A, Churchill, D, Gazzard, B, Nelson, M, Asboe, D, Bulbeck, S, Mandalia, S, Clarke, J, Delpech, V, Anderson, J, Munshi, S, Post, F, Easterbrook, P, Khan, Y, Patel, P, Karim, F, Duffell, S, Gilson, R, Man, SL, Williams, I, Gompels, M, Dooley, D, Schwenk, A, Ainsworth, J, Johnson, M, Youle, M, Lampe, F, Smith, C, Grabowska, H, Chaloner, C, Ismajani Puradiredja, D, Walsh, J, Weber, J, Kemble, C, Mackie, N, Winston, A, Leen, C, Wilson, A, Bezemer, DO, Gras, LAJ, Kesselring, AM, Van Sighem, AI, Zaheri, S, Van Twillert, G, Kortmann, W, Branger, J, Prins, JM, Kuijpers, TW, Scherpbier, HJ, Van Der Meer, JTM, Wit, FWMN, Godfried, MH, Van Der Poll, T, Nellen, FJB, and Lange, JMA
Subjects: Humans, AIDS-Related Opportunistic Infections, HIV Infections, Neoplasms, Anti-Retroviral Agents, Antiretroviral Therapy, Highly Active, Incidence, Developed Countries, Adolescent, Adult, Aged, Middle Aged, United States, Europe, Female, Male, Young Adult, HIV, immune reconstitution inflammatory syndrome, incidence, inverse probability weighting, unmasking, Antiretroviral Therapy, Highly Active, HIV/AIDS, Infectious Diseases, Genetics, Behavioral and Social Science, Infection, Rare Diseases, Lymphoma, Cancer, Hematology, Tuberculosis, Virology, Biological Sciences, Medical and Health Sciences, Psychology and Cognitive Sciences
Abstract: BackgroundThere is little information on the incidence of AIDS-defining events which have been reported in the literature to be associated with immune reconstitution inflammatory syndrome (IRIS) after combined antiretroviral therapy (cART) initiation. These events include tuberculosis, mycobacterium avium complex (MAC), cytomegalovirus (CMV) retinitis, progressive multifocal leukoencephalopathy (PML), herpes simplex virus (HSV), Kaposi sarcoma, non-Hodgkin lymphoma (NHL), cryptococcosis and candidiasis.MethodsWe identified individuals in the HIV-CAUSAL Collaboration, which includes data from six European countries and the US, who were HIV-positive between 1996 and 2013, antiretroviral therapy naive, aged at least 18 years, had CD4 cell count and HIV-RNA measurements and had been AIDS-free for at least 1 month between those measurements and the start of follow-up. For each AIDS-defining event, we estimated the hazard ratio for no cART versus less than 3 and at least 3 months since cART initiation, adjusting for time-varying CD4 cell count and HIV-RNA via inverse probability weighting.ResultsOut of 96 562 eligible individuals (78% men) with median (interquantile range) follow-up of 31 [13,65] months, 55 144 initiated cART. The number of cases varied between 898 for tuberculosis and 113 for PML. Compared with non-cART initiation, the hazard ratio (95% confidence intervals) up to 3 months after cART initiation were 1.21 (0.90-1.63) for tuberculosis, 2.61 (1.05-6.49) for MAC, 1.17 (0.34-4.08) for CMV retinitis, 1.18 (0.62-2.26) for PML, 1.21 (0.83-1.75) for HSV, 1.18 (0.87-1.58) for Kaposi sarcoma, 1.56 (0.82-2.95) for NHL, 1.11 (0.56-2.18) for cryptococcosis and 0.77 (0.40-1.49) for candidiasis.ConclusionWith the potential exception of mycobacterial infections, unmasking IRIS does not appear to be a common complication of cART initiation in high-income countries.
Published: 2014

11. Transient RFI environment of LOFAR-LBA at 72-75 MHz. Impact on ultra-widefield AARTFAAC Cosmic Explorer observations of the redshifted 21-cm signal

Author: Gehlot, B.K., primary, Koopmans, L.V.E., additional, Brackenhoff, S.A., additional, Ceccotti, E., additional, Ghosh, S., additional, Hofer, C., additional, Mertens, F.G., additional, Mevius, M., additional, Munshi, S., additional, Offringa, A.R., additional, Pandey, V.N., additional, Rowlinson, A., additional, Shulevski, A., additional, Wijers, R.A.M.J., additional, Yatawatta, S., additional, and Zaroubi, S., additional
Published: 2023
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12. A novel radio imaging method for physical spectral index modelling

Author: Ceccotti, E, primary, Offringa, A R, additional, Koopmans, L V E, additional, Timmerman, R, additional, Brackenhoff, S A, additional, Gehlot, B K, additional, Mertens, F G, additional, Munshi, S, additional, Pandey, V N, additional, van Weeren, R J, additional, Yatawatta, S, additional, and Zaroubi, S, additional
Published: 2023
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13. Accurate modelling of the Lyman-α coupling for the 21-cm signal, observability with NenuFAR, and SKA

Author: Semelin, B., primary, Mériot, R., additional, Mertens, F., additional, Koopmans, L. V. E., additional, Aubert, D., additional, Barkana, R., additional, Fialkov, A., additional, Munshi, S., additional, and Ocvirk, P., additional
Published: 2023
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14. First upper limits on the 21-cm signal power spectrum from the Cosmic Dawn from one night of observations with NenuFAR

Author: Munshi, S., Mertens, F. G., Koopmans, L. V. E., Offringa, A. R., Semelin, B., Aubert, D., Barkana, R., Bracco, A., Brackenhoff, S. A., Cecconi, B., Ceccotti, E., Corbel, S., Fialkov, A., Gehlot, B. K., Ghara, R., Girard, J. N., Grießmeier, J. M., Höfer, C., Hothi, I., Mériot, R., Mevius, M., Ocvirk, P., Shaw, A. K., Theureau, G., Yatawatta, S., Zarka, P., Zaroubi, S., Munshi, S., Mertens, F. G., Koopmans, L. V. E., Offringa, A. R., Semelin, B., Aubert, D., Barkana, R., Bracco, A., Brackenhoff, S. A., Cecconi, B., Ceccotti, E., Corbel, S., Fialkov, A., Gehlot, B. K., Ghara, R., Girard, J. N., Grießmeier, J. M., Höfer, C., Hothi, I., Mériot, R., Mevius, M., Ocvirk, P., Shaw, A. K., Theureau, G., Yatawatta, S., Zarka, P., and Zaroubi, S.
Abstract: The redshifted 21-cm signal from neutral hydrogen is a direct probe of the physics of the early universe and has been an important science driver of many present and upcoming radio interferometers. In this study, we use a single night of observations with the New Extension in Nan\c{c}ay Upgrading LOFAR (NenuFAR) to place upper limits on the 21-cm power spectrum from the Cosmic Dawn at a redshift of $z$ = 20.3. NenuFAR is a new low-frequency radio interferometer, operating in the 10-85 MHz frequency range, currently under construction at the Nan\c{c}ay Radio Observatory in France. It is a phased array instrument with a very dense uv-coverage at short baselines, making it one of the most sensitive instruments for 21-cm cosmology analyses at these frequencies. Our analysis adopts the foreground subtraction approach, in which sky sources are modeled and subtracted through calibration, and residual foregrounds are subsequently removed using Gaussian process regression (GPR). The final power spectra are constructed from the gridded residual data cubes in the uv-plane. Signal injection tests are performed at each step of the analysis pipeline, and the relevant pipeline settings are optimized to ensure minimal signal loss, and any signal suppression is accounted for through a bias correction on our final upper limits. We obtain a best 2$\sigma$ upper limit of $2.4\times 10^7$ $\text{mK}^{2}$ at $z$ = 20.3 and $k$ = 0.041 $h\,\text{cMpc}^{-1}$. We see a strong excess power in the data, making our upper limits two orders of magnitude higher than the thermal noise limit. We investigate the origin and nature of this excess power and discuss further improvements in the analysis pipeline, which can potentially mitigate it and consequently allow us to reach the thermal noise sensitivity when multiple nights of observations are processed in the future., Comment: 27 pages, 21 figures, and 6 tables; accepted for publication in Astronomy and Astrophysics (A&A)
Published: 2023
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15. Temperature-Dependent Sheet Resistance and Surface Characterization of Thin Copper Films Bonded to FR4 Composite under Mechanical Vibrations

Author: Universitat Rovira i Virgili, Azam, S; Munshi, S; Hassan, MK; Fragoso, A, Universitat Rovira i Virgili, and Azam, S; Munshi, S; Hassan, MK; Fragoso, A
Abstract: Featured Application: Electrical and electronic devices that experience long-term vibrations. Electrical boards, also called printed circuit boards, constitute the basis of most electronic devices. These boards are mainly fabricated of thin copper films bonded to fiber epoxy laminates, such as FR4. Being the most important functional component of these devices, they sometimes undergo mechanical stresses such as shock and vibration during transport and operation that can induce electrical failure and malfunction; hence, studies addressing the effects of vibrations on their electrical properties have important applications. In this paper, small cantilever samples made of bare copper bonded to FR4 with three isolated rectangular zones were studied to analyze, for the first time, variations in electrical properties such as sheet resistance and resistivity before and after 200 k, 500 k, and 800 k vibration cycles at three different temperatures (25, 35, and 45 °C). A significant rise in resistance equivalent to 1657% of the initial value was observed from 0 to 800 k vibration cycles. These changes were accompanied by a 95% decrease in conductivity, from 4.1 × 107 to 2.3 × 106 S/m, whereas very little change in the electrical properties was observed due to temperature rise. Surface analysis by ESEM showed cracks ~1 µm in width and several millimeters in length with a crack density of ~8 cracks per mm after 800 k cycles. The surface composition (100% copper) was not altered even upon a high number of vibration cycles, and static drop contact angle measurements of 117–119 degrees indicated an increase in the hydrophobicity of the surface attributed to increased surface roughness and the accumulation of very small air bubbles on the cracks.
Published: 2023

16. Assessing the impact of two independent direction-dependent calibration algorithms on the LOFAR 21 cm signal power spectrum

Author: Gan, H., primary, Mertens, F. G., additional, Koopmans, L. V. E., additional, Offringa, A. R., additional, Mevius, M., additional, Pandey, V. N., additional, Brackenhoff, S. A., additional, Ceccotti, E., additional, Ciardi, B., additional, Gehlot, B. K., additional, Ghara, R., additional, Giri, S. K., additional, Iliev, I. T., additional, and Munshi, S., additional
Published: 2022
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17. Comparative studies of T = 3 and T = 4 icosahedral RNA insect viruses

Author: Johnson, JE, Munshi, S, Liljas, L, Agrawal, D, Olson, NH, Reddy, V, Fisher, A, McKinney, B, Schmidt, T, and Baker, TS
Subjects: Biochemistry and Cell Biology, Chemical Sciences, Biological Sciences, Crystallography, X-Ray, Insect Viruses, Microscopy, Electron, Models, Molecular, Models, Structural, Molecular Conformation, RNA Viruses, Virology
Abstract: Crystallographic and molecular biological studies of T = 3 nodaviruses (180 identical subunits in the particle) and T = 4 tetraviruses (240 identical subunits in the particle) have revealed similarity in both the architecture of the particles and the strategy for maturation. The comparative studies provide a novel opportunity to examine an apparent evolution of particle size, from smaller (T = 3) to larger (T = 4), with both particles based on similar subunits. The BBV and FHV nodavirus structures are refined at 2.8 A and 3 A respectively, while the N omega V structure is at 6 A resolution. Nevertheless, the detailed comparisons of the noda and tetravirus X-ray electron density maps show that the same type of switching in subunit twofold contacts is used in the T = 3 and T = 4 capsids, although differences must exist between quasi and icosahedral threefold contacts in the T = 4 particle that have not yet been detected. The analyses of primary and tertiary structures of noda and tetraviruses show that N omega V subunits undergo a post assembly cleavage like that observed in nodaviruses and that the cleaved 76 C-terminal residues remain associated with the particle.
Published: 1994

18. Preliminary X-ray data analysis of crystalline cowpea chlorotic mottle virus.

Author: Speir, JA, Munshi, S, Baker, TS, and Johnson, JE
Subjects: Plant Viruses, RNA Viruses, Virion, Crystallization, X-Ray Diffraction, Image Processing, Computer-Assisted, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences, Virology
Abstract: Crystals of cowpea chlorotic mottle virus (CCMV) that diffract X-rays to 3.1 A resolution were grown in a succinate-PEG solution buffered at pH 3.3. The crystals are in space group P2(1)2(1)2(1) with unit cell dimensions of a = 381.26 A, b = 381.26 A, and c = 408.59 A. Four particles occupy the unit cell, placing a single virion in the crystallographic asymmetric unit. Diffraction intensities measured from 196 films collected at the Cornell High Energy Synchrotron Source accounted for 55% of the theoretically possible data to 3.2 A. Unit cell dimensions and rotation function analyses of the X-ray data revealed that the particles were organized in a pseudo-tetragonal relationship with the pseudo-fourfold axis along the crystal c axis. Analysis of electron micrographs of two-dimensional crystals of CCMV revealed a remarkable similarity between these and planes of particles perpendicular to the crystallographic c axis in the three-dimensional crystal.
Published: 1993

19. An Unusual Case of Recurrent Pyocolpos Following Midtrimester Miscarriage Revealed as Obstructed Hemivagina with Ipsilateral Renal Agenesis (OHVIRA) Syndrome

Author: Haldar M, Dasgupta S, Khandaker S, Munshi S, Mondal N, and Adhikari S
Subjects: Uterus didelphys, Obstructed hemivagina, Vaginal septum excision, Ultrasound, MRI, Medicine
Abstract: Obstructed hemivagina with ipsilateral renal agenesis (OHVIRA Syndrome) is a rare congenital anomaly. It mostly presents with severe dysmenorrhea and a palpable mass due to unilateral hematocolpos. Sometime it presents in unusual way with prolonged vaginal bleeding and profuse vaginal discharge. Here we report case of an 18 years old married female with OHVIRA syndrome presenting late with symptoms of recurrent pyocolpos following dilatation and evacuation for midtrimester miscarriage that was diagnosed on the basis of MRI and managed by vaginal septotomy.
Published: 2014

20. Characterization and reactivity study of non-heme high-valent iron-hydroxo complexes

Author: Keshari K., Bera M., Velasco L., Munshi S., Gupta G., Moonshiram D., Paria S. and SP acknowledges Science and Engineering Research Board (ECR/2017/002433) and IIT Delhi for funding. D. M. acknowledges funding from the Severo Ochoa Excellence program (SEV-2016-0686) from the Instituto IMDEA Nanociencia, the Acciones de Dinamización 'Europa Investigacion' grant (EIN2019-103399), and the Spanish Ministerio de Ciencia, Innovacion y Universidades grant (PID2019-111086RA-I00). The research leading to part of the results was further supported by the project CALIPSOplus under the Grant Agreement 730872 from the EU Framework Programme for Research and Innovation HORIZON 2020. We also thank Dr Wolfgang Caliebe for help with experiments at the Petra P64 beamline at DESY, a member of the Helmholtz Association (HGF) (Germany). The DFT calculations (SI) were performed in the Scientic Computing Center-Autonomous University of Madrid (CatDesignProject, PI: D. Moonshiram), thanks to CPU time and other resources granted by the institution. We acknowledge Prof. Kaushik Ghosh, IIT Roorkee for helping with EPR measurements. We thank Prof. Kuntal Manna, IIT Delhi for helping with GC-mass measurements. KK acknowledges MHRD for the fellowship. MB thanks SERB for the Inspire fellowship. GG thanks IIT Delhi for the Institute Post-Doctoral Fellowship.
Published: 2021

21. Characterization and reactivity study of non-heme high-valent iron-hydroxo complexes

Author: Keshari K., Bera M., Velasco L., Munshi S., Gupta G., Moonshiram D., Paria S., Keshari K., Bera M., Velasco L., Munshi S., Gupta G., Moonshiram D., and Paria S.
Published: 2021

22. Cross-wavelet transform as a new paradigm for feature extraction from noisy partial discharge pulses

Author: Dey, D., Chatterjee, B., Chakravorti, S., and Munshi, S.
Subjects: Electric discharges -- Analysis, Electric discharges through gases -- Analysis, Fuzzy algorithms -- Usage, Fuzzy logic -- Usage, Fuzzy systems -- Usage, Neural networks -- Usage, Noise control -- Methods, Fuzzy sets -- Usage, Set theory -- Usage, Fuzzy logic, Neural network, Business, Electronics, Electronics and electrical industries
Published: 2010

23. Rough-granular approach for impulse fault classification of transformers using cross-wavelet transform

Author: Dey, D., Chatterjee, B., Chakravorti, S., and Munshi, S.
Subjects: Wavelet transforms -- Evaluation, Electric fault location -- Methods, Electric transformers -- Design and construction, Business, Electronics, Electronics and electrical industries
Abstract: A novel approach based on information granulation using Rough sets for impulse fault identification of transformers has been proposed. It is found that the location and type of fault within a transformer winding can be classified efficiently by the features extracted from cross-wavelet spectra of current waveforms, obtained from impulse test. Results show that the proposed methodology can localize the fault within 5% of the winding length with a high degree of accuracy. The basic concepts of feature extraction using cross-wavelet transform and the method of classification of those features by rough-granular method are also explained. Index Terms--Cross-wavelet transform, cross-wavelet spectrum, impulse fault identification, information granulation, rough set.
Published: 2008

24. Controlling Structure and Dimensions of a Disordered Protein via Mutations

Author: Munshi, S, Rajendran, D, Ramesh, S, Subramanian, S, Bhattacharjee, K, Kumar, MR, Naganathan, AN, Munshi, S, Rajendran, D, Ramesh, S, Subramanian, S, Bhattacharjee, K, Kumar, MR, and Naganathan, AN
Abstract: The dimensions of intrinsically disordered proteins (IDPs) are sensitive to small energetic-entropic differences between intramolecular and protein-solvent interactions. This is commonly observed on modulating solvent composition and temperature. However, the inherently heterogeneous conformational landscape of IDPs is also expected to be influenced by mutations that can (de)stabilize pockets of local and even global structure, native and non-native, and hence the average dimensions. Here, we show experimental evidence for the remarkably tunable landscape of IDPs by employing the DNA-binding domain of CytR, a high-sequence-complexity IDP, as a model system. CytR exhibits a range of structure and compactness upon introducing specific mutations that modulate microscopic terms, including main-chain entropy, hydrophobicity, and electrostatics. The degree of secondary structure, as monitored by far-UV circular dichroism (CD), is strongly correlated to average ensemble dimensions for 14 different mutants of CytR and is consistent with the Uversky-Fink relation. Our experiments highlight how average ensemble dimensions can be controlled via mutations even in the disordered regime, the prevalence of non-native interactions and provide testable controls for molecular simulations.
Published: 2020

25. Associations between baseline characteristics, CD4 cell count response and virological failure on first-line efavirenz

Author: Stirrup, OT, Sabin, CA, Phillips, AN, Williams, I, Churchill, D, Tostevin, A, Hill, T, Dunn, DT, Asboe, D, Pozniak, A, Cane, P, Chadwick, D, Clark, D, Collins, S, Delpech, V, Douthwaite, S, Dunn, D, Fearnhill, E, Porter, K, Stirrup, O, Fraser, C, Geretti, AM, Gunson, R, Hale, A, Hue, S, Lazarus, L, Leigh-Brown, A, Mbisa, T, Mackie, N, Orkin, C, Nastouli, E, Pillay, D, Phillips, A, Sabin, C, Smit, E, Templeton, K, Tilston, P, Volz, E, Zhang, H, Fairbrother, K, Dawkins, J, O'Shea, S, Mullen, J, Cox, A, Tandy, R, Fawcett, T, Hopkins, M, Booth, C, Garcia-Diaz, A, Renwick, L, Schmid, ML, Payne, B, Hubb, J, Dustan, S, Kirk, S, Bradley-Stewart, A, Ainsworth, J, Allan, S, Anderson, J, Babiker, A, Gazzard, B, Gilson, R, Compels, M, Hay, P, Johnson, M, Jose, S, Kegg, S, Leen, C, Martin, F, Mital, D, Nelson, M, Palfreeman, A, Post, F, Pritchard, J, Schwenk, A, Tariq, A, Trevelion, R, Ustianowski, A, Walsh, J, Thornton, A, Huntington, S, Glabay, A, Shidfar, S, Lynch, J, Hand, J, De Souza, C, Perry, N, Tilbury, S, Youssef, E, Mabika, T, Mandalia, S, Munshi, S, Adefisan, A, Taylor, C, Gleisner, Z, Ibrahim, F, Campbell, L, Baillie, K, Brima, N, Miller, S, Wood, C, Youle, M, Lampe, F, Smith, C, Tsintas, R, Chaloner, C, Hutchinson, S, Winston, A, Weber, J, Ramzan, F, Carder, M, Wilson, A, Morris, S, Gompels, M, Lewszuk, A, Faleye, A, Ogunbiyi, V, Mitchell, S, Kemble, C, Russell-Sharpe, S, Gravely, J, Harte, A, Spencer, H, Jones, R, Cumming, S, Atkinson, C, Edgell, V, Allen, J, Murphy, C, and Gunder, I
Subjects: NNRTI, viral suppression, Science & Technology, drug resistance, MUTATIONS, Immunology, antiretroviral therapy, MODELS, viral failure, HIV, HIV-1 DRUG-RESISTANCE, TIME, INDIVIDUALS, Infectious Diseases, ADHERENCE, NRTI, Virology, INFECTION, UK, COMBINATION ANTIRETROVIRAL THERAPY, UK HIV Drug Resistance Database and the UK Collaborative HIV Cohort, Life Sciences & Biomedicine, ART, SUPPRESSION
Abstract: Objectives The aim of this study was to investigate associations between baseline characteristics and CD4 cell count response on first-line antiretroviral therapy and risk of virological failure (VF) with or without drug resistance. Methods We conducted an analysis of UK Collaborative HIV Cohort data linked to the UK HIV Drug Resistance Database. Inclusion criteria were viral sequence showing no resistance prior to initiation of first-line efavirenz + tenofovir disoproxil fumarate + emtricitabine and virological suppression within 6 months. Outcomes of VF (≥200 copies/mL) with or without drug resistance were assessed using a competing risks approach fitted jointly with a model for CD4 cell count recovery. Hazard ratios for each VF outcome were estimated for baseline CD4 cell count and viral load and characteristics of CD4 cell count response using latent variables on a standard normal scale. Results A total of 3640 people were included with 338 VF events; corresponding viral sequences were available in 134 with ≥1 resistance mutation in 36. VF with resistance was associated with lower baseline CD4 (0.30, 0.09–0.62), lower CD4 recovery (0.04, 0.00–0.17) and higher CD4 variability (4.40, 1.22–12.68). A different pattern of associations was observed for VF without resistance, but the strength of these results was less consistent across sensitivity analyses. Cumulative incidence of VF with resistance was estimated to be
Published: 2019

26. Virological outcomes of boosted protease inhibitor-based first-line ART in subjects harbouring thymidine analogue-associated mutations as the sole form of transmitted drug resistance

Author: Geretti, AM, White, E, Orkin, C, Tostevin, A, Tilston, P, Chadwick, D, Leen, C, Sabin, C, Dunn, DT, Asboe, D, Pozniak, A, Cane, P, Churchill, D, Clark, D, Collins, S, Delpech, V, Douthwaite, S, Dunn, D, Fearnhill, E, Porter, K, Stirrup, O, Fraser, C, Gunson, R, Hale, A, Hue, S, Lazarus, L, Leigh-Brown, A, Mbisa, T, Mackie, N, Nastouli, E, Pillay, D, Phillips, A, Smit, E, Templeton, K, Volz, E, Williams, I, Zhang, H, Dawkins, J, O'Shea, S, Mullen, J, Cox, A, Tandy, R, Fawcett, T, Hopkins, M, Booth, C, Garcia-Diaz, A, Renwick, L, Schmid, ML, Payne, B, Hubb, J, Dustan, S, Kirk, S, Bradley-Stewart, A, Ainsworth, J, Allan, S, Anderson, J, Babiker, A, Gazzard, B, Gilson, R, Gompels, M, Hay, P, Hill, T, Johnson, M, Jose, S, Kegg, S, Martin, F, Mital, D, Nelson, M, Palfreeman, A, Post, F, Pritchard, J, Sabin, CA, Schwenk, A, Tariq, A, Trevelion, R, Ustianowski, A, Walsh, J, Thornton, A, Huntington, S, Glabay, A, Shidfar, S, Lynch, J, Hand, J, De Souza, C, Perry, N, Tilbury, S, Youssef, E, Mabika, T, Mandalia, S, Munshi, S, Adefisan, A, Taylor, C, Gleisner, Z, Ibrahim, F, Campbell, L, Baillie, K, Brima, N, Miller, S, Wood, C, Youle, M, Lampe, F, Smith, C, Tsintas, R, Chaloner, C, Hutchinson, S, Winston, A, Weber, J, Ramzan, F, Carder, M, Wilson, A, Morris, S, Lewszuk, A, Faleye, A, Ogunbiyi, V, Mitchell, S, Kemble, C, Russell-Sharpe, S, Gravely, J, Harte, A, Spencer, H, Jones, R, Cumming, S, Atkinson, C, Edgell, V, Allen, J, Murphy, C, and Gunder, I
Subjects: 0301 basic medicine, Oncology, Male, HIV Infections, Drug resistance, Kaplan-Meier Estimate, chemistry.chemical_compound, 0302 clinical medicine, 1108 Medical Microbiology, Abacavir, Antiretroviral Therapy, Highly Active, INFECTION, Pharmacology (medical), Pharmacology & Pharmacy, 030212 general & internal medicine, Original Research, Proteolytic enzymes, Lamivudine, virus diseases, Viral Load, Prognosis, ANTIRETROVIRAL TREATMENT, Infectious Diseases, Treatment Outcome, Cohort, RNA, Viral, Female, 1115 Pharmacology and Pharmaceutical Sciences, UK HIV Drug Resistance Database and UK CHIC Study, Life Sciences & Biomedicine, Viral load, 0605 Microbiology, medicine.drug, Microbiology (medical), Adult, medicine.medical_specialty, Efavirenz, Genotype, TRANSMISSION, Anti-HIV Agents, 030106 microbiology, REGIMENS, Emtricitabine, Microbiology, 03 medical and health sciences, Internal medicine, Drug Resistance, Viral, medicine, Humans, Protease Inhibitors, Alleles, Pharmacology, Science & Technology, TREATMENT-NAIVE PATIENTS, business.industry, HIV, INDIVIDUALS, chemistry, Amino Acid Substitution, Mutation, HIV-1, business
Abstract: Objectives: In subjects with transmitted thymidine analogue mutations (TAMs), boosted PIs (PI/b) are often chosen to overcome possible resistance to the NRTI backbone. However, data to guide treatment selection are limited. Our aim was to obtain firmer guidance for clinical practice using real-world cohort data.Methods: We analysed 1710 subjects who started a PI/b in combination with tenofovir or abacavir plus emtricitabine or lamivudine, and compared their virological outcomes with those of 4889 patients who started an NNRTI (predominantly efavirenz), according to the presence of ≥1 TAM as the sole form of transmitted drug resistance.Results: Participants with ≥1 TAM comprised predominantly MSM (213 of 269, 79.2%), subjects of white ethnicity (206 of 269, 76.6%) and HIV-1 subtype B infections (234 of 269, 87.0%). Most (203 of 269, 75.5%) had singleton TAMs, commonly a revertant of T215Y or T215F (112 of 269, 41.6%). Over a median of 2.5 years of follow-up, 834 of 6599 (12.6%) subjects experienced viraemia (HIV-1 RNA >50 copies/mL). The adjusted HR for viraemia was 2.17 with PI/b versus NNRTI-based therapy (95% CI 1.88-2.51; P Conclusions: In this cohort, patients harbouring ≥1 TAM as the sole form of transmitted drug resistance gained no apparent virological advantage from starting first-line ART with a PI/b.
Published: 2018

27. Carotid and vertebral artery dissection syndromes

Author: Thanvi, B, Munshi, S K, Dawson, S L, and Robinson, T G
Published: 2005

28. A new self-tuned PID-type fuzzy controller as a combination of two-term controllers

Author: Bhattacharya, S., Chatterjee, A., and Munshi, S.
Published: 2004
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29. Value of routine duodenal biopsy in diagnosing coeliac disease in patients with iron deficiency anaemia

Author: Mandal, A K, Mehdi, I, Munshi, S K, and Lo, T C N
Published: 2004

30. Acceptability of oesophagogastroduodenoscopy without intravenous sedation: patients’ versus endoscopist’s perception with special reference to older patients

Author: Thanvi, B R, Munshi, S K, Vijayakumar, N, Taub, N, and Lo, T C N
Published: 2003

31. Neuropsychiatric non-motor aspects of Parkinson’s disease

Author: Thanvi, B R, Munshi, S K, Vijaykumar, N, and Lo, T C N
Published: 2003

32. Recurrent autumnal psychosis

Author: Joshi, P, Wicks, A C, and Munshi, S K
Published: 2003

33. ACCEPTABILITY OF OESOPHA-GOGASTRODUODENOSCOPY WITHOUT IV SEDATION: PATIENTʼs VERSUS ENDOSCOPISTʼs PERCEPTION WITH SPECIAL REFERENCE TO ELDERLY PATIENTS

Author: THANVI, B. R., MUNSHI, S. K., VIJAYKUMAR, N., TAUB, N., and LO, T. C.N.
Published: 2001

34. EARLY VERSUS LATE MORTALITY IN VERY ELDERLY END-STAGE RENAL DISEASE PATIENTS STARTING DIALYSIS

Author: MUNSHI, S., VIJAYKUMAR, N., PATEL, A., LO, T. C.N., and WARWICK, G.
Published: 2001

35. LIPIDS AND OBESITY IN OLDER PEOPLE

Author: MANGION, D. and MUNSHI, S.
Published: 2001

36. Development and application of a new measure of engagement in out‐patient HIV care

Author: Howarth, AR, Burns, FM, Apea, V, Jose, S, Hill, T, Delpech, VC, Evans, A, Mercer, CH, Michie, S, Morris, S, Sachikonye, M, Sabin, C, Ainsworth, Jonathan, Allan, Sris, Anderson, Jane, Babiker, Abdel, Chadwick, David, Dunn, David, Fisher, Martin, Gazzard, Brian, Gilson, Richard, Gompels, Mark, Hay, Phillip, Johnson, Margaret, Kegg, Stephen, Leen, Clifford, Martin, Fabiola, Nelson, Mark, Orkin, Chloe, Palfreeman, Adrian, Phillips, Andrew, Pillay, Deenan, Post, Frank, Pritchard, Jillian, Schwenk, Achim, Tariq, Anjum, Trevelion, Roy, Walsh, John, Thornton, Alicia, Huntington, Susie, Glabay, Adam, Perry, N., Tilbury, S., Youssef, E., Churchill, D., Everett, R., Asboe, D., Mandalia, S., Korat, H., Taylor, C., Gleisner, Z., Ibrahim, F., Campbell, L., Brima, N., Williams, I., Youle, M., Lampe, F., Smith, C., Tsintas, R., Chaloner, C., Hutchinson, S., Mackie, N., Winston, A., Weber, J., Ramzan, F., Carder, M., Lynch, J., Hand, J., Souza, C., Anderson, J., Munshi, S., Miller, S., Wood, C., Leen, C., Wilson, A., Morris, S., Memon, K., Lewszuk, A., Cope, E., Gibson, J., Main, P., Mitchell, S., Hunter, M., Dhillon, M., Russell‐Sharpe, S., Harte, A., Clay, S., Tariq, A., Spencer, H., Jones, R., Cumming, S., and Atkinson, C.
Subjects: Adult, Male, patient engagement, Adolescent, HIV, HIV Infections, out‐patient care, retention measure, Middle Aged, Patient Acceptance of Health Care, United Kingdom, Cohort Studies, Interviews as Topic, Young Adult, cohort study, Ambulatory Care, Humans, Female, Original Research, Aged
Abstract: Objectives Commonly used measures of engagement in HIV care do not take into account that the frequency of attendance is related to changes in treatment and health status. This study developed a new measure of engagement in care (EIC) incorporating clinical factors. Methods We conducted semi‐structured interviews with eight HIV physicians to identify factors associated with the timing of patients' next scheduled appointments. These factors informed the development of an algorithm to classify each month of follow‐up as “in care” (on or before the time of the next expected attendance) or “out of care” (after the time of the next expected attendance). The EIC algorithm was applied to data from the UK Collaborative HIV Cohort (UK CHIC) study, a large clinical cohort study. Results The interviews indicated that time to next appointment varied depending on psychosocial and physical comorbidities, and clinical factors (time since diagnosis, AIDS diagnosis, treatment status, CD4 count and viral load). The resulting EIC algorithm was applied to 44 432 patients; 83.9% of the 3 021 224 person‐months were “in care”. Greater EIC was independently associated with older age, white ethnicity, HIV acquisition through sex between men, current use of antiretroviral therapy (ART), a higher nadir CD4 count, later calendar year and being seen at the clinic for the first time within the last year. Conclusions This algorithm describing engagement in HIV care incorporates a time‐updated measure of patients' treatment and health status. It adds to the options available for measuring this key performance indicator.
Published: 2016

37. The anti-fecundity effect of 5-azacytidine (5-AzaC) on Schistosoma mansoni is linked to dis-regulated transcription, translation and stem cell activities

Author: Geyer, K.K, Munshi, S., Vickers, Mark A, Squance, M, Wilkinson, Toby, Berrar, D, Chaparro, C, Swain, MT, Hoffmann, K.F, Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Department of Cell Biology, John Innes Centre, Norwich Research Park, The Roslin Institute, University of Edinburgh, Tokyo Institute of Technology [Tokyo] (TITECH), and Université de Perpignan Via Domitia (UPVD)
Subjects: Fecundity, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], lcsh:RC109-216, Epigenetics, 5-Azacytidine, Schistosoma mansoni, RNA-Seq, Stem cells, Protein synthesis, lcsh:Infectious and parasitic diseases
Abstract: Uncontrolled host immunological reactions directed against tissue-trapped eggs precipitate a potentially lethal, pathological cascade responsible for schistosomiasis. Blocking schistosome egg production, therefore, presents a strategy for simultaneously reducing immunopathology as well as limiting disease transmission in endemic or emerging areas. We recently demonstrated that the ribonucleoside analogue 5-azacytidine (5-AzaC) inhibited Schistosoma mansoni oviposition, egg maturation and ovarian development. While these anti-fecundity effects were associated with a loss of DNA methylation, other molecular processes affected by 5-AzaC were not examined at the time. By comparing the transcriptomes of 5-AzaC-treated females to controls, we provide evidence that this ribonucleoside analogue also modulates other crucial aspects of schistosome egg-laying biology. For example, S. mansoni gene products associated with amino acid-, carbohydrate-, fatty acid-, nucleotide- and tricarboxylic acid (TCA)- homeostasis are all dysregulated in 5-AzaC treated females. To validate the metabolic pathway most significantly affected by 5-AzaC, amino acid metabolism, nascent protein synthesis was subsequently quantified in adult schistosomes. Here, 5-AzaC inhibited this process by 68% ±16.7% (SEM) in male- and 81% ±4.8% (SEM) in female-schistosomes. Furthermore, the transcriptome data indicated that adult female stem cells were also affected by 5-AzaC. For instance, 40% of transcripts associated with proliferating schistosome cells were significantly down-regulated by 5-AzaC. This finding correlated with a considerable reduction (95%) in the number of 5-ethynyl-2′-deoxyuridine (EdU) positive cells found in 5-AzaC-treated females. In addition to protein coding genes, the effect that 5-AzaC had on repetitive element expression was also assessed. Here, 46 repeats were found differentially transcribed between 5-AzaC-treated and control females with long terminal repeat (LTR) and DNA transposon classes being amongst the most significant. This study demonstrates that the anti-fecundity activity of 5-AzaC affects more than just DNA methylation in schistosome parasites. Further characterisation of these processes may reveal novel targets for schistosomiasis control. Keywords: Schistosoma mansoni, Epigenetics, 5-Azacytidine, Fecundity, RNA-Seq, Protein synthesis, Stem cells
Published: 2018

38. Risk factors and outcomes for the Q151M and T69 insertion HIV-1 resistance mutations in historic UK data

Author: Stirrup, OT, Dunn, DT, Tostevin, A, Sabin, CA, Pozniak, A, Asboe, D, Cox, A, Orkin, C, Martin, F, Cane, P, Fairbrother, K, Fearnhill, E, Hubb, J, Porter, K, Babiker, A, Lynch, J, Hand, J, De Souza, C, Churchill, D, Perry, N, Tilbury, S, Youssef, E, Clark, D, Gazzard, B, Nelson, M, Mabika, T, Mandalia, S, Anderson, J, Munshi, S, Post, F, Adefisan, A, Taylor, C, Gleisner, Z, Ibrahim, F, Campbell, L, Chadwick, D, Baillie, K, Gilson, R, Brima, N, Williams, I, Ainsworth, J, Schwenk, A, Miller, S, Wood, C, Johnson, M, Youle, M, Lampe, F, Smith, C, Tsintas, R, Chaloner, C, Hutchinson, S, Phillips, A, Hill, T, Jose, S, Huntington, S, Thornton, A, Walsh, J, Mackie, N, Winston, A, Weber, J, Ramzan, F, Carder, M, Leen, C, Wilson, A, Morris, S, Gompels, M, Allan, S, Palfreeman, A, Lewszuk, A, Kegg, S, Faleye, A, Ogunbiyi, V, Mitchell, S, Hay, P, Kemble, C, Russell-Sharpe, S, Gravely, J, Harte, A, Tariq, A, Spencer, H, Jones, R, Pritchard, J, Cumming, S, Atkinson, C, Mital, D, Edgell, V, Allen, J, Ustianowski, A, Murphy, C, and Gunder, I
Subjects: Multi-NRTI resistance, RESOURCE-LIMITED SETTINGS, Science & Technology, 151 complex, HIV, CHILDREN, Multidrug resistance, IMMUNODEFICIENCY-VIRUS TYPE-1, 69 insertion complex, UK Collaborative HIV Cohort, INFECTED INDIVIDUALS, PREVALENCE, EMERGENCE, Infectious Diseases, ANTIRETROVIRAL THERAPY, NRTI, 1ST-LINE REGIMENS, 1107 Immunology, Virology, COHORT, TRANSMITTED DRUG-RESISTANCE, Life Sciences & Biomedicine, UK HIV Drug Resistance Database
Abstract: Background: The prevalence of HIV-1 resistance to antiretroviral therapies (ART) has declined in high-income countries over recent years, but drug resistance remains a substantial concern in many low and middle-income countries. The Q151M and T69 insertion (T69i) resistance mutations in the viral reverse transcriptase gene can reduce susceptibility to all nucleoside/tide analogue reverse transcriptase inhibitors, motivating the present study to investigate the risk factors and outcomes associated with these mutations. Methods: We considered all data in the UK HIV Drug Resistance Database for blood samples obtained in the period 1997-2014. Where available, treatment history and patient outcomes were obtained through linkage to the UK Collaborative HIV Cohort study. A matched case-control approach was used to assess risk factors associated with the appearance of each of the mutations in ART-experienced patients, and survival analysis was used to investigate factors associated with viral suppression. A further analysis using matched controls was performed to investigate the impact of each mutation on survival. Results: A total of 180 patients with Q151M mutation and 85 with T69i mutation were identified, almost entirely from before 2006. Occurrence of both the Q151M and T69i mutations was strongly associated with cumulative period of virological failure while on ART, and for Q151M there was a particular positive association with use of stavudine and negative association with use of boosted-protease inhibitors. Subsequent viral suppression was negatively associated with viral load at sequencing for both mutations, and for Q151M we found a negative association with didanosine use but a positive association with boosted-protease inhibitor use. The results obtained in these analyses were also consistent with potentially large associations with other drugs. Analyses were inconclusive regarding associations between the mutations and mortality, but mortality was high for patients with low CD4 at detection. Conclusions: The Q151M and T69i resistance mutations are now very rare in the UK. Our results suggest that good outcomes are possible for people with these mutations. However, in this historic sample, viral load and CD4 at detection were important factors in determining prognosis.
Published: 2018

39. Virological failure and development of new resistance mutations according to CD4 count at combination antiretroviral therapy initiation

Author: Jose, S., Quinn, K., Dunn, D., Cox, A., Sabin, C., Fidler, S., Fisher, Martin, Gazzard, Brian, Gilson, Richard, Gompels, Mark, Hay, Phillip, Johnson, Margaret, Kegg, Stephen, Leen, C., Martin, Fabiola, Nelson, Mark, Palfreeman, Adrian, Post, F., Pritchard, Jillian, Sachikonye, Memory, Schwenk, Achim, Tariq, Anjum, Walsh, John, Hill, Teresa, Jose, Sophie, Phillips, Andrew, Sabin, Caroline, Thornton, Alicia, Dunn, David, Glabay, Adam, Fisher, M., Perry, N., Tilbury, S., Youssef, E., Churchill, D., Gazzard, B., Nelson, M., Everett, R., Asboe, D., Mandalia, S., Korat, H., Taylor, C., Gleisner, Z., Ibrahim, F., Campbell, L., Gilson, R., Brima, N., Williams, I., Johnson, M., Youle, M., Lampe, F., Smith, C., Tsintas, R., Chaloner, C., Hutchinson, S., Phillips, A., Hill, T., Thornton, A., Huntington, S., Walsh, J., Mackie, N., Winston, A., Weber, J., Ramzan, F., Carder, M., Orkin, C., Lynch, J., Hand, J., de Souza, C., Anderson, J., Munshi, S., Ainsworth, J., Schwenk, A., Miller, S., Wood, C., Wilson, A., Morris, S., Gompels, M., Allan, S., Palfreeman, A., Memon, K., Lewszuk, A., Chadwick, D., Cope, E., Gibson, J., Kegg, S., Main, P., Mitchell, Hunter, Hay, P., Dhillon, M., Martin, F., Russell-Sharpe, S., Harte, A., Clay, S., Tariq, A., Spencer, H., Jones, R., Pritchard, J., Cumming, S., Atkinson, C., Delpech, Valerie, Sachikony, M., Aitken, Celia, Asboe, David, Pozniak, Anton, Cane, Patricia, Chadwick, David, Churchill, Duncan, Clark, Duncan, Collins, Simon, Douthwaite, Samuel, Fearnhill, Esther, Porter, Kholoud, Tostevin, Anna, White, Ellen, Fraser, Christophe, Geretti, Anna Maria, Hale, Antony, Hué, Stéphane, Kaye, Steve, Kellam, Paul, Lazarus, Linda, Leigh-Brown, Andrew, Mbisa, Tamyo, Mackie, Nicola, Moses, Samuel, Orkin, Chloe, Nastouli, Eleni, Pillay, Deenan, Smit, Erasmus, Templeton, Kate, Tilston, Peter, Webster, Daniel, Williams, Ian, Zhang, Hongyi, Greatorex, Jane, O'Shea, Siobhan, Mullen, Jane, Cox, Alison, Tandy, Richard, Fawcett, Tracy, Hopkins, Mark, Ashton, Lynn, Booth, Claire, Garcia-Diaz, Ana, Shepherd, Jill, Schmid, Matthias L., Payne, Brendan, Pereira, Spiro, Hubb, Jonathan, Kirk, Stuart, Gunson, Rory, Bradley-Stewart, Amanda, and Medical Research Council (MRC)
Subjects: 0301 basic medicine, Male, HAART, HIV Infections, Treatment failure, law.invention, 0302 clinical medicine, Randomized controlled trial, law, Antiretroviral Therapy, Highly Active, Pharmacology (medical), 030212 general & internal medicine, Treatment Failure, virological failure, Health Policy, UK CHIC and UK HDRD Steering Committees, Virological failure, 3. Good health, Antiretroviral therapy, Patient benefit, Infectious Diseases, Female, medicine.symptom, Life Sciences & Biomedicine, Viral load, Cart, medicine.medical_specialty, Anti-HIV Agents, Short Communication, antiretroviral therapy, CD4 count, Asymptomatic, 03 medical and health sciences, HIV-INFECTION, Virology, Internal medicine, Drug Resistance, Viral, medicine, Humans, Science & Technology, business.industry, HIV resistance, 1103 Clinical Sciences, 030112 virology, CD4 Lymphocyte Count, Immunology, Mutation, business
Abstract: Objectives No randomized controlled trials have yet reported an individual patient benefit of initiating combination antiretroviral therapy (cART) at CD4 counts > 350 cells/μL. It is hypothesized that earlier initiation of cART in asymptomatic and otherwise healthy individuals may lead to poorer adherence and subsequently higher rates of resistance development. Methods In a large cohort of HIV-positive individuals, we investigated the emergence of new resistance mutations upon virological treatment failure according to the CD4 count at the initiation of cART. Results Of 7918 included individuals, 6514 (82.3%), 996 (12.6%) and 408 (5.2%) started cART with a CD4 count ≤ 350, 351–499 and ≥ 500 cells/μL, respectively. Virological rebound occurred while on cART in 488 (7.5%), 46 (4.6%) and 30 (7.4%) with a baseline CD4 count ≤ 350, 351–499 and ≥ 500 cells/μL, respectively. Only four (13.0%) individuals with a baseline CD4 count > 350 cells/μL in receipt of a resistance test at viral load rebound were found to have developed new resistance mutations. This compared to 107 (41.2%) of those with virological failure who had initiated cART with a CD4 count
Published: 2015

40. TRC150094 attenuates progression of nontraditional cardiovascular risk factors associated with obesity and type 2 diabetes in obese ZSF1 rats

Author: ZAMBAD SP, MUNSHI S, DUBEY A, GUPTA R, BUSIELLO RA, GOGLIA F, GUPTA RC, CHAUTHAIWALE V, DUTT C., LANNI, Antonia, Zambad, Sp, Munshi, S, Dubey, A, Gupta, R, Busiello, Ra, Lanni, Antonia, Goglia, F, Gupta, Rc, Chauthaiwale, V, and Dutt, C.
Subjects: Pharmacology, obesity, TRC150094, CV risk factors, energy expenditure, Internal Medicine, CV risk factor, type 2 diabetes, Targets and Therapy [Diabetes, Metabolic Syndrome and Obesity], Type 2 diabete, fatty acid oxidation, Original Research
Abstract: Shitalkumar P Zambad1, Siralee Munshi2, Amita Dubey3, Ram Gupta1, Rosa Anna Busiello4, Antonia Lanni5, Fernando Goglia6, Ramesh C Gupta7, Vijay Chauthaiwale8, Chaitanya Dutt91Pharmacology, 2Cellular and Molecular Biology, 3Pre-clinical and Safety Evaluation, Torrent Research Centre, Torrent Pharmaceuticals Ltd, Gujarat, India; 4Dipartimento di Biologia, Universita degli Studi di Napoli Federico II, Naples, Italy; 5Dipartimento di Scienze della Vita, Seconda Universita di Napoli, Caserta, Italy; 6Dipartimento di Scienze Biologiche ed Ambientali, Universita del Sannio, Benevento, Italy; 7Medicinal Chemistry, 8Discovery Research, 9Clinical Research, Torrent Research Centre, Torrent Pharmaceuticals Ltd, Gujarat, IndiaAbstract: Chronic overnutrition and consequential visceral obesity is associated with a cluster of risk factors for cardiovascular disease and type 2 diabetes mellitus. Moreover, individuals who have a triad of hypertension, dysglycemia, and elevated triglycerides along with reduced high-density lipoprotein cholesterol have a greater residual cardiovascular risk even after factoring for the traditional risk factors such as age, smoking, diabetes, and elevated low-density lipoprotein cholesterol. In our previous study we demonstrated that TRC150094, when administered to rats receiving a high-fat diet, stimulated mitochondrial fatty acid oxidation (FAO) and reduced visceral adiposity, opening an interesting perspective for a possible clinical application. In the present study, oral administration of TRC150094 to obese Zucker spontaneously hypertensive fatty rats (obese ZSF1) improved glucose tolerance and glycemic profile as well as attenuated a rise in blood pressure. Obese ZSF1 rats treated with TRC150094 also showed reduced hepatic steatosis, reduced progression of nephropathy, and improved skeletal muscle function. At the cellular level, TRC150094 induced a significant increase in mitochondrial respiration as well as an increased FAO in liver and skeletal muscle, ultimately resulting in reduced hepatic as well as total body fat accumulation, as evaluated by magnetic resonance spectroscopy and magnetic resonance imaging, respectively. If reproduced in humans, these results could confirm that TRC150094 may represent an attractive therapeutic agent to counteract multiple residual cardiovascular risk components.Keywords: CV risk factors, energy expenditure, fatty acid oxidation, obesity, TRC150094, type 2 diabetes
Published: 2011

41. Incomplete Reversibility of Estimated Glomerular Filtration Rate Decline Following Tenofovir Disoproxil Fumarate Exposure

Author: Jose, Sophie, Hamzah, Lisa, Campbell, Lucy J., Hill, Teresa, Fisher, Martin, Leen, Clifford, Gilson, Richard, Walsh, John, Nelson, Mark, Hay, Phillip, Johnson, Margaret, Chadwick, David, Nitsch, Dorothea, Jones, Rachael, Sabin, Caroline A., Post, Frank A., Ainsworth, Jonathan, Anderson, Jane, Babiker, Abdel, Delpech, Valerie, Dunn, David, Gazzard, Brian, Gompels, Mark, Kegg, Stephen, Orkin, Chloe, Palfreeman, Adrian, Phillips, Andrew, Pillay, Deenan, Post, Frank, Sabin, Caroline, Sachikonye, Memory, Schwenk, Achim, Huntington, Susie, Josie, Sophie, Thornton, Alicia, Glabay, Adam, Orkin, C., Garrett, N., Lynch, J., Hand, J., de Souza, C., Fisher, M., Perry, N., Tilbury, S., Churchill, D., Gazzard, B., Nelson, M., Waxman, M., Asboe, D., Mandalia, S., Delpech, V., Anderson, J., Munshi, S., Korat, H., Poulton, M., Taylor, C., Gleisner, Z., Campbell, L., Gilson, R., Brima, N., Williams, I., Schwenk, A., Ainsworth, J., Wood, C., Miller, S., Johnson, M., Youle, M., Lampe, F., Smith, C., Grabowska, H., Chaloner, C., Puradiredja, D., Walsh, J., Weber, J., Ramzan, F., Mackie, N., Winston, A., Leen, C., Wilson, A., Gompels, M., Allan, S., Palfreeman, A., Moore, A., Chadwick, D., Wakeman, K., Main, Paul, Mitchell, Hunter, and Dhillon, Mandip
Subjects: Adult, Male, eGFR slopes, kidney, Anti-HIV Agents, Adenine, renal function, Organophosphonates, HIV Infections, highly active antiretroviral therapy, Middle Aged, Viral Load, tenofovir, Drug Administration Schedule, Cohort Studies, Major Articles and Brief Reports, eGFR, HIV/AIDS, Humans, Female, Kidney Diseases, Glomerular Filtration Rate, Proportional Hazards Models
Abstract: Background. Tenofovir disoproxil fumarate (TDF) has been linked to renal impairment, but the extent to which this impairment is reversible is unclear. We aimed to investigate the reversibility of renal decline during TDF therapy. Methods. Cox proportional hazards models assessed factors associated with discontinuing TDF in those with an exposure duration of >6 months. In those who discontinued TDF therapy, linear piecewise regression models estimated glomerular filtration rate (eGFR) slopes before initiation of, during, and after discontinuation of TDF therapy. Factors associated with not achieving eGFR recovery 6 months after discontinuing TDF were assessed using multivariable logistic regression. Results. We observed declines in the eGFR during TDF exposure (mean slopes, −15.7 mL/minute/1.73 m2/year [95% confidence interval {CI}, −20.5 to −10.9] during the first 3 months and −3.1 mL/minute/1.73 m2/year [95% CI, −4.6 to −1.7] thereafter) and evidence of eGFR increases following discontinuation of TDF therapy (mean slopes, 12.5 mL/minute/1.73 m2/year [95% CI, 8.9–16.1] during the first 3 months and 0.8 mL/minute/1.73 m2/year [95% CI, .1–1.5] thereafter). Following TDF discontinuation, 38.6% of patients with a decline in the eGFR did not experience recovery. A higher eGFR at baseline, a lower eGFR after discontinuation of TDF therapy, and more-prolonged exposure to TDF were associated with an increased risk of incomplete recovery 6 months after discontinuation of TDF therapy. Conclusions. This study shows that a decline in the eGFR during TDF therapy was not fully reversible in one third of patients and suggests that prolonged TDF exposure at a low eGFR should be avoided.
Published: 2014

42. A deep learning framework using convolution neural network for classification of impulse fault patterns in transformers with increased accuracy

Author: Dey, D., primary, Chatterjee, B., additional, Dalai, S., additional, Munshi, S., additional, and Chakravorti, S., additional
Published: 2017
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43. Some new Plant Plant Records of Nagpur Region India

Author: Paradkar, S A, Munshi, S K, and BioStor
Published: 1979

44. A simplified protocol for differentiation of electrophysiologically mature neuronal networks from human induced pluripotent stem cells

Author: Gunhanlar, N, primary, Shpak, G, additional, van der Kroeg, M, additional, Gouty-Colomer, L A, additional, Munshi, S T, additional, Lendemeijer, B, additional, Ghazvini, M, additional, Dupont, C, additional, Hoogendijk, W J G, additional, Gribnau, J, additional, de Vrij, F M S, additional, and Kushner, S A, additional
Published: 2017
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45. Cytogenetic Studies on Primary Trisomics of Plantago lanceolata

Author: A Munshi, S Sareen, A Langer and A K Koul
Subjects: lcsh:Q, lcsh:Science
Abstract: Cytogenetic Studies on Primary Trisomics of Plantago lanceolata
Published: 2015

46. Opportunistic infections and AIDS malignancies early after initiating combination antiretroviral therapy in high-income countries

Author: Lodi, Sara, Del Amo, Julia, Moreno, Santiago, Bucher, H. C., Furrer, Hansjakob, Logan, Roger, Sterne, Jonathan, Pérez-Hoyos, Santiago, Jarrín, Inma, Phillips, Andrew, Olson, Ashley, Van Sighem, Ard, Reiss, Peter, Sabin, C., Jose, Sophie, Justice, Amy, Goulet, Joseph, Miró, José M., Ferrer, Elena, Meyer, Laurence, Seng, Rémonie, Vourli, Georgia, Antoniadou, Anastasia, Dabis, Francois, Vandenhede, Mari Anne, Costagliola, Dominique, Abgrall, S., Hernán, Miguel A., Hernan, Miguel, Bansi, L., Hill, T., Dunn, D., Porter, K., Glabay, A., Orkin, C., Thomas, R., Jones, K., Fisher, M., Perry, N., Pullin, A., Churchill, D., Gazzard, B., Nelson, M., Asboe, D., Bulbeck, S., Mandalia, S., Clarke, J., Delpech, V., Anderson, J., Munshi, S., Post, F., Easterbrook, P., Khan, Y., Patel, P., Karim, F., Duffell, S., Gilson, R., Man, S. L., Williams, I., Gompels, M., Dooley, D., Schwenk, A., Ainsworth, J., Johnson, M., Youle, M., Lampe, F., Smith, C., Grabowska, H., Chaloner, C., Ismajani Puradiredja, D., Phillips, A., Walsh, J., Weber, J., Kemble, C., Mackie, N., Winston, A., Leen, C., Wilson, A., Bezemer, D. O., Gras, L. A.J., Kesselring, A. M., Van Sighem, A. I., Zaheri, S., Van Twillert, G., Kortmann, W., Branger, J., Prins, J. M., Kuijpers, T. W., Scherpbier, H. J., Van Der Meer, J. T.M., Wit, F. W.M.N., Godfried, M. H., Reiss, P., Van Der Poll, T., Nellen, F. J.B., Lange, J. M.A., Geerlings, S. E., Van Vugt, M., Pajkrt, D., Bos, J. C., Van Der Valk, M., Grijsen, M. L., Wiersinga, W. J., Brinkman, K., Blok, W. L., Frissen, P. H.J., Schouten, W. E.M., Van Den Berk, G. E.L., Veenstra, J., Lettinga, K. D., Mulder, J. W., Vrouenraets, S. M.E., Lauw, F. N., Van Eeden, A., Verhagen, D. W.M., Van Agtmael, M. A., Perenboom, R. M., Claessen, F. A.P., Bomers, M., Peters, E. J.G., Richter, C., Van Der Berg, J. P., Gisolf, E. H., Schippers, E. F., Van Nieuwkoop, C., Van Elzakker, E. P., Leyten, E. M.S., Gelinck, L. B.S., Pronk, M. J.H., Bravenboer, B., Kootstra, G. J., Delsing, C. E., Sprenger, H. G., Doedens, R., Scholvinck, E. H., Van Assen, S., Bierman, W. F.W., Soetekouw, R., Ten Kate, R. W., Van Vonderen, M. G.A., Van Houte, D. P.F., Kroon, F. P., Van Dissel, J. T., Arend, S. M., De Boer, M. G.J., Jolink, H., Ter Vollaard, H. J.M., Bauer, M. P., Weijer, S., El Moussaoui, R., Lowe, S., Schreij, G., Oude Lashof, A., Posthouwer, D., Koopmans, P. P., Keuter, M., Van Der Ven, A. J.A.M., Ter Hofstede, H. J.M., Dofferhoff, A. S.M., Warris, A., Van Crevel, R., Van Der Ende, M. E., De Vries-Sluijs, T. E.M.S., Schurink, C. A.M., Nouwen, J. L., Nispen Tot Pannerden, M. H., Verbon, A., Rijnders, B. J.A., Van Gorp, E. C.M., Hassing, R. J., Smeulders, A. W.M., Hartwig, N. G., Driessen, G. J.A., Den Hollander, J. G., Pogany, K., Juttmann, J. R., Van Kasteren, M. E.E., Hoepelman, A. I.M., Mudrikova, T., Schneider, M. M.E., Jaspers, C. A.J.J., Ellerbroek, P. M., Oosterheert, J. J., Arends, J. E., Wassenberg, M. W.M., Barth, R. E., Geelen, S. P.M., Wolfs, T. F.W., Bont, L. J., Van Den Berge, M., Stegeman, A., Groeneveld, P. H.P., Alleman, M. A., Bouwhuis, J. W., Barin, F., Burty, C., Duvivier, C., Enel, P., Fredouille-Heripret, L., Gasnault, J., Khuong, M. A., Mahamat, A., Pilorgé, F., Tattevin, P., Salomon, Valérie, Jacquemet, N., Costagliola, D., Grabar, S., Guiguet, M., Lanoy, E., Lièvre, L., Mary-Krause, M., Selinger-Leneman, H., Lacombe, J. M., Potard, V., Bricaire, F., Herson, S., Katlama, C., Simon, A., Desplanque, N., Girard, P. M., Meynard, J. L., Meyohas, M. C., Picard, O., Cadranel, J., Mayaud, C., Pialoux, G., Clauvel, J. P., Decazes, J. M., Gérard, L., Molina, J. M., Diemer, M., Sellier, P., Bentata, M., Honoré, P., Jeantils, V., Tassi, S., Mechali, D., Taverne, B., Bouvet, E., Crickx, B., Ecobichon, J. L., Matheron, S., Picard-Dahan, C., Yeni, P., Berthé, H., Dupont, C., Chandemerle, C., Mortier, E., De Truchis, P., Tisne-Dessus, D., Weiss, L., Salmon, D., Auperin, I., Gilquin, J., Roudière, L., Viard, J. P., Boue, F., Fior, R., Delfraissy, J. F., Goujard, C., Jung, C., Lesprit, Ph, Vittecoq, D., Fraisse, P., Lang, J. M., Rey, D., Beck-Wirth, G., Stahl, J. P., Lecercq, P., Gourdon, F., Laurichesse, H., Fresard, A., Lucht, F., Bazin, C., Verdon, R., Chavanet, P., Arvieux, C., Michelet, C., Choutet, P., Goudeau, A., Maître, M. F., Hoen, B., Eglinger, P., Faller, J. P., Borsa-Lebas, F., Caron, F., Reynes, J., Daures, J. P., May, T., Rabaud, C., Berger, J. L., Rémy, G., Arlet-Suau, E., Cuzin, L., Massip, P., Thiercelin Legrand, M. F., Pontonnier, G., Viget, N., Yasdanpanah, Y., Dellamonica, P., Pradier, C., Pugliese, P., Aleksandrowicz, K., Quinsat, D., Ravaux, I., Tissot-Dupont, H., Delmont, J. P., Moreau, J., Gastaut, J. A., Poizot Martin, I., Retornaz, F., Soubeyrand, J., Galinier, A., Ruiz, J. M., Allegre, T., Blanc, P. A., Bonnet-Montchardon, D., Lepeu, G., Granet-Brunello, P., Esterni, J. P., Pelissier, L., Cohen-Valensi, R., Nezri, M., Chadapaud, S., Laffeuillade, A., Billaud, E., Raffi, F., Boibieux, A., Peyramond, D., Livrozet, J. M., Touraine, J. L., Cotte, L., Trepo, C., Strobel, M., Bissuel, F., Pradinaud, R., Sobesky, M., Cabié, A., Gaud, C., Contant, M., Aubert, V., Barth, J., Battegay, M., Bernasconi, E., Böni, J., Burton-Jeangros, C., Calmy, A., Cavassini, M., Egger, M., Elzi, L., Fehr, J., Fellay, J., Furrer, H., Haerry, D., Fux, C. A., Gorgievski, M., Günthard, H., Hasse, B., Hirsch, H. H., Hösli, I., Kahlert, C., Kaiser, L., Keiser, O., Klimkait, T., Kovari, H., Ledergerber, B., Martinetti, G., Martinez De Tejada, B., Metzner, K., Müller, N., Nadal, D., Pantaleo, G., Rauch, A., Regenass, S., Rickenbach, M., Rudin, C., Schmid, P., Schultze, D., Schöni-Affolter, F., Schüpbach, J., Speck, R., Taffé, P., Tarr, P., Telenti, A., Trkola, A., Vernazza, P., Weber, R., Yerly, S., Casabona, J., Gallois, A., Esteve, A., Podzamczer, D., Murillas, J., Gatell, J. M., Manzardo, C., Tural, C., Clotet, B., Ferrer, E., Riera, M., Segura, F., Navarro, G., Force, L., Vilaró, J., Masabeu, A., García, I., Guadarrama, M., Cifuentes, C., Dalmau, D., Jaen, Agustí, C., Montoliu, A., Pérez, I., Gargoulas, Freyra, Blanco, J. L., Garcia-Alcaide, F., Martínez, E., Mallolas, J., López-Dieguez, M., García-Goez, J. F., Sirera, G., Romeu, J., Jou, A., Negredo, E., Miranda, C., Capitan, M. C., Saumoy, M., Imaz, A., Tiraboschi, J. M., Murillo, O., Bolao, F., Peña, C., Cabellos, C., Masó, M., Vila, A., Sala, M., Cervantes, M., Jose Amengual, Ma, Navarro, M., Penelo, E., Barrufet, P., Bejarano, G., Molina, J., Alvaro, M., Mercadal, J., Fernandez, Juanse, Ospina, Jesus E., Muñoz, M. A., Caro-Murillo, A. M., Sobrino, P., Jarrín, I., Gomez Sirvent, J. L., Rodríguez, P., Aleman, M. R., Alonso, M. M., Lopez, A. M., Hernandez, M. I., Soriano, V., Labarga, P., Barreiro, P., Medrano, J., Rivas, P., Herrero, D., Blanco, F., Vispo, M. E., Martín, L., Ramírez, G., De Diego, M., Rubio, R., Pulido, F., Moreno, V., Cepeda, C., Hervás, Rl, Iribarren, J. A., Arrizabalaga, J., Aramburu, M. J., Camino, X., Rodrí-guez-Arrondo, F., Von Wichmann, M. A., Pascual, L., Goenaga, M. A., Gutierrez, F., Masia, M., Ramos, J. M., Padilla, S., Sanchez-Hellín, V., Bernal, E., Escolano, C., Montolio, F., Peral, Y., Berenguer, J., Lopez, J. C., Miralles, P., Cosín, J., Sanchez, M., Gutierrez, I., Ramírez, M., Padilla, B., Vidal, F., Sanjuan, M., Peraire, J., Veloso, S., Vilades, C., Lopez-Dupla, M., Olona, M., Vargas, M., Aldeguer, J. L., Blanes, M., Lacruz, J., Salavert, M., Montero, M., Cuéllar, S., De Los Santos, I., Sanz, J., Oteo, J. A., Blanco, J. R., Ibarra, V., Metola, L., Sanz, M., Pérez-Martínez, L., Sola, J., Uriz, J., Castiello, J., Reparaz, J., Arriaza, M. J., Irigoyen, C., Moreno, S., Antela, A., Casado, J. L., Dronda, F., Moreno, A., Pérez, M. J., López, D., Gutiérrez, C., Hernández, B., Pumares, M., Martí, P., García, L., Page, C., García, F., Hernández, J., Peña, A., Muñoz, L., Parra, J., Viciana, P., Leal, M., López-Cortés, L. F., Trastoy, M., Mata, R., Justice, A. C., Fiellin, D. A., Rimland, D., Jones-Taylor, C., Oursler, K. A., Titanji, R., Brown, S., Garrison, S., Rodriguez-Barradas, M., Masozera, N., Goetz, M., Leaf, D., Simberkoff, M., Blumenthal, D., Leung, J., Butt, A., Hoffman, E., Gibert, C., Peck, R., Mattocks, K., Braithwaite, S., Brandt, C., Bryant, K., Cook, R., Conigliaro, J., Crothers, K., Chang, J., Crystal, S., Day, N., Erdos, J., Freiberg, M., Kozal, M., Gandhi, N., Gaziano, M., Gerschenson, M., Good, B., Gordon, A., Goulet, J. L., Hernán, M. A., Kraemer, K., Lim, J., Maisto, S., Miller, P., Mole, L., O'Connor, P., Papas, R., Robins, J. M., Rinaldo, C., Roberts, M., Samet, J., Tierney, B., Whittle, J., Babiker, A., Brettle, R., Darbyshire, J., Goldberg, D., Hawkins, D., Jaffe, H., Johnson, A., McLean, K., Pillay, D., Cursley, Adam, Ewings, Fiona, Fairbrother, Keith, Louisa Gnatiuc, S. L., Murphy, Brendan, Douglas, G., Kennedy, N., Pritchard, J., Andrady, U., Rajda, N., Maw, R., McKernan, S., Drake, S., Gilleran, G., White, D., Ross, J., Toomer, S., Hewart, R., Wilding, H., Woodward, R., Dean, G., Heald, L., Horner, P., Glover, S., Bansaal, D., Eduards, S., Carne, C., Browing, M., Das, R., Stanley, B., Estreich, S., Magdy, A., O'Mahony, C., Fraser, P., Hayman, B., Jebakumar, S. P.R., Joshi, U., Ralph, S., Wade, A., Mette, R., Lalik, J., Summerfield, H., El-Dalil, A., France, J. A., White, C., Robertson, R., Gordon, S., McMillan, S., Morris, S., Lean, C., Vithayathil, K., McLean, L., Winter, A., Gale, D., Jacobs, S., Tayal, S., Short, L., Green, S., Williams, G., Sivakumar, K., Bhattacharyya, N. D., Monteiro, E., Minton, J., Dhar, J., Nye, F., De Souza, C. B., Isaksen, A., McDonald, L., Franca, A., William, L., Jendrulek, I., Peters, B., Shaunak, S., El-Gadi, S., Easterbrook, P. J., Mazhude, C., Johnstone, R., Fakoya, A., McHale, J., Waters, A., Kegg, S., Mitchell, S., Byrne, P., Rice, P., Fidler, S., Mullaney, S. A., McCormack, S., David, D., Melville, R., Phillip, K., Balachandran, T., Mabey-Puttock, S., Sukthankar, A., Murphy, C., Wilkins, E., Ahmad, S., Haynes, J., Evans, E., Ong, E., Grey, R., Meaden, J., Bignell, C., Loay, D., Peacock, K., Girgis, M. R., Morgan, B., Palfreeman, A., Wilcox, J., Tobin, J., Tucker, L., Saeed, A. M., Chen, F., Deheragada, A., Williams, O., Lacey, H., Herman, S., Kinghorn, D., Devendra, V. S., Wither, J., Dawson, S., Rowen, D., Harvey, J., Bridgwood, A., Singh, G., Chauhan, M., Kellock, D., Young, S., Dannino, S., Kathir, Y., Rooney, G., Currie, J., FitzGerald, M., Devendra, S., Keane, F., Booth, G., Green, T., Arumainayyagam, J., Chandramani, S., Rajamanoharan, S., Robinson, T., Curless, E., Gokhale, R., Tariq, A., Luzzi, G., Fairley, I., Wallis, F., Smit, E., Ward, F., Loze, B., Morlat, P., Bonarek, M., Bonnet, F., Nouts, C., Louis, I., Reliquet, V., Sauser, F., Biron, C., Mounoury, O., Hue, H., Brosseau, D., Ghosn, J., Rannou, M. T., Bergmann, J. F., Badsi, E., Rami, A., Parrinello, M., Samanon-Bollens, D., Campa, P., Tourneur, M., Desplanques, N., Jeanblanc, F., Chiarello, P., Makhloufi, D., Blanc, A. 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A., Guerrero, R., Rivera, E., Marco, A., Quintana, M., Gonzalez, C., Castilla, J., Guevara, M., De Mendoza, C., Zahonero, N., Ortíz, M., Paraskevis, D., Touloumi, G., Pantazis, N., Bakoyannis, G., Gioukari, V., Antoniadou, A., Papadopoulos, A., Petrikkos, G., Daikos, G., Psichogiou, M., Gargalianos-Kakolyris, P., Xylomenos, G., Katsarou, O., Kouramba, A., Ioannidou, P., Kordossis, T., Kontos, A., Lazanas, M., Chini, M., Tsogas, N., Panos, G., Paparizos, V., Leuow, K., Kourkounti, S., Sambatakou, H., Mariolis, I., Skoutelis, A., Papastamopoulos, V., Baraboutis, I., Internal medicine, APH - Aging & Later Life, Pediatric surgery, CCA - Innovative therapy, ICaR - Circulation and metabolism, ICaR - Ischemia and repair, Graduate School, Paediatric Infectious Diseases / Rheumatology / Immunology, Landsteiner Laboratory, AII - Amsterdam institute for Infection and Immunity, Infectious diseases, Global Health, Center of Experimental and Molecular Medicine, APH - Amsterdam Public Health, AII - Inflammatory diseases, and ARD - Amsterdam Reproduction and Development
Subjects: Adult, Male, medicine.medical_specialty, Adolescent, Opportunistic infection, AIDS-Related Opportunistic Infections, Immunology, Population, Retinitis, HIV Infections, Article, 17 Psychology And Cognitive Sciences, Young Adult, Immune reconstitution inflammatory syndrome, Antiretroviral Therapy, Highly Active, Neoplasms, Virology, Internal medicine, medicine, Humans, Immunology and Allergy, education, Inverse probability weighting, Aged, education.field_of_study, business.industry, Developed Countries, Incidence, Progressive multifocal leukoencephalopathy, Hazard ratio, HIV, virus diseases, 11 Medical And Health Sciences, Middle Aged, 06 Biological Sciences, medicine.disease, United States, Europe, Infectious Diseases, Anti-Retroviral Agents, Unmasking, Female, Cytomegalovirus retinitis, business
Abstract: Background: There is little information on the incidence of AIDS-defining events which have been reported in the literature to be associated with immune reconstitution inflammatory syndrome (IRIS) after combined antiretroviral therapy (cART) initiation. These events include tuberculosis, mycobacterium avium complex (MAC), cytomegalovirus (CMV) retinitis, progressive multifocal leukoencephalopathy (PML), herpes simplex virus (HSV), Kaposi sarcoma, non-Hodgkin lymphoma (NHL), cryptococcosis and candidiasis.Methods: We identified individuals in the HIV-CAUSAL Collaboration, which includes data from six European countries and the US, who were HIV-positive between 1996 and 2013, antiretroviral therapy naive, aged at least 18 years, hadCD4+ cell count and HIV-RNA measurements and had been AIDS-free for at least 1 month between those measurements and the start of follow-up. For each AIDS-defining event, we estimated the hazard ratio for no cART versus less than 3 and at least 3 months since cART initiation, adjusting for time-varying CD4+ cell count and HIV-RNA via inverse probability weighting.Results: Out of 96 562 eligible individuals (78% men) with median (interquantile range) follow-up of 31 [13,65] months, 55 144 initiated cART. The number of cases varied between 898 for tuberculosis and 113 for PML. Compared with non-cART initiation, the hazard ratio (95% confidence intervals) up to 3 months after cART initiation were 1.21 (0.90-1.63) for tuberculosis, 2.61 (1.05-6.49) for MAC, 1.17 (0.34-4.08) for CMV retinitis, 1.18 (0.62-2.26) for PML, 1.21 (0.83-1.75) for HSV, 1.18 (0.87-1.58) for Kaposi sarcoma, 1.56 (0.82-2.95) for NHL, 1.11 (0.56-2.18) for cryptococcosis and 0.77 (0.40-1.49) for candidiasis.Conclusion: With the potential exception of mycobacterial infections, unmasking IRIS does not appear to be a common complication of cART initiation in high-income countries.
Published: 2014

47. Opportunistic infections and AIDS malignancies early after initiating combination antiretroviral therapy in high-income countries

Author: Lodi, S. Del Amo, J. Moreno, S. Bucher, H.C. Furrer, H. Logan, R. Sterne, J. Pérez-Hoyos, S. Jarrín, I. Phillips, A. Olson, A. Van Sighem, A. Reiss, P. Sabin, C. Jose, S. Justice, A. Goulet, J. Miró, J.M. Ferrer, E. Meyer, L. Seng, R. Vourli, G. Antoniadou, A. Dabis, F. Vandenhede, M.-A. Costagliola, D. Abgrall, S. Hernán, M.A. Hernan, M. Bansi, L. Hill, T. Sabin, C. Dunn, D. Porter, K. Glabay, A. Orkin, C. Thomas, R. Jones, K. Fisher, M. Perry, N. Pullin, A. Churchill, D. Gazzard, B. Nelson, M. Asboe, D. Bulbeck, S. Mandalia, S. Clarke, J. Delpech, V. Anderson, J. Munshi, S. Post, F. Easterbrook, P. Khan, Y. Patel, P. Karim, F. Duffell, S. Gilson, R. Man, S.-L. Williams, I. Gompels, M. Dooley, D. Schwenk, A. Ainsworth, J. Johnson, M. Youle, M. Lampe, F. Smith, C. Grabowska, H. Chaloner, C. Ismajani Puradiredja, D. Bansi, L. Hill, T. Phillips, A. Sabin, C. Walsh, J. Weber, J. Kemble, C. Mackie, N. Winston, A. Leen, C. Wilson, A. Bezemer, D.O. Gras, L.A.J. Kesselring, A.M. Van Sighem, A.I. Zaheri, S. Van Twillert, G. Kortmann, W. Branger, J. Prins, J.M. Kuijpers, T.W. Scherpbier, H.J. Van Der Meer, J.T.M. Wit, F.W.M.N. Godfried, M.H. Reiss, P. Van Der Poll, T. Nellen, F.J.B. Lange, J.M.A. Geerlings, S.E. Van Vugt, M. Pajkrt, D. Bos, J.C. Van Der Valk, M. Grijsen, M.L. Wiersinga, W.J. Brinkman, K. Blok, W.L. Frissen, P.H.J. Schouten, W.E.M. Van Den Berk, G.E.L. Veenstra, J. Lettinga, K.D. Mulder, J.W. Vrouenraets, S.M.E. Lauw, F.N. Van Eeden, A. Verhagen, D.W.M. Van Agtmael, M.A. Perenboom, R.M. Claessen, F.A.P. Bomers, M. Peters, E.J.G. Richter, C. Van Der Berg, J.P. Gisolf, E.H. Schippers, E.F. Van Nieuwkoop, C. Van Elzakker, E.P. Leyten, E.M.S. Gelinck, L.B.S. Pronk, M.J.H. Bravenboer, B. Kootstra, G.J. Delsing, C.E. Sprenger, H.G. Doedens, R. Scholvinck, E.H. Van Assen, S. Bierman, W.F.W. Soetekouw, R. Ten Kate, R.W. Van Vonderen, M.G.A. Van Houte, D.P.F. Kroon, F.P. Van Dissel, J.T. Arend, S.M. De Boer, M.G.J. Jolink, H. Ter Vollaard, H.J.M. 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Waters, A. Kegg, S. Mitchell, S. Byrne, P. Johnson, M. Rice, P. Fidler, S. Mullaney, S.A. McCormack, S. David, D. Melville, R. Phillip, K. Balachandran, T. Mabey-Puttock, S. Sukthankar, A. Murphy, C. Wilkins, E. Ahmad, S. Tayal, S. Haynes, J. Evans, E. Ong, E. Das, R. Grey, R. Meaden, J. Bignell, C. Loay, D. Peacock, K. Girgis, M.R. Morgan, B. Palfreeman, A. Wilcox, J. Tobin, J. Tucker, L. Saeed, A.M. Chen, F. Deheragada, A. Williams, O. Lacey, H. Herman, S. Kinghorn, D. Devendra, V.S. Wither, J. Dawson, S. Rowen, D. Harvey, J. Wilkins, E. Bridgwood, A. Singh, G. Chauhan, M. Kellock, D. Young, S. Dannino, S. Kathir, Y. Rooney, G. Currie, J. Fitzgerald, M. Devendra, S. Keane, F. Booth, G. Green, T. Arumainayyagam, J. Chandramani, S. Rajamanoharan, S. Robinson, T. Curless, E. Gokhale, R. Tariq, A. Roberts, M. Williams, O. Luzzi, G. FitzGerald, M. Fairley, I. Wallis, F. Smit, E. Ward, F. Molina, J.M. Loze, B. Morlat, P. Bonarek, M. Bonnet, F. Nouts, C. Louis, I. Raffi, F. Reliquet, V. Sauser, F. Biron, C. Mounoury, O. Hue, H. Brosseau, D. Delfraissy, J.F. Goujard, C. Ghosn, J. Rannou, M.T. Bergmann, J.F. Badsi, E. Rami, A. Diemer, M. Parrinello, M. Girard, P.M. Samanon-Bollens, D. Campa, P. Tourneur, M. Desplanques, N. Livrozet, J.M. Jeanblanc, F. Chiarello, P. Makhloufi, D. Blanc, A.P. Allègre, T. Reynes, J. Baillat, V. Lemoing, V. Merle De Boever, C. Tramoni, C. Cabié, A. Sobesky, G. Abel, S. Beaujolais, V. Pialoux, G. Slama, L. Chakvetadze, C. Berrebi, V. Yeni, P. Bouvet, E. Fournier, I. Gerbe, J. Trepo, C. Koffi, K. Augustin-Normand, C. Miailhes, P. Thoirain, V. Brochier, C. Thomas, R. Souala, F. Ratajczak, M. Beytoux, J. Jacomet, C. Gourdon, F. Rouveix, E. Morelon, S. Dupont, C. Olivier, C. Lortholary, O. Dupont, B. Viard, J.P. Maignan, A. Ragnaud, J.M. Raymond, I. Leport, C. Jadand, C. Jestin, C. Longuet, P. Boucherit, S. Sereni, D. Lascoux, C. Prevoteau, F. Sobel, A. Levy, Y. Lelièvre, J.D. Lascaux, A.S. Dominguez, S. Dumont, C. Aumâitre, H. Delmas, B. Saada, M. Medus, M. Guillevin, L. Salmon, D. Tahi, T. Yazdanpanah, Y. Pavel, S. Marien, M.C. Drenou, B. Beck-Wirth, G. Beck, C. Benomar, M. Katlama, C. Tubiana, R. Ait Mohand, H. Chermak, A. Ben Abdallah, S. Bentata, M. Touam, F. Hoen, B. Drobacheff, C. Folzer, A. Massip, P. Obadia, M. Prudhomme, L. Bonnet, E. Balzarin, F. Pichard, E. Chennebault, J.M. Fialaire, P. Loison, J. Galanaud, P. Boué, F. Bornarel, D. Verdon, R. Bazin, C. Six, M. Ferret, P. Weiss, L. Batisse, D. Gonzales-Canali, G. Tisne-Dessus, D. Devidas, A. Chevojon, P. Turpault, I. Lafeuillade, A. Cheret, A. Philip, G. Morel, P. Timsit, J. Herson, S. Amirat, N. Simon, A. Brancion, C. Cabane, J. Picard, O. Tredup, J. Stein, A. Ravault, I. Chavanet, C. Buisson, M. Treuvetot, S. Choutet, P. Nau, P. Bastides, F. May, T. Boyer, L. Wassoumbou, S. Oksenhendeler, E. Gérard, L. Bernard, L. De Truchis, P. Berthé, H. Domart, Y. Merrien, D. Greder Belan, A. Gayraud, M. Bodard, L. Meudec, A. Beuscart, C. Daniel, C. Pape, E. Vinceneux, P. Simonpoli, A.M. Zeng, A. Fournier, L. Fuzibet, J.G. Sohn, C. Rosenthal, E. Quaranta, M. Dellamonica, P. Chaillou, S. Sabah, M. Audhuy, B. Schieber, A. Moreau, P. Niault, M. Vaillant, O. Huchon, G. Compagnucci, A. De Lacroix Szmania, I. Richier, L. Lamaury, I. Saint-Dizier, F. Garipuy, D. Gastaut, J.A. Drogoul, M.P. Poizot Martin, I. Fabre, G. Lambert De Cursay, G. Abraham, B. Perino, C. Lagarde, P. David, F. Roche-Sicot, J. Saraux, J.L. Leprêtre, A. Fampin, B. Uludag, A. Morin, A.S. Bletry, O. Zucman, D. Regnier, A. Girard, J.J. Quinsat, D.T. Heripret, L. Grihon, F. Houlbert, D. Ruel, M. Chemlal, K. Caron, F. Debab, Y. Tremollieres, F. Perronne, V. Lepeu, G. Slama, B. Perré, P. Miodovski, C. Guermonprez, G. Dulioust, A. Boudon, P. Malbec, D. Patey, O. Semaille, C. Deville, J. Remy, G. Béguinot, I. Galanaud, P. Boue, F. Chambrin, V. Pignon, C. Estocq, G.A. Levy, A. Delfraissy, J.F. Goujard, C. Duracinsky, M. Le Bras, P. Ngussan, M.S. Peretti, D. Medintzeff, N. Lambert, T. Segeral, O. Lezeau, P. Laurian, Y. Weiss, L. Buisson, M. Piketty, C. Karmochkine, M. Batisse, D. Eliaszewitch, M. Jayle, D. Tisne-Dessus, D. Kazatchkine, M. Leport, C. Colasante, U. Jadand, C. Jestin, C. Duval, X. Nouaouia, W. Boucherit, S. Vilde, J.L. Girard, P.M. Bollens, D. Binet, D. Diallo, B. Meyohas, M.C. Fonquernie, L. Lagneau, J.L. Salmon, D. Guillevin, L. Tahi, T. Launay, O. Pietrie, M.P. Sicard, D. Stieltjes, N. Michot, J. Sobel, A. Levy, Y. Bourdillon, F. Lascaux, A.S. Lelievre, J.D. Dumont, C. Dupont, B. Obenga, G. Viard, J.P. Maignan, A. Vittecoq, D. Escaut, L. Bolliot, C. Bricaire, F. Katlama, C. Schneider, L. Herson, S. Simon, A. Iguertsira, M. Stein, A. Tomei, C. Ravaux, I. Dhiver, C. Tissot Dupont, H. Vallon, A. Gallais, J. Gallais, H. Gastaut, J.A. Drogoul, M.P. Fabre, G. Dellamonica, P. Durant, J. Mondain, V. Perbost, I. Cassuto, J.P. Karsenti, J.M. Venti, H. Fuzibet, J.G. Rosenthal, E. Ceppi, C. Quaranta, M. Krivitsky, J.A. Bentata, M. Bouchaud, O. Honore, P. Sereni, D. Lascoux, C. Delgado, J. Rouzioux, C. Burgard, M. Boufassa, L. Peynet, J. Pérez-Hoyos, S. Del Amo, J. Alvarez, D. Monge, S. Muga, R. Sanvisens, A. Clotet, B. Tor, J. Bolao, F. Rivas, I. Vallecillo, G. Del Romero, J. Raposo, P. Rodríguez, C. Vera, M. Hurtado, I. Belda, J. Fernandez, E. Alastrue, I. Santos, C. Tasa, T. Juan, A. Trullen, J. Garcia De Olalla, P. Cayla, J. Masdeu, E. Knobel, H. Mirò, J.M. Sambeat, M.A. Guerrero, R. Rivera, E. Guerrero, R. Marco, A. Quintana, M. Gonzalez, C. Castilla, J. Guevara, M. De Mendoza, C. Zahonero, N. Ortíz, M. Paraskevis, D. Touloumi, G. Pantazis, N. Bakoyannis, G. Gioukari, V. Antoniadou, A. Papadopoulos, A. Petrikkos, G. Daikos, G. Psichogiou, M. Gargalianos-Kakolyris, P. Xylomenos, G. Katsarou, O. Kouramba, A. Ioannidou, P. Kordossis, T. Kontos, A. Lazanas, M. Chini, M. Tsogas, N. Panos, G. Paparizos, V. Leuow, K. Kourkounti, S. Sambatakou, H. Mariolis, I. Skoutelis, A. Papastamopoulos, V. Baraboutis, I. The HIV-CAUSAL Collaboration
Subjects: virus diseases
Abstract: Background: There is little information on the incidence of AIDS-defining events which have been reported in the literature to be associated with immune reconstitution inflammatory syndrome (IRIS) after combined antiretroviral therapy (cART) initiation. These events include tuberculosis, mycobacterium avium complex (MAC), cytomegalovirus (CMV) retinitis, progressive multifocal leukoencephalopathy (PML), herpes simplex virus (HSV), Kaposi sarcoma, non-Hodgkin lymphoma (NHL), cryptococcosis and candidiasis. Methods: We identified individuals in the HIV-CAUSAL Collaboration, which includes data from six European countries and the US, who were HIV-positive between 1996 and 2013, antiretroviral therapy naive, aged at least 18 years, hadCD4+ cell count and HIV-RNA measurements and had been AIDS-free for at least 1 month between those measurements and the start of follow-up. For each AIDS-defining event, we estimated the hazard ratio for no cART versus less than 3 and at least 3 months since cART initiation, adjusting for time-varying CD4+ cell count and HIV-RNA via inverse probability weighting. Results: Out of 96 562 eligible individuals (78% men) with median (interquantile range) follow-up of 31 [13,65] months, 55 144 initiated cART. The number of cases varied between 898 for tuberculosis and 113 for PML. Compared with non-cART initiation, the hazard ratio (95% confidence intervals) up to 3 months after cART initiation were 1.21 (0.90-1.63) for tuberculosis, 2.61 (1.05-6.49) for MAC, 1.17 (0.34-4.08) for CMV retinitis, 1.18 (0.62-2.26) for PML, 1.21 (0.83-1.75) for HSV, 1.18 (0.87-1.58) for Kaposi sarcoma, 1.56 (0.82-2.95) for NHL, 1.11 (0.56-2.18) for cryptococcosis and 0.77 (0.40-1.49) for candidiasis. Conclusion: With the potential exception of mycobacterial infections, unmasking IRIS does not appear to be a common complication of cART initiation in high-income countries. © 2014 Wolters Kluwer Health | Lippincott Williams & Wilkins.
Published: 2014

48. Combination of three rapid tests: An alternative approach to confirmatory laboratory diagnosis of HIV infection in Bangladesh

Author: Munshi, S., Ahmed, J., Ahmed, M., Nessa, A., and Tabassum, S.
Subjects: Enzyme-linked immunosorbent assay -- Health aspects, HIV (Viruses) -- Health aspects, Health
Abstract: Dear Editor, Laboratory diagnosis of human immunodeficiency virus (HIV) infection depends mostly on detection of antibodies against HIV in plasma or serum using a sequential two-test algorithm; Enzyme Linked Immunosorbent [...]
Published: 2009

49. High prevalence of Hepatitis A virus antibody among Bangladeshi children and young adults warrants pre-immunization screening of antibody in HAV vaccination strategy

Author: Ahmed, M., Munshi, S., Nessa, A., Ullah, M., Tabassum, S., and Islam, M.
Subjects: Flexible response (Strategy), Vaccination, Prevalence studies (Epidemiology), Hepatitis A, Immunoglobulins, Deterrence (Strategy), Hepatitis A virus, Health
Abstract: Serum samples from 465 subjects aged between 1 and 25 years were tested for antibody against hepatitis A virus (HAV) [anti-HAV IgG and IgM] to determine the seroprevalence of HAV [...]
Published: 2009

50. HBV, HCV and syphilis co-infections in human immunodeficiency virus positive Bangladeshi patients: Observation at two reference laboratories

Author: Munshi, S., Hoque, M., Mondol, Mea, Jalaluddin, M., Tabassum, S., and Islam, M.
Subjects: HIV (Viruses) -- Care and treatment, HIV (Viruses) -- Health aspects, Syphilis -- Care and treatment, Syphilis -- Health aspects, HIV patients -- Care and treatment, HIV patients -- Health aspects, Hepatitis C -- Care and treatment, Hepatitis C -- Health aspects, Laboratories -- Health aspects, Infection -- Care and treatment, Infection -- Health aspects, Health
Abstract: Dear editor, Human Immunodeficiency Virus (HIV), Hepatitis B virus (HBV), Hepatitis C virus (HCV) and syphilis share certain epidemiological characteristics . In the post highly active antiretroviral therapy (HAART) era, [...]
Published: 2008

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