Barriers and facilitators to next-generation sequencing use in United States oncology settings: a systematic review.

Next-generation sequencing (NGS) of solid tumors can inform treatment decisions; however, uptake remains low. This objective of this systematic review was to identify barriers to and facilitators of NGS in US oncology settings. Embase and MEDLINE were searched in March 2023 for articles published from 2012 to 2023 on barriers and facilitators of NGS adoption for solid tumors.

Molecular Dynamical and Quantum Mechanical Exploration of the Site-Specific Dynamics of Cy3 Dimers Internally Linked to dsDNA.

Performing spectroscopic measurements on biomolecules labeled with fluorescent probes is a powerful approach to locating the molecular behavior and dynamics of large systems at specific sites within their local environments. The indocarbocyanine dye Cy3 has emerged as one of the most commonly used chromophores. The incorporation of Cy3 dimers into DNA enhances experimental resolution owing to the spectral characteristics influenced by the geometric orientation of excitonically coupled monomeric units.

Bottlenecks to Learning Evidence-Based Practice: Recommendations for Nursing Faculty.

Background: Evidence-based practice (EBP) competency is an expected outcome of baccalaureate education; however, research indicates nursing graduates enter practice with competency gaps.

Purpose: The purpose of this study was to explore the challenges accelerated baccalaureate students experience when learning the steps of EBP.

Methods: A qualitative, descriptive design was used to identify bottlenecks to student learning.

Positive selection underlies repeated knockout of ORF8 in SARS-CoV-2 evolution.

Knockout of the ORF8 protein has repeatedly spread through the global viral population during SARS-CoV-2 evolution. Here we use both regional and global pathogen sequencing to explore the selection pressures underlying its loss. In Washington State, we identified transmission clusters with ORF8 knockout throughout SARS-CoV-2 evolution, not just on novel, high fitness viral backbones.

Exploring kidney dialysis costs in the United States: a scoping review.

Aims: The increasing prevalence of end-stage renal disease (ESRD) in the United States (US) represents a considerable economic burden due to the high cost of dialysis treatment. This review examines data from real-world studies to identify cost drivers and explore areas where dialysis costs could be reduced.

Methods: We identified and synthesized evidence published from 2016-2023 reporting direct dialysis costs in adult US patients from a comprehensive literature search of MEDLINE, Embase, and grey literature sources (e.

Spectroscopic approaches for studies of site-specific DNA base and backbone 'breathing' using exciton-coupled dimer-labeled DNA.

DNA regulation and repair processes require direct interactions between proteins and DNA at specific sites. Local fluctuations of the sugar-phosphate backbones and bases of DNA (a form of DNA 'breathing') play a central role in such processes. Here we review the development and application of novel spectroscopic methods and analyses - both at the ensemble and single-molecule levels - to study structural and dynamic properties of exciton-coupled cyanine and fluorescent nucleobase analogue dimer-labeled DNA constructs at key positions involved in protein-DNA complex assembly and function.

Using transition density models to interpret experimental optical spectra of exciton-coupled cyanine (iCy3)2 dimer probes of local DNA conformations at or near functional protein binding sites.

Exciton-coupled chromophore dimers are an emerging class of optical probes for studies of site-specific biomolecular interactions. Applying accurate theoretical models for the electrostatic coupling of a molecular dimer probe is a key step for simulating its optical properties and analyzing spectroscopic data. In this work, we compare experimental absorbance and circular dichroism (CD) spectra of 'internally-labeled' (iCy3)2 dimer probes inserted site-specifically into DNA fork constructs to theoretical calculations of the structure and geometry of these exciton-coupled dimers.

An atlas of continuous adaptive evolution in endemic human viruses.

Through antigenic evolution, viruses such as seasonal influenza evade recognition by neutralizing antibodies. This means that a person with antibodies well tuned to an initial infection will not be protected against the same virus years later and that vaccine-mediated protection will decay. To expand our understanding of which endemic human viruses evolve in this fashion, we assess adaptive evolution across the genome of 28 endemic viruses spanning a wide range of viral families and transmission modes.

Epidemiology of clinically significant forms of alpha- and beta-thalassemia: A global map of evidence and gaps.

This systematic literature review assessed the global prevalence and birth prevalence of clinically significant forms of alpha- and beta-thalassemia. Embase, MEDLINE, and the Cochrane Library were searched for observational studies published January 1, 2000, to September 21, 2021. Of 2093 unique records identified, 69 studies reported across 70 publications met eligibility criteria, including 6 records identified from bibliography searches.

Utilisation, effectiveness, and safety of immediate postpartum intrauterine device insertion: a systematic literature review.

Background: Intrauterine devices (IUDs) are highly effective contraception. IUDs inserted directly following delivery provide immediate birth control and may decrease unintended pregnancies, including short-interval pregnancies, thereby mitigating health risks and associated economic burden.

Methods: This systematic literature review included published global data on the utilisation, effectiveness, and safety of postpartum intrauterine devices (PPIUDs) of any type.

Systematic Literature Review of Real-World Effectiveness Results Data for First-Line Ibrutinib in Chronic Lymphocytic Leukemia and Small Lymphocytic Lymphoma.

Background And Objective: Ibrutinib, an oral Bruton's tyrosine kinase inhibitor, has demonstrated efficacy as a first-line treatment for chronic lymphocytic leukemia in multiple, phase III, randomized clinical trials. This systematic literature review assessed the clinical effectiveness of ibrutinib in the first-line treatment of chronic lymphocytic leukemia in real-world clinical settings.

Methods: MEDLINE, EMBASE, and relevant conference websites were searched for articles published in the USA from 1 January, 2014 to 30 June, 2020.

Burden of neutropenia and leukopenia among adult kidney transplant recipients: A systematic literature review of observational studies.

Background: Leukopenia and neutropenia (L/N) may affect treatment decisions, potentially resulting in poor clinical and economic outcomes among kidney transplant recipients (KTRs). The burden of L/N is poorly quantified systematically. This systematic literature review aimed to summarize the incidence of, risk factors for, and clinical and economic outcomes associated with L/N post-KT.

A Bayesian approach to infer recombination patterns in coronaviruses.

As shown during the SARS-CoV-2 pandemic, phylogenetic and phylodynamic methods are essential tools to study the spread and evolution of pathogens. One of the central assumptions of these methods is that the shared history of pathogens isolated from different hosts can be described by a branching phylogenetic tree. Recombination breaks this assumption.

Cost-sharing and adherence, clinical outcomes, health care utilization, and costs: A systematic literature review.

US health plans are adopting benefit designs that shift greater financial burden to patients through higher deductibles, additional copay tiers, and coinsurance. Prior systematic reviews found that higher cost was associated with reductions in both appropriate and inappropriate medications. However, these reviews were conducted prior to contemporary benefit design and medication utilization.

Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2.

The SARS-CoV-2 pandemic has resulted in numerous virus variants, some of which have altered receptor-binding or antigenic phenotypes. Here, we quantify the degree to which adaptive evolution is driving the accumulation of mutations across the genome. We correlate clade growth with mutation accumulation, compare rates of nonsynonymous to synonymous divergence, assess temporal clustering of mutations, and evaluate the evolutionary success of individual mutations.

Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2.

Given the importance of variant SARS-CoV-2 viruses with altered receptor-binding or antigenic phenotypes, we sought to quantify the degree to which adaptive evolution is driving accumulation of mutations in the SARS-CoV-2 genome. Here we assessed adaptive evolution across genes in the SARS-CoV-2 genome by correlating clade growth with mutation accumulation as well as by comparing rates of nonsynonymous to synonymous divergence, clustering of mutations across the SARS-CoV-2 phylogeny and degree of convergent evolution of individual mutations. We find that spike S1 is the focus of adaptive evolution, but also identify positively-selected mutations in other genes that are sculpting the evolutionary trajectory of SARS-CoV-2.

Accurate Modeling of Excitonic Coupling in Cyanine Dye Cy3.

Accurate modeling of excitonic coupling in molecules is of great importance for inferring the structures and dynamics of coupled systems. Cy3 is a cyanine dye that is widely used in molecular spectroscopy. Its well-separated excitation bands, high sensitivity to the surroundings, and the high energy transfer efficiency make it a perfect choice for excitonic coupling experiments.

Application of the Threshold Concept Framework in Nursing: An Integrative Review.

Background: The shift to concept-based curricula requires nurse educators to be selective with disciplinary content to avoid overburdening curricula. Although educators strive to make these concepts explicit, some learners find them troublesome. These troublesome concepts are often threshold concepts, which are critical to understanding disciplinary knowledge.

Recombination patterns in coronaviruses.

As shown during the SARS-CoV-2 pandemic, phylogenetic and phylodynamic methods are essential tools to study the spread and evolution of pathogens. One of the central assumptions of these methods is that the shared history of pathogens isolated from different hosts can be described by a branching phylogenetic tree. Recombination breaks this assumption.

Global incidence of intraventricular hemorrhage among extremely preterm infants: a systematic literature review.

Objectives: To conduct a systematic literature review to evaluate the global incidence of intraventricular hemorrhage grade 2-4 among extremely preterm infants.

Methods: We performed searches in MEDLINE and Embase for intraventricular hemorrhage and prematurity cited in English language observational studies published from May 2006 to October 2017. Included studies analyzed data from infants born at ≤28 weeks' gestational age and reported on intraventricular hemorrhage epidemiology.

An integrative review of threshold concepts in doctoral education: Implications for PhD nursing programs.

Objective: To critically analyze published research addressing threshold concepts in doctoral education, explore factors affecting conceptual threshold crossing by doctoral students, and consider the application of these findings in doctoral nursing education.

Background: Mastery of concepts specific to the research-focused doctorate is critical in order for doctoral students to become independent researchers. These threshold concepts can be challenging, or troublesome, and students may find themselves 'stuck' during the learning journey.

Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229e.

Seasonal coronaviruses (OC43, 229E, NL63, and HKU1) are endemic to the human population, regularly infecting and reinfecting humans while typically causing asymptomatic to mild respiratory infections. It is not known to what extent reinfection by these viruses is due to waning immune memory or antigenic drift of the viruses. Here we address the influence of antigenic drift on immune evasion of seasonal coronaviruses.

Antiviral treatment approaches for cytomegalovirus prevention in kidney transplant recipients: A systematic review of randomized controlled trials.

Various CMV anti-viral (AV) preventive strategies have been utilized in KTRs. We examined efficacy, safety and costs of CMV-AV prevention strategies in KTRs using a systematic literature review (SLR) of randomized controlled trials (RCTs) publications indexed in MEDLINE and Embase (from inception to November 2018). Thirty RCTs met inclusion criteria with 22 unique AV preventive strategies.