Protocol to longitudinally quantify SARS-CoV-2 RNA in wastewater using RT-qPCR and pepper mild mottle virus normalization.

Wastewater surveillance allows severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection levels to be tracked in a community. Here, we present a protocol to longitudinally quantify SARS-CoV-2 RNA in wastewater using quantitative reverse-transcription PCR (RT-qPCR) and pepper mild mottle virus (PMMoV) normalization. We describe steps for the pasteurization of wastewater samples, solids separation, supernatant filtration, viral precipitation and concentration, and RNA extraction. We then detail procedures for RT-qPCR, viral concentration extrapolation, PMMoV normalization, and longitudinal analysis. This protocol has the potential to be used for surveillance of other microorganisms. For complete details on the use and execution of this protocol, please refer to Sanchez Jimenez et al.1.

Inferring population dynamics in macaque cortex.

Objective.The proliferation of multi-unit cortical recordings over the last two decades, especially in macaques and during motor-control tasks, has generated interest in neural 'population dynamics': the time evolution of neural activity across a group of neurons working together. A good model of these dynamics should be able to infer the activity of unobserved neurons within the same population and of the observed neurons at future times. Accordingly, Pandarinath and colleagues have introduced a benchmark to evaluate models on these two (and related) criteria: four data sets, each consisting of firing rates from a population of neurons, recorded from macaque cortex during movement-related tasks.Approach.Since this is a discriminative-learning task, we hypothesize that general-purpose architectures based on recurrent neural networks (RNNs) trained with masking can outperform more 'bespoke' models. To capture long-distance dependencies without sacrificing the autoregressive bias of recurrent networks, we also propose a novel, hybrid architecture ('TERN') that augments the RNN with self-attention, as in transformer networks.Main results.Our RNNs outperform all published models on all four data sets in the benchmark. The hybrid architecture improves performance further still. Pure transformer models fail to achieve this level of performance, either in our work or that of other groups.Significance.We argue that the autoregressive bias imposed by RNNs is critical for achieving the highest levels of performance, and establish the state of the art on the neural latents benchmark. We conclude, however, by proposing that the benchmark be augmented with an alternative evaluation of latent dynamics that favors generative over discriminative models like the ones we propose in this report.

Wastewater surveillance in the COVID-19 post-emergency pandemic period: A promising approach to monitor and predict SARS-CoV-2 surges and evolution.

On May 24, 2023, approximately 3.5 years into the pandemic, the World Health Organization (WHO) declared the end of the COVID-19 global health emergency. However, as there are still ∼3000 COVID-19 deaths per day in May 2023, robust surveillance systems are still warranted to return to normalcy in times of low risk and respond appropriately in times of high risk. The different phases of the pandemic have been defined by infection numbers and variants, both of which have been determined through clinical tests that are subject to many biases. Unfortunately, the end of the COVID-19 emergency threatens to exasperate these biases, thereby warranting alternative tracking methods. We hypothesized that wastewater surveillance could be used as a more accurate and comprehensive method to track SARS-CoV-2 in the post-emergency pandemic period (PEPP). SARS-CoV-2 was quantified and sequenced from wastewater between June 2022 and March 2023 to research the anticipated 2022/23 winter surge. However, in the 2022/23 winter, there was lower-than-expected SARS-CoV-2 circulation, which was hypothesized to be due to diagnostic testing biases but was confirmed by our wastewater analysis, thereby emphasizing the unpredictable nature of SARS-CoV-2 surges while also questioning its winter seasonality. Even in times of low baseline circulation, we found wastewater surveillance to be sensitive enough to detect minor changes in circulation levels ∼30-46 days prior to diagnostic tests, suggesting that wastewater surveillance may be a more appropriate early warning system to prepare for unpredictable surges in the PEPP. Furthermore, sequencing of wastewater detected variants of concern that were positively correlated with clinical samples and also provided a method to identify mutations with a high likelihood of appearing in future variants, necessary for updating vaccines and therapeutics prior to novel variant circulation. Together, these data highlight the effectiveness of wastewater surveillance in the PEPP to limit the global health burden of SARS-CoV-2 due to increases in circulation and/or viral evolution.

Novel pathway for the sonochemical synthesis of silver nanoparticles with near-spherical shape and high stability in aqueous media.

The present study shows the development of a novel sonochemical synthesis pathway of sub-15 nm silver nanoparticles (AgNPs) with quasi-spherical shape and high stability in aqueous suspension. Different analytical techniques such as on-line UV-Vis spectroscopy, Atomic Force Microscopy (AFM), and Transmission Electron Microscopy (TEM) were complementarily used to characterize the evolution of the properties of AgNPs synthesized with this new route. Furthermore, different centrifugation conditions were studied to establish a practical, simple and straightforward purification method. Particle size was determined by TEM employing two different deposition methods, showing that purified AgNPs have a size of 8.1 nm ± 2.4 nm with a narrow dispersion of the size distribution (95% coverage interval from 3.4 to 13 nm). Critical information of the shape and crystalline structure of these sub-15 nm AgNPs, provided by shape descriptors (circularity and roundness) using TEM and high resolution (HR)-TEM measurements, confirmed the generation of AgNPs with quasi-spherical shapes with certain twin-fault particles promoted by the high energy of the ultrasonic treatment. Elemental analysis by TEM-EDS confirmed the high purity of the sub-15 nm AgNPs, consisting solely of Ag. At the optical level, these AgNPs showed a bandgap energy of (2.795 ± 0.002) eV. Finally, the evaluation of the effects of ultraviolet radiation (UVC: 254 nm and UVA: 365 nm) and storage temperature on the spectral stability revealed high stability of the optical properties and subsequently dimensional properties of sub-15 nm AgNPs in the short-term (600 min) and long-term (24 weeks).

New advances in the method validation, extraction methods and measurement uncertainty for the determination of water-soluble hexavalent chromium in hydraulic cement.

The quantification of Cr (VI) in the cement matrix is highly important, given the possibility of suffering illnesses including dermatitis, induced nasal carcinoma, and DNA damage produced by inhalation of and/or direct contact with this substance by construction workers. This study presents an analytical validation of the determination of water-soluble Cr (VI) using Ultraviolet-Visible Spectroscopy (UV-Vis) with 1.5-diphenylcarbazide. To do so, different performance characteristics were determined: working interval, analytical sensitivity, linearity, limits of detection (LOD) and quantification (LOQ), as well as measurement uncertainty, in order to provide better metrological information about the performance of this method. The study also focused on evaluating the impact of use of different types of standard sands (ASTM C-778 and CEN) for preparing mortar cement and extracting water soluble Cr (VI) present in the cement. For this purpose, two cements with different concentrations (2.01 ± 0.21 and 0.75 ± 0.09 mg-kg-1) of Cr (IV) were created to evaluate extraction using three types of treatments: oxidized with potassium peroxidisulfite, non-oxidized, and an alternative method using cement paste. It was observed that mortar cement using ASTM C-778 sand tends to underestimate Cr (IV) content when concentrations are below 0.8 mg kg-1, while at higher concentrations of ~2.0 mg kg-1 it does not generate different results compared to those obtained using mortar cement made with CEN-standard sand. An alternative method called "paste extraction" also showed statistically comparable results with respect to standard mortar for both concentration levels evaluated. Finally, samples of cement marketed in Costa Rica were analyzed using different types of water soluble Cr (IV) extraction methods. The results show concentrations between 0.70 ± 0.13 mg kg-1 and 1.30 ± 0.13 mg kg-1, demonstrating that they comply with the limits established by international standards and national regulations in Costa Rica.

Improving the quality control of drinking water in Nicaragua through proficiency testing in a metrological multilateral cooperation project.

The United Nations General Assembly explicitly recognized the human right to water and sanitation and acknowledged that drinking water is essential to the realization of all human rights in a 2010 resolution. Supporting and strengthening the quality infrastructure in countries throughout the world guarantees more reliable water quality analyses, thus reducing the risks to consumers' health. The present paper describes a multilateral cooperation project developed in Nicaragua to improve the country's quality infrastructure and, in turn, the quality control of drinking water. The project was developed with the support of National Metrology Institutes (NMIs) from the Inter-American Metrology System (SIM), the Physikalisch Technische Bundesanstalt (PTB) and the participation of research institutes and laboratories in Nicaragua. Several mechanisms such as awareness seminars, workshops, metrological screenings, peer review of the laboratories' quality systems, and organizing proficiency testing (PT) were used to successfully achieve the cooperation goal. As a result, technical infrastructure for the organization of PT rounds in Nicaragua was implemented to evaluate the relevant physicochemical parameters such as pH, chloride (Cl-), and nitrate (NO3-) in drinking water. The results from the PT rounds which took place during the two-year cooperation project showed substantial improvement in the performances of the participating laboratories, and therefore, in their measurement methods. Finally, this article shows how multilateral cooperation projects can strengthen the quality infrastructure, improving and ensuring the quality control of drinking water.

Delineation of Tumor Habitats based on Dynamic Contrast Enhanced MRI.

Tumor heterogeneity can be elucidated by mapping subregions of the lesion with differential imaging characteristics, called habitats. Dynamic Contrast Enhanced (DCE-)MRI can depict the tumor microenvironments by identifying areas with variable perfusion and vascular permeability, since individual tumor habitats vary in the rate and magnitude of the contrast uptake and washout. Of particular interest is identifying areas of hypoxia, characterized by inadequate perfusion and hyper-permeable vasculature. An automatic procedure for delineation of tumor habitats from DCE-MRI was developed as a two-part process involving: (1) statistical testing in order to determine the number of the underlying habitats; and (2) an unsupervised pattern recognition technique to recover the temporal contrast patterns and locations of the associated habitats. The technique is examined on simulated data and DCE-MRI, obtained from prostate and brain pre-clinical cancer models, as well as clinical data from sarcoma and prostate cancer patients. The procedure successfully identified habitats previously associated with well-perfused, hypoxic and/or necrotic tumor compartments. Given the association of tumor hypoxia with more aggressive tumor phenotypes, the obtained in vivo information could impact management of cancer patients considerably.

Silver Nanoparticles: Technological Advances, Societal Impacts, and Metrological Challenges.

Silver nanoparticles (AgNPs) show different physical and chemical properties compared to their macroscale analogs. This is primarily due to their small size and, consequently, the exceptional surface area of these materials. Presently, advances in the synthesis, stabilization, and production of AgNPs have fostered a new generation of commercial products and intensified scientific investigation within the nanotechnology field. The use of AgNPs in commercial products is increasing and impacts on the environment and human health are largely unknown. This article discusses advances in AgNP production and presents an overview of the commercial, societal, and environmental impacts of this emerging nanoparticle (NP), and nanomaterials in general. Finally, we examine the challenges associated with AgNP characterization, discuss the importance of the development of NP reference materials (RMs) and explore their role as a metrological mechanism to improve the quality and comparability of NP measurements.