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1. Building an open source software ecosystem for cross-disciplinary plasma research and education

Author

Murphy, Nicholas A., Stańczak, Dominik, Leonard, Andrew J., Parashar, Tulasi, Kozlowski, Pawel M., Alterman, B. L., Roberts, D. Aaron, Christe, S. D., Conners, Martin, Bobra, Monica, Mason, James Paul, Barnes, Will, McGranaghan, Ryan M., Bhatt, Asti, Erikson, Philip J., Lind, Frank D., Volz, Ryan, Swoboda, John, Hatzigeorgiu, Nick, Inglis, Andrew, deOliveira-Lopes, Felipe Nathan, Ireland, Jack, Coxon, John C., Murray, Sophie A., Yates, Japheth N., Cheung, Mark C. M., Klenzing, Jeff, Stansby, David, He, Han, Huang, Yi-Min, Dong, Chuanfei, Winter, Henry, Buitrago-Casas, Juan-Camilo, Kaur, Manjit, Smith, Sterling, Dudson, Benjamin, Seaton, Daniel B., Comisso, Luca, Halford, Alexa J., Barnak, D. H., Weigel, R. S., Tavant, A., Vandegriff, Jon D., de Val-Borro, Miguel, and Savcheva, Antonia

Subjects
scientific reproducibility, ComputerSystemsOrganization_COMPUTERSYSTEMIMPLEMENTATION, ComputingMethodologies_SIMULATIONANDMODELING, plasma physics, software sustainability, ComputingMethodologies_SYMBOLICANDALGEBRAICMANIPULATION, MathematicsofComputing_NUMERICALANALYSIS, open source scientific software
Abstract

We propose that the plasma physics community and funding agencies invest in an open source software ecosystem for plasma research and education., This community paper was submitted to the Plasma 2020 decadal review of plasma physics., {"references":["D. Muna et al. (2016), \"The Astropy Problem,\" arXiv:1610.03159","Astropy Collaboration et al. (2018), \"The Astropy Project: Building an Open-science Project and Status of the v2.0 Core Package,\" Astronomical Journal 156, 123, doi:10.3847/1538-3881/aabc4f","SunPy Community et al. (2015), \"SunPy – Python for solar physics,\" Computational Science and Discovery 8, 1, doi:10.1088/1749-4699/8/1/014009","A. Burrell et al. (2018), \"Snakes on a Spaceship – An Overview of Python in Heliophysics,\" Journal of Geophysical Research 123, 10384, doi:10.1029/2018JA025877","PlasmaPy Community et al. (2018), \"PlasmaPy: an open source community-developed Python package for plasma physics,\" Zenodo, doi:10.5281/zenodo.1238132","National Academies of Sciences, Engineering, and Medicine, \"Open Source Software Policy Options for NASA Earth and Space Sciences\" (National Academies Press, 2018).","S. Hettrick (2016), \"Research Software Sustainability: Report on a Knowledge Exchange Workshop.\"","Mark D. Wilkinson et al. (2016), \"The FAIR Guiding Principles for scientific data management and stewardship,\" Scientific Data 3, sdata201618, doi:10.1038/sdata.2016.18","Engineering and Physical Sciences Research Council, \"Software as an infrastructure,\" (2012).","G. Wilson et al. (2014), \"Best Practices for Scientific Computing,\" PLOS Biology 12, 1, doi:10.1371/journal.pbio.1001745","A. Scopatz and K. D. Huff, \"Effective Computation in Physics: Field Guide to Research with Python\" (O'Reilly Media, 2015).","B. K. Spears et al. (2018), \"Deep learning: A guide for practitioners in the physical sciences,\" Physics of Plasmas 25, 080901, doi:10.1063/1.5020791","D. R. Smith et al., \"Highlights from the community white paper 'Enhancing US fusion science with data- centric technologies',\" in APS DPP Meeting Abstracts (2018)."]}

Published
2019

2. Variability of growth in children starting antiretroviral treatment in southern Africa

Author

Gsponer T., Weigel R., Davies M. A., Bolton C., Moultrie H., Vaz P., Rabie H., Technau K., Ndirangu J., Eley B., Garone D., Wellington M., Giddy J., Ehmer J., Egger M., Keiser O., and Ie D. E. A. Southern Africa

Abstract

BACKGROUND: Poor growth is an indication for antiretroviral therapy (ART) and a criterion for treatment failure. We examined variability in growth response to ART in 12 programs in Malawi Zambia Zimbabwe Mozambique and South Africa. METHODS: Treatment naive children aged /= 1. For HAZ the corresponding range was 2.33 (95 CI: 2.62 to 2.02) to 1.27 (95 CI: 1.58 to 1.00) for baseline HAZ /= 1. CONCLUSIONS: Despite a sustained growth response and catch up growth in children with advanced HIV disease treated with ART normal weights and heights are not achieved over 3 years of ART.

Published
2013

3. Characteristics of adults and children diagnosed with tuberculosis in Lilongwe, Malawi: findings from an integrated HIV/TB clinic

Author

Feldacker C, Tweya H, Keiser O, Weigel R, Kalulu M, Fenner L, Egger M, Manda E, Mwafilaso J B, Kamba C, and Phiri S

Subjects
Adult, Male, Malawi, Adolescent, Coinfection, Infant, HIV Infections, Middle Aged, Article, Young Adult, Anti-Retroviral Agents, Child, Preschool, HIV Seropositivity, Humans, Tuberculosis, Female, Child, Retrospective Studies
Abstract

Objectives To describe initial registration characteristics of adult and paediatric TB patients at a large public integrated TB and HIV clinic in Lilongwe Malawi between January 2008 and December 2010. Methods Routine data on patient with TB category and TB type stratified by HIV and ART status were used to explore differences in proportions among TB only TB/HIV co infected patients not on ART and TB/HIV co infected patients on ART using chi square tests. Trends over time illustrate strengths and weaknesses of integrated service provision. Results Among 10 143 adults HIV ascertainment and ART uptake were high and increased over time. The proportion of relapse was highest among those on ART (5). The proportion of smear positive pulmonary TB (PTB) was highest among HIV negative patients with TB (34.9); extra pulmonary TB (EPTB) was lowest among TB only (16.2). Among 338 children

Published
2012

4. A biregional survey and review of first-line treatment failure and second-line paediatric antiretroviral access and use in Asia and southern Africa

Author

Saphonn, V., Saramony, S., Vibol, U., Sophan, S., Tucker, J., Zhang, F. J., Han, N., Kumarasamy, N., Saghayam, S., Kurniati, N., Muktiarti, D., Fong, S. M., Thien, M., Yusoff, N. K. N., Hai, L. C., Razali, K., Rahman, N. F. A., Nallusamy, R., Chan, K. C., Sirisanthana, V., Aurpibul, L., Hansudewechakul, R., Khongponoi, A., Lumbiganon, P., Kosalaraksa, P., Jourdain, Gonzague, Ananworanich, J., Suwanlerk, T., Chokephaibulkit, K., Wittawatmongkol, O., Truong, H. K., Mai, D. A. N., Do, C. V., Ha, M. T., Bui, H. V., Nguyen, V. L., Le, O. N., Sohn, A. H., Messerschmidt, L., Pang, J., Cooper, D. A., Law, M. G., Kariminia, A., Davies, M. A., Eley, B., Giddy, J., Moultrie, H., Pascoe, M., Rabie, H., Technau, K., Van Cutsem, G., Vaz, P., Weigel, R., and Wood, R.

Abstract

Background: To better understand the need for paediatric second-line antiretroviral therapy (ART), an ART management survey and a cross-sectional analysis of second-line ART use were conducted in the TREAT Asia Paediatric HIV Observational Database and the IeDEA Southern Africa (International Epidemiologic Databases to Evaluate AIDS) regional cohorts. Methods: Surveys were conducted in April 2009. Analysis data from the Asia cohort were collected in March 2009 from 12 centres in Cambodia, India, Indonesia, Malaysia, and Thailand. Data from the IeDEA Southern Africa cohort were finalized in February 2008 from 10 centres in Malawi, Mozambique, South Africa and Zimbabwe. Results: Survey responses reflected inter-regional variations in drug access and national guidelines. A total of 1301 children in the TREAT Asia and 4561 children in the IeDEA Southern Africa cohorts met inclusion criteria for the cross-sectional analysis. Ten percent of Asian and 3.3% of African children were on second-line ART at the time of data transfer. Median age (interquartile range) in months at second-line initiation was 120 (78-145) months in the Asian cohort and 66 (29-112) months in the southern African cohort. Regimens varied, and the then current World Health Organization-recommended nucleoside reverse transcriptase combination of abacavir and didanosine was used in less than 5% of children in each region. Conclusions: In order to provide life-long ART for children, better use of current first-line regimens and broader access to heat-stable, paediatric second-line and salvage formulations are needed. There will be limited benefit to earlier diagnosis of treatment failure unless providers and patients have access to appropriate drugs for children to switch to.

Published
2011

6. Nuklearmedizinische Untersuchungen zur Bestimmung des Rechts-Links-Shunts und der Lungendurchblutung am Lungen- und Ganzkörperszintigramm bei Säuglingen und Kindern mit angeborenen zyanotischen Herzvitien

Author

Anger K, Weigel R, Stunkat R, Löser H, and Seboldt H

Subjects
Pulmonary and Respiratory Medicine, medicine.medical_specialty, Heart disease, business.industry, Cardiac shunting, Total body, Lung scan, medicine.disease, Text mining, Internal medicine, Cardiology, Medicine, Surgery, Cardiology and Cardiovascular Medicine, business, Perfusion, Right-to-left
Published
1974

7. Bestimmung des Rechts-Links-Shunts bei cyanotischen Herzvitien durch Differenzierung von Lungen- und Restkörperaktivitäten im Ganzkörperszintigramm nach Gabe von mit 99mTc-markierten Albuminmikrosphären

Author

Löser H, Stunkat R, Anger K, Weigel R, and Seboldt H

Abstract

Durch Differenzierung von Lungen- und Restkorperaktivitaten im Ganzkorperszintigramm (Ganzkorperscanner der Firma Ohio-Nuclear) nach Gabe von mit 99mTc markierten Albumin­mikrospharen (250 bis 500 μCi) sollte bei cyanotischen Vitien der Anteil venosen Blutes am arteriellen Systemkreislauf sichtbar gemacht werden. Dabei konnte auf der Basis gangiger szintigraphischer Untersuchungsmethoden (3 bis 11, 13) mit Hilfe computergesteuerter Diagnostik ein neues Verfahren entwickelt werden, das ohne grosere Belastung der Sauglinge und Kinder sowohl zur praoperativen Shuntbeurteilung bei cyanotischen Herzfehlern geeignet ist, als auch den Operationserfolg und die Wirksamkeit von palliativen Anastomosenoperatio­nen dokumentiert.

Published
1974

24. e1e2phi-Consistency

Author

Silaghi, M.-C., Sam-Haroud, D., Weigel, R., Vu, X.-H., and Faltings, B. V.

25. Evidence for ice particles in the tropical stratosphere from in-situ measurements

Author

Reus, M., Borrmann, S., Bansemer, A., Heymsfield, A. J., Weigel, R., Schiller, C., Mitev, V., Frey, W., Kunkel, D., Kürten, A., Curtius, J., Sitnikov, N. M., Ulanovsky, A., and Fabrizio Ravegnani

Subjects
lcsh:Chemistry, lcsh:QD1-999, ddc:550, Life Science, lcsh:Physics, lcsh:QC1-999
Abstract

In-situ ice crystal size distribution measurements are presented within the tropical troposphere and lower stratosphere. The measurements were performed using a combination of a Forward Scattering Spectrometer Probe (FSSP-100) and a Cloud Imaging Probe (CIP), which were installed on the Russian high altitude research aircraft M55 "Geophysica" during the SCOUT-O3 campaign in Darwin, Australia. One of the objectives of the campaign was to characterise the Hector convective system, which appears on an almost daily basis during the pre-monsoon season over the Tiwi Islands, north of Darwin. In total 90 encounters with ice clouds, between 10 and 19 km altitude were selected from the dataset and were analysed. Six of these encounters were observed in the lower stratosphere, up to 1.4 km above the local tropopause. Concurrent lidar measurements on board "Geophysica" indicate that these ice clouds were a result of overshooting convection. Large ice crystals, with a maximum dimension up to 400 μm, were observed in the stratosphere. The stratospheric ice clouds included an ice water content ranging from 7.7×10−5 to 8.5×10−4 g m−3 and were observed at ambient relative humidities (with respect to ice) between 75 and 157%. Three modal lognormal size distributions were fitted to the average size distributions for different potential temperature intervals, showing that the shape of the size distribution of the stratospheric ice clouds are similar to those observed in the upper troposphere. In the tropical troposphere the effective radius of the ice cloud particles decreases from 100 μm at about 10 km altitude, to 3 μm at the tropopause, while the ice water content decreases from 0.04 to 10−5 g m−3. No clear trend in the number concentration was observed with altitude, due to the thin and inhomogeneous characteristics of the observed cirrus clouds. The ice water content calculated from the observed ice crystal size distribution is compared to the ice water content derived from two hygrometer instruments. This independent measurement of the ice water content agrees within the combined uncertainty of the instruments for ice water contents exceeding 3×10−4g m−3. Stratospheric residence times, calculated based on gravitational settling, and evaporation rates show that the ice crystals observed in the stratosphere over the Hector storm system had a high potential of humidifying the stratosphere locally. Utilizing total aerosol number concentration measurements from a four channel condensation particle counter during two separate campaigns, it can be shown that the fraction of ice particles to the number of aerosol particles remaining ranges from 1:300 to 1:30 000 for tropical upper tropospheric ice clouds with ambient temperatures below −75°C.

28. Design of a cold vacuum chamber for diagnostics

Author

Casalbuoni, S., Baumbach, T., Grau, A. W., Hagelstein, M., Rossmanith, R., Vincent Baglin, Jenninger, B., Cimino, R., Cox, M. P., Mashkina, E. M., Wallen, E. J., and Weigel, R.

39. Eu project resolution: Reconfigurable systems for mobile local communication and positioning

Author

Ellinger, F., Carls, J., Wehrli, S., Jäckel, H., Kromer, C., Wiebking, L., Dabek, A., Hüttner, J., Roskosch, R., Gierlich, R., Seisenberger, C., Huemer, M., Mosshammer, R., Ußmüller, T., Weigel, R., Subramanian, V., Krcmar, M., Böck, G., Doumenis, D., Kounoudes, A., Kurek, K., Yevhen Yashchyshyn, Szumny, R., Kalis, A., Avatagelou, E., Garbi, A., and Spiegel, S.

43. Comparison of dual nucleoside-analogue reverse-transcriptase inhibitor regimens with HIV-1 who have not previously been treated: the PENTA 5 randomized trial

Author

J. P. Aboulker, A. Babiker, A. Compagnucci, J. H. Darbyshire, M. Debré, C. Giaquinto, D. M. Gibb, L. Harper, Y. Saidi, AS Walker, J. Darbyshire, D. Johnson, P. Kelleher, L. McGee, A Newberry, A. Poland, A. S. Walker, J P. Aboulker, I. Carrière, V. Eliette, S. Leonardo, M. Gersten, A. Jones, S. Blanche, A. B. Bohlin, K Butler, G. Castelli Gattinara, P. Clayden, R De Groot, A. Faye, C. Griscelli, I Grosch Wörner, C. Kind, H. Lyall, J. Levy, M. Mellado Pena, D. Nadal, C Peckham, J. T. Ramos Amador, L. Rosado, C. Rudin, H. Scherpbier, M Sharland, P. A. Tovo, G. Tudor Williams, N. Valerius, A. Volny Anne, U Wintergerst, V. Wahn, C. Hill, P Lepage, A. Pozniak, S. Vella, M. Hainaut, A. Peltier, S. Carlier, G. Zissis, M. Della Negra, W. Queiroz, L. P. Feitosa, D Oliveira, F. Mechinaud, F. Ballerau, A. Lepelletier, S. Billaudel, V. Ferre, I. Grosch Wörner, R. Weigel, K. Seel, C. Feiterna Sperling, D. Ohlendorf, G. Riße, C. Müller, T. Niehues, J. Ndagijimana, G. Horneff, N. Vente, R. Ganschow, T. Simon, R. Vossen, H Pfister, U. Wintergerst, G. Notheis, G. Strotmann, S Schlieben, K. Butler, E. Hayes, M. O’Mara, J. Fanning, F. Goggins, S. Moriarty, M. Byrne, L. Battisti, M. Duse, S. Timpano, E. Uberti, P. Crispino, P. Carrara, F. Fomia, A. Manca, L. Galli, M. de Martino, F. Fioredda, E. Pontali, M. Cellini, C. Baraldi, M. Portolani, M. Meacci, P. Pietrosemoli, R. Berni Canani, P. Laccetti, M. Gobbo, V. Giacomet, R. D’Elia, O. Rampon, E. Ruga, A. de Rossi, M. Zanchetta, D. Caselli, A. Maccabruni, E. Cattaneo, V Landini, S. Bernardi, A. Krzysztofiak, C. Tancredi, P. Rossi, L. Pansani, E. Palomba, C. Gabiano, A. Mazza, G. Rossetti, R. Nicolin, A. Timillero, F. Candeias, G Santos, M. L. Ramos Ribeiro, M. C. Almeida, M. H. Lourenço, R. Antunes, M. J. Mellado Pena, M L. Carillo de Albornoz, P. Martinez Santos, L. Ciria Calavia, J. Serra Devecchi, O. Delgado, N. Matamoros, A. Foot, H. Kershaw, C. Kelly, O. Caul, W. Tarnow Mordi, J. Petrie, A. McDowell, P. McIntyre, K. Appleyard, K. Sloper, V. Shah, K. Cheema, A. Aali, J. Mok, R. Russell, A. Brewster, N. Richardson, S. Burns, D. Gibb, V. Novelli, N. Klein, S. Ewen, V. Yeung, C. Ball, K. Himid, D. Nayagam, D. Graham, A. Barrie, K. Stringer, S. Jones, N. Weerasooriya, M. Zuckerman, P. Bracken, E. Cooper, T. Fisher, R. Barrie, U. Patel, V. Van Someren, K. Moshal, L. Perry, T. Gundlach, J. Norman, M. Sharland, M. Richardson, S. Donaghy, Z. Mitchla, C. Wells, J. Booth, A. Shipp, J. White, S. Head, S. Lambers, K. O’Hara, C. Stainsby, G. Du Mont, T. Solanki, S. Swanton, S. O’Shea, A. Tilsey, S. Kaye, A. Finn, S. Choo, R. Lakshman, L. Barr, G. Bell, A. Siddens, GUARINO, ALFREDO, SPAGNUOLO, MARIA IMMACOLATA, Aboulker, J. P., Babiker, A., Compagnucci, A., Darbyshire, J. H., Debré, M., Giaquinto, C., Gibb, D. M., Harper, L., Saidi, Y., Walker, A, Darbyshire, J., Johnson, D., Kelleher, P., Mcgee, L., Newberry, A, Poland, A., Walker, A. S., Aboulker, J P., Carrière, I., Eliette, V., Leonardo, S., Gersten, M., Jones, A., Blanche, S., Bohlin, A. B., Butler, K, Castelli Gattinara, G., Clayden, P., R De Groot, Faye, A., Griscelli, C., I Grosch Wörner, Kind, C., Lyall, H., Levy, J., Mellado Pena, M., Nadal, D., Peckham, C, Ramos Amador, J. T., Rosado, L., Rudin, C., Scherpbier, H., Sharland, M, Tovo, P. A., Tudor Williams, G., Valerius, N., Volny Anne, A., Wintergerst, U, Wahn, V., Hill, C., Lepage, P, Pozniak, A., Vella, S., Hainaut, M., Peltier, A., Carlier, S., Zissis, G., Della Negra, M., Queiroz, W., Feitosa, L. P., Oliveira, D, Mechinaud, F., Ballerau, F., Lepelletier, A., Billaudel, S., Ferre, V., Grosch Wörner, I., Weigel, R., Seel, K., Feiterna Sperling, C., Ohlendorf, D., Riße, G., Müller, C., Niehues, T., Ndagijimana, J., Horneff, G., Vente, N., Ganschow, R., Simon, T., Vossen, R., Pfister, H, Wintergerst, U., Notheis, G., Strotmann, G., Schlieben, S, Butler, K., Hayes, E., O’Mara, M., Fanning, J., Goggins, F., Moriarty, S., Byrne, M., Battisti, L., Duse, M., Timpano, S., Uberti, E., Crispino, P., Carrara, P., Fomia, F., Manca, A., Galli, L., de Martino, M., Fioredda, F., Pontali, E., Cellini, M., Baraldi, C., Portolani, M., Meacci, M., Pietrosemoli, P., Guarino, Alfredo, Spagnuolo, MARIA IMMACOLATA, Berni Canani, R., Laccetti, P., Gobbo, M., Giacomet, V., D’Elia, R., Rampon, O., Ruga, E., de Rossi, A., Zanchetta, M., Caselli, D., Maccabruni, A., Cattaneo, E., Landini, V, Bernardi, S., Krzysztofiak, A., Tancredi, C., Rossi, P., Pansani, L., Palomba, E., Gabiano, C., Mazza, A., Rossetti, G., Nicolin, R., Timillero, A., Candeias, F., Santos, G, Ramos Ribeiro, M. L., Almeida, M. C., Lourenço, M. H., Antunes, R., Mellado Pena, M. J., Carillo de Albornoz, M L., Martinez Santos, P., Ciria Calavia, L., Serra Devecchi, J., Delgado, O., Matamoros, N., Foot, A., Kershaw, H., Kelly, C., Caul, O., Tarnow Mordi, W., Petrie, J., Mcdowell, A., Mcintyre, P., Appleyard, K., Sloper, K., Shah, V., Cheema, K., Aali, A., Mok, J., Russell, R., Brewster, A., Richardson, N., Burns, S., Gibb, D., Novelli, V., Klein, N., Ewen, S., Yeung, V., Ball, C., Himid, K., Nayagam, D., Graham, D., Barrie, A., Stringer, K., Jones, S., Weerasooriya, N., Zuckerman, M., Bracken, P., Cooper, E., Fisher, T., Barrie, R., Patel, U., Van Someren, V., Moshal, K., Perry, L., Gundlach, T., Norman, J., Sharland, M., Richardson, M., Donaghy, S., Mitchla, Z., Wells, C., Booth, J., Shipp, A., White, J., Head, S., Lambers, S., O’Hara, K., Stainsby, C., Du Mont, G., Solanki, T., Swanton, S., O’Shea, S., Tilsey, A., Kaye, S., Finn, A., Choo, S., Lakshman, R., Barr, L., Bell, G., and Siddens, A.

Abstract

Introduction Treatment options for children with HIV-1 are limited. We aimed to compare activity and safety of three dualnucleoside analogue reverse-transcriptase inhibitor (NRTI) regimens with or without a protease inhibitor in previously untreated children with HIV-1. Methods In our multicentre trial, we randomly assigned 36 children to zidovudine and lamivudine, 45 to zidovudine and abacavir, and 47 to lamivudine and abacavir. Children who were symptomfree (n=55) were also randomly assigned to receive nelfinavir or placebo. Children with more advanced disease received open-label nelfinavir (73). Primary endpoints were change in plasma HIV-1 RNA at 24 and 48 weeks for the NRTI comparison and occurrence of serious adverse events for both randomised comparisons. Analyses were by intention to treat. Findings Children had a median CD4 percentage of 22% (IQR 15–29) and a mean HIV-1 RNA concentration of 5·0 log copies/mL (SD 0·8). One child was lost to follow-up and one died of sepsis. At 48 weeks, in the zidovudine/lamivudine, zidovudine/abacavir, and lamivudine/abacavir groups, mean HIV-1 RNA had decreased by 1·71, 2·19, and 2·63 log copies/mL, respectively (estimated in absence of nelfinavir) (p=0·02 after adjustment for baseline factors). One child had a hypersensitivity reaction to abacavir; and three with possible reactions stopped abacavir. There were 24 serious adverse events—six in the symptom-free children (all on nelfinavir), but none were attributed to nelfinavir. Interpretation Regimens containing abacavir were more effective than zidovudine/lamivudine. Such regimens could be combined with protease inhibitors and non-nucleoside reverse transcriptase inhibitors for safe and effective treatment of previously untreated children with HIV-1.

Published
2002

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