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8. Association of the COVID‐19 Outbreak with Acute Stroke Care in Switzerland

Author

De Marchis, Gian Marco, Wright, Patrick R., Michel, Patrik, Strambo, Davide, Carrera, Emmanuel, Dirren, Elisabeth, Luft, Andreas R, Wegener, Susanne, Cereda, Carlo W, K��gi, Georg, Vehoff, Jochen, Gensicke, Henrik, Lyrer, Philippe, Nedeltchev, Krassen, Khales, Timo, Bolognese, Manuel, Salmen, Stephan, Sturzenegger, Rolf, Bonvin, Christophe, Berger, Christian, Schelosky, Ludwig, Mono, Marie���Luise, Rodic, Biljana, von Reding, Andrea, Schwegler, Guido, Tarnutzer, Alexander A., Medlin, Friedrich, Humm, Andrea M., Peters, Nils, Beyeler, Morin, Kriemler, Lilian, Bervini, David, Fandino, Javier, Hemkens, Lars G., Mordasini, Pasquale, Arnold, Marcel, Fischer, Urs, Bonati, Leo H., and Swiss Stroke Registry Investigators

Subjects
Stroke, Neurology, SARS-CoV-2, Communicable Disease Control, COVID-19, Humans, 610 Medicine & health, Neurology (clinical), Pandemics, Retrospective Studies, Stroke/epidemiology, Stroke/therapy, Switzerland/epidemiology, epidemiology, stroke, 610 Medizin und Gesundheit, Switzerland
Abstract

In Switzerland, the COVID-19 incidence during the first pandemic wave was high. Our aim was to assess the association of the outbreak with acute stroke care in Switzerland in spring 2020. This was a retrospective analysis based on the Swiss Stroke Registry, which includes consecutive patients with acute cerebrovascular events admitted to Swiss Stroke Units and Stroke Centers. A linear model was fitted to the weekly admission from 2018 and 2019 and was used to quantify deviations from the expected weekly admissions from 13 March to 26 April 2020 (the "lockdown period"). Characteristics and 3-month outcome of patients admitted during the lockdown period were compared with patients admitted during the same calendar period of 2018 and 2019. In all, 28,310 patients admitted between 1 January 2018 and 26 April 2020 were included. Of these, 4491 (15.9%) were admitted in the periods March 13-April 26 of the years 2018-2020. During the lockdown in 2020, the weekly admissions dropped by up to 22% compared to rates expected from 2018 and 2019. During three consecutive weeks, weekly admissions fell below the 5% quantile (likelihood 0.38%). The proportion of intracerebral hemorrhage amongst all registered admissions increased from 7.1% to 9.3% (p = 0.006), and numerically less severe strokes were observed (median National Institutes of Health Stroke Scale from 3 to 2, p = 0.07). Admissions and clinical severity of acute cerebrovascular events decreased substantially during the lockdown in Switzerland. Delivery and quality of acute stroke care were maintained.

Published
2022
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9. Distribution of Aspergillus Species and Prevalence of Azole Resistance in Respiratory Samples From Swiss Tertiary Care Hospitals

Author

Ragozzino, Silvio; https://orcid.org/0000-0002-8100-2096, Goldenberger, Daniel, Wright, Patrick R; https://orcid.org/0000-0002-1153-0846, Zimmerli, Stefan, Mühlethaler, Konrad, Neofytos, Dionysios; https://orcid.org/0000-0001-6970-2869, Riat, Arnaud; https://orcid.org/0000-0001-5171-6816, Boggian, Katia, Nolte, Oliver; https://orcid.org/0000-0002-1761-0812, Conen, Anna; https://orcid.org/0000-0002-5216-4109, Fankhauser, Hans, Schreiber, Peter W; https://orcid.org/0000-0001-8123-2601, Zbinden, Reinhard, Lamoth, Frederic, Khanna, Nina; https://orcid.org/0000-0002-2642-419X, Ragozzino, Silvio; https://orcid.org/0000-0002-8100-2096, Goldenberger, Daniel, Wright, Patrick R; https://orcid.org/0000-0002-1153-0846, Zimmerli, Stefan, Mühlethaler, Konrad, Neofytos, Dionysios; https://orcid.org/0000-0001-6970-2869, Riat, Arnaud; https://orcid.org/0000-0001-5171-6816, Boggian, Katia, Nolte, Oliver; https://orcid.org/0000-0002-1761-0812, Conen, Anna; https://orcid.org/0000-0002-5216-4109, Fankhauser, Hans, Schreiber, Peter W; https://orcid.org/0000-0001-8123-2601, Zbinden, Reinhard, Lamoth, Frederic, and Khanna, Nina; https://orcid.org/0000-0002-2642-419X

Abstract

Among 400 Aspergillus species from respiratory samples in Switzerland, Aspergillus fumigatus was the most frequent species. Non-fumigatus Aspergillus spp were more prevalent among solid organ transplant recipients and after azole exposure. Azole resistance was detected in 4 A fumigatus isolates, 3 of them with the "environmental" mutation TR$_{34}$/L98H in the cyp51A gene.

Published
2022

10. Association of the COVID-19 outbreak with acute stroke care in Switzerland

Author

De Marchis, Gian Marco; https://orcid.org/0000-0002-0342-9780, Wright, Patrick R, Michel, Patrik, et al, Luft, Andreas R; https://orcid.org/0000-0001-9865-7382, Wegener, Susanne; https://orcid.org/0000-0003-4369-7023, Mono, Marie-Luise, Peters, Nils, De Marchis, Gian Marco; https://orcid.org/0000-0002-0342-9780, Wright, Patrick R, Michel, Patrik, et al, Luft, Andreas R; https://orcid.org/0000-0001-9865-7382, Wegener, Susanne; https://orcid.org/0000-0003-4369-7023, Mono, Marie-Luise, and Peters, Nils

Abstract

Background and purpose: In Switzerland, the COVID-19 incidence during the first pandemic wave was high. Our aim was to assess the association of the outbreak with acute stroke care in Switzerland in spring 2020. Methods: This was a retrospective analysis based on the Swiss Stroke Registry, which includes consecutive patients with acute cerebrovascular events admitted to Swiss Stroke Units and Stroke Centers. A linear model was fitted to the weekly admission from 2018 and 2019 and was used to quantify deviations from the expected weekly admissions from 13 March to 26 April 2020 (the "lockdown period"). Characteristics and 3-month outcome of patients admitted during the lockdown period were compared with patients admitted during the same calendar period of 2018 and 2019. Results: In all, 28,310 patients admitted between 1 January 2018 and 26 April 2020 were included. Of these, 4491 (15.9%) were admitted in the periods March 13-April 26 of the years 2018-2020. During the lockdown in 2020, the weekly admissions dropped by up to 22% compared to rates expected from 2018 and 2019. During three consecutive weeks, weekly admissions fell below the 5% quantile (likelihood 0.38%). The proportion of intracerebral hemorrhage amongst all registered admissions increased from 7.1% to 9.3% (p = 0.006), and numerically less severe strokes were observed (median National Institutes of Health Stroke Scale from 3 to 2, p = 0.07). Conclusions: Admissions and clinical severity of acute cerebrovascular events decreased substantially during the lockdown in Switzerland. Delivery and quality of acute stroke care were maintained. Keywords: COVID-19; epidemiology; stroke

Published
2022

11. Effect of admission time on provision of acute stroke treatment at stroke units and stroke centers-An analysis of the Swiss Stroke Registry

Author

Altersberger, Valerian L; https://orcid.org/0000-0002-0610-9328, Wright, Patrick R, Schaedelin, Sabine A, et al, Wegener, Susanne; https://orcid.org/0000-0003-4369-7023, Mono, Marie-Luise, Peters, Nils, Luft, Andreas R; https://orcid.org/0000-0001-9865-7382, Altersberger, Valerian L; https://orcid.org/0000-0002-0610-9328, Wright, Patrick R, Schaedelin, Sabine A, et al, Wegener, Susanne; https://orcid.org/0000-0003-4369-7023, Mono, Marie-Luise, Peters, Nils, and Luft, Andreas R; https://orcid.org/0000-0001-9865-7382

Abstract

Introduction Rapid treatment of acute ischemic stroke (AIS) depends on sufficient staffing which differs between Stroke Centers and Stroke Units in Switzerland. We studied the effect of admission time on performance measures of AIS treatment and related temporal trends over time. Patients and methods We compared treatment rates, door-to-image-time, door-to-needle-time, and door-to-groin-puncture-time in stroke patients admitted during office hours (Monday-Friday 8:00-17:59) and non-office hours at all certified Stroke Centers and Stroke Units in Switzerland, as well as secular trends thereof between 2014 and 2019, using data from the Swiss Stroke Registry. Secondary outcomes were modified Rankin Scale and mortality at 3 months. Results Data were eligible for analysis in 31,788 (90.2%) of 35,261 patients. Treatment rates for IVT/EVT were higher during non-office hours compared with office hours in Stroke Centers (40.8 vs 36.5%) and Stroke Units (21.8 vs 18.5%). Door-to-image-time and door-to-needle-time increased significantly during non-office hours. Median (IQR) door-to-groin-puncture-time at Stroke Centers was longer during non-office hours compared to office hours (84 (59-116) vs 95 (66-130) minutes). Admission during non-office hours was independently associated with worse functional outcome (1.11 [95%CI: 1.04-1.18]) and increased mortality (1.13 [95%CI: 1.01-1.27]). From 2014 to 2019, median door-to-groin-puncture-time improved and the treatment rate for wake-up strokes increased. Discussion and Conclusion Despite differences in staffing, patient admission during non-office hours delayed IVT to a similar, modest degree at Stroke Centers and Stroke Units. A larger delay of EVT was observed during non-office hours, but Stroke Centers sped up delivery of EVT over time. Patients admitted during non-office hours had worse functional outcomes, which was not explained by treatment delays.

Published
2022

12. Endovascular Treatment for Acute Ischemic Stroke With or Without General Anesthesia: A Matched Comparison

Author

Wagner, Benjamin, primary, Lorscheider, Johannes, additional, Wiencierz, Andrea, additional, Blackham, Kristine, additional, Psychogios, Marios, additional, Bolliger, Daniel, additional, De Marchis, Gian Marco, additional, Engelter, Stefan T., additional, Lyrer, Philippe, additional, Wright, Patrick R., additional, Fischer, Urs, additional, Mordasini, Pasquale, additional, Nannoni, Stefania, additional, Puccinelli, Francesco, additional, Kahles, Timo, additional, Bianco, Giovanni, additional, Carrera, Emmanuel, additional, Luft, Andreas R., additional, Cereda, Carlo W., additional, Kägi, Georg, additional, Weber, Johannes, additional, Nedeltchev, Krassen, additional, Michel, Patrik, additional, Gralla, Jan, additional, Arnold, Marcel, additional, Bonati, Leo H., additional, Anon, Javier, additional, Clarke, Sandra, additional, Diepers, Michael, additional, Gruber, Philipp, additional, Martin, Eileen, additional, Remonda, Luca, additional, Schweikert, Andreas, additional, Zupa., Vedrana, additional, Altersberger, Valerian, additional, Brehm, Alex, additional, Dittrich, Tolga, additional, El Mekabaty, Amgad, additional, Fladt, Joachim, additional, Fisch, Urs, additional, Gensicke, Henrik, additional, Hert, Lisa, additional, Manuzzi, Sabrina, additional, Maurer, Marina, additional, Meya, Louisa, additional, Peters, Nils, additional, Polymeris, Alexandros, additional, Thilemann, Sebastian, additional, Traenka, Christopher, additional, Tsogkas, Ioannes, additional, Zietz, Anaelle, additional, Goeldlin, Martina, additional, Heldner, Mirjam, additional, Jung, Simon, additional, Kaesmacher, Johannes, additional, Mamaari, Basel, additional, Meinel, Thomas, additional, Mueller, Madlaine, additional, Sarykaya, Hakan, additional, Seiffge, David, additional, Siepen, Bernhard, additional, Vynkier, Jan, additional, Eskandari, Ashraf, additional, Pantazou, Vasiliki, additional, Strambo, Davide, additional, Frangi, Jane, additional, Sihabdeen, Shairin, additional, Vehoff, Jochen, additional, Katan, Mira, additional, Mueller, Achim, additional, and Wegener, Susanne, additional

Published
2022
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13. Effect of admission time on provision of acute stroke treatment at stroke units and stroke centers—An analysis of the Swiss Stroke Registry

Author

Altersberger, Valerian L, primary, Wright, Patrick R, additional, Schaedelin, Sabine A, additional, De Marchis, Gian Marco, additional, Gensicke, Henrik, additional, Engelter, Stefan T, additional, Psychogios, Marios, additional, Kahles, Timo, additional, Goeldlin, Martina, additional, Meinel, Thomas R, additional, Mordasini, Pasquale, additional, Kaesmacher, Johannes, additional, von Hessling, Alexander, additional, Vehoff, Jochen, additional, Weber, Johannes, additional, Wegener, Susanne, additional, Salmen, Stephan, additional, Sturzenegger, Rolf, additional, Medlin, Friedrich, additional, Berger, Christian, additional, Schelosky, Ludwig, additional, Renaud, Susanne, additional, Niederhauser, Julien, additional, Bonvin, Christophe, additional, Schaerer, Michael, additional, Mono, Marie-Luise, additional, Rodic, Biljana, additional, Schwegler, Guido, additional, Peters, Nils, additional, Bolognese, Manuel, additional, Luft, Andreas R, additional, Cereda, Carlo W, additional, Kägi, Georg, additional, Michel, Patrick, additional, Carrera, Emmanuel, additional, Arnold, Marcel, additional, Fischer, Urs, additional, Nedeltchev, Krassen, additional, and Bonati, Leo H, additional

Published
2022
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14. Distribution of Aspergillus Species and Prevalence of Azole Resistance in Respiratory Samples From Swiss Tertiary Care Hospitals

Author

Ragozzino, Silvio, Goldenberger, Daniel, Wright, Patrick R, Zimmerli, Stefan, Mühlethaler, Konrad, Neofytos, Dionysios, Riat, Arnaud, Boggian, Katia, Nolte, Oliver, Conen, Anna, Fankhauser, Hans, Schreiber, Peter W, Zbinden, Reinhard, Lamoth, Frederic, Khanna, Nina, University of Zurich, and Khanna, Nina

Subjects
ddc:616, TR34/L98H mutation, Aspergillus fumigatus, Cyp51A gene, 610 Medicine & health, bacterial infections and mycoses, azole resistance, cyp51A gene, non-fumigatus Aspergillus spp, 10234 Clinic for Infectious Diseases, 2728 Neurology (clinical), Infectious Diseases, Oncology, Azole resistance, 2730 Oncology, skin and connective tissue diseases, Non-fumigatus Aspergillus spp
Abstract

Among 400 Aspergillus species from respiratory samples in Switzerland, Aspergillus fumigatus was the most frequent species. Non-fumigatus Aspergillus spp were more prevalent among solid organ transplant recipients and after azole exposure. Azole resistance was detected in 4 A fumigatus isolates, 3 of them with the “environmental” mutation TR34/L98H in the cyp51A gene.

Published
2022
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15. sj-docx-1-eso-10.1177_23969873221094408 – Supplemental material for Effect of admission time on provision of acute stroke treatment at stroke units and stroke centers—An analysis of the Swiss Stroke Registry

Author

Altersberger, Valerian L, Wright, Patrick R, Schaedelin, Sabine A, De Marchis, Gian Marco, Gensicke, Henrik, Engelter, Stefan T, Psychogios, Marios, Kahles, Timo, Goeldlin, Martina, Meinel, Thomas R, Mordasini, Pasquale, Kaesmacher, Johannes, von Hessling, Alexander, Vehoff, Jochen, Weber, Johannes, Wegener, Susanne, Salmen, Stephan, Sturzenegger, Rolf, Medlin, Friedrich, Berger, Christian, Schelosky, Ludwig, Renaud, Susanne, Niederhauser, Julien, Bonvin, Christophe, Schaerer, Michael, Mono, Marie-Luise, Rodic, Biljana, Schwegler, Guido, Peters, Nils, Bolognese, Manuel, Luft, Andreas R, Cereda, Carlo W, Kägi, Georg, Michel, Patrick, Carrera, Emmanuel, Arnold, Marcel, Fischer, Urs, Nedeltchev, Krassen, and Bonati, Leo H

Subjects
FOS: Clinical medicine, Cardiology, Medicine, 110904 Neurology and Neuromuscular Diseases
Abstract

Supplemental material, sj-docx-1-eso-10.1177_23969873221094408 for Effect of admission time on provision of acute stroke treatment at stroke units and stroke centers—An analysis of the Swiss Stroke Registry by Valerian L Altersberger, Patrick R Wright, Sabine A Schaedelin, Gian Marco De Marchis, Henrik Gensicke, Stefan T Engelter, Marios Psychogios, Timo Kahles, Martina Goeldlin, Thomas R Meinel, Pasquale Mordasini, Johannes Kaesmacher, Alexander von Hessling, Jochen Vehoff, Johannes Weber, Susanne Wegener, Stephan Salmen, Rolf Sturzenegger, Friedrich Medlin, Christian Berger, Ludwig Schelosky, Susanne Renaud, Julien Niederhauser, Christophe Bonvin, Michael Schaerer, Marie-Luise Mono, Biljana Rodic, Guido Schwegler, Nils Peters, Manuel Bolognese, Andreas R Luft, Carlo W Cereda, Georg Kägi, Patrick Michel, Emmanuel Carrera, Marcel Arnold, Urs Fischer, Krassen Nedeltchev and Leo H Bonati in European Stroke Journal

Published
2022
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17. Distribution of Aspergillus Species and Prevalence of Azole Resistance in Respiratory Samples From Swiss Tertiary Care Hospitals

Author

Ragozzino, Silvio, primary, Goldenberger, Daniel, additional, Wright, Patrick R, additional, Zimmerli, Stefan, additional, Mühlethaler, Konrad, additional, Neofytos, Dionysios, additional, Riat, Arnaud, additional, Boggian, Katia, additional, Nolte, Oliver, additional, Conen, Anna, additional, Fankhauser, Hans, additional, Schreiber, Peter W, additional, Zbinden, Reinhard, additional, Lamoth, Frederic, additional, and Khanna, Nina, additional

Published
2021
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18. Body composition analysis in patients with acute heart failure: the Scale Heart Failure trial

Author

De Ieso, Fiorangelo, primary, Mutke, Markus Reinhold, additional, Brasier, Noe Karl, additional, Raichle, Christina Janitha, additional, Keller, Bettina, additional, Sucker, Celine, additional, Abdelhamid, Khaled, additional, Bloch, Tiziano, additional, Reissenberger, Pamela, additional, Schönenberg, Ladina, additional, Fischer, Sandro Kevin, additional, Saboz, Jonas, additional, Weber, Nora, additional, Schädelin, Sabine, additional, Bruni, Nicole, additional, Wright, Patrick R., additional, and Eckstein, Jens, additional

Published
2021
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19. Impact of Sodium Levels on Functional Outcomes in Patients With Stroke – A Swiss Stroke Registry Analysis

Author

Potasso, Laura, primary, Refardt, Julie, additional, De Marchis, Gian Marco, additional, Wiencierz, Andrea, additional, Wright, Patrick R, additional, Wagner, Benjamin, additional, Dittrich, Tolga, additional, Polymeris, Alexandros A, additional, Gensicke, Henrik, additional, Bonati, Leo H, additional, and Christ-Crain, Mirjam, additional

Published
2021
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20. Clinical Data Management System (CDMS) Evaluation

Author

Bochud, Yves, primary, Huf, Christina, additional, Helmers, Muriel, additional, Wright, Patrick R., additional, Saccilotto, Ramon, additional, Mostaguir, Khaled, additional, Fares, Fady, additional, and Lengwiler, Daniel, additional

Published
2021
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23. Impact of Sodium Levels on Functional Outcomes in Patients With Stroke – A Swiss Stroke Registry Analysis.

Author

Potasso, Laura, Refardt, Julie, De Marchis, Gian Marco, Wiencierz, Andrea, Wright, Patrick R., Wagner, Benjamin, Dittrich, Tolga, Polymeris, Alexandros A., Gensicke, Henrik, Bonati, Leo H., and Christ-Crain, Mirjam

Subjects
SODIUM, HYPONATREMIA, HEALTH outcome assessment
Abstract

Context: Correction of hyponatremia might represent an additional treatment for improving stroke patients’ clinical outcomes. Objective: Admission hyponatremia is associated with worse clinical outcome in stroke patients, but whether normalization of hyponatremia improves outcome is unknown. We investigated whether normalization of hyponatremia affects patients’ disability, mortality, and stroke recurrence within 3 months; length of hospitalization; and discharge destination. Design: This was a registry-based analysis of data collected between January 2016 and December 2018. We linked data from Swiss Stroke Registry (SSR) with electronic patients’ records for extracting sodium values. Setting: We analyzed data of hospitalized patients treated at University Hospital of Basel. Patients: Stroke patients whose data and informed consent were available. Main outcome measure: Modified Rankin Scale (mRS) score at 3 months. The tested hypothesis was formulated after SSR data collection but before linkage with electronic patients’ records. Results: Of 1995 patients, 144 (7.2%) had hyponatremia on admission; 102 (70.8%) reached normonatremia, and 42 (29.2%) remained hyponatremic at discharge. An increase of initial sodium was associated with better functional outcome at 3 months (odds ratio [OR] 0.94; 95% CI, 0.90-0.99, for a shift to higher mRS per 1 mmol/L sodium increase). Compared with normonatremic patients, patients who remained hyponatremic at discharge had a worse functional outcome at 3 months (odds ratio 2.46; 95% CI, 1.20- 5.03, for a shift to higher mRS). No effect was found on mortality, recurrence, or length of hospitalization. Conclusions: In hospitalized acute stroke patients, persistent hyponatremia is associated with worse functional outcome. Whether active correction of hyponatremia improves outcome remains to be determined in prospective studies. [ABSTRACT FROM AUTHOR]

Published
2022
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25. Freiburg RNA tools: a central online resource for RNA-focused research and teaching

Author

Raden, Martin, primary, Ali, Syed M, additional, Alkhnbashi, Omer S, additional, Busch, Anke, additional, Costa, Fabrizio, additional, Davis, Jason A, additional, Eggenhofer, Florian, additional, Gelhausen, Rick, additional, Georg, Jens, additional, Heyne, Steffen, additional, Hiller, Michael, additional, Kundu, Kousik, additional, Kleinkauf, Robert, additional, Lott, Steffen C, additional, Mohamed, Mostafa M, additional, Mattheis, Alexander, additional, Miladi, Milad, additional, Richter, Andreas S, additional, Will, Sebastian, additional, Wolff, Joachim, additional, Wright, Patrick R, additional, and Backofen, Rolf, additional

Published
2018
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27. Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq – ryhB encodes the regulatory RNA RyhB and a peptide, RyhP

Author

Neuhaus, Klaus, Landstorfer, Richard, Simon, Svenja, Schober, Steffen, Wright, Patrick R., Smith, Cameron, Backofen, Rolf, Wecko, Romy, Keim, Daniel A., and Scherer, Siegfried

Subjects
Phenotype, Base Sequence, Sequence Analysis, RNA, Gene Expression Profiling, Genetics, RNA, Small Untranslated, ddc:004, Escherichia coli O157, Peptides, Ribosomes, Biotechnology, Research Article
Abstract

Background While NGS allows rapid global detection of transcripts, it remains difficult to distinguish ncRNAs from short mRNAs. To detect potentially translated RNAs, we developed an improved protocol for bacterial ribosomal footprinting (RIBOseq). This allowed distinguishing ncRNA from mRNA in EHEC. A high ratio of ribosomal footprints per transcript (ribosomal coverage value, RCV) is expected to indicate a translated RNA, while a low RCV should point to a non-translated RNA. Results Based on their low RCV, 150 novel non-translated EHEC transcripts were identified as putative ncRNAs, representing both antisense and intergenic transcripts, 74 of which had expressed homologs in E. coli MG1655. Bioinformatics analysis predicted statistically significant target regulons for 15 of the intergenic transcripts; experimental analysis revealed 4-fold or higher differential expression of 46 novel ncRNA in different growth media. Out of 329 annotated EHEC ncRNAs, 52 showed an RCV similar to protein-coding genes, of those, 16 had RIBOseq patterns matching annotated genes in other enterobacteriaceae, and 11 seem to possess a Shine-Dalgarno sequence, suggesting that such ncRNAs may encode small proteins instead of being solely non-coding. To support that the RIBOseq signals are reflecting translation, we tested the ribosomal-footprint covered ORF of ryhB and found a phenotype for the encoded peptide in iron-limiting condition. Conclusion Determination of the RCV is a useful approach for a rapid first-step differentiation between bacterial ncRNAs and small mRNAs. Further, many known ncRNAs may encode proteins as well. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3586-9) contains supplementary material, which is available to authorized users.

Published
2017

30. Bioconda: A sustainable and comprehensive software distribution for the life sciences

Author

Grüning, Björn, primary, Dale, Ryan, additional, Sjödin, Andreas, additional, Chapman, Brad A., additional, Rowe, Jillian, additional, Tomkins-Tinch, Christopher H., additional, Valieris, Renan, additional, Caprez, Adam, additional, Batut, Bérénice, additional, Haudgaard, Mathias, additional, Cokelaer, Thomas, additional, Beauchamp, Kyle A., additional, Pedersen, Brent S, additional, Hoogstrate, Youri, additional, Bretaudeau, Anthony, additional, Ryan, Devon, additional, Corguillé, Gildas Le, additional, Yusuf, Dilmurat, additional, Luna-Valero, Sebastian, additional, Kirchner, Rory, additional, Brinda, Karel, additional, Wollmann, Thomas, additional, Raden, Martin, additional, Heeringen, Simon J. van, additional, Soranzo, Nicola, additional, Pantano, Lorena, additional, Charlop-Powers, Zachary, additional, Unneberg, Per, additional, Smet, Matthias De, additional, Martin, Marcel, additional, Kuster, Greg Von, additional, Antao, Tiago, additional, Miladi, Milad, additional, Thornton, Kevin, additional, Brueffer, Christian, additional, Beek, Marius van den, additional, Maticzka, Daniel, additional, Blank, Clemens, additional, Will, Sebastian, additional, Gravouil, K´evin, additional, Wolff, Joachim, additional, Holtgrewe, Manuel, additional, Fallmann, Jörg, additional, Piro, Vitor C., additional, Shlyakhter, Ilya, additional, Yousif, Ayman, additional, Mabon, Philip, additional, Zhang, Xiao-Ou, additional, Shen, Wei, additional, Cabral, Jennifer, additional, Thomas, Cristel, additional, Enns, Eric, additional, Brown, Joseph, additional, Boekel, Jorrit, additional, Hollander, Mattias de, additional, Kelleher, Jerome, additional, Turaga, Nitesh, additional, Ruiter, Julian R. de, additional, Bouvier, Dave, additional, Gladman, Simon, additional, Choudhary, Saket, additional, Harding, Nicholas, additional, Eggenhofer, Florian, additional, Kratz, Arne, additional, Fang, Zhuoqing, additional, Kleinkauf, Robert, additional, Timm, Henning, additional, Cock, Peter J. A., additional, Seiler, Enrico, additional, Brislawn, Colin, additional, Nguyen, Hai, additional, Stovner, Endre Bakken, additional, Ewels, Philip, additional, Chambers, Matt, additional, Johnson, James E., additional, Hägglund, Emil, additional, Ye, Simon, additional, Guimera, Roman Valls, additional, Pruesse, Elmar, additional, Dunn, W. Augustine, additional, Parsons, Lance, additional, Patro, Rob, additional, Koppstein, David, additional, Grassi, Elena, additional, Wohlers, Inken, additional, Reynolds, Alex, additional, Cornwell, MacIntosh, additional, Stoler, Nicholas, additional, Blankenberg, Daniel, additional, He, Guowei, additional, Bargull, Marcel, additional, Junge, Alexander, additional, Farouni, Rick, additional, Freeberg, Mallory, additional, Singh, Sourav, additional, Bogema, Daniel R., additional, Cumbo, Fabio, additional, Wang, Liang-Bo, additional, Larson, David E, additional, Workentine, Matthew L., additional, Devisetty, Upendra Kumar, additional, Laurent, Sacha, additional, Roger, Pierrick, additional, Garnier, Xavier, additional, Agren, Rasmus, additional, Khan, Aziz, additional, Eppley, John M, additional, Li, Wei, additional, Stöcker, Bianca Katharina, additional, Rausch, Tobias, additional, Taylor, James, additional, Wright, Patrick R., additional, Taranto, Adam P., additional, Chicco, Davide, additional, Sennblad, Bengt, additional, Baaijens, Jasmijn A., additional, Gopez, Matthew, additional, Abdennur, Nezar, additional, Milne, Iain, additional, Preussner, Jens, additional, Pinello, Luca, additional, Srivastava, Avi, additional, Chande, Aroon T., additional, Kensche, Philip Reiner, additional, Pirola, Yuri, additional, Knudsen, Michael, additional, Bruijn, Ino de, additional, Blin, Kai, additional, Gonnella, Giorgio, additional, Enache, Oana M., additional, Rai, Vivek, additional, Waters, Nicholas R., additional, Hiltemann, Saskia, additional, Bendall, Matthew L., additional, Stahl, Christoph, additional, Miles, Alistair, additional, Boursin, Yannick, additional, Perez-Riverol, Yasset, additional, Schmeier, Sebastian, additional, Clarke, Erik, additional, Arvai, Kevin, additional, Jung, Matthieu, additional, Domenico, Tom´as Di, additional, Seiler, Julien, additional, Rasche, Eric, additional, Kornobis, Etienne, additional, Beisser, Daniela, additional, Rahmann, Sven, additional, Mikheyev, Alexander S, additional, Tran, Camy, additional, Capellades, Jordi, additional, Schröder, Christopher, additional, Salatino, Adrian Emanuel, additional, Dirmeier, Simon, additional, Webster, Timothy H., additional, Moskalenko, Oleksandr, additional, Stephen, Gordon, additional, and Köster, Johannes, additional

Published
2017
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36. Salimabromide: Unexpected Chemistry from the Obligate Marine MyxobacteriumEnhygromxya salina

Author

Felder, Stephan, Dreisigacker, Sandra, Kehraus, Stefan, Neu, Edith, Bierbaum, Gabriele, Wright, Patrick R., Menche, Dirk, Schäberle, Till F., König, Gabriele M., Felder, Stephan, Dreisigacker, Sandra, Kehraus, Stefan, Neu, Edith, Bierbaum, Gabriele, Wright, Patrick R., Menche, Dirk, Schäberle, Till F., and König, Gabriele M.

Abstract

Marine myxobacteria (Enhygromyxa, Plesiocystis, Pseudoenhygromyxa, Haliangium) are phylogenetically distant from their terrestrial counterparts. Salimabromide is the first natural product from the Plesiocystis/Enhygromyxa clade of obligatory marine myxobacteria. Salimabromide has a new tetracyclic carbon skeleton, comprising a brominated benzene ring, a furano lactone residue, and a cyclohexane ring, bridged by a seven-membered cyclic moiety. The absolute configuration was deduced from experimental and calculated CD data. Salimabromide revealed antibiotic activity towards Arthrobacter cristallopoietes.

Published
2013
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38. Comparative analysis of the antioxidant properties of Icelandic and Hawaiian lichens.

Author

Hagiwara, Kehau, Wright, Patrick R., Tabandera, Nicole K., Kelman, Dovi, Backofen, Rolf, Ómarsdóttir, Sesselja, and Wright, Anthony D.

Subjects
*ANTIOXIDANTS, *LICHENS, *SYMBIOSIS, *GREEN algae
Abstract

Antioxidant activity of symbiotic organisms known as lichens is an intriguing field of research because of its strong contribution to their ability to withstand extremes of physical and biological stress (e.g. desiccation, temperature, UV radiation and microbial infection). We present a comparative study on the antioxidant activities of 76 Icelandic and 41 Hawaiian lichen samples assessed employing the DPPH- and FRAP-based antioxidant assays. Utilizing this unprecedented sample size, we show that while highest individual sample activity is present in the Icelandic dataset, the overall antioxidant activity is higher for lichens found in Hawaii. Furthermore, we report that lichens from the genus P eltigera that have been described as strong antioxidant producers in studies on Chinese, Russian and Turkish lichens also show high antioxidant activities in both Icelandic and Hawaiian lichen samples. Finally, we show that opportunistic sampling of lichens in both Iceland and Hawaii will yield high numbers of lichen species that exclusively include green algae as photobiont. [ABSTRACT FROM AUTHOR]

Published
2016
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41. Workflow for a Computational Analysis of an sRNA Candidate in Bacteria.

Author

Wright PR and Georg J

Subjects
Workflow, Computational Biology methods, Cyanobacteria genetics, Genome, Bacterial, Genomics methods, RNA, Bacterial genetics, RNA, Small Untranslated genetics
Abstract

Computational methods can often facilitate the functional characterization of individual sRNAs and furthermore allow high-throughput analysis on large numbers of sRNA candidates. This chapter outlines a potential workflow for computational sRNA analyses and describes in detail methods for homolog detection, target prediction, and functional characterization based on enrichment analysis. The cyanobacterial sRNA IsaR1 is used as a specific example. All methods are available as webservers and easily accessible for nonexpert users.

Published
2018
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