Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping.

Bacterial plasmids are extensively involved in the rapid global spread of antibiotic resistance. We here present an assay, based on optical DNA mapping of single plasmids in nanofluidic channels, which provides detailed information about the plasmids present in a bacterial isolate. In a single experiment, we obtain the number of different plasmids in the sample, the size of each plasmid, an optical barcode that can be used to identify and trace the plasmid of interest and information about which plasmid that carries a specific resistance gene. Gene identification is done using CRISPR/Cas9 loaded with a guide-RNA (gRNA) complementary to the gene of interest that linearizes the circular plasmids at a specific location that is identified using the optical DNA maps. We demonstrate the principle on clinically relevant extended spectrum beta-lactamase (ESBL) producing isolates. We discuss how the gRNA sequence can be varied to obtain the desired information. The gRNA can either be very specific to identify a homogeneous group of genes or general to detect several groups of genes at the same time. Finally, we demonstrate an example where we use a combination of two gRNA sequences to identify carbapenemase-encoding genes in two previously not characterized clinical bacterial samples

an evaluation of data sources to determine the number of people living with HIV who are receiving antiretroviral therapy in Germany

Background This study aimed to determine the number of people living with HIV receiving antiretroviral therapy (ART) between 2006 and 2013 in Germany by using the available numbers of antiretroviral drug prescriptions and treatment data from the ClinSurv HIV cohort (CSH). Methods The CSH is a multi-centre, open, long-term observational cohort study with an average number of 10.400 patients in the study period 2006–2013. ART has been documented on average for 86% of those CSH patients and medication history is well documented in the CSH. The antiretroviral prescription data (APD) are reported by billing centres for pharmacies covering >99% of nationwide pharmacy sales of all individuals with statutory health insurance (SHI) in Germany (~85%). Exactly one thiacytidine-containing medication (TCM) with either emtricitabine or lamivudine is present in all antiretroviral fixed-dose combinations (FDCs). Thus, each daily dose of TCM documented in the APD is presumed to be representative of one person per day receiving ART. The proportion of non-TCM regimen days in the CSH was used to determine the corresponding number of individuals in the APD. Results The proportion of CSH patients receiving TCMs increased continuously over time (from 85% to 93%; 2006–2013). In contrast, treatment interruptions declined remarkably (from 11% to 2%; 2006–2013). The total number of HIV-infected people with ART experience in Germany increased from 31,500 (95% CI 31,000-32,000) individuals to 54,000 (95% CI 53,000-55,500) over the observation period (including 16.3% without SHI and persons who had interrupted ART). An average increase of approximately 2,900 persons receiving ART was observed annually in Germany. Conclusions A substantial increase in the number of people receiving ART was observed from 2006 to 2013 in Germany. Currently, the majority (93%) of antiretroviral regimens in the CSH included TCMs with ongoing use of FDCs. Based on these results, the future number of people receiving ART could be estimated by exclusively using TCM prescriptions, assuming that treatment guidelines will not change with respect to TCM use in ART regimens

Capital C, geometric optimization of a free-form steel gridshell towards planar quadrilateral glass units

The former Diamond-exchange building in Amsterdam, now called Capital C, is restored to its former glory and currently undergoing a major renovation. This listed building has been returned to its original design and topped with a spatial gridshell roof structure of glass and steel, designed by renowned architect office ZJA Zwarts & Jansma Architects. This paper focuses on the geometric optimization of the free-form gridshell towards planar quad glass units.   The final shape of the gridshell is determined by a parametric computer model. With a by ZJA in-house written program, the boundary conditions were defined, where after the software searches the ideal shape. In the case of Capital C, the ideal shape was a geometrical free-form shape but with planar or minimal curved quadrilateral glass. This to represent the faceted aesthetics of the diamond, representing the building’s heritage. In addition to the look, optimizing to planar glass panes also increased the feasibility and cost-efficiency of the design. During this process Octatube, as a specialist Design and Build contractor, was approached and challenged to realize this innovative and complex design.   In principle the gridshell has one repetitive structural steel connection. However due to its shape every connection is unique and itself composed of many unique parts. In the final design, approximately 1000 different steel elements and 200 different glass units are applied. With a traditional design method, where all elements are modelled one by one, a minor change to the geometric shape of the shell would lead to a large amount of labour. A time-consuming and error-prone job. Therefore the design is automated, by means of an in-house developed parametric tool by Octatube, which converts the complex basic geometry into a FEM-model and detailed production model.   The applied methods of parametric design and engineering allowed the team to not only optimize the glass-design until late in the engineering phase, incorporating a file-to-factory workflow, it also allowed for fast and very precise pre-fabrication. Not unimportant when installing a free-form glass and steel gridshell on top of a listed building in the heart of Amsterdam

Protein phosphatase 4 controls circadian clock dynamics by modulating CLOCK/BMAL1 activity

In all organisms with circadian clocks, post-translational modifications of clock proteins control the dynamics of circadian rhythms, with phosphorylation playing a dominant role. All major clock proteins are highly phosphorylated, and many kinases have been described to be responsible. In contrast, it is largely unclear whether and to what extent their counterparts, the phosphatases, play an equally crucial role. To investigate this, we performed a systematic RNAi screen in human cells and identified protein phosphatase 4 (PPP4) with its regulatory subunit PPP4R2 as critical components of the circadian system in both mammals an

Nanoconfined circular and linear DNA - equilibrium conformations and unfolding kinetics

Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of DNA from the circular to linear configuration as a light-induced double strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to which extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results fall between theoretical predictions for the extended de Gennes regime at weaker confinement and the Odijk regime at stronger confinement. We show that it is possible to directly distinguish between circular and linear DNA molecules by measuring the emission intensity from the DNA. Finally, we determine the rate of unfolding and show that this rate is larger for more confined DNA, possibly reflecting the corresponding larger difference in entropy between the circular and linear configurations.Comment: 21 pages, 7 figures, 1 tabl

Field-scale demonstration of in situ immobilization of heavy metals by injecting iron oxide nanoparticle adsorption barriers in groundwater

Remediation of heavy metal-contaminated aquifers is a challenging process because they cannot be degraded by microorganisms. Together with the usually limited effectiveness of technologies applied today for treatment of heavy metal contaminated groundwater, this creates a need for new remediation technologies. We therefore developed a new treatment, in which permeable adsorption barriers are established in situ in aquifers by the injection of colloidal iron oxides. These adsorption barriers aim at the immobilization of heavy metals in aquifers groundwater, which was assessed in a large-scale field study in a brownfield site. Colloidal iron oxide (goethite) nanoparticles were used to install an in situ adsorption barrier in a very het-erogeneous, contaminated aquifer of a brownfield in Asturias, Spain. The groundwater contained high concen-trations of heavy metals with up to 25 mg/L zinc, 1.3 mg/L lead, 40 mg/L copper, 0.1 mg/L nickel and other minor heavy metal pollutants below 1 mg/L. High amounts of zinc (>900 mg/kg), lead (>2000 mg/kg), nickel (>190 mg/kg) were also present in the sediment. Ca. 1500 kg of goethite nanoparticles of 461 ±266 nm diameter were injected at low pressure (<0.6 bar) into the aquifer through nine screened injection wells. For each injection well, a radius of influence of at least 2.5 m was achieved within 8 h, creating an in situ barrier of 22 ×3 ×9 m. Despite the extremely high heavy metal contamination and the strong heterogeneity of the aquifer, successful immobilization of contaminants was observed in the tested area. The contaminant concentrations were strongly reduced immediately after the injection and the abatement of the heavy metals continued for a total post- injection monitoring period of 189 days. The iron oxide particles were found to adsorb heavy metals even at pH-values between 4 and 6, where low adsorption would have been expected. The study demonstrated the applicability of iron oxide nanoparticles for installing adsorption barriers for containment of heavy metals in contaminated groundwater under real conditions

Field-scale demonstration of in situ immobilization of heavy metals by injecting iron oxide nanoparticle adsorption barriers in groundwater

Remediation of heavy metal-contaminated aquifers is a challenging process because they cannot be degraded by microorganisms. Together with the usually limited effectiveness of technologies applied today for treatment of heavy metal contaminated groundwater, this creates a need for new remediation technologies. We therefore developed a new treatment, in which permeable adsorption barriers are established in situ in aquifers by the injection of colloidal iron oxides. These adsorption barriers aim at the immobilization of heavy metals in aquifers groundwater, which was assessed in a large-scale field study in a brownfield site. Colloidal iron oxide (goethite) nanoparticles were used to install an in situ adsorption barrier in a very heterogeneous, contaminated aquifer of a brownfield in Asturias, Spain. The groundwater contained high concentrations of heavy metals with up to 25 mg/L zinc, 1.3 mg/L lead, 40 mg/L copper, 0.1 mg/L nickel and other minor heavy metal pollutants below 1 mg/L. High amounts of zinc (>900 mg/kg), lead (>2000 mg/kg), nickel (>190 mg/kg) were also present in the sediment. Ca. 1500 kg of goethite nanoparticles of 461 ± 266 nm diameter were injected at low pressure (< 0.6 bar) into the aquifer through nine screened injection wells. For each injection well, a radius of influence of at least 2.5 m was achieved within 8 h, creating an in situ barrier of 22 × 3 × 9 m. Despite the extremely high heavy metal contamination and the strong heterogeneity of the aquifer, successful immobilization of contaminants was observed in the tested area. The contaminant concentrations were strongly reduced immediately after the injection and the abatement of the heavy metals continued for a total post-injection monitoring period of 189 days. The iron oxide particles were found to adsorb heavy metals even at pH-values between 4 and 6, where low adsorption would have been expected. The study demonstrated the applicability of iron oxide nanoparticles for installing adsorption barriers for containment of heavy metals in contaminated groundwater under real conditions.This work was supported by H2020 EU project “Reground” Grant Agreement N◦ 641768. (www.reground-project.eu/). The authors gratefully acknowledge the valuable contribution of Sofia Credaro, who assisted in the proofreading and language editing of the manuscript. The authors thank the constructive comments by two anonymous reviewers

Hemophagocytic lymphohistiocytosis: how common and how severe is it as a complication of malaria? Retrospective case series and review of the literature

&lt;jats:title&gt;Abstract&lt;/jats:title&gt;&lt;jats:sec&gt;&lt;jats:title&gt;Background&lt;/jats:title&gt;&lt;jats:p&gt;Infection-associated secondary hemophagocytic lymphohistiocytosis (sHLH) is a potentially life-threatening hyperinflammatory condition caused by various infectious diseases. Malaria has rarely been described as trigger. The aim of this study is to collect data on frequency, clinical spectrum, and outcome of sHLH induced by malaria.&lt;/jats:p&gt;&lt;/jats:sec&gt;&lt;jats:sec&gt;&lt;jats:title&gt;Methods&lt;/jats:title&gt;&lt;jats:p&gt;We collected case numbers on malaria and malaria-associated sHLH from specialized centers in Germany from 2015 to 2022. In addition, we conducted a literature search on published cases of malaria-associated sHLH and systematically analyzed the literature regarding clinical and diagnostic criteria.&lt;/jats:p&gt;&lt;/jats:sec&gt;&lt;jats:sec&gt;&lt;jats:title&gt;Results&lt;/jats:title&gt;&lt;jats:p&gt;We obtained data from 13 centers treating 1461 malaria cases with different&lt;jats:italic&gt;Plasmodium&lt;/jats:italic&gt;species, of which 5 patients (0.34%) also were diagnosed with sHLH. The literature search revealed detailed case reports from further 51 patients and case series comprising the description of further 24 patients with malaria-associated sHLH. Most cases (48/80; 60%) were reported from Asia. The median time interval between onset of malaria symptoms and hospital admission was 7 days. Severe complications of sHLH were documented in 36% (20/56) of patients, including two patients with multiple organ failure in our case series. Only 41% (23/56) of patients received specific treatment for sHLH, nevertheless the mortality rate (CFR) of 5% is lower compared to the CFR reported for sHLH triggered by other infectious diseases (e.g., 25% in sHLH due to EBV infection).&lt;/jats:p&gt;&lt;/jats:sec&gt;&lt;jats:sec&gt;&lt;jats:title&gt;Conclusion&lt;/jats:title&gt;&lt;jats:p&gt;Malaria-associated sHLH appears to have a comparatively good prognosis but may still represent an underdiagnosed and potentially fatal complication of malaria, especially in resource-poor settings.&lt;/jats:p&gt;&lt;/jats:sec&gt

Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England.

BACKGROUND: Since its emergence in Autumn 2020, the SARS-CoV-2 Variant of Concern (VOC) B.1.1.7 (WHO label Alpha) rapidly became the dominant lineage across much of Europe. Simultaneously, several other VOCs were identified globally. Unlike B.1.1.7, some of these VOCs possess mutations thought to confer partial immune escape. Understanding when and how these additional VOCs pose a threat in settings where B.1.1.7 is currently dominant is vital. METHODS: We examine trends in the prevalence of non-B.1.1.7 lineages in London and other English regions using passive-case detection PCR data, cross-sectional community infection surveys, genomic surveillance, and wastewater monitoring. The study period spans from 31st January 2021 to 15th May 2021. FINDINGS: Across data sources, the percentage of non-B.1.1.7 variants has been increasing since late March 2021. This increase was initially driven by a variety of lineages with immune escape. From mid-April, B.1.617.2 (WHO label Delta) spread rapidly, becoming the dominant variant in England by late May. INTERPRETATION: The outcome of competition between variants depends on a wide range of factors such as intrinsic transmissibility, evasion of prior immunity, demographic specificities and interactions with non-pharmaceutical interventions. The presence and rise of non-B.1.1.7 variants in March likely was driven by importations and some community transmission. There was competition between non-B.1.17 variants which resulted in B.1.617.2 becoming dominant in April and May with considerable community transmission. Our results underscore that early detection of new variants requires a diverse array of data sources in community surveillance. Continued real-time information on the highly dynamic composition and trajectory of different SARS-CoV-2 lineages is essential to future control efforts. FUNDING: National Institute for Health Research, Medicines and Healthcare products Regulatory Agency, DeepMind, EPSRC, EA Funds programme, Open Philanthropy, Academy of Medical Sciences Bill,Melinda Gates Foundation, Imperial College Healthcare NHS Trust, The Novo Nordisk Foundation, MRC Centre for Global Infectious Disease Analysis, Community Jameel, Cancer Research UK, Imperial College COVID-19 Research Fund, Medical Research Council, Wellcome Sanger Institute

FUTURE-AI: International consensus guideline for trustworthy and deployable artificial intelligence in healthcare

Despite major advances in artificial intelligence (AI) for medicine and healthcare, the deployment and adoption of AI technologies remain limited in real-world clinical practice. In recent years, concerns have been raised about the technical, clinical, ethical and legal risks associated with medical AI. To increase real world adoption, it is essential that medical AI tools are trusted and accepted by patients, clinicians, health organisations and authorities. This work describes the FUTURE-AI guideline as the first international consensus framework for guiding the development and deployment of trustworthy AI tools in healthcare. The FUTURE-AI consortium was founded in 2021 and currently comprises 118 inter-disciplinary experts from 51 countries representing all continents, including AI scientists, clinicians, ethicists, and social scientists. Over a two-year period, the consortium defined guiding principles and best practices for trustworthy AI through an iterative process comprising an in-depth literature review, a modified Delphi survey, and online consensus meetings. The FUTURE-AI framework was established based on 6 guiding principles for trustworthy AI in healthcare, i.e. Fairness, Universality, Traceability, Usability, Robustness and Explainability. Through consensus, a set of 28 best practices were defined, addressing technical, clinical, legal and socio-ethical dimensions. The recommendations cover the entire lifecycle of medical AI, from design, development and validation to regulation, deployment, and monitoring. FUTURE-AI is a risk-informed, assumption-free guideline which provides a structured approach for constructing medical AI tools that will be trusted, deployed and adopted in real-world practice. Researchers are encouraged to take the recommendations into account in proof-of-concept stages to facilitate future translation towards clinical practice of medical AI