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Article ; Online: Portable Nanopore sequencing solution for next-generation HIV drug resistance testing.

Park, Sung Yong / Faraci, Gina / Ganesh, Kevin / Dubé, Michael P / Lee, Ha Youn

Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology

2024 Volume 171, Page(s) 105639

Abstract: Background: Tackling HIV drug resistance is one of major challenges for ending AIDS epidemic, but the elevated expense of cutting-edge genomics hampers the advancement of HIV genotype testing for clinical care.: Methods: We developed a HIV genotype ... ...

Abstract	Background: Tackling HIV drug resistance is one of major challenges for ending AIDS epidemic, but the elevated expense of cutting-edge genomics hampers the advancement of HIV genotype testing for clinical care. Methods: We developed a HIV genotype testing pipeline that centers on a cost-efficient portable Nanopore sequencer. Accuracy verification was conducted through comparison with parallel data obtained via fixed-site Pacbio sequencing. Our complete pol-gene sequencing strategy coupled with portable high-throughput sequencing was applied to identify drug resistance mutations across 58 samples sourced from the ART-treated Los Angeles General Medical Center Rand Schrader Clinic (LARSC) cohort (7 samples from 7 individuals) and the ART-naïve Center for HIV/AIDS Vaccine Immunology (CHAVI) cohort (51 samples from 38 individuals). Results: A total of 472 HIV consensus sequences, each tagged with a unique molecular identifier, were produced from over 1.4 million bases acquired through portable Nanopore sequencing, which matched those obtained independently via Pacbio sequencing. With this desirable accuracy, we first documented the linkage of multidrug cross-resistance mutations across Integrase Strand Transfer inhibitors (INSTIs) and Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs) from an individual failing a second-generation INSTI regimen. By producing more than 500 full-length HIV pol gene sequences in a single portable sequencing run, we detected Protease Inhibitor (PI), Nucleoside Reverse Transcriptase Inhibitor (NRTI), NNRTI and INSTI resistance mutations. All drug resistance mutations identified through portable sequencing were cross-validated using fixed-site Pacbio sequencing. Conclusions: Our accurate and affordable HIV drug resistance testing solution is adaptable for both individual patient care and large-scale surveillance initiatives.
MeSH term(s)	Humans ; HIV Infections/drug therapy ; Nanopore Sequencing ; HIV-1/genetics ; Reverse Transcriptase Inhibitors/therapeutic use ; Anti-HIV Agents/pharmacology ; Anti-HIV Agents/therapeutic use ; Genotype ; HIV Integrase Inhibitors/therapeutic use ; Mutation ; Drug Resistance ; Drug Resistance, Viral/genetics ; HIV Integrase/genetics
Chemical Substances	Reverse Transcriptase Inhibitors ; Anti-HIV Agents ; HIV Integrase Inhibitors ; HIV Integrase (EC 2.7.7.-)
Language	English
Publishing date	2024-01-09
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1446080-4
ISSN	1873-5967 ; 1386-6532
ISSN (online)	1873-5967
ISSN	1386-6532
DOI	10.1016/j.jcv.2024.105639
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Article ; Online: Full-spectrum HIV drug resistance mutation detection by high-resolution complete pol gene sequencing.

Faraci, Gina / Park, Sung Yong / Dubé, Michael P / Lee, Ha Youn

Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology

2023 Volume 164, Page(s) 105491

Abstract: Background: Drug resistance mutation testing is a key element for HIV clinical management, informing effective treatment regimens. However, resistance screening in current clinical practice is limited in reporting linked cross-class resistance mutations ...

Abstract	Background: Drug resistance mutation testing is a key element for HIV clinical management, informing effective treatment regimens. However, resistance screening in current clinical practice is limited in reporting linked cross-class resistance mutations and minority variants, both of which may increase the risk of virological failure. Methods: To address these limitations, we obtained 358 full-length pol gene sequences from 52 specimens of 20 HIV infected individuals by combining microdroplet amplification, unique molecular identifier (UMI) labeling, and long-read high-throughput sequencing. Results: We conducted a rigorous assessment of the accuracy of our pipeline for precision drug resistance mutation detection, verifying that a sequencing depth of 35 high-throughput reads achieved complete, error-free pol gene sequencing. We detected 26 distinct drug resistance mutations to Protease Inhibitors (PIs), Nucleoside Reverse Transcriptase Inhibitors (NRTIs), Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs), and Integrase Strand Transfer Inhibitors (INSTIs). We detected linked cross-class drug resistance mutations (PI+NRTI, PI+NNRTI, and NRTI+NNRTI) that confer cross-resistance to multiple drugs in different classes. Fourteen different types of minority mutations were also detected with frequencies ranging from 3.2% to 19%, and the presence of these mutations was verified by Sanger reference sequencing. We detected a putative transmitted drug resistance mutation (TDRM) in one individual that persisted for over seven months from the first sample collected at the acute stage of infection prior to seroconversion. Conclusions: Our comprehensive drug resistance mutation profiling can advance clinical practice by reporting mutation linkage and minority variants to better guide antiretroviral therapy options.
MeSH term(s)	Humans ; Reverse Transcriptase Inhibitors/therapeutic use ; Anti-HIV Agents/pharmacology ; Anti-HIV Agents/therapeutic use ; Genes, pol ; HIV-1/genetics ; Drug Resistance, Viral/genetics ; HIV Infections/drug therapy ; Mutation ; Genotype
Chemical Substances	Reverse Transcriptase Inhibitors ; Anti-HIV Agents
Language	English
Publishing date	2023-05-06
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1446080-4
ISSN	1873-5967 ; 1386-6532
ISSN (online)	1873-5967
ISSN	1386-6532
DOI	10.1016/j.jcv.2023.105491
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Article ; Online: Precision detection of recent HIV infections using high-throughput genomic incidence assay.

Faraci, Gina / Park, Sung Yong / Love, Tanzy M T / Dubé, Michael P / Lee, Ha Youn

Microbiology spectrum

2023 , Page(s) e0228523

Abstract: HIV incidence is a key measure for tracking disease spread and identifying populations and geographic regions where new infections are most concentrated. The HIV sequence population provides a robust signal for the stage of infection. Large-scale and ... ...

Abstract	HIV incidence is a key measure for tracking disease spread and identifying populations and geographic regions where new infections are most concentrated. The HIV sequence population provides a robust signal for the stage of infection. Large-scale and high-precision HIV sequencing is crucial for effective genomic incidence surveillance. We produced 1,034 full-length envelope gene sequences from a seroconversion cohort by conducting HIV microdrop sequencing and measuring the genomic incidence assay's genome similarity index (GSI) dynamics. The measured dynamics of 9 of 12 individuals aligned with the GSI distribution estimated independently using 417 publicly available incident samples. We enhanced the capacity to identify individuals with recent infections, achieving predicted detection accuracies of 92% (89%-94%) for cases within 6 months and 81% (74%-87%) for cases within 9 months. These accuracy levels agreed with the observed detection accuracy intervals of an independent validation data set. Additionally, we produced 131 full-length envelope gene sequences from eight individuals with chronic HIV infection. This analysis confirmed a false recency rate (FRR) of 0%, which was consistent with 162 publicly available chronic samples. The mean duration of recent infection (MDRI) was 238 (209-267) days, indicating an 83% improvement in performance compared to current recent infection testing algorithms. The shifted Poisson mixture model was then used to estimate the time since infection, and the model estimates showed an 88% consistency with the days post infection derived from HIV RNA test dates and/or seroconversion dates. HIV microdrop sequencing provides unique prospects for large-scale incidence surveillance using high-throughput sequencing. IMPORTANCE Accurate identification of recently infected individuals is vital for prioritizing specific populations for interventions, reducing onward transmission risks, and optimizing public health services. However, current HIV-specific antibody-based methods have not been satisfactory in accurately identifying incident cases, hindering the use of HIV recency testing for prevention efforts and partner protection. Genomic incidence assays offer a promising alternative for identifying recent infections. In our study, we used microdroplet technologies to produce a large number of complete HIV envelope gene sequences, enabling the accurate detection of early infection signs. We assessed the dynamics of the incidence assay's metrics and compared them with statistical models. Our approach demonstrated high accuracy in identifying individuals with recent infections, achieving predicted detection rates exceeding 90% within 6 months and over 80% within 9 months of infection. This high-resolution method holds significant potential for enhancing the effectiveness of HIV incidence screening for case-based surveillance in public health initiatives.
Language	English
Publishing date	2023-09-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.02285-23
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Article ; Online: Informing efforts beyond tailored promotional campaigns by understanding contextual factors shaping vaccine hesitancy among equity-deserving populations in Canada: an exploratory qualitative study.

Nascimento, Lena G / Dubé, Ève / Burns, Kathleen E / Brown, Patrick / Calnan, Michael / Ward, Paul R / Filice, Eric / Herati, Hoda / Ike, Nnenna A U / Rotolo, Bobbi / Meyer, Samantha B

International journal for equity in health

2023 Volume 22, Issue 1, Page(s) 209

Abstract: Background: Vaccine hesitancy exists on a continuum ranging between complete adherence and complete refusal due to doubts or concerns within a heterogeneous group of individuals. Despite widespread acknowledgement of the contextual factors influencing ... ...

Abstract	Background: Vaccine hesitancy exists on a continuum ranging between complete adherence and complete refusal due to doubts or concerns within a heterogeneous group of individuals. Despite widespread acknowledgement of the contextual factors influencing attitudes and beliefs shaping COVID-19 vaccine hesitancy, qualitative research with equity-deserving groups, accounting for unique lived experiences, remains a gap in the literature. We aim to identify and begin to understand and document the unique contextual factors shaping hesitancy by equity-deserving groups as it relates to relationships with government and health authorities. Methods: Participants were recruited and interviewed between Aug-Dec 2021. Semi-structured interviews using a convergent interviewing technique were conducted with individuals from the general population, as well as individuals who identify as First Nations, Métis, or Inuit, members of the LGBT2SQ + community, low-income Canadians, Black Canadians, and newcomers. Interviews were audio recorded and transcribed by a team of researchers. Memos were written following interviews and used to complement the thematic analysis of the interview data. Themes are presented in the results section. Results: The rationale for hesitancy among equity-deserving groups is consistent with literature documenting hesitancy in the general population. Contextual factors surrounding equity-deserving groups' attitudes and beliefs, however, are unique and relate to a history of oppression, discrimination, and genocide. We identified factors unique to subgroups; for example, religious or fatalistic beliefs among participant who identify as FNMI, fear associated with lack of testing and speed of vaccines' production among participants who identify as FNMI, Black, and LGBT2SQ + , distrust of the healthcare system for LGBT2SQ + and Black Canadians, and distrust of the government and opposition to vaccine mandates for participating who identify as LGBT2SQ + , low-income, FNMI, or Black Canadian. Newcomers stood out as very trusting of the government and accepting of COVID-19 vaccination. Conclusions: While our data on vaccine hesitancy largely mirror concerns reported in the vast body of literature citing rationale for COVID-19 hesitancy in high-income countries, the contextual factors identified in our work point to the need for wider systemic change. Our results may be used to support efforts, beyond tailored promotion campaigns, to support the confident acceptance of vaccines for COVID-19 and the acceptance of novel vaccines as future infectious diseases emerge.
MeSH term(s)	Humans ; COVID-19 Vaccines ; Canada ; Vaccination Hesitancy ; Government ; COVID-19/prevention & control ; Vaccination
Chemical Substances	COVID-19 Vaccines
Language	English
Publishing date	2023-10-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2092056-8
ISSN	1475-9276 ; 1475-9276
ISSN (online)	1475-9276
ISSN	1475-9276
DOI	10.1186/s12939-023-02025-y
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Article ; Online: Considerations for designing and implementing combination HIV cure trials: findings from a qualitative in-depth interview study in the United States.

Dubé, Karine / Kanazawa, John / Dee, Lynda / Taylor, Jeff / Sauceda, John A / Gianella, Sara / Smith, Davey / Deeks, Steven G / Peluso, Michael J

AIDS research and therapy

2021 Volume 18, Issue 1, Page(s) 75

Abstract: Background: An increasing number of HIV cure trials involve combining multiple potentially curative interventions. Until now, considerations for designing and implementing complex combination HIV cure trials have not been thoroughly considered.: ... ...

Abstract	Background: An increasing number of HIV cure trials involve combining multiple potentially curative interventions. Until now, considerations for designing and implementing complex combination HIV cure trials have not been thoroughly considered. Methods: We used a purposive method to select key informants for our study. Informants included biomedical HIV cure researchers, regulators, policy makers, bioethicists, and community members. We used in-depth interviews to generate ethical and practical considerations to guide the design and implementation of combination HIV cure research. We analyzed the qualitative data using conventional content analysis focused on inductive reasoning. Results: We interviewed 11 biomedical researchers, 4 community members, 2 regulators, 1 policy researcher, and 1 bioethicist. Informants generated considerations for designing and implementing combination interventions towards an HIV cure, focused on ethical aspects, as well as considerations to guide trial design, benefit/risk determinations, regulatory requirements, prioritization and sequencing and timing of interventions, among others. Informants also provided considerations related to combining specific HIV cure research modalities, such as broadly neutralizing antibodies (bNAbs), cell and gene modification products, latency-reversing agents and immune-based interventions. Finally, informants provided suggestions to ensure meaningful therapeutic improvements over standard antiretroviral therapy, overcome challenges of designing combination approaches, and engage communities around combination HIV cure research. Conclusion: The increasing number of combination HIV cure trials brings with them a host of ethical and practical challenges. We hope our paper will inform meaningful stakeholder dialogue around the use of combinatorial HIV cure research approaches. To protect the public trust in HIV cure research, considerations should be periodically revisited and updated with key stakeholder input as the science continues to advance.
MeSH term(s)	HIV Infections/drug therapy ; Humans ; Qualitative Research ; Research Personnel ; United States
Language	English
Publishing date	2021-10-18
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2173450-1
ISSN	1742-6405 ; 1742-6405
ISSN (online)	1742-6405
ISSN	1742-6405
DOI	10.1186/s12981-021-00401-8
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Article ; Online: SARS-CoV-2 Booster Vaccination for Participants in "HIV Cure"-Related Clinical Trials.

Peluso, Michael J / Williams, Meghann C / Campbell, Danielle M / Dee, Lynda / Taylor, Jeff / Ngo, Lynn H / Hoh, Rebecca / Dubé, Karine / Sauceda, John A / Deeks, Steven G

Journal of acquired immune deficiency syndromes (1999)

2022 Volume 89, Issue 3, Page(s) e30

MeSH term(s)	Antibodies, Viral ; COVID-19 ; Clinical Trials as Topic ; HIV Infections/drug therapy ; HIV Infections/prevention & control ; Humans ; SARS-CoV-2 ; Vaccination
Chemical Substances	Antibodies, Viral
Language	English
Publishing date	2022-02-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	645053-2
ISSN	1944-7884 ; 1077-9450 ; 0897-5965 ; 0894-9255 ; 1525-4135
ISSN (online)	1944-7884 ; 1077-9450
ISSN	0897-5965 ; 0894-9255 ; 1525-4135
DOI	10.1097/QAI.0000000000002875
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Article ; Online: Tumor bed extending to margins in breast cancer specimens after neoadjuvant chemotherapy: Incidence and clinical significance.

Ngo, Marie-Hélène / Gervais, Mai-Kim / Leblanc, Guy / Dubé, Pierre / Sidéris, Lucas / Yassa, Michael / Guilbert, Marie-Christine

Annals of diagnostic pathology

2022 Volume 61, Page(s) 152060

Abstract: Background: Pathologic examination of post-neoadjuvant chemotherapy (NAC) breast surgical specimens includes assessment of margins. It has been recommended that tumor bed (TB) changes extending to margins should be documented; however, its' incidence ... ...

Abstract	Background: Pathologic examination of post-neoadjuvant chemotherapy (NAC) breast surgical specimens includes assessment of margins. It has been recommended that tumor bed (TB) changes extending to margins should be documented; however, its' incidence and clinical significance have not yet been established. The aim of our study was to gather prognostic data on this histological finding. Design: We retrospectively identified all cases where TB was reported at margin. Cases where margins were also positive for invasive carcinoma or DCIS were excluded. Results: From 2016 to 2019, 115 cases of NAC treated breast cancers were identified with 21 having at least one margin positive for TB after initial surgery (incidence of 18.3 %). Five cases were estrogen receptor (ER)-/HER2-, 9 were HER2+ and 7 were ER+/HER2-. Nineteen patients underwent partial mastectomy and 2 underwent total mastectomy. Nine patients had a pathological complete response (pCR).Ten cases had more than one positive margin for TB. None of the 21 patients underwent a second surgery for margin re-excision. Twenty patients received adjuvant therapy. With an average follow-up of 28.1 months, there has been one local recurrence. Four other patients developed metastatic disease, one of which died of the disease. The rates of locoregional and distant recurrence and mortality were statistically similar to those from patients whose margins were negative for TB. Conclusions: Our results suggest low risk of local recurrence when a positive margin for TB is not re-excised. Further data and follow-up will be needed to confirm the adequacy of conservative management in this setting.
MeSH term(s)	Humans ; Female ; Neoadjuvant Therapy ; Breast Neoplasms/drug therapy ; Breast Neoplasms/surgery ; Breast Neoplasms/pathology ; Incidence ; Retrospective Studies ; Mastectomy ; Mastectomy, Segmental/methods ; Margins of Excision ; Receptors, Estrogen ; Neoplasm Recurrence, Local/pathology
Chemical Substances	Receptors, Estrogen
Language	English
Publishing date	2022-10-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	1440011-x
ISSN	1532-8198 ; 1092-9134
ISSN (online)	1532-8198
ISSN	1092-9134
DOI	10.1016/j.anndiagpath.2022.152060
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Article ; Online: Informing efforts beyond tailored promotional campaigns by understanding contextual factors shaping vaccine hesitancy among equity-deserving populations in Canada

Lena G. Nascimento / Ève Dubé / Kathleen E. Burns / Patrick Brown / Michael Calnan / Paul R. Ward / Eric Filice / Hoda Herati / Nnenna A. U. Ike / Bobbi Rotolo / Samantha B. Meyer

International Journal for Equity in Health, Vol 22, Iss 1, Pp 1-

an exploratory qualitative study

2023 Volume 13

Abstract: Abstract Background Vaccine hesitancy exists on a continuum ranging between complete adherence and complete refusal due to doubts or concerns within a heterogeneous group of individuals. Despite widespread acknowledgement of the contextual factors ... ...

Abstract	Abstract Background Vaccine hesitancy exists on a continuum ranging between complete adherence and complete refusal due to doubts or concerns within a heterogeneous group of individuals. Despite widespread acknowledgement of the contextual factors influencing attitudes and beliefs shaping COVID-19 vaccine hesitancy, qualitative research with equity-deserving groups, accounting for unique lived experiences, remains a gap in the literature. We aim to identify and begin to understand and document the unique contextual factors shaping hesitancy by equity-deserving groups as it relates to relationships with government and health authorities. Methods Participants were recruited and interviewed between Aug-Dec 2021. Semi-structured interviews using a convergent interviewing technique were conducted with individuals from the general population, as well as individuals who identify as First Nations, Métis, or Inuit, members of the LGBT2SQ + community, low-income Canadians, Black Canadians, and newcomers. Interviews were audio recorded and transcribed by a team of researchers. Memos were written following interviews and used to complement the thematic analysis of the interview data. Themes are presented in the results section. Results The rationale for hesitancy among equity-deserving groups is consistent with literature documenting hesitancy in the general population. Contextual factors surrounding equity-deserving groups’ attitudes and beliefs, however, are unique and relate to a history of oppression, discrimination, and genocide. We identified factors unique to subgroups; for example, religious or fatalistic beliefs among participant who identify as FNMI, fear associated with lack of testing and speed of vaccines’ production among participants who identify as FNMI, Black, and LGBT2SQ + , distrust of the healthcare system for LGBT2SQ + and Black Canadians, and distrust of the government and opposition to vaccine mandates for participating who identify as LGBT2SQ + , low-income, FNMI, or Black Canadian. Newcomers stood ...
Keywords	COVID-19 ; Equity-deserving groups ; Marginalized groups ; Canada ; Vaccine hesitancy ; Contextual factors ; Public aspects of medicine ; RA1-1270
Subject code	360
Language	English
Publishing date	2023-10-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: A collaborative, multidisciplinary approach to HIV transmission risk mitigation during analytic treatment interruption.

Peluso, Michael J / Dee, Lynda / Campbell, Danielle / Taylor, Jeff / Hoh, Rebecca / Rutishauser, Rachel L / Sauceda, John / Deeks, Steven G / Dubé, Karine

Journal of virus eradication

2020 Volume 6, Issue 1, Page(s) 34–37

Abstract: Analytic treatment interruptions (ATIs) are currently the standard for assessing the impact of experimental interventions aimed at inducing sustained antiretroviral therapy (ART)-free remission in trials related to HIV cure. ATIs are associated with ... ...

Abstract	Analytic treatment interruptions (ATIs) are currently the standard for assessing the impact of experimental interventions aimed at inducing sustained antiretroviral therapy (ART)-free remission in trials related to HIV cure. ATIs are associated with substantial risk to both study participants and their sexual partner(s). Two documented HIV transmissions occurring in the context of ATIs have been recently reported, but recommendations for mitigating the risk of such events during ATIs are limited. We outline a practical approach to risk mitigation during ATI studies and describe strategies we are utilising in an upcoming clinical trial that may be applicable to other centres.
Language	English
Publishing date	2020-02-20
Publishing country	England
Document type	Editorial
ZDB-ID	2868549-0
ISSN	2055-6659 ; 2055-6640
ISSN (online)	2055-6659
ISSN	2055-6640
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Article ; Online: Supramolecular Relay-Control of Organocatalysis with a Hemithioindigo-Based Molecular Motor.

Grill, Kerstin / Dube, Henry

Journal of the American Chemical Society

2020 Volume 142, Issue 45, Page(s) 19300–19307

Abstract: ... without direct interference by the motor. As an example the organocatalysed Michael addition reaction between ... of this approach presents further advantages, e.g., for easy tailoring of conditions or facile exchange ...

Abstract	Integration of individual molecular components such as molecular motors or switches into larger meta-functional systems represents a current challenge at the forefront of molecular machine research. Here we present a modular supramolecular approach to relay the photoinduced geometry changes of a hemithioindigo based molecular motor into catalytic efficiency of a chemical reaction. Using the intrinsic chemical nature of the motor for recognition of different hydrogen-bonding organocatalysts a greater than 10-fold modulation in binding affinity is achieved upon photoisomerization. This change in affinity is then translated effectively into control of catalytic competence of the organocatalysts without direct interference by the motor. As an example the organocatalysed Michael addition reaction between nitrostyrene and 3-methoxy-dimethyl aniline was modulated in situ by visible light irradiation. Thus, dynamic and reversible remote control of catalytic processes by the switching capacity of a hemithioindigo molecular motor is established in a multicomponent chemical system. The high intrinsic modularity of this approach presents further advantages, e.g., for easy tailoring of conditions or facile exchange of catalysts and reactions. These results represent a first stepping stone into integrated chemical networks regulated by molecular machines in a fully dynamic way.
Language	English
Publishing date	2020-10-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.0c09519
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