Phylogenomics and the rise of the angiosperms.

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5-7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.

Polypharmacy, over-the-counter medications, and aromatase inhibitor adherence in early-stage breast cancer.

PURPOSE: Polypharmacy is associated with negative health outcomes and decreased medication adherence. Polypharmacy is common in cancer populations, but few studies have evaluated the relationship between polypharmacy and aromatase inhibitor (AI) adherence. No studies have evaluated the relationship between over-the-counter (OTC) supplements and AI adherence. Our primary hypothesis was that polypharmacy would be associated with increased risk of premature AI discontinuation. METHODS: This exploratory analysis used data from the Exemestane and Letrozole Pharmacogenetics (ELPh) trial, a prospective, multicenter, randomized controlled trial that enrolled participants from 2005 to 2009. Included patients were female, postmenopausal, with stage 0-III breast cancer, who had completed indicated chemotherapy, surgery, and radiation. Participants were randomized to adjuvant exemestane or letrozole and completed serial clinical examinations and questionnaires for two years. Concomitant medication data were collected prospectively. Cox proportion models were used for statistical analysis of the relationship between polypharmacy, OTCs, medication class, and AI adherence. RESULTS: In the 490 analyzed participants, use of any prescription medications at baseline was associated with decreased risk of premature AI discontinuation (HR 0.56, p = 0.02). Use of selective serotonin reuptake inhibitors (SSRIs) or selective serotonin and norepinephrine reuptake inhibitors (SNRIs) at baseline was associated with decreased risk of premature AI discontinuation (HR 0.67, p = 0.04). Use of any OTCs was not associated with AI discontinuation. CONCLUSION: Baseline use of prescription medications but not OTCs was associated with increased AI persistence. Future research is needed to understand how this can be utilized to promote AI adherence.

Phylogenomic analyses of Sapindales support new family relationships, rapid Mid-Cretaceous Hothouse diversification, and heterogeneous histories of gene duplication.

Sapindales is an angiosperm order of high economic and ecological value comprising nine families, c. 479 genera, and c. 6570 species. However, family and subfamily relationships in Sapindales remain unclear, making reconstruction of the order's spatio-temporal and morphological evolution difficult. In this study, we used Angiosperms353 target capture data to generate the most densely sampled phylogenetic trees of Sapindales to date, with 448 samples and c. 85% of genera represented. The percentage of paralogous loci and allele divergence was characterized across the phylogeny, which was time-calibrated using 29 rigorously assessed fossil calibrations. All families were supported as monophyletic. Two core family clades subdivide the order, the first comprising Kirkiaceae, Burseraceae, and Anacardiaceae, the second comprising Simaroubaceae, Meliaceae, and Rutaceae. Kirkiaceae is sister to Burseraceae and Anacardiaceae, and, contrary to current understanding, Simaroubaceae is sister to Meliaceae and Rutaceae. Sapindaceae is placed with Nitrariaceae and Biebersteiniaceae as sister to the core Sapindales families, but the relationships between these families remain unclear, likely due to their rapid and ancient diversification. Sapindales families emerged in rapid succession, coincident with the climatic change of the Mid-Cretaceous Hothouse event. Subfamily and tribal relationships within the major families need revision, particularly in Sapindaceae, Rutaceae and Meliaceae. Much of the difficulty in reconstructing relationships at this level may be caused by the prevalence of paralogous loci, particularly in Meliaceae and Rutaceae, that are likely indicative of ancient gene duplication events such as hybridization and polyploidization playing a role in the evolutionary history of these families. This study provides key insights into factors that may affect phylogenetic reconstructions in Sapindales across multiple scales, and provides a state-of-the-art phylogenetic framework for further research.

Association between nociplastic pain and premature endocrine therapy discontinuation in breast cancer patients.

PURPOSE: At least 5 years of adjuvant endocrine therapy (ET) is recommended for patients with hormone receptor-positive invasive breast cancer to reduce cancer recurrence risk. Up to half of patients prematurely discontinue ET, often due to musculoskeletal pain. Nociplastic pain is abnormal central nervous system pain processing without evidence of tissue or neuronal damage. This study aimed to evaluate the relationship between baseline nociplastic pain and ET discontinuation. METHODS: This was a retrospective, single center, cohort study. Included patients were female, had stage 0-III invasive breast cancer, did not receive neoadjuvant therapy, and completed quality of life questionnaires prior to breast surgery, including Fibromyalgia Survey for nociplastic pain. Clinical data including duration of ET were abstracted from the medical record. Patient characteristics were analyzed with t-tests and Chi-squared tests, as appropriate. Univariate and multivariable regressions were performed with Cox proportional hazard models. RESULTS: Six hundred eighty-one patients diagnosed between 2012 and 2019 met inclusion criteria; 480 initiated ET and were included in the analysis. Of these 480 patients, 203 (42.3%) prematurely discontinued initial ET therapy. On univariate analysis, tamoxifen use (hazard ratio [HR] 0.70, p = 0.021) and premenopausal status (HR 0.73, p = 0.04) were inversely associated with ET discontinuation, while Fibromyalgia Score was positively associated (HR 1.04, p = 0.043). On multivariable analysis, baseline Fibromyalgia Score remained associated with ET discontinuation. CONCLUSION: Nociplastic pain present prior to surgery was associated with premature ET discontinuation. Fibromyalgia Score screening may be useful for evaluating ET discontinuation risk. Treatments targeting nociplastic pain may be more effective for treating ET-emergent pain.

Length of Anticoagulation in Provoked Venous Thromboembolism: A Multicenter Study of How Real-World Practice Mirrors Guideline Recommendations.

Background For more than a decade, guidelines have recommended a limited 3 months of anticoagulation for the treatment of provoked venous thromboembolism (VTE). How closely real-world practice follows guideline recommendations is not well described. Methods and Results In our multicenter, retrospective cohort study, we evaluated trends in anticoagulation duration for patients enrolled in the MAQI2 (Michigan Anticoagulation Quality Improvement Initiative) registry who were receiving anticoagulation for a provoked VTE. The MAQI2 registry comprises 6 centers in Michigan that manage patients' long-term anticoagulation. We identified 474 patients on warfarin and 302 patients on direct oral anticoagulants who were receiving anticoagulation for a primary indication of provoked VTE between 2008 and 2020. Using a predefined threshold of 120 days (3 months plus a buffer period), predictors of extended anticoagulant use were identified using multivariable logistic regression. Most patients received >120 days of anticoagulation, regardless of which medication was used. The median (25th-75th percentile) length of treatment for patients taking warfarin was 142 (91-234) days and for direct oral anticoagulants was 180 (101-360) days. Recurrent VTE (odds ratio [OR], 2.75 [95% CI, 1.67-4.53]), history of myocardial infarction (OR, 3.92 [95% CI, 1.32-11.7]), and direct oral anticoagulant rather than warfarin use (OR, 2.22 [95% CI, 1.59-3.08]) were independently associated with prolonged anticoagulation. Conclusions In our cohort of patients with provoked VTE, most patients received anticoagulation for longer than the guideline-recommended 3 months. This demonstrates a potential opportunity to improve care delivery and reduce anticoagulant-associated bleeding risk.

Genetic characterization of outbred Sprague Dawley rats and utility for genome-wide association studies.

Sprague Dawley (SD) rats are among the most widely used outbred laboratory rat populations. Despite this, the genetic characteristics of SD rats have not been clearly described, and SD rats are rarely used for experiments aimed at exploring genotype-phenotype relationships. In order to use SD rats to perform a genome-wide association study (GWAS), we collected behavioral data from 4,625 SD rats that were predominantly obtained from two commercial vendors, Charles River Laboratories and Harlan Sprague Dawley Inc. Using double-digest genotyping-by-sequencing (ddGBS), we obtained dense, high-quality genotypes at 291,438 SNPs across 4,061 rats. This genetic data allowed us to characterize the variation present in Charles River vs. Harlan SD rats. We found that the two populations are highly diverged (FST > 0.4). Furthermore, even for rats obtained from the same vendor, there was strong population structure across breeding facilities and even between rooms at the same facility. We performed multiple separate GWAS by fitting a linear mixed model that accounted for population structure and using meta-analysis to jointly analyze all cohorts. Our study examined Pavlovian conditioned approach (PavCA) behavior, which assesses the propensity for rats to attribute incentive salience to reward-associated cues. We identified 46 significant associations for the various metrics used to define PavCA. The surprising degree of population structure among SD rats from different sources has important implications for their use in both genetic and non-genetic studies.

Patient and practitioner perspectives on the design of a simulated affective touch device to reduce procedural anxiety associated with radiotherapy: a qualitative study.

OBJECTIVE: The aim of this study was to elicit the views of relevant stakeholders on the design of a device using simulated affective touch to reduce procedural anxiety surrounding radiotherapy and imaging. DESIGN: This qualitative study collected data from focus groups which were then analysed using inductive thematic analysis in line with Braun and Clarke's methods. PARTICIPANTS AND SETTING: Twenty patients and carers were recruited, as well as 10 healthcare practitioners involved in either delivering radiotherapy or imaging procedures. RESULTS: Patients, carers and healthcare practitioners agreed on some aspects of the device design, such as ensuring the device is warm and flexible in where it can be used on the body. However, patient and healthcare practitioner cohorts had at times differing viewpoints. For example, healthcare practitioners provided professional perspectives and required easy cleaning of the device. Meanwhile patients focused on anxiety-relieving factors, such as the tactile sensation of the device being either a vibration or pulsation. There was no consensus on who should control the device. CONCLUSIONS: The desired features of a simulated affective touch device have been investigated. Different priorities of patients and their carers and healthcare practitioners were evident. Any design must incorporate such features as to appease both groups. Areas where no consensus was reached could be further explored, alongside including further patient and public involvement in the form of a project advisory group.

Not as simple as "fear of the unknown": A qualitative study exploring anxiety in the radiotherapy department.

OBJECTIVE: Little is understood about the anxiety experienced by cancer patients undergoing radiotherapy or investigative imaging. Our aim was to identify sources of anxiety, the points along the cancer journey where anxiety occurred and methods to alleviate it. METHODS: Six focus groups were conducted with cancer patients (n = 17), caregivers (n = 3) and healthcare practitioners (HCPs; n = 10) in the radiotherapy department. Patients described specific elements in the care pathway which induced anxiety, while HCPs focused on their perception of the patient experience. Thematic analysis was used to analyse data. RESULTS: Three broad themes emerged: The Environment, The Individual and The Unknown. The physical environment of the hospital, inside the scanner for example, emerged as a key source of anxiety. The impact of cancer on patients' individual lives was significant, with many feeling isolated. The majority of participants described anxiety associated with the unknown. HCPs reported difficulty in identifying the anxious patient. CONCLUSIONS: Anxiety is experienced throughout the cancer pathway. Common sources include the physical environment and the uncertainty associated with having cancer. Identifying both anxiety-inducing factors, and the anxious patients themselves, is crucial to enable targeted interventions to alleviate anxiety.

New targets acquired: Improving locus recovery from the Angiosperms353 probe set.

PREMISE: Universal target enrichment kits maximize utility across wide evolutionary breadth while minimizing the number of baits required to create a cost-efficient kit. The Angiosperms353 kit has been successfully used to capture loci throughout the angiosperms, but the default target reference file includes sequence information from only 6-18 taxa per locus. Consequently, reads sequenced from on-target DNA molecules may fail to map to references, resulting in fewer on-target reads for assembly, and reducing locus recovery. METHODS: We expanded the Angiosperms353 target file, incorporating sequences from 566 transcriptomes to produce a 'mega353' target file, with each locus represented by 17-373 taxa. This mega353 file is a drop-in replacement for the original Angiosperms353 file in HybPiper analyses. We provide tools to subsample the file based on user-selected taxon groups, and to incorporate other transcriptome or protein-coding gene data sets. RESULTS: Compared to the default Angiosperms353 file, the mega353 file increased the percentage of on-target reads by an average of 32%, increased locus recovery at 75% length by 49%, and increased the total length of the concatenated loci by 29%. DISCUSSION: Increasing the phylogenetic density of the target reference file results in improved recovery of target capture loci. The mega353 file and associated scripts are available at: https://github.com/chrisjackson-pellicle/NewTargets.

HybPhaser: A workflow for the detection and phasing of hybrids in target capture data sets.

PREMISE: Hybrids contain divergent alleles that can confound phylogenetic analyses but can provide insights into reticulated evolution when identified and phased. We developed a workflow to detect hybrids in target capture data sets and phase reads into parental lineages using a similarity and phylogenetic framework. METHODS: We used Angiosperms353 target capture data for Nepenthes, including known hybrids to test the novel workflow. Reference mapping was used to assess heterozygous sites across the data set and to detect hybrid accessions and paralogous genes. Hybrid samples were phased by mapping reads to multiple references and sorting reads according to similarity. Phased accessions were included in the phylogenetic framework. RESULTS: All known Nepenthes hybrids and nine additional samples had high levels of heterozygous sites, had reads associated with multiple divergent clades, and were phased into accessions resembling divergent haplotypes. Phylogenetic analysis including phased accessions increased clade support and confirmed parental lineages of hybrids. DISCUSSION: HybPhaser provides a novel approach to detect and phase hybrids in target capture data sets, which can provide insights into reticulations by revealing origins of hybrids and reduce conflicting signal, leading to more robust phylogenetic analyses.

Emotion in remediation: A scoping review of the medical education literature.

OBJECTIVES: Remediation can be crucial and high stakes for medical learners, and experts agree it is often not optimally conducted. Research from other fields indicates that explicit incorporation of emotion improves education because of emotion's documented impacts on learning. Because this could present an important opportunity for improving remediation, we aimed to investigate how the literature on remediation interventions in medical education discusses emotion. METHODS: The authors used Arksey and O'Malley's framework to conduct a scoping literature review of records describing remediation interventions in medical education, using PubMed, CINAHL Complete, ERIC, Web of Science and APA PsycInfo databases, including all English-language publications through 1 May 2020 meeting search criteria. They included publications discussing remediation interventions either empirically or theoretically, pertaining to physicians or physician trainees of any level. Two independent reviewers used a standardised data extraction form to report descriptive information; they reviewed included records for the presence of mentions of emotion, described the mentions and analysed results thematically. RESULTS: Of 1644 records, 199 met inclusion criteria and were reviewed in full. Of those, 112 (56%) mentioned emotion in some way; others focused solely on cognitive aspects of remediation. The mentions of emotion fell into three themes based on when the emotion was cited as present: during regular coursework or practice, upon referral for remediation and during remediation. One-quarter of records (50) indicated potential intentional incorporation of emotion into remediation programme design, but they were non-specific as to how emotions related to the learning process itself. CONCLUSION: Even though emotion is omnipresent in remediation, medical educators frequently do not factor emotion into the design of remediation approaches and rarely explicitly utilise emotion to improve the learning process. Applications from other fields may help medical educators leverage emotion to improve learning in remediation, including strategies to frame and design remediation.

Safety of fluoroscopically guided pain procedures in patients receiving cytotoxic chemotherapy: a retrospective analysis.

PURPOSE: To examine the incidence of bleeding and infectious adverse events (AEs) in patients undergoing interventional, fluoroscopic-guided axial spine procedures to modulate pain. METHODS: Retrospective data of patients undergoing fluoroscopically guided axial spine injections at a single tertiary care medical center Cancer Rehabilitation program in the USA were reviewed. AEs, type of chemotherapy, type of tumor, age, platelet and absolute neutrophil counts (ANC) prior to the procedure, and relevant past medical history were collected. Descriptive statistical analyses were performed. RESULTS: Sixty-three separately identifiable procedures across 28 patients met inclusion criteria. Zero AEs were recorded. Platelet and ANC were generally above the recommended safety threshold, but granulocyte colony stimulating factor was administered prior to four procedures to boost ANC levels. Multiple myeloma was the most common cancer diagnosis (64.3%). Various solid tumors made up the remaining cancer diagnoses. Epidural steroid injections (n=23) and medial branch blocks (n=23) were the most common procedures performed and lumbar (n=35) was the most common location of procedures. Three patients died within 30 days of the procedures but their deaths were not directly attributable to the injections. CONCLUSION: This provides preliminary data to support the safety of injections in patients receiving cytotoxic chemotherapy. Larger, multicenter studies are required before firm conclusions can be drawn.

Interventional and Non-interventional Medical Rehabilitation Approaches to Axial Spine Pain in Vertebral Metastatic Disease.

As targeted therapies help patients with advanced cancer live longer, interventions for management of axial spine pain will become more common. Unfortunately, the indications for and safety of these procedures have been relatively unexplored compared with non-cancer adults. This review focuses on the following aspects of axial spine pain management in patients with vertebral metastatic disease: (1) pathophysiology and symptoms of cancer- and non-cancer-related spine pain; (2) safety and efficacy of non-interventional rehabilitation approaches to treat this pain; (3) considerations for interventional pain approaches to acute and chronic pain in patients with vertebral metastatic disease. This review also summarizes gaps in the literature and describes specific cases in which the described interventions have been applied.

Checklist of the vascular flora of the Sunda-Sahul Convergence Zone.

Background The Sunda-Sahul Convergence Zone, defined here as the area comprising Australia, New Guinea, and Southeast Asia (Indonesia to Myanmar), straddles the Sunda and Sahul continental shelves and is one of the most biogeographically famous and important regions in the world. Floristically, it is thought to harbour a large amount of the world's diversity. Despite the importance of the area, a checklist of the flora has never before been published. Here we present the first working checklist of vascular plants for the Sunda-Sahul Convergence Zone. The list was compiled from 24 flora volumes, online databases and unpublished plot data. Taxonomic nomenclature was updated, and each species was coded into nested biogeographic regions. The list includes 60,415 species in 5,135 genera and 363 families of vascular plants. New information This is the first species-level checklist of the region and presents an updated census of the region's floristic biodiversity. The checklist confirms that species richness of the SSCZ is comparable to that of the Neotropics, and highlights areas in need of further documentation and taxonomic work. This checklist provides a novel dataset for studying floristic ecology and evolution in this biogeographically important region of very high global biodiversity.

Quantification of conjunctival TNF-α in aqueous-deficient dry eye.

PURPOSE: This study aimed to quantify and compare conjunctival epithelial tumor necrosis factor (NF) α mRNA expression in Sjögren syndrome (SS), non-Sjögren syndrome aqueous-deficient dry eye (non-SS DE), and non-dry eye (NDE) control subjects. METHODS: A total of 76 subjects were recruited for this study: 25 SS (confirmed via American-European Consensus Criteria 2002), 25 non-SS DE (confirmed by symptoms and Schirmer scores ≤ 10 mm), and 26 NDE. Superior and temporal bulbar conjunctival epithelial cells were collected via impression cytology. Epithelial RNA was extracted, and TNF-α mRNA expression was quantified by real-time quantitative polymerase chain reaction. RESULTS: The expression of TNF-α mRNA was found to be significantly higher in the SS group (2.48 ± 1.79) compared to both non-SS DE (0.95 ± 1.18; p < 0.05) and NDE (0.84 ± 0.51; p < 0.05) groups. No difference in TNF-α mRNA expression was found between the non-SS DE and NDE groups (p = 0.67). CONCLUSIONS: These results demonstrate that SS-associated aqueous-deficient dry eye is associated with a significant upregulation of conjunctival epithelial TNF-α mRNA relative to both non-SS DE and control groups. The degree to which TNF-α mRNA is upregulated in SS may contribute to the severe ocular surface damage observed in these patients.

Release of Ciprofloxacin-HCl and Dexamethasone Phosphate by Hyaluronic Acid Containing Silicone Polymers.

The purpose of this study was to determine the effect of the covalent incorporation of hyaluronic acid (HA) into conventional hydrogel and hydrogels containing silicone as models for contact lens materials on the uptake and release of the fluoroquinolone antibiotic ciprofloxacin and the anti-inflammatory steroid dexamethasone phosphate. A 3 mg/mL ciprofloxacin solution (0.3% w/v) and a 1 mg/mL dexamethasone phosphate solution (0.1%) was prepared in borate buffered saline. Three hydrogel material samples (pHEMA; pHEMA TRIS; DMAA TRIS) were prepared with and without the covalent incorporation of HA of molecular weight (MW) 35 or 132 kDa. Hydrogel discs were punched from a sheet of material with a uniform diameter of 5 mm. Uptake kinetics were evaluated at room temperature by soaking the discs for 24 h. Release kinetics were evaluated by placing the drug-loaded discs in saline at 34 °C in a shaking water bath. At various time points over 6-7 days, aliquots of the release medium were assayed for drug amounts. The majority of the materials tested released sufficient drug to be clinically relevant in an ophthalmic application, reaching desired concentrations for antibiotic or anti-inflammatory activity in solution. Overall, the silicone-based hydrogels (pHEMA TRIS and DMAA TRIS), released lower amounts of drug than the conventional pHEMA material (p < 0.001). Materials with HA MW132 released more ciprofloxacin compared to materials with HA MW35 and lenses without HA (p < 0.02). Some HA-based materials were still releasing the drug after 6 days.

MUC1 expression in Sjogren's syndrome, KCS, and control subjects.

PURPOSE: To quantify and compare human mucin 1 (MUC1) protein and mRNA expression in tears and conjunctival epithelial cells collected from Sjogren's syndrome (SS), non-Sjogren's keratoconjunctivitus sicca (KCS) and non-dry eyed (NDE) control subjects. METHODS: Seventy-six subjects were recruited for this study: 25 SS (confirmed via American-European Consensus Criteria 2002), 25 KCS (confirmed by symptoms and Schirmer scores < or = 10 mm) and 26 NDE. Tears were collected using an eye-wash technique. Impression cytology was used to gather protein and mRNA from conjunctival epithelial cells. Soluble and membrane bound MUC1 were quantified via western blotting and MUC1 mRNA was quantified by real time qPCR. RESULTS: The SS group demonstrated significantly higher concentrations of soluble MUC1 (0.12 +/- 0.11 [SS]; 0.013 +/- 0.02 [KCS; p=0.001]; 0.0023 +/- 0.0024 [NDE; p<0.001]) and MUC1 mRNA (3.18 +/- 1.44 [SS]; 1.79 +/- 1.18 [KCS; p<0.05]; 1.60 +/- 0.74 [NDE; p<0.05]) compared to both KCS and NDE groups. Soluble MUC1 expression was also higher in the KCS group compared to the NDE group (p=0.02), where as MUC1 mRNA expression was similar in both KCS and NDE groups. Membrane bound MUC1 expression differed only between the SS and NDE groups (0.005 +/- -0.003 [SS]; 0.003 +/- 0.002 [NDE; p=0.002]). CONCLUSIONS: These results demonstrate that SS subjects express greater quantities of MUC1 protein and mRNA compared to both KCS and control subjects. Increased soluble MUC1 expression was also found in KCS subjects compared to controls. Membrane bound MUC1 was present in higher concentration in SS versus NDE only. These significant changes in MUC1 expression may represent compensatory or protective responses to chronic insult to the ocular surface.