Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin.

Metagenomic inferences of bacterial strain diversity and infectious disease transmission studies largely assume a dominant, within-individual haplotype. We hypothesize that within-individual bacterial population diversity is critical for homeostasis of a healthy microbiome and infection risk. We characterized the evolutionary trajectory and functional distribution of Staphylococcus epidermidis-a keystone skin microbe and opportunistic pathogen. Analyzing 1,482 S. epidermidis genomes from 5 healthy individuals, we found that skin S. epidermidis isolates coalesce into multiple founder lineages rather than a single colonizer. Transmission events, natural selection, and pervasive horizontal gene transfer result in population admixture within skin sites and dissemination of antibiotic resistance genes within-individual. We provide experimental evidence for how admixture can modulate virulence and metabolism. Leveraging data on the contextual microbiome, we assess how interspecies interactions can shape genetic diversity and mobile gene elements. Our study provides insights into how within-individual evolution of human skin microbes shapes their functional diversification.

Charting the Complexity of the Marine Microbiome through Single-Cell Genomics.

Marine bacteria and archaea play key roles in global biogeochemistry. To improve our understanding of this complex microbiome, we employed single-cell genomics and a randomized, hypothesis-agnostic cell selection strategy to recover 12,715 partial genomes from the tropical and subtropical euphotic ocean. A substantial fraction of known prokaryoplankton coding potential was recovered from a single, 0.4 mL ocean sample, which indicates that genomic information disperses effectively across the globe. Yet, we found each genome to be unique, implying limited clonality within prokaryoplankton populations. Light harvesting and secondary metabolite biosynthetic pathways were numerous across lineages, highlighting the value of single-cell genomics to advance the identification of ecological roles and biotechnology potential of uncultured microbial groups. This genome collection enabled functional annotation and genus-level taxonomic assignments for >80% of individual metagenome reads from the tropical and subtropical surface ocean, thus offering a model to improve reference genome databases for complex microbiomes.

De novo structural mutation rates and gamete-of-origin biases revealed through genome sequencing of 2,396 families.

Each human genome includes de novo mutations that arose during gametogenesis. While these germline mutations represent a fundamental source of new genetic diversity, they can also create deleterious alleles that impact fitness. Whereas the rate and patterns of point mutations in the human germline are now well understood, far less is known about the frequency and features that impact de novo structural variants (dnSVs). We report a family-based study of germline mutations among 9,599 human genomes from 33 multigenerational CEPH-Utah families and 2,384 families from the Simons Foundation Autism Research Initiative. We find that de novo structural mutations detected by alignment-based, short-read WGS occur at an overall rate of at least 0.160 events per genome in unaffected individuals, and we observe a significantly higher rate (0.206 per genome) in ASD-affected individuals. In both probands and unaffected samples, nearly 73% of de novo structural mutations arose in paternal gametes, and we predict most de novo structural mutations to be caused by mutational mechanisms that do not require sequence homology. After multiple testing correction, we did not observe a statistically significant correlation between parental age and the rate of de novo structural variation in offspring. These results highlight that a spectrum of mutational mechanisms contribute to germline structural mutations and that these mechanisms most likely have markedly different rates and selective pressures than those leading to point mutations.

Ultrasound-guided nerve blocks in emergency medicine practice: 2022 updates.

OBJECTIVES: In the Emergency Department (ED), ultrasound-guided nerve blocks (UGNBs) have become a cornerstone of multimodal pain regimens. We investigated current national practices of UGNBs across academic medical center EDs, and how these trends have changed over time. METHODS: We conducted a cross-sectional electronic survey of academic EDs with ultrasound fellowships across the United States. Twenty-item questionnaires exploring UGNB practice patterns, training, and complications were distributed between November 2021-June 2022. Data was manually curated, and descriptive statistics were performed. The survey results were then compared to results from Amini et al. 2016 UGNB survey to identify trends. RESULTS: The response rate was 80.5% (87 of 108 programs). One hundred percent of responding programs perform UGNB at their institutions, with 29% (95% confidence interval (CI), 20%-39%) performing at least 5 blocks monthly. Forearm UGNB are most commonly performed (96% of programs (95% CI, 93%-100%)). Pain control for fractures is the most common indication (84%; 95% CI, 76%-91%). Eighty-five percent (95% CI, 77%-92%) of programs report at least 80% of UGNB performed are effective. Eighty-five percent (95% CI, 66%-85%) of programs have had no reported complications from UGNB performed by emergency providers at their institution. The remaining 15% (95% CI, 8%-23%) report an average of 1 complication annually. CONCLUSIONS: All programs participating in our study report performing UGNB in their ED, which is a 16% increase over the last 5 years. UGNB's are currently performed safely and effectively in the ED, however practice improvements can still be made. Creating multi-disciplinary committees at local and national levels can standardize guidelines and practice policies to optimize patient safety and outcomes.

Improving the Care and Cost of Treating Community-Acquired Stage 3 and 4 Decubitus Ulcers.

INTRODUCTION: The healthcare costs for treatment of community-acquired decubitus ulcers accounts for $11.6 billion in the United States annually. Patients with stage 3 and 4 decubitus ulcers are often treated inefficiently prior to reconstructive surgery while physicians attempt to optimize their condition (debridement, fecal/urinary diversion, physical therapy, nutrition, and obtaining durable medical goods). We hypothesized that hospital costs for inpatient optimization of decubitus ulcers would significantly differ from outpatient optimization costs, resulting in significant financial losses to the hospital and that transitioning optimization to an outpatient setting could reduce both total and hospital expenditures. In this study, we analyzed and compared the financial expenditures of optimizing patients with decubitus ulcers in an inpatient setting versus maximizing outpatient utilization of resources prior to reconstruction. METHODS: Encounters of patients with stage 3 or 4 decubitus ulcers over a 5-year period were investigated. These encounters were divided into two groups: Group 1 included patients who were optimized totally inpatient prior to reconstructive surgery; group 2 included patients who were mostly optimized in an outpatient setting and this encounter was a planned admission for their reconstructive surgery. Demographics, comorbidities, paralysis status, and insurance carriers were collected for all patients. Financial charges and reimbursements were compared among the groups. RESULTS: Forty-five encounters met criteria for inclusion. Group 1's average hospital charges were $500,917, while group 2's charges were $134,419. The cost of outpatient therapeutic items for patient optimization prior to wound closure was estimated to be $10,202 monthly. When including an additional debridement admission for group 2 patients (average of $108,031), the maximal charges for total care was $252,652, and hospital reimbursements were similar between group 1 and group 2 ($65,401 vs $50,860 respectively). CONCLUSIONS: The data derived from this investigation strongly suggests that optimizing patients in an outpatient setting prior to decubitus wound closure versus managing the patients totally on an inpatient basis will significantly reduce hospital charges, and hence costs, while minimally affecting reimbursements to the hospital.

Confidence intervals in molecular dating by maximum likelihood.

Molecular dating has been widely used to infer the times of past evolutionary events using molecular sequences. This paper describes three bootstrap methods to infer confidence intervals under a penalized likelihood framework. The basic idea is to use data pseudoreplicates to infer uncertainty in the branch lengths of a phylogeny reconstructed with molecular sequences. The three specific bootstrap methods are nonparametric (direct tree bootstrapping), semiparametric (rate smoothing), and parametric (Poisson simulation). Our extensive simulation study showed that the three methods perform generally well under a simple strict clock model of molecular evolution; however, the results were less positive with data simulated using an uncorrelated or a correlated relaxed clock model. Several factors impacted, possibly in interaction, the performance of the confidence intervals. Increasing the number of calibration points had a positive effect, as well as increasing the sequence length or the number of sequences although both latter effects depended on the model of evolution. A case study is presented with a molecular phylogeny of the Felidae (Mammalia: Carnivora). A comparison was made with a Bayesian analysis: the results were very close in terms of confidence intervals and there was no marked tendency for an approach to produce younger or older bounds compared to the other.

Deposition of Ultrathin MgB2 Films from a Suspension Using Cosolvent Marangoni Flow.

Magnesium diboride (MgB2) has demonstrated, theoretically and experimentally, promise as a candidate material for hydrogen storage and has thus attracted much contemporary research interest. To study hydrogen gas adsorption on MgB2 thin films using a quartz crystal microbalance (QCM)─a workhorse apparatus for this specific experiment─MgB2 must be deposited uniformly on the active surface of the QCM without damaging the quartz's performance. In work presented here, a wet-chemistry colloid synthesis and deposition process of a MgB2 thin film on a gold (Au) surface was established to avoid the extreme conditions of conventional physical deposition methods. This process also counteracts the unwanted phenomena of drying droplets on a solid surface, particularly the coffee-ring effect. To verify the normal function of the QCM after MgB2 deposition and its ability to obtain meaningful data, simple gas adsorption tests were conducted on the QCM, and the MgB2 film on the QCM was characterized with X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM) for elemental analysis and surface roughness, respectively. To obtain information about the thickness and the involvement of the coffee-ring effect, the same synthesis route was applied on a similar gold substrate─an evaporated Au film on glass. XPS characterization of the film and its precursor suspension shows the potential existence of both MgB2 and its oxide forms. The film's thickness on evaporated Au was measured by scanning transmission electron microscopy (STEM) to be 3.9 nm. The resulting samples show mitigation of the coffee-ring effect through roughness measurements with AFM at two scan sizes of 50 × 50 and 1 × 1 µm2.

Interaction energy and isosteric heat of adsorption between hydrogen and magnesium diboride.

Hydrogen storage materials form a crucial research topic for future energy utilization employing hydrogen and among those of interest magnesium diboride (MgB2) has shown its prevalence. In this study, a first-principles analytical adsorption model of one hydrogen molecule in the vicinity of various magnesium diboride crystal surfaces was developed in order to obtain surface thermodynamic properties as a function of molecular and lattice properties. Henry's law constant (KH) and isosteric heat of adsorption (ΔHads) indicators of the affinity between a gaseous molecule and a solid surface are thus calculated. The results in this paper not only address questions pertaining to the first stage of hydrogen storage processes but also advance the understanding of physisorption thermodynamics of a neutral molecule (H2) coming in contact with a layered metallic-like surface (MgB2). Although the model is built from a framework of classical calculations, quantum effects are incorporated as the fractional charge of the ions on the free surfaces, which is essential for the calculation of analytic thermodynamic values that approximate calculations from other methods. To benchmark our theoretical models, periodic density functional calculations were performed to determine the interactions between H2 and different MgB2 surfaces from first-principles. By considering both the top and sublayers of MgB2 in calculating interaction energy, we have analytically and computationally calculated the interaction energies of H2 molecules and MgB2's terminated planes, and witnessed the strong dependence of interaction energies on surface charges. We have also observed a dipole flipping phenomenon which explains the discontinuity seen in the interaction energy graph of Mg(0001). Both analytical and computational results showed heat of adsorption at zero coverage varying at a very low range (<7 kJ mol-1).

Assessing the Impact of Provider Training and Perceived Barriers on the Provision of Spiritual Care: a Mixed Methods Study.

The current study evaluated formal training around spiritual care for healthcare providers and the relationships between that training, perceived barriers to spiritual care, and frequency of inquiry around spiritual topics. A mixed methods explanatory sequential design was used. Quantitative methods included an online survey administered to providers at The Ohio State University Comprehensive Cancer Center. Main and interactive effects of formal training and barriers to spiritual care on frequency of inquiry around spiritual topics were assessed with two-way ANOVA. Qualitative follow-up explored provider strategies to engage spiritual topics. Among 340 quantitative participants, most were female (82.1%) or White (82.6%) with over one-half identifying as religious (57.5%). The majority were nurses (64.7%) and less than 10% of all providers (n = 26) indicated formal training around spiritual care. There were main effects on frequency of inquiry around spiritual topics for providers who indicated "personal discomfort" as a barrier (p < 0.001), but not formal training (p = 0.526). Providers who indicated "personal discomfort" as a barrier inquired about spirituality less frequently, regardless of receiving formal training (M = 8.0, SD = 1.41) or not (M = 8.76, SD = 2.96). There were no interactive effects between training and "may offend patients" or "personal discomfort" (p = 0.258 and 0.125, respectively). Qualitative analysis revealed four strategies with direct and indirect approaches: (1) permission-giving, (2) self-awareness/use-of-self, (3) formal assessment, and (4) informal assessment. Training for providers should emphasize self-awareness to address intrapersonal barriers to improve the frequency and quality of spiritual care for cancer patients.

Evaluation and updates to the Leggett model for pharmacokinetic modeling of exposure to lead in the workplace - Part II adjustments to the adult exposure model, confirmation of Leggett+, and modeling of workplace exposure.

California's Office of Environmental Health Hazard Assessment has updated the comprehensive age-specific model of lead metabolism in humans published by Richard W. Leggett in 1993. The updated model, called Leggett+, was introduced in a peer-reviewed report in 2013. The Leggett + model simulates the relationship between blood lead and exposure in the workplace. Leggett + includes a workplace exposure model comprising respiratory tract intake (workplace lead inhaled by a worker) and uptake (lead absorbed into the blood from the respiratory tract plus uptake from ambient air and diet). The latter is calculated as intake times an inhalation transfer coefficient plus background uptake. An adjusted adult systemic model describes the metabolism of the absorbed lead. This paper provides details about the workplace exposure and uptake elements of Leggett+, an updated approach to calibrating an inhalation transfer coefficient, confirmation of the model's performance in predicting blood lead levels from workplace studies, and predictions of blood lead levels from simulated exposures to workplace airborne lead over a working lifetime. Blood lead relative to airborne lead concentrations in a standard workplace scenario predicted by Leggett + was similar to corresponding relationships from four published workplace studies. Leggett + predictions displayed a good fit to regression equations when other key factors were considered such as pre-employment blood lead and ongoing background intake of lead, workplace air concentration, lead aerosol characteristics, and worker activity levels. The comprehensive Leggett + model can simulate plausible workplace air-blood lead relationships from a broad range of worker exposures. The inhalation transfer coefficient of 0.30, derived from empirical data described in the 2013 report has been reexamined. The original estimate continues to represent a plausible mid-point for a coefficient derived from an expanded range of theoretical particle size distributions deposited in the upper and lower regions of the respiratory tract considering intake during sedentary and outdoor activity breathing scenarios. This coefficient is slightly lower than the value of 0.35 estimated for unknown forms of lead by Leggett in 1993.

Palladium-Mediated Incorporation of Carboranes into Small Molecules, Peptides, and Proteins.

Carboranes represent a class of compounds with increasing therapeutic potential. However, few general approaches to readily embed carboranes into small molecules, peptides, and proteins are available. We report a strategy based on palladium-mediated C-X (X = C, S, and N) bond formation for the installation of carborane-containing moieties onto small molecules and peptides. We demonstrate the ability of Pd-based reagents with appropriate ligands to overcome the high hydrophobicity of the carborane group and enable chemoselective conjugation of cysteine residues at room temperature in aqueous buffer. Accordingly, carboranes can be efficiently installed on proteins by employing a combination of a bis-sulfonated biarylphosphine-ligated Pd reagent in an aqueous histidine buffer. This method is successfully employed on nanobodies, a fully synthetic affibody, and the antibody therapeutics trastuzumab and cetuximab. The conjugates of the affibody ZHER2 and the trastuzumab antibody retained binding to their target antigens. Conjugated proteins maintain their activity in cell-based functional assays in HER2-positive BT-474 cell lines. This approach enables the rapid incorporation of carborane moieties into small molecules, peptides, and proteins for further exploration in boron neutron capture therapy, which requires the targeted delivery of boron-dense groups.

Intersectionality in cancer care: A systematic review of current research and future directions.

OBJECTIVES: The objective of the current review was to synthesize the literature on intersectionality relative to disparities across the cancer care continuum. A model to support future intersectional cancer research was proposed. METHODS: Web-based discovery services and discipline-specific databases were queried for both peer-reviewed and gray literature. Study screening and data extraction were facilitated through the Covidence software platform. RESULTS: Among 497 screened studies, 28 met study inclusion criteria. Most articles were peer-reviewed empirical studies (n = 22) that focused on pre-diagnosis/screening (n = 19) and included marginalized racial/ethnic (n = 22) identities. Pre-cancer diagnosis, sexual orientation and race influenced women's screening and vaccine behaviors. Sexual minority women, particularly individuals of color, were less likely to engage in cancer prevention behaviors prior to diagnosis. Race and socioeconomic status (SES) were important factors in patient care/survivorship with worse outcomes among non-white women of low SES. Emergent themes in qualitative results emphasized the importance of patient intersectional identities, as well as feelings of marginalization, fears of discrimination, and general discomfort with providers as barriers to seeking cancer care. CONCLUSIONS: Patients with intersectional identities often experience barriers to cancer care that adversely impact screening, diagnosis, treatment, as well as survivorship. The use of an "intersectional lens" as a future clinical and research framework will facilitate a more multidimensional and holistic approach to the care of cancer patients.

Comparison of surveillance trapping methods to monitor Culicoides biting midge activity in Trinidad, West Indies.

Culicoides biting midges (Diptera: Ceratopogonidae) are biting nuisances and arbovirus vectors of both public health and veterinary significance in Trinidad. We compared sampling methods to define the behaviour and bionomics of adult Culicoides populations at a commercial dairy goat farm. Three static trap designs were compared: (a) Centre for Disease Control (CDC) downdraft UV trap; (b) CDC trap with an incandescent bulb and (c) CDC trap with semiochemical lure consisting of R-(-)-1-octen-3-ol and CO2 (no bulb). Sweep netting was used to define diel periodicity. A total of 30,701 biting midges were collected using static traps, dominated by female Culicoides furens (>70% of trap collections across all three designs). There was no significant difference in the Margalef's index between the three traps; however, trap designs A and C collected a significantly greater number of individuals than trap B, and trap C gained highest species richness. The greatest species richness and abundance of Culicoides collected by sweep net was observed between 6:00 and 6:15 pm and notable differences in the crepuscular activity pattern of several species were identified. Comparative data on Culicoides species richness, abundance, sex and reproductive status is discussed and can be used to improve surveillance strategies, research designs and risk management.

Specialization in a Nitrogen-Fixing Symbiosis: Proteome Differences Between Sinorhizobium medicae Bacteria and Bacteroids.

Using tandem mass spectrometry (MS/MS), we analyzed the proteome of Sinorhizobium medicae WSM419 growing as free-living cells and in symbiosis with Medicago truncatula. In all, 3,215 proteins were identified, over half of the open reading frames predicted from the genomic sequence. The abundance of 1,361 proteins displayed strong lifestyle bias. In total, 1,131 proteins had similar levels in bacteroids and free-living cells, and the low levels of 723 proteins prevented statistically significant assignments. Nitrogenase subunits comprised approximately 12% of quantified bacteroid proteins. Other major bacteroid proteins included symbiosis-specific cytochromes and FixABCX, which transfer electrons to nitrogenase. Bacteroids had normal levels of proteins involved in amino acid biosynthesis, glycolysis or gluconeogenesis, and the pentose phosphate pathway; however, several amino acid degradation pathways were repressed. This suggests that bacteroids maintain a relatively independent anabolic metabolism. Tricarboxylic acid cycle proteins were highly expressed in bacteroids and no other catabolic pathway emerged as an obvious candidate to supply energy and reductant to nitrogen fixation. Bacterial stress response proteins were induced in bacteroids. Many WSM419 proteins that are not encoded in S. meliloti Rm1021 were detected, and understanding the functions of these proteins might clarify why S. medicae WSM419 forms a more effective symbiosis with M. truncatula than S. meliloti Rm1021.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Phylogenetic Conflicts, Combinability, and Deep Phylogenomics in Plants.

Studies have demonstrated that pervasive gene tree conflict underlies several important phylogenetic relationships where different species tree methods produce conflicting results. Here, we present a means of dissecting the phylogenetic signal for alternative resolutions within a data set in order to resolve recalcitrant relationships and, importantly, identify what the data set is unable to resolve. These procedures extend upon methods for isolating conflict and concordance involving specific candidate relationships and can be used to identify systematic error and disambiguate sources of conflict among species tree inference methods. We demonstrate these on a large phylogenomic plant data set. Our results support the placement of Amborella as sister to the remaining extant angiosperms, Gnetales as sister to pines, and the monophyly of extant gymnosperms. Several other contentious relationships, including the resolution of relationships within the bryophytes and the eudicots, remain uncertain given the low number of supporting gene trees. To address whether concatenation of filtered genes amplified phylogenetic signal for relationships, we implemented a combinatorial heuristic to test combinability of genes. We found that nested conflicts limited the ability of data filtering methods to fully ameliorate conflicting signal amongst gene trees. These analyses confirmed that the underlying conflicting signal does not support broad concatenation of genes. Our approach provides a means of dissecting a specific data set to address deep phylogenetic relationships while also identifying the inferential boundaries of the data set. [Angiosperms; coalescent; gene-tree conflict; genomics; phylogenetics; phylogenomics.].

Systems analysis of miRNA biomarkers to inform drug safety.

microRNAs (miRNAs or miRs) are short non-coding RNA molecules which have been shown to be dysregulated and released into the extracellular milieu as a result of many drug and non-drug-induced pathologies in different organ systems. Consequently, circulating miRs have been proposed as useful biomarkers of many disease states, including drug-induced tissue injury. miRs have shown potential to support or even replace the existing traditional biomarkers of drug-induced toxicity in terms of sensitivity and specificity, and there is some evidence for their improved diagnostic and prognostic value. However, several pre-analytical and analytical challenges, mainly associated with assay standardization, require solutions before circulating miRs can be successfully translated into the clinic. This review will consider the value and potential for the use of circulating miRs in drug-safety assessment and describe a systems approach to the analysis of the miRNAome in the discovery setting, as well as highlighting standardization issues that at this stage prevent their clinical use as biomarkers. Highlighting these challenges will hopefully drive future research into finding appropriate solutions, and eventually circulating miRs may be translated to the clinic where their undoubted biomarker potential can be used to benefit patients in rapid, easy to use, point-of-care test systems.

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data.

BACKGROUND: Metagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments; however, the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers. RESULTS: Here we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome data. Abundance estimates at genome resolution are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license. CONCLUSIONS: ATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas.

Evolution of Portulacineae Marked by Gene Tree Conflict and Gene Family Expansion Associated with Adaptation to Harsh Environments.

Several plant lineages have evolved adaptations that allow survival in extreme and harsh environments including many families within the plant clade Portulacineae (Caryophyllales) such as the Cactaceae, Didiereaceae, and Montiaceae. Here, using newly generated transcriptomic data, we reconstructed the phylogeny of Portulacineae and examined potential correlates between molecular evolution and adaptation to harsh environments. Our phylogenetic results were largely congruent with previous analyses, but we identified several early diverging nodes characterized by extensive gene tree conflict. For particularly contentious nodes, we present detailed information about the phylogenetic signal for alternative relationships. We also analyzed the frequency of gene duplications, confirmed previously identified whole genome duplications (WGD), and proposed a previously unidentified WGD event within the Didiereaceae. We found that the WGD events were typically associated with shifts in climatic niche but did not find a direct association with WGDs and diversification rate shifts. Diversification shifts occurred within the Portulacaceae, Cactaceae, and Anacampserotaceae, and whereas these did not experience WGDs, the Cactaceae experienced extensive gene duplications. We examined gene family expansion and molecular evolutionary patterns with a focus on genes associated with environmental stress responses and found evidence for significant gene family expansion in genes with stress adaptation and clades found in extreme environments. These results provide important directions for further and deeper examination of the potential links between molecular evolutionary patterns and adaptation to harsh environments.

Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion.

Phylogenomic research is accelerating the publication of landmark studies that aim to resolve deep divergences of major organismal groups. Meanwhile, systems for identifying and integrating the products of phylogenomic inference-such as newly supported clade concepts-have not kept pace. However, the ability to verbalize node concept congruence and conflict across multiple, in effect simultaneously endorsed phylogenomic hypotheses, is a prerequisite for building synthetic data environments for biological systematics and other domains impacted by these conflicting inferences. Here we develop a novel solution to the conflict verbalization challenge, based on a logic representation and reasoning approach that utilizes the language of Region Connection Calculus (RCC-5) to produce consistent alignments of node concepts endorsed by incongruent phylogenomic studies. The approach employs clade concept labels to individuate concepts used by each source, even if these carry identical names. Indirect RCC-5 modeling of intensional (property-based) node concept definitions, facilitated by the local relaxation of coverage constraints, allows parent concepts to attain congruence in spite of their differentially sampled children. To demonstrate the feasibility of this approach, we align two recent phylogenomic reconstructions of higher-level avian groups that entail strong conflict in the "neoavian explosion" region. According to our representations, this conflict is constituted by 26 instances of input "whole concept" overlap. These instances are further resolvable in the output labeling schemes and visualizations as "split concepts", which provide the labels and relations needed to build truly synthetic phylogenomic data environments. Because the RCC-5 alignments fundamentally reflect the trained, logic-enabled judgments of systematic experts, future designs for such environments need to promote a culture where experts routinely assess the intensionalities of node concepts published by our peers-even and especially when we are not in agreement with each other.

Decomplexation as a rate limitation in the thiol-Michael addition of N-acrylamides.

The thiol-Michael addition is a popular, selective, high-yield "click" reaction utilized for applications ranging from small-molecule synthesis to polymer or surface modification. Here, we combined experimental and quantum mechanical modeling approaches using density functional theory (DFT) to examine the thiol-Michael reaction of N-allyl-N-acrylamide monomers used to prepare sequence-defined oligothioetheramides (oligoTEAs). Experimentally, the reaction was evaluated with two fluorous tagged thiols and several monomers at room temperature (22 °C and 40 °C). Using the Eyring equation, the activation energies (enthalpies) were calculated, observing a wide range of energy barriers ranging from 28 kJ mol-1 to 108 kJ mol-1 within the same alkene class. Computationally, DFT coupled with the Nudged Elastic Band method was used to calculate the entire reaction coordinate of each monomer reaction using the B97-D3 functional and a hybrid implicit-explicit methanol solvation approach. The thiol-Michael reaction is traditionally rate-limited by the propagation or chain-transfer steps. However, our test case with N-acrylamides and fluorous thiols revealed experimental and computational data produced satisfactory agreement only when we considered a previously unconsidered step that we termed "product decomplexation", which occurs as the product physically dissociates from other co-reactants after chain transfer. Five monomers were investigated to support this finding, capturing a range of functional groups varying in alkyl chain length (methyl to hexyl) and aromaticity (benzyl and ethylenephenyl). Increased substrate alkyl chain length increased activation energy, explained by the inductive effect. Aromatic ring-stacking configurations significantly impacted the activation energy and contributed to improved molecular packing density. Hydrogen-bonding between reactants increased the activation energy emphasizing the rate-limitation of the product decomplexation. Our findings begin to describe a new structure-kinetic relationship for thiol-Michael acceptors to enable further design of reactive monomers for synthetic polymers and biomaterials.