RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse.

Eukaryotic genomes contain many nongenic elements that function in gene regulation, chromosome organization, recombination, repair, or replication, and mutation of those elements can affect genome function and cause disease. Although numerous epigenomic studies provide high coverage of gene regulatory regions, those data are not usually exposed in traditional genome annotation and can be difficult to access and interpret without field-specific expertise. The National Center for Biotechnology Information (NCBI) therefore provides RefSeq Functional Elements (RefSeqFEs), which represent experimentally validated human and mouse nongenic elements derived from the literature. The curated data set is comprised of richly annotated sequence records, descriptive records in the NCBI Gene database, reference genome feature annotation, and activity-based interactions between nongenic regions, target genes, and each other. The data set provides succinct functional details and transparent experimental evidence, leverages data from multiple experimental sources, is readily accessible and adaptable, and uses a flexible data model. The data have multiple uses for basic functional discovery, bioinformatics studies, genetic variant interpretation; as known positive controls for epigenomic data evaluation; and as reference standards for functional interactions. Comparisons to other gene regulatory data sets show that the RefSeqFE data set includes a wider range of feature types representing more areas of biology, but it is comparatively smaller and subject to data selection biases. RefSeqFEs thus provide an alternative and complementary resource for experimentally assayed functional elements, with future data set growth expected.

Amplification- and Enzyme-Free Magnetic Diagnostics Circuit for Whole-Genome Detection of SARS-CoV-2 RNA.

Polymerase chain reaction (PCR) requires thermal cycling and enzymatic reactions for sequence amplification, hampering their applications in point-of-care (POC) settings. Magnetic bioassays based on magnetic particle spectroscopy (MPS) and magnetic nanoparticles (MNPs) are isothermal, wash-free, and can be quantitative. Realizing them amplification- and enzyme-free on a benchtop device, they will become irreplaceable for POC applications. Here we demonstrate a first-in-class magnetic signal amplification circuit (MAC) that enables detection of whole genome of SARS-CoV-2 by combining the specificity of toehold-mediated DNA strand displacement with the magnetic response of MNPs to declustering processes. Using MAC, we detect the N gene of SARS-CoV-2 samples at a concentration of 104 RNA copies/µl as determined by droplet digital PCR. Further, we demonstrate that MAC can reliably distinguish between SARS-CoV-2 and other human coronaviruses. Being a wash-, amplification- and enzyme-free biosensing concept and working at isothermal conditions (25 °C) on a low-cost benchtop MPS device, our MAC biosensing concept offers several indispensable features for translating nucleic acid detection to POC applications.

Decoupling the Characteristics of Magnetic Nanoparticles for Ultrahigh Sensitivity.

Immunoassays exploiting magnetization dynamics of magnetic nanoparticles are highly promising for mix-and-measure, quantitative, and point-of-care diagnostics. However, how single-core magnetic nanoparticles can be employed to reduce particle concentration and concomitantly maximize assay sensitivity is not fully understood. Here, we design monodisperse Néel and Brownian relaxing magnetic nanocubes (MNCs) of different sizes and compositions. We provide insights into how to decouple physical properties of these MNCs to achieve ultrahigh sensitivity. We find that tricomponent-based Zn0.06Co0.80Fe2.14O4 particles, with out-of-phase to initial magnetic susceptibility χ″/χ0 ratio of 0.47 out of 0.50 for magnetically blocked ideal particles, show the ultrahigh magnetic sensitivity by providing a rich magnetic particle spectroscopy (MPS) harmonics spectrum despite bearing lower saturation magnetization than dicomponent Zn0.1Fe2.9O4 having high saturation magnetization. The Zn0.06Co0.80Fe2.14O4 MNCs, coated with catechol-based poly(ethylene glycol) ligands, measured by our benchtop MPS show 3 orders of magnitude better particle LOD than that of commercial nanoparticles of comparable size.

Scale-dependent particle diffusivity and apparent viscosity in polymer solutions as probed by dynamic magnetic nanorheology.

In several upcoming rheological approaches, including methods of micro- and nanorheology, the measurement geometry is of critical impact on the interpretation of the results. The relative size of the probe objects employed (as compared to the intrinsic length scales of the sample to be investigated) becomes of crucial importance, and there is increasing interest to investigate the dynamic processes and mobility in nanostructured materials. A combination of different rheological approaches based on the rotation of magnetically blocked nanoprobes is used to systematically investigate the size-dependent diffusion behavior in aqueous poly(ethylene glycol) (PEG) solutions with special attention paid to the relation of probe size to characteristic length scales within the polymer solutions. We employ two types of probe particles: nickel rods of hydrodynamic length Lh between 200 nm and 650 nm, and cobalt ferrite spheres with diameter dh between 13 nm and 23 nm, and examine the influence of particle size and shape on the nanorheological information obtained in model polymer solutions based on two related, dynamic-magnetic approaches. The results confirm that as long as the investigated solutions are not entangled, and the particles are much larger than the macromolecular correlation length, a good accordance between macroscopic and nanoscopic results, whereas a strong size-dependent response is observed in cases where the particles are of similar size or smaller than the radius of gyration Rg or the correlation length ξ of the polymer solution.

Magnetic nanoparticle-based biomolecule imaging with a scanning magnetic particle spectrometer.

This study reports on a wash-free, inexpensive and sensitive approach of biomolecule imaging with magnetic nanoparticles (MNPs) via a custom-built scanning magnetic particle spectrometer (SMPS). Streptavidin-coated MNPs are used as magnetic biomarkers for the detection of Immunoglobulin G (IgG) conjugated with biotin (IgG-Biotin) while five samples with different-concentration IgG-Biotin are prepared for experiments. The measurements of the ac susceptibility indicate that the conjugation of the IgG-Biotin onto the surface of the MNPs forms cross-linking between the MNPs, thus increasing the characteristic Brownian relaxation time from 0.627 to 1.448 ms. The ratio of the 3rd to the 1st harmonics is measured on the samples with different-concentration IgG-Biotin in ac magnetic fields with a frequency ranging from about 300 Hz to 2 kHz. It shows that the measurement sensitivity of the IgG-Biotin concentration decreases from 4.62 × 10-3 to 0.39 × 10-3 nM-1 with increasing excitation frequency. Phantom images of the harmonic ratio, measured with the SMPS, indicate that unbound and bound MNPs can be easily distinguished. Furthermore, the excitation frequency dependence of the contrast-to-noise ratio of the images is discussed based on the measurement sensitivity and the standard deviation of the measured image intensity. This study demonstrates the feasibility of the SMPS for imaging biomolecules bound onto the MNPs, which is of great interest to disease diagnostics and therapy.

Fe2+ Deficiencies, FeO Subdomains, and Structural Defects Favor Magnetic Hyperthermia Performance of Iron Oxide Nanocubes into Intracellular Environment.

Herein, by studying a stepwise phase transformation of 23 nm FeO-Fe3O4 core-shell nanocubes into Fe3O4, we identify a composition at which the magnetic heating performance of the nanocubes is not affected by the medium viscosity and aggregation. Structural and magnetic characterizations reveal the transformation of the FeO-Fe3O4 nanocubes from having stoichiometric phase compositions into Fe2+-deficient Fe3O4 phases. The resultant nanocubes contain tiny compressed and randomly distributed FeO subdomains as well as structural defects. This phase transformation causes a 10-fold increase in the magnetic losses of the nanocubes, which remain exceptionally insensitive to the medium viscosity as well as aggregation unlike similarly sized single-phase magnetite nanocubes. We observe that the dominant relaxation mechanism switches from Néel in fresh core-shell nanocubes to Brownian in partially oxidized nanocubes and once again to Néel in completely treated nanocubes. The Fe2+ deficiencies and structural defects appear to reduce the magnetic energy barrier and anisotropy field, thereby driving the overall relaxation into Néel process. The magnetic losses of these nanoparticles remain unchanged through a progressive internalization/association to ovarian cancer cells. Moreover, the particles induce a significant cell death after being exposed to hyperthermia treatment. Here, we present the largest heating performance that has been reported to date for 23 nm iron oxide nanoparticles under intracellular conditions. Our findings clearly demonstrate the positive impacts of the Fe2+ deficiencies and structural defects in the Fe3O4 structure on the heating performance into intracellular environment.

Homogeneous Biosensing Based on Magnetic Particle Labels.

The growing availability of biomarker panels for molecular diagnostics is leading to an increasing need for fast and sensitive biosensing technologies that are applicable to point-of-care testing. In that regard, homogeneous measurement principles are especially relevant as they usually do not require extensive sample preparation procedures, thus reducing the total analysis time and maximizing ease-of-use. In this review, we focus on homogeneous biosensors for the in vitro detection of biomarkers. Within this broad range of biosensors, we concentrate on methods that apply magnetic particle labels. The advantage of such methods lies in the added possibility to manipulate the particle labels by applied magnetic fields, which can be exploited, for example, to decrease incubation times or to enhance the signal-to-noise-ratio of the measurement signal by applying frequency-selective detection. In our review, we discriminate the corresponding methods based on the nature of the acquired measurement signal, which can either be based on magnetic or optical detection. The underlying measurement principles of the different techniques are discussed, and biosensing examples for all techniques are reported, thereby demonstrating the broad applicability of homogeneous in vitro biosensing based on magnetic particle label actuation.

Prehospital anaesthesia performed by physician/critical care paramedic teams in a major trauma network in the UK: a 12†month review of practice.

INTRODUCTION: In the West Midlands region of the UK, delivery of pre-hospital care has been remodelled through introduction of a 24 h Medical Emergency Response Incident Team (MERIT). Teams including physicians and critical care paramedics (CCP) are deployed to incidents on land-based and helicopter-based platforms. Clinical practice, including delivery of rapid sequence induction of anaesthesia (RSI), is underpinned by standard operating procedures (SOP). This study describes the first 12 months experience of prehospital RSI in the MERIT scheme in the West Midlands. METHODS: Retrospective review of the MERIT clinical database for the 12 months following the launch of the scheme. Data was collected relating to the number of RSIs performed; indication for RSI; number of intubation attempts; grade of view on laryngoscopy and the base speciality/grade of the operator performing intubation. RESULTS: MERIT teams were activated 1619 times, attending scene in 1029 cases. RSI was performed 142 times (13.80% of scene attendances). There was one recorded case of failure to intubate requiring insertion of a supraglottic airway device (0.70%). In over a third of RSI cases, CCPs performed laryngoscopy and intubation (n=53, 37.32%). Proficiency of obtaining Grade I view at laryngoscopy was similar for physicians (74.70%) and CCPs (77.36%). Intubation was successful at the first attempt in over 90% of cases. CONCLUSIONS: This study demonstrates that operation within a system that provides high levels of exposure, underpinned by comprehensive and robust training and governance frameworks, promotes levels of performance in successful prehospital RSI regardless of base speciality or profession.

Classification of Magnetic Nanoparticle Systems--Synthesis, Standardization and Analysis Methods in the NanoMag Project.

This study presents classification of different magnetic single- and multi-core particle systems using their measured dynamic magnetic properties together with their nanocrystal and particle sizes. The dynamic magnetic properties are measured with AC (dynamical) susceptometry and magnetorelaxometry and the size parameters are determined from electron microscopy and dynamic light scattering. Using these methods, we also show that the nanocrystal size and particle morphology determines the dynamic magnetic properties for both single- and multi-core particles. The presented results are obtained from the four year EU NMP FP7 project, NanoMag, which is focused on standardization of analysis methods for magnetic nanoparticles.

Polymer/Iron Oxide Nanoparticle Composites--A Straight Forward and Scalable Synthesis Approach.

Magnetic nanoparticle systems can be divided into single-core nanoparticles (with only one magnetic core per particle) and magnetic multi-core nanoparticles (with several magnetic cores per particle). Here, we report multi-core nanoparticle synthesis based on a controlled precipitation process within a well-defined oil in water emulsion to trap the superparamagnetic iron oxide nanoparticles (SPION) in a range of polymer matrices of choice, such as poly(styrene), poly(lactid acid), poly(methyl methacrylate), and poly(caprolactone). Multi-core particles were obtained within the Z-average size range of 130 to 340 nm. With the aim to combine the fast room temperature magnetic relaxation of small individual cores with high magnetization of the ensemble of SPIONs, we used small (<10 nm) core nanoparticles. The performed synthesis is highly flexible with respect to the choice of polymer and SPION loading and gives rise to multi-core particles with interesting magnetic properties and magnetic resonance imaging (MRI) contrast efficacy.

Direct protein detection in the sample solution by monitoring rotational dynamics of nickel nanorods.

The feasibility of a recently introduced homogeneous immunodiagnostic approach to directly detect analyte binding by optical observation of the hydrodynamic properties of magnetically rotated nanorods ("PlasMag") is demonstrated experimentally. Specifically, it is shown that the phase lag of the long axis of nickel nanorods (magnetic core parameters: length 182 nm, diameter 26 nm) with respect to externally applied rotating magnetic fields significantly increases on the adhesion of bovine serum albumin (BSA) protein to their surfaces. To validate these results, the amount of bound protein molecules is independently determined by analysis of the electrophoretic mobility of the nanorods. Furthermore, the data also demonstrate the applicability of recently developed empirical models based on numerical solutions of the Fokker-Planck equation for describing the dynamics of magnetic nanoparticles in rotating magnetic fields.

Self-consistent magnetic properties of magnetite tracers optimized for magnetic particle imaging measured by ac susceptometry, magnetorelaxometry and magnetic particle spectroscopy.

Sensitivity and spatial resolution in Magnetic Particle Imaging are affected by magnetic properties of the nanoparticle tracers used during imaging. Here, we have carried out a comprehensive magnetic characterization of single-core iron oxide nanoparticles that were designed for MPI. We used ac susceptometry, fluxgate magnetorelaxometry, and magnetic particle spectroscopy to evaluate the tracer's magnetic core size, hydrodynamic size, and magnetic anisotropy. Our results present a self-consistent set of magnetic and structural parameters for the tracers that is consistent with direct measurements of size using transmission electron microscopy and dynamic light scattering and that can be used to better understand their MPI performance.

Tuning the magnetic properties of metal oxide nanocrystal heterostructures by cation exchange.

For three types of colloidal magnetic nanocrystals, we demonstrate that postsynthetic cation exchange enables tuning of the nanocrystal's magnetic properties and achieving characteristics not obtainable by conventional synthetic routes. While the cation exchange procedure, performed in solution phase approach, was restricted so far to chalcogenide based semiconductor nanocrystals, here ferrite-based nanocrystals were subjected to a Fe(2+) to Co(2+) cation exchange procedure. This allows tracing of the compositional modifications by systematic and detailed magnetic characterization. In homogeneous magnetite nanocrystals and in gold/magnetite core shell nanocrystals the cation exchange increases the coercivity field, the remanence magnetization, as well as the superparamagnetic blocking temperature. For core/shell nanoheterostructures a selective doping of either the shell or predominantly of the core with Co(2+) is demonstrated. By applying the cation exchange to FeO/CoFe(2)O(4) core/shell nanocrystals the Neél temperature of the core material is increased and exchange-bias effects are enhanced so that vertical shifts of the hysteresis loops are obtained which are superior to those in any other system.

Cooperative dynamics of DNA-grafted magnetic nanoparticles optimize magnetic biosensing and coupling to DNA origami.

Magnetic nanoparticles (MNPs) provide new opportunities for enzyme-free biosensing of nucleic acid biomarkers and magnetic actuation by patterning on DNA origami, yet how the DNA grafting density affects their dynamics and accessibility remains poorly understood. Here, we performed surface functionalization of MNPs with single-stranded DNA (ssDNA) via click chemistry with a tunable grafting density, which enables the encapsulation of single MNPs inside a functional polymeric layer. We used several complementary methods to show that particle translational and rotational dynamics exhibit a sigmoidal dependence on the ssDNA grafting density. At low densities, ssDNA strands adopt a coiled conformation that results in minor alterations to particle dynamics, while at high densities, they organize into polymer brushes that collectively influence particle dynamics. Intermediate ssDNA densities, where the dynamics are most sensitive to changes, show the highest magnetic biosensing sensitivity for the detection of target nucleic acids. Finally, we demonstrate that MNPs with high ssDNA grafting densities are required to efficiently couple to DNA origami. Our results establish ssDNA grafting density as a critical parameter for the functionalization of MNPs for magnetic biosensing and functionalization of DNA nanostructures.

Robust approaches for model-free small-angle scattering data analysis.

The small-angle neutron scattering data of nanostructured magnetic samples contain information regarding their chemical and magnetic properties. Often, the first step to access characteristic magnetic and structural length scales is a model-free investigation. However, due to measurement uncertainties and a restricted q range, a direct Fourier transform usually fails and results in ambiguous distributions. To circumvent these problems, different methods have been introduced to derive regularized, more stable correlation functions, with the indirect Fourier transform being the most prominent approach. Here, the indirect Fourier transform is compared with the singular value decomposition and an iterative algorithm. These approaches are used to determine the correlation function from magnetic small-angle neutron scattering data of a powder sample of iron oxide nanoparticles; it is shown that with all three methods, in principle, the same correlation function can be derived. Each method has certain advantages and disadvantages, and thus the recommendation is to combine these three approaches to obtain robust results.

New Insights in the Occurrence of Venous Thromboembolism in Critically Ill Patients with COVID-19-A Large Postmortem and Clinical Analysis.

Critically ill COVID-19 patients are at high risk for venous thromboembolism (VTE), namely deep vein thrombosis (DVT) and/or pulmonary embolism (PE), and death. The optimal anticoagulation strategy in critically ill patients with COVID-19 remains unknown. This study investigated the ante mortem incidence as well as postmortem prevalence of VTE, the factors predictive of VTE, and the impact of changed anticoagulation practice on patient survival. We conducted a consecutive retrospective analysis of postmortem COVID-19 (n = 64) and non-COVID-19 (n = 67) patients, as well as ante mortem COVID-19 (n = 170) patients admitted to the University Medical Center Hamburg-Eppendorf (Hamburg, Germany). Baseline patient characteristics, parameters related to the intensive care unit (ICU) stay, and the clinical and autoptic presence of VTE were evaluated and statistically compared between groups. The occurrence of VTE in critically ill COVID-19 patients is confirmed in both ante mortem (17%) and postmortem (38%) cohorts. Accordingly, comparing the postmortem prevalence of VTE between age- and sex-matched COVID-19 (43%) and non-COVID-19 (0%) cohorts, we found the statistically significant increased prevalence of VTE in critically ill COVID-19 cohorts (p = 0.001). A change in anticoagulation practice was associated with the statistically significant prolongation of survival time (HR: 2.55, [95% CI 1.41-4.61], p = 0.01) and a reduction in VTE occurrence (54% vs. 25%; p = 0.02). In summary, in the autopsy as well as clinical cohort of critically ill patients with COVID-19, we found that VTE was a frequent finding. A change in anticoagulation practice was associated with a statistically significantly prolonged survival time.

Toward Rapid and Sensitive Detection of SARS-CoV-2 with Functionalized Magnetic Nanoparticles.

The outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) threatens global medical systems and economies and rules our daily living life. Controlling the outbreak of SARS-CoV-2 has become one of the most important and urgent strategies throughout the whole world. As of October 2020, there have not yet been any medicines or therapies to be effective against SARS-CoV-2. Thus, rapid and sensitive diagnostics is the most important measures to control the outbreak of SARS-CoV-2. Homogeneous biosensing based on magnetic nanoparticles (MNPs) is one of the most promising approaches for rapid and highly sensitive detection of biomolecules. This paper proposes an approach for rapid and sensitive detection of SARS-CoV-2 with functionalized MNPs via the measurement of their magnetic response in an ac magnetic field. For proof of concept, mimic SARS-CoV-2 consisting of spike proteins and polystyrene beads are used for experiments. Experimental results demonstrate that the proposed approach allows the rapid detection of mimic SARS-CoV-2 with a limit of detection of 0.084 nM (5.9 fmole). The proposed approach has great potential for designing a low-cost and point-of-care device for rapid and sensitive diagnostics of SARS-CoV-2.

Point-of-need detection of pathogen-specific nucleic acid targets using magnetic particle spectroscopy.

The ongoing COVID-19 pandemic stresses the need for widely available diagnostic tests for the presence of SARS-CoV-2 in individuals. Due to the limited availability of vaccines, diagnostic assays which are cheap, easy-to-use at the point-of-need, reliable and fast, are currently the only way to control the pandemic situation. Here we present a diagnostic assay for the detection of pathogen-specific nucleic acids based on changes of the magnetic response of magnetic nanoparticles: The target-mediated hybridization of modified nanoparticles leads to an increase in the hydrodynamic radius. This resulting change in the magnetic behaviour in an ac magnetic field can be measured via magnetic particle spectroscopy (MPS), providing a viable tool for the accurate detection of target nucleic acids. In this work we show that single stranded DNA can be detected in a concentration-dependent manner by these means. In addition to detecting synthetic DNA with an arbitrary sequence in a concentration down to 500 pM, we show that RNA and SARS-CoV-2-specific DNA as well as saliva as a sample medium can be used for an accurate assay. These proof-of-principle experiments show the potential of MPS based assays for the reliable and fast diagnostics of pathogens like SARS-CoV-2 in a point-of-need fashion without the need of complex sample preparation.

Static magnetic response of multicore particles.

We present theoretical calculations of the characteristics of the static magnetic response of multicore magnetic nanoparticles. These particles contain a considerable number (∼10^{2}) of single-domain magnetic nanocrystallites, which are modeled as uniformly magnetized balls with uniaxial magnetocrystalline anisotropy, the energetic barrier of which is comparable with the thermal energy. Thus, we model a multicore magnetic nanoparticle as an ensemble of superparamagnetic nanoparticles, the position and the easy magnetization axis of which are fixed but randomly distributed. Summing up the magnetic moments of the nanocrystallites inside a multicore particle, we thus obtain the magnetic moment of the multicore particle under the assumption that magnetic interactions between the nanocrystallites can be neglected. It is found that the weak-field magnetic response of these multicore particles is independent of anisotropy constant. The model is compared with recent experimental data and good agreement is found.

The Dissociation Rate of Acetylacetonate Ligands Governs the Size of Ferrimagnetic Zinc Ferrite Nanocubes.

Magnetic nanoparticles are critical to a broad range of applications from medical diagnostics and therapeutics to biotechnological processes and single-molecule manipulation. To advance these applications, facile and robust routes to synthesize highly magnetic nanoparticles over a wide size range are needed. Here, we demonstrate that changing the degassing temperature of thermal decomposition of metal acetylacetonate precursors from 90 to 25 °C tunes the size of ferrimagnetic ZnxFe3-xO4 nanocubes from 25 to 100 nm, respectively. We show that degassing at 90 °C nearly entirely removes acetylacetone ligands from the reaction, which results in an early formation of monomers and a reaction-controlled growth following LaMer's model toward small nanocubes. In contrast, degassing at 25 °C only partially dissociates acetylacetone ligands from the metal center and triggers a delayed formation of monomers, which leads to intermediate assembled structures made of tiny irregular crystallites and an eventual formation of large nanocubes via a diffusion-controlled growth mechanism. Using complementary techniques, we determine the substitution fraction x of Zn2+ to be in the range of 0.35-0.37. Our method reduces the complexity of the thermal decomposition method by narrowing the synthesis parameter space to a single physical parameter and enables fabrication of highly magnetic and uniform zinc ferrite nanocubes over a broad size range. The resulting particles are promising for a range of applications from magnetic fluid hyperthermia to actuation of macromolecules.