Search

Abstract Background Shared decision making in healthcare is a fundamental right for patients. Healthcare professionals' perception of their own abilities to enable shared decision making is crucial for implementing shared decision making within service. IcanSDM (I can shared decision making) is a brief measure to investigate healthcare professionals' perception of shared decision making approaches to their practices. It was developed in Canada with French and English versions, and recently translated into German. This study aims to adapt the IcanSDM measure for Danish-speaking healthcare professionals, and evaluate its psychometric properties. Methods Cultural adaptation and translation based on Beaton et al.'s approach was applied. A forward translation by ten people and a backward translation by two people were performed. To assess comprehensibility, cognitive interviews were conducted with 24 healthcare professionals. Eighty healthcare professionals who were trained in shared decision making for either one hour (n = 65) or one day (n = 15) participated in the psychometric evaluation. The evaluation concerned acceptance, item characteristics, skewness, item difficulties, corrected item-total correlations, inter-item correlations, factorial structure, internal consistency, and responsiveness. Results The forward and backward translation revealed few discrepancies, and participants understood the items well. The psychometric evaluation showed a high completion rate and acceptable item difficulties and discrimination values. Both the factor analysis and the internal consistency showed a 2-factor structure: 1) healthcare professionals' capacity to implement shared decision making; and 2) healthcare professionals' capacity to practise shared decision making. The IcanSDM_Danish obtained a Cronbach’s alpha coefficient of 0.74. The evaluation of responsiveness showed improvement, but was not statistically significant. Conclusion The IcanSDM_Danish has good cross-cultural validity and internal consistency, and a 2-factor structure. The IcanSDM_Danish is capable of providing reliable and valid measurement when evaluating constructed knowledge about shared decision making, and may be able to support the implementation of shared decision making training and evaluation of its impact.

Abstract Background The use of 3D imaging techniques, such as X-ray CT, in root phenotyping has become more widespread in recent years. However, due to the complexity of the root structure, analyzing the resulting 3D volumes to obtain detailed architectural root traits remains a challenging computational problem. When it comes to image-based phenotyping of excavated maize root crowns, two types of root features that are notably missing from existing methods are the whorls and soil line. Whorls refer to the distinct areas located at the base of each stem node from which roots sprout in a circular pattern (Liu S, Barrow CS, Hanlon M, Lynch JP, Bucksch A. Dirt/3D: 3D root phenotyping for field-grown maize (zea mays). Plant Physiol. 2021;187(2):739–57. https://doi.org/10.1093/plphys/kiab311 .). The soil line is where the root stem meets the ground. Knowledge of these features would give biologists deeper insights into the root system architecture (RSA) and the below- and above-ground root properties. Results We developed TopoRoot+, a computational pipeline that produces architectural traits from 3D X-ray CT volumes of excavated maize root crowns. Building upon the TopoRoot software (Zeng D, Li M, Jiang N, Ju Y, Schreiber H, Chambers E, et al. Toporoot: A method for computing hierarchy and fine-grained traits of maize roots from 3D imaging. Plant Methods. 2021;17(1). https://doi.org/10.1186/s13007-021-00829-z .) for computing fine-grained root traits, TopoRoot + adds the capability to detect whorls, identify nodal roots at each whorl, and compute the soil line location. The new algorithms in TopoRoot + offer an additional set of fine-grained traits beyond those provided by TopoRoot. The addition includes internode distances, root traits at every hierarchy level associated with a whorl, and root traits specific to above or below the ground. TopoRoot + is validated on a diverse collection of field-grown maize root crowns consisting of nine genotypes and spanning across three years. TopoRoot + runs in minutes for a typical volume size of $$\:40{0}^{3}$$ on a desktop workstation. Our software and test dataset are freely distributed on Github. Conclusions TopoRoot + advances the state-of-the-art in image-based phenotyping of excavated maize root crowns by offering more detailed architectural traits related to whorls and soil lines. The efficiency of TopoRoot + makes it well-suited for high-throughput image-based root phenotyping.

Abstract The complex life cycle of Plasmodium falciparum requires coordinated gene expression regulation to allow host cell invasion, transmission, and immune evasion. Increasing evidence now suggests a major role for epigenetic mechanisms in gene expression in the parasite. In eukaryotes, many lncRNAs have been identified to be pivotal regulators of genome structure and gene expression. To investigate the regulatory roles of lncRNAs in P. falciparum we explore the intergenic lncRNA distribution in nuclear and cytoplasmic subcellular locations. Using nascent RNA expression profiles, we identify a total of 1768 lncRNAs, of which 718 (~41%) are novels in P. falciparum. The subcellular localization and stage-specific expression of several putative lncRNAs are validated using RNA-FISH. Additionally, the genome-wide occupancy of several candidate nuclear lncRNAs is explored using ChIRP. The results reveal that lncRNA occupancy sites are focal and sequence-specific with a particular enrichment for several parasite-specific gene families, including those involved in pathogenesis and sexual differentiation. Genomic and phenotypic analysis of one specific lncRNA demonstrate its importance in sexual differentiation and reproduction. Our findings bring a new level of insight into the role of lncRNAs in pathogenicity, gene regulation and sexual differentiation, opening new avenues for targeted therapeutic strategies against the deadly malaria parasite.

Summary: Background: While vaccines have established utility against COVID-19, phase 3 efficacy studies have generally not comprehensively evaluated protection provided by previous infection or hybrid immunity (previous infection plus vaccination). Individual patient data from US government-supported harmonized vaccine trials provide an unprecedented sample population to address this issue. We characterized the protective efficacy of previous SARS-CoV-2 infection and hybrid immunity against COVID-19 early in the pandemic over three-to six-month follow-up and compared with vaccine-associated protection. Methods: In this post-hoc cross-protocol analysis of the Moderna, AstraZeneca, Janssen, and Novavax COVID-19 vaccine clinical trials, we allocated participants into four groups based on previous-infection status at enrolment and treatment: no previous infection/placebo; previous infection/placebo; no previous infection/vaccine; and previous infection/vaccine. The main outcome was RT-PCR-confirmed COVID-19 >7–15 days (per original protocols) after final study injection. We calculated crude and adjusted efficacy measures. Findings: Previous infection/placebo participants had a 92% decreased risk of future COVID-19 compared to no previous infection/placebo participants (overall hazard ratio [HR] ratio: 0.08; 95% CI: 0.05–0.13). Among single-dose Janssen participants, hybrid immunity conferred greater protection than vaccine alone (HR: 0.03; 95% CI: 0.01–0.10). Too few infections were observed to draw statistical inferences comparing hybrid immunity to vaccine alone for other trials. Vaccination, previous infection, and hybrid immunity all provided near-complete protection against severe disease. Interpretation: Previous infection, any hybrid immunity, and two-dose vaccination all provided substantial protection against symptomatic and severe COVID-19 through the early Delta period. Thus, as a surrogate for natural infection, vaccination remains the safest approach to protection. Funding: National Institutes of Health.

Plain English summary More and more patients are taking part in research as patient partners. However, researchers have little guidance on how to bring patient partners into research studies and at what levels. There are many ways to do this. It can be hard to choose the way most appropriate for a specific project, especially for newer researchers. We (11 researchers at different career levels) developed guidance through six workshops to help new researchers choosing the way to engage patient partners most appropriate for their project. The guidance resulted in two different resources. Resource I gives five international approaches for bringing patient partners into research. Resource II describes methods for engaging patient partners at different levels. Fourteen researchers and five PhD students tested the guidance and scored how usable it is. It had excellent usability. The two resources did help researchers to decide on the best ways to engage patient partners in research. We now need to test how the guidance can be used to talk to patients about taking part in specific research projects.

The directed evolution of antibodies yields important tools for research and therapy. Here the authors develop a periplasmic phage-assisted continuous evolution platform for improvement of protein-protein interactions in the disulfidecompatible E. coli periplasm.

Abstract Background The patients’ and the carers’ roles in health service research has changed from being solely participants in studies to also being active partners and co-designers in the research process. Research carried out with or by patient partners is an increasingly accepted component of health service research in many countries, but how researchers can best approach engaging patient partners in the research process is still not clear. There is a need for guidance to support researchers when engaging patient partners and assess how such engagement impacts on research outputs. The aim of this paper is to present a protocol for a scoping review of published literature on how to engage patient partners effectively in the research process. Investigating this aim implies examining: a) how to engage patient partners in the research process; and b) what impact such engagement has on research outputs. This scoping review protocol is the first to examine how to engage patient partners effectively across different diseases and research areas. Methods A scoping review using a systematic process informed by Arksey and O’Malley’s framework will be carried out across six electronic databases using the terms ‘patient participation’, ‘community participation’, ‘research personnel’, ‘patient and public involvement’ and ‘patient partner’. We will include published reviews concerning engagement of patient partners in the research process in healthcare settings, and exclude studies assessing engagement in treatment and healthcare. Two reviewers will screen the titles and abstracts of articles independently for inclusion, and extract data from articles that meet the inclusion criteria. Where there is disagreement, a third reviewer will be consulted to facilitate consensus. The data elicited will include: author and study characteristics; research aims and findings; description of patient engagement in the research process; and assessment impact. Descriptive data and narrative analysis will synthesize findings. Discussion To understand how to engage patient partners effectively in the research process, the impact of such engagement must be taken into consideration to give a qualified suggestion for future guidance. We hope this review will raise awareness of which common elements constitute effective engagement of patient partners in the research process.

Abstract Background Global but predictable changes impact the DNA methylome as we age, acting as a type of molecular clock. This clock can be hastened by conditions that decrease lifespan, raising the question of whether it can also be slowed, for example, by conditions that increase lifespan. Mice are particularly appealing organisms for studies of mammalian aging; however, epigenetic clocks have thus far been formulated only in humans. Results We first examined whether mice and humans experience similar patterns of change in the methylome with age. We found moderate conservation of CpG sites for which methylation is altered with age, with both species showing an increase in methylome disorder during aging. Based on this analysis, we formulated an epigenetic-aging model in mice using the liver methylomes of 107 mice from 0.2 to 26.0 months old. To examine whether epigenetic aging signatures are slowed by longevity-promoting interventions, we analyzed 28 additional methylomes from mice subjected to lifespan-extending conditions, including Prop1df/df dwarfism, calorie restriction or dietary rapamycin. We found that mice treated with these lifespan-extending interventions were significantly younger in epigenetic age than their untreated, wild-type age-matched controls. Conclusions This study shows that lifespan-extending conditions can slow molecular changes associated with an epigenetic clock in mice livers.

Abstract Background Age-associated epigenetic changes are implicated in aging. Notably, age-associated DNA methylation changes comprise a so-called aging “clock”, a robust biomarker of aging. However, while genetic, dietary and drug interventions can extend lifespan, their impact on the epigenome is uncharacterised. To fill this knowledge gap, we defined age-associated DNA methylation changes at the whole-genome, single-nucleotide level in mouse liver and tested the impact of longevity-promoting interventions, specifically the Ames dwarf Prop1 df/df mutation, calorie restriction and rapamycin. Results In wild-type mice fed an unsupplemented ad libitum diet, age-associated hypomethylation was enriched at super-enhancers in highly expressed genes critical for liver function. Genes harbouring hypomethylated enhancers were enriched for genes that change expression with age. Hypermethylation was enriched at CpG islands marked with bivalent activating and repressing histone modifications and resembled hypermethylation in liver cancer. Age-associated methylation changes are suppressed in Ames dwarf and calorie restricted mice and more selectively and less specifically in rapamycin treated mice. Conclusions Age-associated hypo- and hypermethylation events occur at distinct regulatory features of the genome. Distinct longevity-promoting interventions, specifically genetic, dietary and drug interventions, suppress some age-associated methylation changes, consistent with the idea that these interventions exert their beneficial effects, in part, by modulation of the epigenome. This study is a foundation to understand the epigenetic contribution to healthy aging and longevity and the molecular basis of the DNA methylation clock.

Acinetobacter species are non-fermentative Gram-negative coccobacilli that are ubiquitous in the environment. The archetype pathogen within the genus is Acinetobacter baumannii, however, other species have the potential to cause human infection, especially in the hospital setting. We describe a patient with infection due to Acinetobacter radioresistens, a rare agent of human disease, which is often misidentified using biochemical methods. Acinetobacter radioresistens is the source of the Class D OXA-23 carbapenemase that can confer carbapenem resistance in A. baumannii. Therefore, accurate identification of A. radioresistens is important for clinical management and to potentially prevent the spread of carbapenem resistance. Keywords: Acinetobacter radioresistens, Bacteremia, MALDI-TOF MS, OXA-23, Pneumonia

The PIF4 transcription factor mediates the response of Arabidopsis seedlings to elevated temperature. Here the authors show that PIF4 interacts with the circadian clock component TOC1 which acts to suppress the PIF4-mediated temperature response in the evening.

Background and objectives: The aims of this study were to delineate the contribution of specific fascial layers of the myofascial unit to myofascial pain and introduce the use of ultrasound-guided fascial layer-specific hydromanipulation (FLuSH) as a novel technique in the treatment of myofascial pain. Materials and Methods: The clinical data of 20 consecutive adult patients who underwent myofascial injections using FLuSH technique for the treatment of myofascial pain were reviewed. The FLuSH technique involved measuring the pain pressure threshold using an analog algometer initially and after each ultrasound guided injection of normal saline into the specific layers of the myofascial unit (superficial fascia, deep fascia, or muscle) in myofascial points corresponding with Centers of Coordination/Fusion (Fascial Manipulation®). The outcome measured was the change in pain pressure threshold after injection of each specific fascial layer. Results: Deep fascia was involved in 73%, superficial fascia in 55%, and muscle in 43% of points. A non-response to treatment of all three layers occurred in 10% of all injected points. The most common combinations of fascial layer involvement were deep fascia alone in 23%, deep fascia and superficial fascia in 22%, and deep fascia and muscle in 18% of injected points. Each individual had on average of 3.0 ± 1.2 different combinations of fascial layers contributing to myofascial pain. Conclusions: The data support the hypothesis that multiple fascial layers are responsible for myofascial pain. In particular, for a given patient, pain may develop from discrete combinations of fascial layers unique to each myofascial point. Non-response to treatment of the myofascial unit may represent a centralized pain process. Adequate treatment of myofascial pain may require treatment of each point as a distinct pathologic entity rather than uniformly in a given patient or across patients.

Genome sequences diverge more rapidly in mammals than in other animal lineages, such as birds or insects. However, the effect of this rapid divergence on transcriptional evolution remains unclear. Recent reports have indicated a faster divergence of transcription factor binding in mammals than in insects, but others found the reverse for mRNA expression. Here, we show that these conflicting interpretations resulted from differing methodologies. We performed an integrated analysis of transcriptional network evolution by examining mRNA expression, transcription factor binding and cis-regulatory motifs across >25 animal species, including mammals, birds and insects. Strikingly, we found that transcriptional networks evolve at a common rate across the three animal lineages. Furthermore, differences in rates of genome divergence were greatly reduced when restricting comparisons to chromatin-accessible sequences. The evolution of transcription is thus decoupled from the global rate of genome sequence evolution, suggesting that a small fraction of the genome regulates transcription.

Plasmodium vivax infects a hundred million people annually and endangers 40% of the world's population. Unlike Plasmodium falciparum, P. vivax parasites can persist as a dormant stage in the liver, known as the hypnozoite, and these dormant forms can cause malaria relapses months or years after the initial mosquito bite. Here we analyze whole genome sequencing data from parasites in the blood of a patient who experienced consecutive P. vivax relapses over 33 months in a non-endemic country. By analyzing patterns of identity, read coverage, and the presence or absence of minor alleles in the initial polyclonal and subsequent monoclonal infections, we show that the parasites in the three infections are likely meiotic siblings. We infer that these siblings are descended from a single tetrad-like form that developed in the infecting mosquito midgut shortly after fertilization. In this natural cross we find the recombination rate for P. vivax to be 10 kb per centimorgan and we further observe areas of disequilibrium surrounding major drug resistance genes. Our data provide new strategies for studying multiclonal infections, which are common in all types of infectious diseases, and for distinguishing P. vivax relapses from reinfections in malaria endemic regions. This work provides a theoretical foundation for studies that aim to determine if new or existing drugs can provide a radical cure of P. vivax malaria.

Genetic polymorphisms can shape the global landscape of DNA methylation, by either changing substrates for DNA methyltransferases or altering the DNA binding affinity of cis-regulatory proteins. The interactions between CpG methylation and genetic polymorphisms have been previously investigated by methylation quantitative trait loci (mQTL) and allele-specific methylation (ASM) analysis. However, it remains unclear whether these approaches can effectively and comprehensively identify all genetic variants that contribute to the inter-individual variation of DNA methylation levels. Here we used three independent approaches to systematically investigate the influence of genetic polymorphisms on variability in DNA methylation by characterizing the methylation state of 96 whole blood samples in 52 parent-child trios from 22 nuclear pedigrees. We performed targeted bisulfite sequencing with padlock probes to quantify the absolute DNA methylation levels at a set of 411,800 CpG sites in the human genome. With mid-parent offspring analysis (MPO), we identified 10,593 CpG sites that exhibited heritable methylation patterns, among which 70.1% were SNPs directly present in methylated CpG dinucleotides. We determined the mQTL analysis identified 49.9% of heritable CpG sites for which regulation occurred in a distal cis-regulatory manner, and that ASM analysis was only able to identify 5%. Finally, we identified hundreds of clusters in the human genome for which the degree of variation of CpG methylation, as opposed to whether or not CpG sites were methylated, was associated with genetic polymorphisms, supporting a recent hypothesis on the genetic influence of phenotypic plasticity. These results show that cis-regulatory SNPs identified by mQTL do not comprise the full extent of heritable CpG methylation, and that ASM appears overall unreliable. Overall, the extent of genome-methylome interactions is well beyond what is detectible with the commonly used mQTL and ASM approaches, and is likely to include effects on plasticity.

During a lytic gammaherpesvirus infection, host gene expression is severely restricted by the global degradation and altered 3' end processing of mRNA. This host shutoff phenotype is orchestrated by the viral SOX protein, yet its functional significance to the viral lifecycle has not been elucidated, in part due to the multifunctional nature of SOX. Using an unbiased mutagenesis screen of the murine gammaherpesvirus 68 (MHV68) SOX homolog, we isolated a single amino acid point mutant that is selectively defective in host shutoff activity. Incorporation of this mutation into MHV68 yielded a virus with significantly reduced capacity for mRNA turnover. Unexpectedly, the MHV68 mutant showed little defect during the acute replication phase in the mouse lung. Instead, the virus exhibited attenuation at later stages of in vivo infections suggestive of defects in both trafficking and latency establishment. Specifically, mice intranasally infected with the host shutoff mutant accumulated to lower levels at 10 days post infection in the lymph nodes, failed to develop splenomegaly, and exhibited reduced viral DNA levels and a lower frequency of latently infected splenocytes. Decreased latency establishment was also observed upon infection via the intraperitoneal route. These results highlight for the first time the importance of global mRNA degradation during a gammaherpesvirus infection and link an exclusively lytic phenomenon with downstream latency establishment.

Introduction. Little is known about how shifting hospital visitor restrictions issued by national health authorities were communicated, managed, and adapted by hospital charge nurses during the COVID-19 pandemic. Aims. To describe the shifting visitor restrictions and the passing on of restrictions from the national authority level to charge nurses and secondly describe charge nurses' management of the restrictions and their challenges when enforcing them. Methods. The study consisted of a document analysis and a cross-sectional survey including open-ended questions. Descriptive statistics and qualitative content analysis were used. The survey was distributed online to 88 charge nurses in somatic units in a Danish university hospital from March 2020 to April 2021. Results. Restrictions were communicated from national authority level in an effective administrative cascade. The charge nurses led their enforcement in each unit. In total, 71 charge nurses (81%) responded to the survey. For 70%, the wording of the restrictions was clear, while 31% found them challenging to handle. On a weekly or daily basis, 68% of the charge nurses deviated from the restrictions. They identified both upsides and downsides to the absence of relatives. Communication, collaboration, and leadership were experienced as key tools in the ongoing processes of adapting to shifting restrictions. Conclusion. During this severe health crisis, essential information was passed on through well-defined management levels in an effective communication pathway. Charge nurses and their professional values were challenged when balancing shifting national restrictions against individual needs of patients and relatives. Implications for Nursing Management. Charge nurses serve as vital intermediaries between national authorities and frontline nursing practice in managing shifting visitor restrictions during a pandemic. Their experiences can contribute to further qualifying nurse managers' considerations when designing family-centred hospital visitor policies for the future. Also, they may strengthen the handling of future sudden major organizational changes. [ABSTRACT FROM AUTHOR]