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Book ; Online ; Thesis: Visualization of the HIV-1 Nuclear Preintegration Complex Structure by High Precision Correlative Light - and Electron Microscopy and - Tomography

Burk, Robin [Verfasser] / Kräusslich, Hans-Georg [Akademischer Betreuer]

2020

Author's details	Robin Burk ; Betreuer: Hans-Georg Kräusslich
Keywords	Biowissenschaften, Biologie ; Life Science, Biology
Subject code	sg570
Language	English
Publisher	Universitätsbibliothek Heidelberg
Publishing place	Heidelberg
Document type	Book ; Online ; Thesis
Database	Digital theses on the web

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Article ; Online: Correction: Comparison of Four Active SARS-CoV-2 Surveillance Strategies in Representative Population Sample Points: Two-Factor Factorial Randomized Controlled Trial.

Deckert, Andreas / Anders, Simon / Morales, Ivonne / De Allegri, Manuela / Nguyen, Hoa Thi / Souares, Aurélia / McMahon, Shannon / Meurer, Matthias / Burk, Robin / Lou, Dan / Brugnara, Lucia / Sand, Matthias / Koeppel, Lisa / Maier-Hein, Lena / Ross, Tobias / Adler, Tim J / Brenner, Stephan / Dyer, Christopher / Herbst, Konrad /

Ovchinnikova, Svetlana / Marx, Michael / Schnitzler, Paul / Knop, Michael / Bärnighausen, Till / Denkinger, Claudia M

JMIR public health and surveillance

2024 Volume 10, Page(s) e57203

Abstract: This corrects the article DOI: 10.2196/44204.]. ...

Abstract	[This corrects the article DOI: 10.2196/44204.].
Language	English
Publishing date	2024-02-16
Publishing country	Canada
Document type	Published Erratum
ISSN	2369-2960
ISSN (online)	2369-2960
DOI	10.2196/57203
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Article ; Online: Cost and cost-effectiveness of four different SARS-CoV-2 active surveillance strategies: evidence from a randomised control trial in Germany.

Nguyen, Hoa Thi / Denkinger, Claudia M / Brenner, Stephan / Koeppel, Lisa / Brugnara, Lucia / Burk, Robin / Knop, Michael / Bärnighausen, Till / Deckert, Andreas / De Allegri, Manuela

The European journal of health economics : HEPAC : health economics in prevention and care

2023 Volume 24, Issue 9, Page(s) 1545–1559

Abstract: Introduction: The COVID-19 pandemic has entered its third year and continues to affect most countries worldwide. Active surveillance, i.e. testing individuals irrespective of symptoms, presents a promising strategy to accurately measure the prevalence ... ...

Abstract	Introduction: The COVID-19 pandemic has entered its third year and continues to affect most countries worldwide. Active surveillance, i.e. testing individuals irrespective of symptoms, presents a promising strategy to accurately measure the prevalence of SARS-CoV-2. We aimed to identify the most cost-effective active surveillance strategy for COVID-19 among the four strategies tested in a randomised control trial between 18th November 2020 and 23rd December 2020 in Germany. The four strategies included: (A1) direct testing of individuals; (A2) direct testing of households; (B1) testing conditioned on upstream COVID-19 symptom pre-screening of individuals; and (B2) testing conditioned on upstream COVID-19 symptom pre-screening of households. Methods: We adopted a health system perspective and followed an activity-based approach to costing. Resource consumption data were collected prospectively from a digital individual database, daily time records, key informant interviews and direct observations. Our cost-effectiveness analysis compared each strategy with the status quo and calculated the average cost-effective ratios (ACERs) for one primary outcome (sample tested) and three secondary outcomes (responder recruited, case detected and asymptomatic case detected). Results: Our results showed that A2, with cost per sample tested at 52,89 EURO, had the lowest ACER for the primary outcome, closely followed by A1 (63,33 EURO). This estimate was much higher for both B1 (243,84 EURO) and B2 (181,06 EURO). Conclusion: A2 (direct testing at household level) proved to be the most cost-effective of the four evaluated strategies and should be considered as an option to strengthen the routine surveillance system in Germany and similar settings.
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19/epidemiology ; Cost-Benefit Analysis ; Pandemics/prevention & control ; Watchful Waiting
Language	English
Publishing date	2023-01-19
Publishing country	Germany
Document type	Randomized Controlled Trial ; Journal Article
ZDB-ID	2045253-6
ISSN	1618-7601 ; 1618-7598
ISSN (online)	1618-7601
ISSN	1618-7598
DOI	10.1007/s10198-022-01561-8
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Article ; Online: From disgusting and complicated to simple and brilliant: Implementation perspectives and lessons learned from users and rejectors of mail-in SARS-CoV-2 gargle tests.

Röhr, Freda / Uellner, Ferdinand / Deckert, Andreas / Anders, Simon / Burk, Robin / Knop, Michael / Brugnara, Lucia / Bärnighausen, Till / Jahn, Albrecht / McMahon, Shannon / Souares, Aurélia

Frontiers in public health

2023 Volume 10, Page(s) 1024525

Abstract: Background: Despite the important role of testing as a measure against the COVID-19 pandemic, user perspectives on SARS-CoV-2 tests remain scarce, inhibiting an improvement of testing approaches. As the world enters the third year of the pandemic, more ... ...

Abstract	Background: Despite the important role of testing as a measure against the COVID-19 pandemic, user perspectives on SARS-CoV-2 tests remain scarce, inhibiting an improvement of testing approaches. As the world enters the third year of the pandemic, more nuanced perspectives of testing, and opportunities to expand testing in a feasible and affordable manner merit consideration. Methods: Conducted amid the second pandemic wave (late 2020-early 2021) during and after a multi-arm trial evaluating SARS-CoV-2 surveillance strategies in the federal state Baden-Württemberg, Germany, this qualitative sub-study aimed to gain a deeper understanding of how test users and test rejectors perceived mail-in SARS-CoV-2 gargle tests. We conducted 67 semi-structured in-depth interviews (mean duration: 60 min) Results: Respondents generally described gargle sampling as simple and comfortable. However, individual perceptions of the testing method and its feasibility varied widely from disgusting and complicated to simple and brilliant. Self-sampling was appreciated for lowering infection risks during testing, but also considered more complex. Gargle-sampling increased participants' self-efficacy to sample correctly. Communication (first contact, quantity and content of information, reminders, support system) and trust (in the study, its institutional affiliation and test method) decisively influenced the intervention's acceptability. Conclusion: User-driven insights on how to streamline testing include: consider communication, first impressions of tests and information as key for successful mail-in testing; pay attention to the role of mutual trust between those taking and administering tests; implement gargle self-sampling as a pleasant alternative to swab testing; offer multiple test methods to increase test up-take.
MeSH term(s)	Humans ; COVID-19/diagnosis ; Emotions ; Pandemics ; Postal Service ; SARS-CoV-2 ; Implementation Science ; Specimen Handling
Language	English
Publishing date	2023-01-05
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2711781-9
ISSN	2296-2565 ; 2296-2565
ISSN (online)	2296-2565
ISSN	2296-2565
DOI	10.3389/fpubh.2022.1024525
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Thesis ; Online: Toward a theory-based natural language capability in robots and other embodied agents

Burk, Robin K.

Evaluating Hausser's SLIM theory and database semantics

2010

Abstract: Computational natural language understanding and generation have been a goal of artificial intelligence since McCarthy, Minsky, Rochester and Shannon first proposed to spend the summer of 1956 studying this and related problems. Although statistical ... ...

Abstract	Computational natural language understanding and generation have been a goal of artificial intelligence since McCarthy, Minsky, Rochester and Shannon first proposed to spend the summer of 1956 studying this and related problems. Although statistical approaches dominate current natural language applications, two current research trends bring renewed focus on this goal. The nascent field of artificial general intelligence (AGI) seeks to evolve intelligent agents whose multi-subagent architectures are motivated by neuroscience insights into the modular functional structure of the brain and by cognitive science insights into human learning processes. Rapid advances in cognitive robotics also entail multi-agent software architectures that attempt to parallel in many ways the sensory and cognitive processes of humans. Natural language capability is a key objective for both types of software, whether embodied in a physical robot or in a virtual world that emulates features of the physical environment. Hausser's SLIM theory of natural language communication and associated Database Semantics computational instantiation are an ambitious attempt to bridge the gap between formal theory approaches to computational natural language capability and an embodied approach to language and meaning which requires integration of language with sensory perception, planning and social interaction. This dissertation evaluates Hausser's approach to the development of human-level computational natural language capability in embodied and socially situated agents and argues that a theoretical basis for such capability is emerging as a result of recent evidence from linguistics, cognitive science and neuroscience.
Keywords	Linguistics\|Information science\|Artificial intelligence
Subject code	401
Language	ENG
Publishing date	2010-01-01 00:00:01.0
Publisher	State University of New York at Albany
Publishing country	us
Document type	Thesis ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Comparison of Four Active SARS-CoV-2 Surveillance Strategies in Representative Population Sample Points: Two-Factor Factorial Randomized Controlled Trial.

Ovchinnikova, Svetlana / Marx, Michael / Schnitzler, Paul / Knop, Michael / Bärnighausen, Till / Denkinger, Claudia M

JMIR public health and surveillance

2023 Volume 9, Page(s) e44204

Abstract: Background: The COVID-19 pandemic is characterized by rapid increases in infection burden owing to the emergence of new variants with higher transmissibility and immune escape. To date, monitoring the COVID-19 pandemic has mainly relied on passive ... ...

Abstract	Background: The COVID-19 pandemic is characterized by rapid increases in infection burden owing to the emergence of new variants with higher transmissibility and immune escape. To date, monitoring the COVID-19 pandemic has mainly relied on passive surveillance, yielding biased epidemiological measures owing to the disproportionate number of undetected asymptomatic cases. Active surveillance could provide accurate estimates of the true prevalence to forecast the evolution of the pandemic, enabling evidence-based decision-making. Objective: This study compared 4 different approaches of active SARS-CoV-2 surveillance focusing on feasibility and epidemiological outcomes. Methods: A 2-factor factorial randomized controlled trial was conducted in 2020 in a German district with 700,000 inhabitants. The epidemiological outcome comprised SARS-CoV-2 prevalence and its precision. The 4 study arms combined 2 factors: individuals versus households and direct testing versus testing conditioned on symptom prescreening. Individuals aged ≥7 years were eligible. Altogether, 27,908 addresses from 51 municipalities were randomly allocated to the arms and 15 consecutive recruitment weekdays. Data collection and logistics were highly digitized, and a website in 5 languages enabled low-barrier registration and tracking of results. Gargle sample collection kits were sent by post. Participants collected a gargle sample at home and mailed it to the laboratory. Samples were analyzed with reverse transcription loop-mediated isothermal amplification (RT-LAMP); positive and weak results were confirmed with real-time reverse transcription-polymerase chain reaction (RT-PCR). Results: Recruitment was conducted between November 18 and December 11, 2020. The response rates in the 4 arms varied between 34.31% (2340/6821) and 41.17% (2043/4962). The prescreening classified 16.61% (1207/7266) of the patients as COVID-19 symptomatic. Altogether, 4232 persons without prescreening and 7623 participating in the prescreening provided 5351 gargle samples, of which 5319 (99.4%) could be analyzed. This yielded 17 confirmed SARS-CoV-2 infections and a combined prevalence of 0.36% (95% CI 0.14%-0.59%) in the arms without prescreening and 0.05% (95% CI 0.00%-0.108%) in the arms with prescreening (initial contacts only). Specifically, we found a prevalence of 0.31% (95% CI 0.06%-0.58%) for individuals and 0.35% (95% CI 0.09%-0.61%) for households, and lower estimates with prescreening (0.07%, 95% CI 0.0%-0.15% for individuals and 0.02%, 95% CI 0.0%-0.06% for households). Asymptomatic infections occurred in 27% (3/11) of the positive cases with symptom data. The 2 arms without prescreening performed the best regarding effectiveness and accuracy. Conclusions: This study showed that postal mailing of gargle sample kits and returning home-based self-collected liquid gargle samples followed by high-sensitivity RT-LAMP analysis is a feasible way to conduct active SARS-CoV-2 population surveillance without burdening routine diagnostic testing. Efforts to improve participation rates and integration into the public health system may increase the potential to monitor the course of the pandemic. Trial registration: Deutsches Register Klinischer Studien (DRKS) DRKS00023271; https://tinyurl.com/3xenz68a. International registered report identifier (irrid): RR2-10.1186/s13063-021-05619-5.
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19/epidemiology ; Pandemics/prevention & control ; Specimen Handling ; Laboratories
Language	English
Publishing date	2023-08-17
Publishing country	Canada
Document type	Randomized Controlled Trial ; Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2369-2960
ISSN (online)	2369-2960
DOI	10.2196/44204
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Article ; Online: Development of a commercial scale process for production of 1,4-butanediol from sugar.

Burgard, Anthony / Burk, Mark J / Osterhout, Robin / Van Dien, Stephen / Yim, Harry

Current opinion in biotechnology

2016 Volume 42, Page(s) 118–125

Abstract: A sustainable bioprocess for the production of 1,4-butanediol (BDO) from carbohydrate feedstocks was developed. BDO is a chemical intermediate that goes into a variety of products including automotive parts, electronics, and apparel, and is currently ... ...

Abstract	A sustainable bioprocess for the production of 1,4-butanediol (BDO) from carbohydrate feedstocks was developed. BDO is a chemical intermediate that goes into a variety of products including automotive parts, electronics, and apparel, and is currently manufactured commercially through energy-intensive petrochemical processes using fossil raw materials. This review highlights the development of an Escherichia coli strain and an overall process that successfully performed at commercial scale for direct production of bio-BDO from dextrose. Achieving such high level performance required an integrated technology platform enabling detailed engineering of enzyme, pathway, metabolic network, and organism, as well as development of effective fermentation and downstream recovery processes.
MeSH term(s)	Animals ; Butylene Glycols/metabolism ; Carbohydrate Metabolism/physiology ; Commerce ; Drug Industry/economics ; Drug Industry/methods ; Drug Industry/trends ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Fermentation ; Glucose/metabolism ; Humans ; Metabolic Engineering/methods ; Metabolic Networks and Pathways ; Sucrose/metabolism
Chemical Substances	Butylene Glycols ; Sucrose (57-50-1) ; 1,4-butanediol (7XOO2LE6G3) ; Glucose (IY9XDZ35W2)
Language	English
Publishing date	2016-12
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1052045-4
ISSN	1879-0429 ; 0958-1669
ISSN (online)	1879-0429
ISSN	0958-1669
DOI	10.1016/j.copbio.2016.04.016
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Article ; Online: Re-visiting the functional Relevance of the highly conserved Serine 40 Residue within HIV-1 p6(Gag).

Radestock, Benjamin / Burk, Robin / Müller, Barbara / Kräusslich, Hans-Georg

Retrovirology

2014 Volume 11, Page(s) 114

Abstract: Background: HIV-1 formation is driven by the viral structural polyprotein Gag, which assembles at the plasma membrane into a hexagonal lattice. The C-terminal p6(Gag) domain harbors short peptide motifs, called late domains, which recruit the cellular ... ...

Abstract	Background: HIV-1 formation is driven by the viral structural polyprotein Gag, which assembles at the plasma membrane into a hexagonal lattice. The C-terminal p6(Gag) domain harbors short peptide motifs, called late domains, which recruit the cellular endosomal sorting complex required for transport and promote HIV-1 abscission from the plasma membrane. Similar to late domain containing proteins of other viruses, HIV-1 p6 is phosphorylated at multiple residues, including a highly conserved serine at position 40. Previously published studies showed that an S40F exchange in p6(Gag) severely affected virus infectivity, while we had reported that mutation of all phosphorylatable residues in p6(Gag) had only minor effects. Findings: We introduced mutations into p6(Gag) without affecting the overlapping pol reading frame by using an HIV-1 derivative where gag and pol are genetically uncoupled. HIV-1 derivatives with a conservative S40N or a non-conservative S40F exchange were produced. The S40F substitution severely affected virus maturation and infectivity as reported before, while the S40N exchange caused no functional defects and the variant was fully infectious in T-cell lines and primary T-cells. Conclusions: An HIV-1 variant carrying a conservative S40N exchange in p6(Gag) is fully functional in tissue culture demonstrating that neither S40 nor its phosphorylation are required for HIV-1 release and maturation. The phenotype of the S40F mutation appears to be caused by the bulky hydrophobic residue introduced into a flexible region.
MeSH term(s)	Amino Acid Substitution ; HIV-1/genetics ; HIV-1/physiology ; Mutagenesis, Site-Directed ; Serine/genetics ; Serine/metabolism ; Virus Assembly ; gag Gene Products, Human Immunodeficiency Virus/genetics ; gag Gene Products, Human Immunodeficiency Virus/metabolism
Chemical Substances	gag Gene Products, Human Immunodeficiency Virus ; p6 gag protein, Human immunodeficiency virus 1 ; Serine (452VLY9402)
Language	English
Publishing date	2014-12-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1742-4690
ISSN (online)	1742-4690
DOI	10.1186/s12977-014-0114-8
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Article ; Online: Scalable RT-LAMP-based SARS-CoV-2 testing for infection surveillance with applications in pandemic preparedness.

Lou, Dan / Meurer, Matthias / Ovchinnikova, Svetlana / Burk, Robin / Denzler, Anna / Herbst, Konrad / Papaioannou, Ioannis A / Duan, Yuanqiang / Jacobs, Max L / Witte, Victoria / Ürge, Daniel / Kirrmaier, Daniel / Krogemann, Michelle / Gubicza, Krisztina / Boerner, Kathleen / Bundschuh, Christian / Weidner, Niklas M / Merle, Uta / Knorr, Britta /

Welker, Andreas / Denkinger, Claudia M / Schnitzler, Paul / Kräusslich, Hans-Georg / Dao Thi, Viet Loan / De Allegri, Manuela / Nguyen, Hoa Thi / Deckert, Andreas / Anders, Simon / Knop, Michael

EMBO reports

2023 Volume 24, Issue 5, Page(s) e57162

Abstract: Throughout the SARS-CoV-2 pandemic, limited diagnostic capacities prevented sentinel testing, demonstrating the need for novel testing infrastructures. Here, we describe the setup of a cost-effective platform that can be employed in a high-throughput ... ...

Abstract	Throughout the SARS-CoV-2 pandemic, limited diagnostic capacities prevented sentinel testing, demonstrating the need for novel testing infrastructures. Here, we describe the setup of a cost-effective platform that can be employed in a high-throughput manner, which allows surveillance testing as an acute pandemic control and preparedness tool, exemplified by SARS-CoV-2 diagnostics in an academic environment. The strategy involves self-sampling based on gargling saline, pseudonymized sample handling, automated RNA extraction, and viral RNA detection using a semiquantitative multiplexed colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay with an analytical sensitivity comparable with RT-qPCR. We provide standard operating procedures and an integrated software solution for all workflows, including sample logistics, analysis by colorimetry or sequencing, and communication of results. We evaluated factors affecting the viral load and the stability of gargling samples as well as the diagnostic sensitivity of the RT-LAMP assay. In parallel, we estimated the economic costs of setting up and running the test station. We performed > 35,000 tests, with an average turnover time of < 6 h from sample arrival to result announcement. Altogether, our work provides a blueprint for fast, sensitive, scalable, cost- and labor-efficient RT-LAMP diagnostics, which is independent of potentially limiting clinical diagnostics supply chains.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19/diagnosis ; COVID-19/epidemiology ; COVID-19 Testing ; Clinical Laboratory Techniques/methods ; Pandemics/prevention & control ; Sensitivity and Specificity ; RNA, Viral/genetics
Chemical Substances	RNA, Viral
Language	English
Publishing date	2023-03-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2020896-0
ISSN	1469-3178 ; 1469-221X
ISSN (online)	1469-3178
ISSN	1469-221X
DOI	10.15252/embr.202357162
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Zs.A 5433: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Book: UNIX unleashed

Burk, Robin

[the comprehensive solution!]

1998

Author's details	Robin Burk
Language	English
Size	XXXVIII, 1664 S, graph. Darst, 24 cm
Edition	3. ed
Publisher	Sams
Publishing place	Indianapolis, Ind
Document type	Book
Accompanying material	1 CD-ROM
ISBN	0672314118 ; 9780672314117
Database	Former special subject collection: coastal and deep sea fishing

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