RT-PCR/MALDI-TOF diagnostic target performance reflects circulating SARS-CoV-2 variant diversity in New York City

As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to circulate, multiple variants of concern (VOC) have emerged. New variants pose challenges for diagnostic platforms since sequence diversity can alter primer/probe binding sites (PBS), causing false-negative results. The Agena MassARRAY® SARS-CoV-2 Panel utilizes reverse-transcription polymerase chain reaction and mass-spectrometry to detect five multiplex targets across N and ORF1ab genes. Herein, we utilize a dataset of 256 SARS-CoV-2-positive specimens collected between April 11, 2021-August 28, 2021 to evaluate target performance with paired sequencing data. During this timeframe, two targets in the N gene (N2, N3) were subject to the greatest sequence diversity. In specimens with N3 dropout, 69% harbored the Alpha-specific A28095U polymorphism that introduces a 3’-mismatch to the N3 forward PBS and increases risk of target dropout relative to specimens with 28095A (relative risk (RR): 20.02; p<0.0001; 95% Confidence Interval (CI): 11.36-35.72). Furthermore, among specimens with N2 dropout, 90% harbored the Delta-specific G28916U polymorphism that creates a 3’-mismatch to the N2 probe PBS and increases target dropout risk (RR: 11.92; p<0.0001; 95% CI: 8.17-14.06). These findings highlight the robust capability of Agena MassARRAY® SARS-CoV-2 Panel target results to reveal circulating virus diversity and underscore the power of multi-target design to capture VOC.

A Curated Cacophony: Implementing an Intangible

<p>This research investigates a progression away from acoustics formed by spaces and towards spaces that are driven by target acoustics. Despite architecture and acoustics’ shared consideration of form, materiality and inhabitation, too often acoustics is neglected from design and so is treated remedially, nullifying creativity. A case study project was undertaken to investigate the opportunities and limitations of two parametric tools, Galapagos (a generative solver) and Pachyderm (an acoustic simulation tool), to develop acoustic qualities in early architectural design. Yet, what are these acoustic qualities and how could they be measured? Testing of cafes in the Wellington CBD was undertaken to investigate these questions. Six cafes were acoustically tested and five patrons from each of these completed a subjective survey. The café testing suggested that Reverberation Time (RT) could be an effective acoustic measure to direct architectural design. The café with the lowest patron enjoyment rating also recorded the longest RT and highest Sound Pressure Level (SPL), reinforcing the relationship between these three elements. Through these findings, patron enjoyment was concluded to be dependent on SPL and SPL was concluded to be dependent on RT (Whitlock and Dodd, 424). In order to increase patron enjoyment, Galapagos was utilised to explore possible forms that met a target design RT of 0.7 seconds. An RT of 0.7 seconds was chosen as it was shorter than the AS/NZS 2107 (2000) maximum and was comparable to the cafés with the two highest subjective enjoyment ratings. Through a parametric and analogue design methodology, Galapagos and Pachyderm were used to investigate how acoustic goals could shape a café design. The case study project produced a design that not only meets this acoustic criterion but harnesses form to sculpt sound. Instead of applying absorption to flat surfaces, the convex curves on the north and east facades disperse sound, producing both a diffuse environment and an engaging architectural element. This integrated investigation demonstrated that a parametric and analogue design process can be implemented to create a acoustically and architecturally effective design.</p>

A Curated Cacophony: Implementing an Intangible

<p>This research investigates a progression away from acoustics formed by spaces and towards spaces that are driven by target acoustics. Despite architecture and acoustics’ shared consideration of form, materiality and inhabitation, too often acoustics is neglected from design and so is treated remedially, nullifying creativity. A case study project was undertaken to investigate the opportunities and limitations of two parametric tools, Galapagos (a generative solver) and Pachyderm (an acoustic simulation tool), to develop acoustic qualities in early architectural design. Yet, what are these acoustic qualities and how could they be measured? Testing of cafes in the Wellington CBD was undertaken to investigate these questions. Six cafes were acoustically tested and five patrons from each of these completed a subjective survey. The café testing suggested that Reverberation Time (RT) could be an effective acoustic measure to direct architectural design. The café with the lowest patron enjoyment rating also recorded the longest RT and highest Sound Pressure Level (SPL), reinforcing the relationship between these three elements. Through these findings, patron enjoyment was concluded to be dependent on SPL and SPL was concluded to be dependent on RT (Whitlock and Dodd, 424). In order to increase patron enjoyment, Galapagos was utilised to explore possible forms that met a target design RT of 0.7 seconds. An RT of 0.7 seconds was chosen as it was shorter than the AS/NZS 2107 (2000) maximum and was comparable to the cafés with the two highest subjective enjoyment ratings. Through a parametric and analogue design methodology, Galapagos and Pachyderm were used to investigate how acoustic goals could shape a café design. The case study project produced a design that not only meets this acoustic criterion but harnesses form to sculpt sound. Instead of applying absorption to flat surfaces, the convex curves on the north and east facades disperse sound, producing both a diffuse environment and an engaging architectural element. This integrated investigation demonstrated that a parametric and analogue design process can be implemented to create a acoustically and architecturally effective design.</p>

Response Spectrum with Uncertain Damping Using Artificial Neural Networks

It is evident that the response of linear structures under dynamic loads depends to two important dynamics parameters of structures, namely, the natural periods and structural damping. These parameters always characterize the oscillation and the energy dissipation of buildings. In fact, the values of these parameters differ significantly, before, during and after an earthquake from values selected during the design phase. This phenomenon, among other, introduces uncertainty into the building simulation process, which remarkably influences the structural response and associated performance of the structure under dynamic loads. This paper develops a new methodology to estimate the maximum absolute response for linear structures with uncertain damping using the Artificial Neural Networks (ANN) and the Monte Carlo method. The proposed method is illustrated using the target design response spectra corresponding to the EC8 for linear structures exposed to seismic loads. The numerical results revealed the practical applicability of the proposed methodology and the crucial influence of accounting the damping uncertainty in structural dynamics. Additionally, the method can be used in practice, mainly for important and special structures where uncertainty could lead to significant changes in structural response.

Structuring Free-Standing Foils for Laser-Driven Particle Acceleration Experiments

The recent development of petawatt-class laser systems sets a focus on the development of ultra-thin free-standing targets to access enhanced particle acceleration schemes vital for future applications, such as, medical and laser-driven nuclear physics. Specific strategies are required to improve the laser-to-particle energy conversion efficiency and increase the maximum particle energy. One of the promising approaches is based on the target design optimization; either by tuning key parameters which will strongly affect the laser-matter interaction process (e.g., material, composition, density, thickness, lateral dimensions, and shape) or by using micro/nanostructures on the target surface. At ELI-NP, considerable efforts are dedicated to extend the target capabilities beyond simple planar target design and develop complex targets with tailored properties suitable for high-power laser-plasma interaction experiments, as well as for studies with gamma and positrons beams. The paper provides an overview of the manufacturing capabilities currently available within ELI-NP Targets Laboratory for providing users with certain types of solid targets, specifically micro/nanostructured gold and copper foils and microns thick, porous anodized alumina. Also, optimization studies of alternative patterns (micro/nanodots) on silicon substrate are presented for future implementation on metallic free-standing thin foils.

Robust clinical detection of SARS-CoV-2 variants by RT-PCR/MALDI-TOF multi-target approach

The COVID-19 pandemic sparked rapid development of SARS-CoV-2 diagnostics. However, emerging variants pose the risk for target dropout and false-negative results secondary to primer/probe binding site (PBS) mismatches. The Agena MassARRAY SARS-CoV-2 Panel combines RT-PCR and MALDI-TOF mass-spectrometry to probe for five targets across N and ORF1ab genes, which provides a robust platform to accommodate PBS mismatches in divergent viruses. Herein, we utilize a deidentified dataset of 1,262 SARS-CoV-2-positive specimens from Mount Sinai Health System (New York City) from December 2020 through April 2021 to evaluate target results and corresponding sequencing data. Overall, the level of PBS mismatches was greater in specimens with target dropout. Of specimens with N3 target dropout, 57% harbored an A28095T substitution that is highly-specific for the alpha (B.1.1.7) variant of concern. These data highlight the benefit of redundancy in target design and the potential for target performance to illuminate the dynamics of circulating SARS-CoV-2 variants.

Generation of Tri-Directional Spectra-Compatible Time Histories Coupling the Influence Matrix Method and Gram–Schmidt Orthogonalization

This study presents a new approach for obtaining a set of tri-directional time histories compatible with target design spectra by modifying real recorded earthquake ground motions. The influence matrix method (IMM) based on eigenfunction expansion is improved for typical design response spectra with different shapes and employed in order to achieve accurate matching with the target design spectra. By applying the Gram–Schmidt orthogonalization in each iteration of the IMM procedure, the correlation coefficient between any two components can be guaranteed to be strictly zero. Hence, the generated three components in the orthogonal directions are statistically independent. The generated time histories satisfy the requirements of current codes and standards. Two examples are presented to illustrate the procedure and the superiority of the proposed method, with the maximum relative error between the generated time histories and target design spectra being less than 0.2% in [0.6, 100] Hz, and the code requirements being satisfied strictly.

Production of Cyclotron-Based Gallium-68 With Low Energy Protons: Preliminary Target Design and Cyclotron Shielding Considerations

Nuclear reactors, cyclotrons and generators are being used to produce nuclear medicine radionuclides. Radiopharmaceuticals based on Gallium-68 are widely used both experimentally and clinically in Positron Emission Tomography (PET). Currently Ga-68 is mainly produced via 68Ge/68Ga generators, which are expensive. An alternative method is by cyclotron using high enriched Zinc-68 via the 68Zn(p,n)68Ga reaction. Investigations have been conducted for producing Ga-68 using a solid target impacted with a proton beam in energies between (13–14) MeV or higher. The main interest of this work is to produce Ga-68 using energies within a lower range, therefore Ga-68 can be accessed to locations with cyclotrons of lower energy. In this article, an approach to a novel target design to get Ga-68 with low energy protons is conducted. Adequate shielding to avoid extra doses outer the cyclotron is also considered. Monte Carlo code FLUKA is used to simulate the processes of interaction of radiation with matter and the radioactive isotope production. For a beam energy of 11 MeV and current on target of 40 μA the simulated produced activity is about 69.1 GBq. The results show the feasibility of producing Ga-68 with low energy protons and self-shielding system guarantees the regulation-based dose exposition outer the cyclotron.

Systematic decomposition of sequence determinants governing CRISPR/Cas9 specificity

The specificity of CRISPR/Cas9 genome editing is largely determined by the sequences of guide RNA (gRNA) and the targeted DNA, yet the sequence-dependent rules underlying off-target effects are not fully understood. Here we systematically investigated the sequence determinants governing CRISPR/Cas9 specificity by measuring the off-on ratios of 1,902 gRNAs on 13,314 target sequences using an improved synthetic system with dual-target design. Our study revealed a comprehensive set of rules including 3 factors in CRISPR/Cas9 off-targeting: 1) the nucleotide context and position of a single mismatch; 2) an epistasis-like combinatorial effect of multiple mismatches; and 3) a guide-intrinsic mismatch tolerance (GMT) independent of the mismatch context. Notably, the combinatorial effect and GMT are associated with the free-energy landscape in R-loop formation and are explainable by a multi-state kinetic model. Based on these rules, we developed a model-based off-target prediction tool (MOFF), which showed superior performance compared to the existing methods.