The Anti-Histamine Azelastine, Identified by Computational Drug Repurposing, Inhibits Infection by Major Variants of SARS-CoV-2 in Cell Cultures and Reconstituted Human Nasal Tissue.

The COVID-19 pandemic continues to pose challenges, especially with the emergence of new SARS-CoV-2 variants that are associated with higher infectivity and/or compromised protection afforded by the current vaccines. There is a high demand for additional preventive and therapeutic strategies effective against this changing virus. Repurposing of approved or clinically tested drugs can provide an immediate solution.

Nurse-Driven Assessment, Prevention, and Management of Delirium on an Acute Inpatient Neurology Unit.

Background: Delirium commonly affects hospitalized patients and is associated with increased hospital length of stay, discharge to skilled care, cost, morbidity, and mortality.

Local Problem: At our organization, there was no formal delirium assessment performed by the nursing staff outside of the intensive care unit.

Methods: Assessment of nurses' knowledge about delirium, a nurse-driven delirium screening protocol, and patient education were implemented on an adult inpatient neurology unit.

Biokinetics of Plutonium in Nonhuman Primates.

A major source of data on metabolism, excretion and retention of plutonium comes from experimental animal studies. Although old world monkeys are one of the closest living relatives to humans, certain physiological differences do exist between these nonhuman primates and humans. The objective of this paper was to describe the metabolism of plutonium in nonhuman primates using the bioassay and retention data obtained from macaque monkeys injected with plutonium citrate.

Strontium-90 Biokinetics from Simulated Wound Intakes in Non-human Primates Compared with Combined Model Predictions from National Council on Radiation Protection and Measurements Report 156 and International Commission on Radiological Protection Publication 67.

This study had a goal to evaluate the predictive capabilities of the National Council on Radiation Protection and Measurements (NCRP) wound model coupled to the International Commission on Radiological Protection (ICRP) systemic model for 90Sr-contaminated wounds using non-human primate data. Studies were conducted on 13 macaque (Macaca mulatta) monkeys, each receiving one-time intramuscular injections of 90Sr solution. Urine and feces samples were collected up to 28 d post-injection and analyzed for 90Sr activity.

Five-step authorship framework to improve transparency in disclosing contributors to industry-sponsored clinical trial publications.

Authorship guidelines have established criteria to guide author selection based on significance of contribution and helped to define associated responsibilities and accountabilities for the published findings. However, low awareness, variable interpretation, and inconsistent application of these guidelines can lead to confusion and a lack of transparency when recognizing those who merit authorship. This article describes a research project led by the Medical Publishing Insights and Practices (MPIP) Initiative to identify current challenges when determining authorship for industry-sponsored clinical trials and develop an improved approach to facilitate decision-making when recognizing authors from related publications.

Phylogeny and evolution of RNA structure.

Darwin's conviction that all living beings on Earth are related and the graph of relatedness is tree-shaped has been essentially confirmed by phylogenetic reconstruction first from morphology and later from data obtained by molecular sequencing. Limitations of the phylogenetic tree concept were recognized as more and more sequence information became available. The other path-breaking idea of Darwin, natural selection of fitter variants in populations, is cast into simple mathematical form and extended to mutation-selection dynamics.

Sec16 determines the size and functioning of the Golgi in the protist parasite, Trypanosoma brucei.

The Sec16 homologue in Trypanosoma brucei has been identified and characterized. TbSec16 colocalizes with COPII components at the single endoplasmic reticulum exit site (ERES), which is next to the single Golgi stack in the insect (procyclic) form of this organism. Depletion of TbSec16 reduces the size of the ERES and the Golgi, and slows growth and transport of a secretory marker to the cell surface; conversely, overexpression of TbSec16 increases the size of the ERES and Golgi but has no effect on growth or secretion.

Widespread purifying selection on RNA structure in mammals.

Evolutionarily conserved RNA secondary structures are a robust indicator of purifying selection and, consequently, molecular function. Evaluating their genome-wide occurrence through comparative genomics has consistently been plagued by high false-positive rates and divergent predictions. We present a novel benchmarking pipeline aimed at calibrating the precision of genome-wide scans for consensus RNA structure prediction.

Dynamic landscapes: a model of context and contingency in evolution.

Although the basic mechanics of evolution have been understood since Darwin, debate continues over whether macroevolutionary phenomena are driven by the fitness structure of genotype space or by ecological interaction. In this paper we propose a simple model capturing key features of fitness-landscape and ecological models of evolution. Our model describes evolutionary dynamics in a high-dimensional, structured genotype space with interspecies interaction.

ImOSM: intermittent evolution and robustness of phylogenetic methods.

Among the criteria to evaluate the performance of a phylogenetic method, robustness to model violation is of particular practical importance as complete a priori knowledge of evolutionary processes is typically unavailable. For studies of robustness in phylogenetic inference, a utility to add well-defined model violations to the simulated data would be helpful. We therefore introduce ImOSM, a tool to imbed intermittent evolution as model violation into an alignment.

PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences.

Motivation: Predicting RNA-RNA interactions is essential for determining the function of putative non-coding RNAs. Existing methods for the prediction of interactions are all based on single sequences. Since comparative methods have already been useful in RNA structure determination, we assume that conserved RNA-RNA interactions also imply conserved function.

Independent evaluation of optically stimulated luminescence (OSL) 'dot' dosemeters for environmental monitoring.

Optically stimulated luminescence (OSL) 'dot' dosemeters (manufactured by Landauer®) are reported to have a high degree of environmental stability, high level of sensitivity and provide wide range of dose measuring capabilities from 0.05 mGy to 100 Gy. The optical read out method is fast and relatively simple and permits repeated read out, but few studies have been performed about its application in monitoring radiation in the environment.

Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts.

An unexpectedly high number of regulatory RNAs have been recently discovered that fine-tune the function of genes at all levels of expression. We employed Genomic SELEX, a method to identify protein-binding RNAs encoded in the genome, to search for further regulatory RNAs in Escherichia coli. We used the global regulator protein Hfq as bait, because it can interact with a large number of RNAs, promoting their interaction.

Monitoring genomic sequences during SELEX using high-throughput sequencing: neutral SELEX.

Background: SELEX is a well established in vitro selection tool to analyze the structure of ligand-binding nucleic acid sequences called aptamers. Genomic SELEX transforms SELEX into a tool to discover novel, genomically encoded RNA or DNA sequences binding a ligand of interest, called genomic aptamers. Concerns have been raised regarding requirements imposed on RNA sequences undergoing SELEX selection.

The impact of single substitutions on multiple sequence alignments.

We introduce another view of sequence evolution. Contrary to other approaches, we model the substitution process in two steps. First we assume (arbitrary) scaled branch lengths on a given phylogenetic tree.

Dinucleotide controlled null models for comparative RNA gene prediction.

Background: Comparative prediction of RNA structures can be used to identify functional noncoding RNAs in genomic screens. It was shown recently by Babak et al. [BMC Bioinformatics.

Variations in backscatter observed in PMMA whole-body dosimetry slab phantoms.

Polymethyl methacrylate (PMMA) is a useful material for dosimetry phantoms in many ways including approximate tissue equivalence, stability, accessibility and ease of use. However, recent studies indicate that PMMA may have some unanticipated variation in backscatter from one phantom to another. While the reasons behind the variations have not been identified, it has been demonstrated that the backscatter from one phantom to another may vary by as much as 15%, resulting in a dosemeter response variation of as much as 5%.

Quality assurance methods and procedures used to verify consistency in calculating dose coefficients.

The development of a spallation neutron source with a mercury target will lead to the production of rare radionuclides. The dose coefficients for many of these radionuclides have not yet been published. A collaboration of universities and national labs has taken on the task of calculating dose coefficients for the rare radionuclides using the software package DCAL.

Calculation of dose coefficients for radionuclides produced in a spallation neutron source utilizing NUBASE and the evaluated nuclear structure data file databases.

Based on a mercury spallation neutron source target, the UNLV Transmutation Research Program has identified 72 radionuclides with a half-life greater than or equal to a minute as lacking an appropriate reference for a published dose coefficient according to existing radiation safety dose coefficient databases. A method was developed to compare the nuclear data presented in the ENSDF and NUBASE databases for these 72 radionuclides. Due to conflicting or lacking nuclear data in one or more of the databases, internal and external dose coefficient values have been calculated for only 14 radionuclides, which are not currently presented in Federal Guidance Reports Nos.

In silico sequence evolution with site-specific interactions along phylogenetic trees.

Motivation: A biological sequence usually has many sites whose evolution depends on other positions of the sequence, but this is not accounted for by commonly used models of sequence evolution. Here we introduce a Markov model of nucleotide sequence evolution in which the instantaneous substitution rate at a site depends on the states of other sites. Based on the concept of neighbourhood systems, our model represents a universal description of arbitrarily complex dependencies among sites.

Residential radon exposure and lung cancer: risk in nonsmokers.

Lung cancer is a disease that is almost entirely caused by smoking; hence, it is almost totally preventable. Yet there are a small percentage of cases, perhaps as many as 5 to 15%, where there are other causes. Risk factors identified for this other group include passive smoking, occupational exposure to certain chemicals and ionizing radiation, diet, and family history of cancer.

Manipulation of pulmonary prostacyclin synthase expression prevents murine lung cancer.

Inhibition of cyclooxygenase (COX) activity decreases eicosanoid production and prevents lung cancer in animal models. Prostaglandin (PG) I(2) (PGI(2), prostacyclin) is a PGH(2) metabolite with anti-inflammatory, antiproliferative, and antimetastatic properties. The instability of PGI(2) has limited its evaluation in animal models of cancer.