Metals from spacecraft reentry in stratospheric aerosol particles.

Large increases in the number of low earth orbit satellites are projected in the coming decades [L. Schulz, K.-H. Glassmeier, Adv. Space Res. 67, 1002-1025 (2021)] with perhaps 50,000 additional satellites in orbit by 2030 [GAO, Large constellations of satellites: Mitigating environmental and other effects (2022)]. When spent rocket bodies and defunct satellites reenter the atmosphere, they produce metal vapors that condense into aerosol particles that descend into the stratosphere. So far, models of spacecraft reentry have focused on understanding the hazard presented by objects that survive to the surface rather than on the fate of the metals that vaporize. Here, we show that metals that vaporized during spacecraft reentries can be clearly measured in stratospheric sulfuric acid particles. Over 20 elements from reentry were detected and were present in ratios consistent with alloys used in spacecraft. The mass of lithium, aluminum, copper, and lead from the reentry of spacecraft was found to exceed the cosmic dust influx of those metals. About 10% of stratospheric sulfuric acid particles larger than 120 nm in diameter contain aluminum and other elements from spacecraft reentry. Planned increases in the number of low earth orbit satellites within the next few decades could cause up to half of stratospheric sulfuric acid particles to contain metals from reentry. The influence of this level of metallic content on the properties of stratospheric aerosol is unknown.

Towards increased accuracy and reproducibility in SARS-CoV-2 next generation sequence analysis for public health surveillance

During the COVID-19 pandemic, SARS-CoV-2 surveillance efforts integrated genome sequencing of clinical samples to identify emergent viral variants and to support rapid experimental examination of genome-informed vaccine and therapeutic designs. Given the broad range of methods applied to generate new viral genomes, it is critical that consensus and variant calling tools yield consistent results across disparate pipelines. Here we examine the impact of sequencing technologies (Illumina and Oxford Nanopore) and 7 different downstream bioinformatic protocols on SARS-CoV-2 variant calling as part of the NIH Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV) Tracking Resistance and Coronavirus Evolution (TRACE) initiative, a public-private partnership established to address the COVID-19 outbreak. Our results indicate that bioinformatic workflows can yield consensus genomes with different single nucleotide polymorphisms, insertions, and/or deletions even when using the same raw sequence input datasets. We introduce the use of a specific suite of parameters and protocols that greatly improves the agreement among pipelines developed by diverse organizations. Such consistency among bioinformatic pipelines is fundamental to SARS-CoV-2 and future pathogen surveillance efforts. The application of analysis standards is necessary to more accurately document phylogenomic trends and support data-driven public health responses.

Remdesivir and GS-441524 retain antiviral activity against Delta, Omicron, and other emergent SARS-CoV-2 variants

Genetic variation of SARS-CoV-2 has resulted in the emergence and rapid spread of multiple variants throughout the pandemic, of which Omicron is currently the predominant variant circulating worldwide. SARS-CoV-2 variants of concern or interest (VOC/VOI) have evidence of increased viral transmission, disease severity, or decreased effectiveness of vaccines and neutralizing antibodies. Remdesivir (RDV, VEKLURY(R)) is a nucleoside analog prodrug and the first FDA-approved antiviral treatment of COVID-19. Here we present a comprehensive antiviral activity assessment of RDV and its parent nucleoside, GS-441524, against 10 current and former SARS-CoV-2 VOC/VOI clinical isolates by nucleoprotein ELISA and plaque reduction assay. Delta and Omicron variants remained susceptible to RDV and GS-441524, with EC50 values 0.31 to 0.62-fold of those observed against the ancestral WA1 isolate. All other tested variants exhibited EC50 values ranging from 0.15 to 2.3-fold of the observed EC50 values against WA1. Analysis of nearly 6 million publicly available variant isolate sequences confirmed that Nsp12, the RNA-dependent RNA polymerase (RdRp) target of RDV and GS-441524, is highly conserved across variants with only 2 prevalent changes (P323L and G671S). Using recombinant viruses, both RDV and GS-441524 retained potency against all viruses containing frequent variant substitutions or their combination. Taken together, these results highlight the conserved nature of SARS-CoV-2 Nsp12 and provide evidence of sustained SARS-CoV-2 antiviral activity of RDV and GS-441524 across the tested variants. The observed pan-variant activity of RDV supports its continued use for the treatment of COVID-19 regardless of the SARS-CoV-2 variant.

Genetic Conservation of SARS-CoV-2 RNA Replication Complex in Globally Circulating Isolates from Humans and Minks Predicts Minimal Pre-Existing Resistance to Remdesivir

Remdesivir (RDV) exhibits potent antiviral activity against SARS-CoV-2 and is currently the only drug approved for the treatment of COVID-19. However, little is currently known about the potential for pre-existing resistance to RDV and the possibility of SARS-CoV-2 genetic diversification that might impact RDV efficacy as the virus continue to spread globally. In this study, >90,000 SARS-CoV-2 sequences from globally circulating clinical isolates, including sequences from recently emerged United Kingdom and South Africa variants, and >300 from mink isolates were analyzed for genetic diversity in the RNA replication complex (nsp7, nsp8, nsp10, nsp12, nsp13, and nsp14) with a focus on the RNA-dependent RNA polymerase (nsp12), the molecular target of RDV. Overall, low genetic variation was observed with only 12 amino acid substitutions present in the entire RNA replication complex in [≥]0.5% of analyzed sequences with the highest overall frequency (82.2%) observed for nsp12 P323L that consistently increased over time. Low sequence variation in the RNA replication complex was also observed among the mink isolates. Importantly, the coronavirus Nsp12 mutations previously selected in vitro in the presence of RDV were identified in only 2 isolates (0.002%) within all the analyzed sequences. In addition, among the sequence variants observed in [≥]0.5% clinical isolates, including P323L, none were located near the established polymerase active site or sites critical for the RDV mechanism of inhibition. In summary, the low diversity and high genetic stability of the RNA replication complex observed over time and in the recently emerged SARS-CoV-2 variants suggests a minimal global risk of pre-existing SARS-CoV-2 resistance to RDV.

Verification of a Rapidly Multiplexed Circuit for Scalable Action Potential Recording.

This report presents characterizations of in vivo neural recordings performed with a CMOS multichannel neural recording chip that uses rapid multiplexing directly at the electrodes, without any pre-amplification or buffering. Neural recordings were taken from a 16-channel microwire array implanted in rodent cortex, with comparison to a gold-standard commercial bench-top recording system. We were able to record well-isolated threshold crossings from 10 multiplexed electrodes and typical local field potential waveforms from 16, with strong agreement with the standard system (average SNR = 2.59 and 3.07 respectively). For 10 electrodes, the circuit achieves an effective area per channel of 0.0077 mm2, which is >5x smaller than typical multichannel chips. Extensive characterizations of noise and signal quality are presented and compared to fundamental theory, as well as results from in vivo and in vitro experiments. By demonstrating the validation of rapid multiplexing directly at the electrodes, this report confirms it as a promising approach for reducing circuit area in massively-multichannel neural recording systems, which is crucial for scaling recording site density and achieving large-scale sensing of brain activity with high spatiotemporal resolution.

An Open, Object-Based Framework for Generating Anisotropy in Sedimentary Subsurface Models.

The spatial distribution of hydraulic properties in the subsurface controls groundwater flow and solute transport. However, many approaches to modeling these distributions do not produce geologically realistic results and/or do not model the anisotropy of hydraulic conductivity caused by bedding structures in sedimentary deposits. We have developed a flexible object-based package for simulating hydraulic properties in the subsurface-the Hydrogeological Virtual Realities (HyVR) simulation package. This implements a hierarchical modeling framework that takes into account geological rules about stratigraphic bounding surfaces and the geometry of specific sedimentary structures to generate realistic aquifer models, including full hydraulic-conductivity tensors. The HyVR simulation package can create outputs suitable for standard groundwater modeling tools (e.g., MODFLOW), is written in Python, an open-source programming language, and is openly available at an online repository. This paper presents an overview of the underlying modeling principles and computational methods, as well as an example simulation based on the Macrodispersion Experiment site in Columbus, Mississippi. Our simulation package can currently simulate porous media that mimic geological conceptual models in fluvial depositional environments, and that include fine-scale heterogeneity in distributed hydraulic parameter fields. The simulation results allow qualitative geological conceptual models to be converted into digital subsurface models that can be used in quantitative numerical flow-and-transport simulations, with the aim of improving our understanding of the influence of geological realism on groundwater flow and solute transport.

Urinary beta-trace protein gene expression analysis in type 2 diabetes mellitus patients / Análise da expressão do gene da proteína beta-traço na urina de pacientes com diabetes mellitus tipo 2

ABSTRACT Objective: To evaluate the gene expression of beta-trace protein in urine of diabetic patients, with no reduction in glomerular filtration rate, which was defined as below 60mL/min/1.73m2. Methods: Type 2 diabetes mellitus patients were recruited, and a group of non-diabetic individuals served as control. Beta-trace protein gene expression was analyzed by quantitative PCR. Blood samples were collected to establish glucose levels and baseline kidney function. Accuracy was analyzed using ROC curves. Results: Ninety type 2 diabetes mellitus patients and 20 non-diabetic individuals were recruited. The area under the curve was 0.601, sensitivity of 20% and specificity of 89.47%. Among diabetic participants, 18% showed an expression above the cutoff point. Conclusion: These results of accuracy of beta-trace protein gene expression in urine of diabetic patients are promising, although they did not achieve a higher area under the curve level.

RESUMO Objetivo: Avaliar a expressão do gene da proteína beta-traço na urina de pacientes diabéticos, sem redução na taxa de filtração glomerular, definida como abaixo de 60mL/min/1,73m2. Métodos: Foram recrutados pacientes com diabetes mellitus tipo 2, e um grupo de indivíduos não diabéticos serviu como controle. A expressão do gene da proteína beta-traço foi analisada por PCR quantitativa. Amostras de sangue foram coletadas para estabelecer níveis de glicemia e função renal inicial. A acurácia foi analisada utilizando curvas ROC. Resultados: Foram recrutados 90 pacientes com diabetes mellitus tipo 2 e 20 não diabéticos. A área sob a curva foi de 0,601, com sensibilidade de 20% e especificidade de 89,47%. Entre os diabéticos, 18% apresentaram expressão acima do ponto de corte. Conclusão: Estes resultados de acurácia da expressão do gene da proteína beta-traço na urina de pacientes diabéticos são promissores, apesar de não terem atingido um nível alto na área sob a curva.

Cadmium losses in overland flow from an agricultural soil.

Cadmium (Cd) transport in overland flow from agricultural soils is potentially important when trying to predict future soil Cd concentrations, but at present there is little information on the magnitude of loss from this pathway. This study measured Cd concentrations and fluxes in overland flow from a catchment where cattle winter-grazed a forage crop (kale) (Brassica oleracea) in year one and measurements continued in year two when the catchment was returned to pasture and grazed by sheep. Flow-weighted mean concentrations (FWMC) of total, particulate and dissolved Cd in overland flow events from the forage crop were 0.49, 0.41 and 0.08 µg L-1, respectively. In contrast, no dissolved Cd was detected in overland flow from pasture, with a FWMC of total Cd of 0.09 µg L-1. In line with the Cd concentrations, total Cd fluxes were greater from the forage crop (0.06 g Cd ha-1 year-1) than from pasture (0.04 g Cd ha-1 year-1). Cadmium losses in overland flow were relatively minor compared with those reported for other pathways such as plant uptake or subsurface flow. Further, compared to the amount of Cd that is currently added to soil in a maintenance application of phosphate fertiliser (30 kg P ha-1 year-1) which is on average 5.5 g Cd ha-1, Cd losses in overland flow represented < 1% of inputs. Measurement of Cd losses in overland flow should be undertaken at other sites to confirm the low Cd losses found in this study, along with the distribution between dissolved and particulate fractions.

Analysis of Structure-Activity Relationships Based on the Hepatitis†C Virus SLIIb Internal Ribosomal Entry Sequence RNA-Targeting GGHYRFK⋠Cu Complex.

New therapeutics for targeting the hepatitis C virus (HCV) have been released in recent years. Although they are less prone to resistance, they are still administered in cocktails as a combination of drugs targeting various aspects of the viral life cycle. Herein, we aim to contribute to an arsenal of new HCV therapeutics by targeting the HCV internal ribosomal entry sequence (IRES) RNA through the development of catalytic metallodrugs that function to degrade rather than inhibit the target molecule. Based on a previously characterized HCV IRES stem-loop IIb RNA-targeting metallopeptide Cu-GGHYrFK (1⋅Cu), an all-l analogue (3⋅Cu) and a series of additional complexes with single alanine substitutions in the targeting domain were prepared and screened to determine the influence each amino acid side chain on RNA localization and recognition, and catalytic reactivity toward the RNA. Additional substitutions of the tyrosine position in complex 3⋅Cu were also investigated. Good agreement between calculated and measured binding affinities provided support for in silico modeling of the SLIIb RNA binding site and correlations with RNA cleavage sites. Examination of the cleavage products from reaction of the Cu complexes with SLIIb provided mechanistic insights, with the first observation of the 5'-geminal diol and 5'-phosphopropenal as products through the use of a Cu⋅ATCUN catalytic motif. Together, the data yielded insights into structure-function relationships that will guide future optimization efforts.

Subsurface cadmium loss from a stony soil-effect of cow urine application.

Cadmium (Cd) losses in subsurface flow from stony soils that have received cow urine are potentially important, but poorly understood. This study investigated Cd loss from a soil under a winter dairy-grazed forage crop that was grazed either conventionally (24 h) or with restricted grazing (6 h). This provided an opportunity to test the hypothesis that urine inputs could increase Cd concentrations in drainage. It was thought this would be a result of cow urine either (i) enhancing dissolved organic carbon (DOC) concentrations via an increase in soil pH, resulting in the formation of soluble Cd-organic carbon complexes and, or (ii) greater inputs of chloride (Cl) via cow urine, promoting the formation of soluble Cd-Cl complexes. Cadmium concentrations in subsurface flow were generally low, with a spike above the water quality guidelines for a month after the 24-h grazing. Cadmium fluxes were on average 0.30 g Cd ha-1 year-1 (0.27-0.32 g Cd ha-1 year-1), in line with previous estimates for agricultural soils. The mean Cd concentration in drainage from the 24-h grazed plots was significantly higher (P < 0.05) than 6-h plots. No increase in DOC concentrations between the treatments was found. However, Cl concentrations in drainage were significantly higher (P < 0.001) from the 24-h than the 6-h grazed treatment plots, and positively correlated with Cd concentrations, and therefore, a possible mechanism increasing Cd mobility in soil. Further study is warranted to confirm the mechanisms involved and quantities of Cd lost from other systems.

Urinary beta-trace protein gene expression analysis in type 2 diabetes mellitus patients.

OBJECTIVE: To evaluate the gene expression of beta-trace protein in urine of diabetic patients, with no reduction in glomerular filtration rate, which was defined as below 60mL/min/1.73m2. METHODS: Type 2 diabetes mellitus patients were recruited, and a group of non-diabetic individuals served as control. Beta-trace protein gene expression was analyzed by quantitative PCR. Blood samples were collected to establish glucose levels and baseline kidney function. Accuracy was analyzed using ROC curves. RESULTS: Ninety type 2 diabetes mellitus patients and 20 non-diabetic individuals were recruited. The area under the curve was 0.601, sensitivity of 20% and specificity of 89.47%. Among diabetic participants, 18% showed an expression above the cutoff point. CONCLUSION: These results of accuracy of beta-trace protein gene expression in urine of diabetic patients are promising, although they did not achieve a higher area under the curve level.

Catalytic metallodrugs based on the LaR2C peptide target HCV SLIV IRES RNA.

Prior work has demonstrated the potential effectiveness of a new class of metallopeptides as catalytic metallodrugs that target HCV IRES SLIIb RNA (Cu-GGHYrFK, 1). Herein new catalytic metallodrugs (GGHKYKETDLLILFKDDYFAKKNEERK, 2; and GGHKYKETDL, 3) are described based on the LaR2C peptide that has been shown to bind to the SLIV HCV IRES domain. In vitro fluorescence assays yielded KD values ∼10 µM for both peptides and reaction of the copper derivatives with SLIV RNA demonstrated initial rates comparable across different assays as well as displaying pseudo-Michaelis-Menten behavior. The sites of reaction and cleavage mechanisms were determined by MALDI-TOF mass spectrometry. The primary site of copper-promoted SLIV cleavage is shown to occur in the vicinity of the 5'-G17C18A19C20-3' sequence that corresponds to a known binding site of the RM2 motif of the human La protein and has previously been reported to be important for viral translation. This domain also flanks the internal start codon (AUG). Both copper complexes also showed efficacy in an HCV replicon assay (IC50 = 0.75 µM for 2-Cu, and 2.17 µM for 3-Cu) and show potential for treatment of hepatitis C, complementing other marketed drugs by acting on a distinct therapeutic target by a novel mechanism of action.

The impact of lipocalin-type-prostaglandin-D-synthase as a predictor of kidney disease in patients with type 2 diabetes.

Hypertension and diabetes are clinical conditions which contribute to the development of chronic kidney disease as well as risk factors for cardiovascular events. In recent years, lipocalin-type-prostaglandin-D-synthase (beta trace protein; BTP) has increasingly been studied as an alternative to creatinine for the evaluation of renal function as well as for being a possible biomarker for cardiovascular disease. It is expected that the levels of BTP in patients with cardiovascular disease are elevated, as is the case with patients with renal dysfunction. The objective of this study is to realize a systematic review of the pertinent literature in respect to BTP as a biomarker of renal dysfunction in diabetic patients. Using the database MEDLINE, a search up to year 2014 was conducted using the follow descriptors: "lipocalin type prostaglandin d synthase" AND "diabetes"; "lipocalin type prostaglandin d synthase" and "diabetic nephropathy"; "beta trace protein" AND "diabetes"; "beta trace protein" AND "diabetic nephropathy". The criteria used for inclusion were the presence of the referring to terms in title or abstract and study conducted in humans. About 17 articles were selected, of which six articles were duplicates, and of which six articles did not investigate any possible relationship between the protein (BTP) and either diabetes or nephropathy. The final result yielded five articles to be analyzed. This review found BTP is not influenced by race, by body mass index nor by patient's sex. BTP can be considered as a reliable early biomarker of renal dysfunction in diabetics. BTP is associated with metabolic syndrome and is also associated with greater cardiovascular risk. Prospective data establishing a correlation between BTP and mortality would have been of great interest, but such articles were not found in this review.

Insight into the recognition, binding, and reactivity of catalytic metallodrugs targeting stem loop†IIb of hepatitis†C IRES RNA.

The complex Cu-GGHYrFK-amide (1-Cu) was previously reported as a novel metallotherapeutic that catalytically inactivates stem loop IIb (SLIIb) of the hepatitis C virus (HCV) internal ribosomal entry site (IRES) RNA and demonstrates significant antiviral activity in a cellular HCV replicon assay. Herein we describe additional studies focused on understanding the cleavage mechanism as well as the relationship of catalyst configuration to structural recognition and site-selective cleavage of the structured RNA motif. These are advanced by use of a combination of MALDI-TOF mass spectrometry, melting temperature determinations, and computational analysis to develop a structural model for binding and reactivity toward SLIIb of the IRES RNA. In addition, the binding, reactivity, and structural chemistry of the all-D-amino acid form of this metallopeptide, complex 2-Cu, are reported and compared with those of complex 1-Cu. In vitro RNA binding and cleavage assays for complex 2-Cu show a KD value of 76 ± 3 nM, and Michaelis-Menten parameters of kcat =0.14 ± 0.01 min(-1) and KM =7.9 ± 1.2 µM, with a turnover number exceeding 40. In a luciferase-based cellular replicon assay Cu-GGhyrfk-amide shows activity similar to that of the 1-Cu parent peptide, with an IC50 value of 1.9 ± 0.4 µM and cytotoxicity exceeding 100 µM. RT-PCR experiments confirm a significant decrease in HCV RNA levels in replicon assays for up to nine days when treated with complex 1-Cu in three-day dosing increments. This study shows the influence that the α-carbon stereocenter has for this new class of compounds, while detailed mass spectrometry and computational analyses provide new insight into the mechanisms of recognition, binding, and reactivity.

Clearspeech: a display reader for the visually handicapped.

Many domestic appliances and much office equipment is controlled using a keypad and a small digital display. Programming such devices is problematical for the blind and visually handicapped. In this paper, we describe a device that may be used to read the displays on these devices. The device is designed to accept a description of the display being read, which specifies the types and locations of elements of the display. Images are captured using a handheld webcam. Images are processed to remove the distortions due to the camera orientation. The elements of the screen are interpreted and a suitable audio output is generated. In suitably illuminated scenes, the display data is interpreted correctly in approximately 90% of the cases investigated.