Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression.

Our understanding of the evolutionary history of primates is undergoing continual revision due to ongoing genome sequencing efforts. Bolstered by growing fossil evidence, these data have led to increased acceptance of once controversial hypotheses regarding phylogenetic relationships, hybridization and introgression, and the biogeographical history of primate groups. Among these findings is a pattern of recent introgression between species within all major primate groups examined to date, though little is known about introgression deeper in time. To address this and other phylogenetic questions, here, we present new reference genome assemblies for 3 Old World monkey (OWM) species: Colobus angolensis ssp. palliatus (the black and white colobus), Macaca nemestrina (southern pig-tailed macaque), and Mandrillus leucophaeus (the drill). We combine these data with 23 additional primate genomes to estimate both the species tree and individual gene trees using thousands of loci. While our species tree is largely consistent with previous phylogenetic hypotheses, the gene trees reveal high levels of genealogical discordance associated with multiple primate radiations. We use strongly asymmetric patterns of gene tree discordance around specific branches to identify multiple instances of introgression between ancestral primate lineages. In addition, we exploit recent fossil evidence to perform fossil-calibrated molecular dating analyses across the tree. Taken together, our genome-wide data help to resolve multiple contentious sets of relationships among primates, while also providing insight into the biological processes and technical artifacts that led to the disagreements in the first place.

A Review of the Popular Uses, Anatomical, Chemical, and Biological Aspects of Kalanchoe (Crassulaceae): A Genus of Plants Known as "Miracle Leaf".

Species of the genus Kalanchoe have a long history of therapeutic use in ethnomedicine linked to their remarkable healing properties. Several species have chemical and anatomical similarities, often leading to confusion when they are used in folk medicine. This review aims to provide an overview and discussion of the reported traditional uses, botanical aspects, chemical constituents, and pharmacological potential of the Kalanchoe species. Published scientific materials were collected from the PubMed and SciFinder databases without restriction regarding the year of publication through April 2023. Ethnopharmacological knowledge suggests that these species have been used to treat infections, inflammation, injuries, and other disorders. Typically, all parts of the plant are used for medicinal purposes either as crude extract or juice. Botanical evaluation can clarify species differentiation and can enable correct identification and validation of the scientific data. Flavonoids are the most common classes of secondary metabolites identified from Kalanchoe species and can be correlated with some biological studies (antioxidant, anti-inflammatory, and antimicrobial potential). This review summarizes several topics related to the Kalanchoe genus, supporting future studies regarding other unexplored research areas. The need to conduct further studies to confirm the popular uses and biological activities of bioactive compounds is also highlighted.

Systems of Precision: Coherent Probabilities on Pre-Dynkin Systems and Coherent Previsions on Linear Subspaces.

In the literature on imprecise probability, little attention is paid to the fact that imprecise probabilities are precise on a set of events. We call these sets systems of precision. We show that, under mild assumptions, the system of precision of a lower and upper probability form a so-called (pre-)Dynkin system. Interestingly, there are several settings, ranging from machine learning on partial data over frequential probability theory to quantum probability theory and decision making under uncertainty, in which, a priori, the probabilities are only desired to be precise on a specific underlying set system. Here, (pre-)Dynkin systems have been adopted as systems of precision, too. We show that, under extendability conditions, those pre-Dynkin systems equipped with probabilities can be embedded into algebras of sets. Surprisingly, the extendability conditions elaborated in a strand of work in quantum probability are equivalent to coherence from the imprecise probability literature. On this basis, we spell out a lattice duality which relates systems of precision to credal sets of probabilities. We conclude the presentation with a generalization of the framework to expectation-type counterparts of imprecise probabilities. The analogue of pre-Dynkin systems turns out to be (sets of) linear subspaces in the space of bounded, real-valued functions. We introduce partial expectations, natural generalizations of probabilities defined on pre-Dynkin systems. Again, coherence and extendability are equivalent. A related but more general lattice duality preserves the relation between systems of precision and credal sets of probabilities.

Solution cis-Proline Conformation of IPCs Inhibitor Aureobasidin A Elucidated via NMR-Based Conformational Analysis.

Aureobasidin A (abA) is a natural depsipeptide that inhibits inositol phosphorylceramide (IPC) synthases with significant broad-spectrum antifungal activity. abA is known to have two distinct conformations in solution corresponding to trans- and cis-proline (Pro) amide bond rotamers. While the trans-Pro conformation has been studied extensively, cis-Pro conformers have remained elusive. Conformational properties of cyclic peptides are known to strongly affect both potency and cell permeability, making a comprehensive characterization of abA conformation highly desirable. Here, we report a high-resolution 3D structure of the cis-Pro conformer of aureobasidin A elucidated for the first time using a recently developed NMR-driven computational approach. This approach utilizes ForceGen's advanced conformational sampling of cyclic peptides augmented by sparse distance and torsion angle constraints derived from NMR data. The obtained 3D conformational structure of cis-Pro abA has been validated using anisotropic residual dipolar coupling measurements. Support for the biological relevance of both the cis-Pro and trans-Pro abA configurations was obtained through molecular similarity experiments, which showed a significant 3D similarity between NMR-restrained abA conformational ensembles and another IPC synthase inhibitor, pleofungin A. Such ligand-based comparisons can further our understanding of the important steric and electrostatic characteristics of abA and can be utilized in the design of future therapeutics.

Mutation Accumulation in an Asexual Relative of Arabidopsis.

Asexual populations experience weaker responses to natural selection, which causes deleterious mutations to accumulate over time. Additionally, stochastic loss of individuals free of deleterious mutations can lead to an irreversible increase in mutational load in asexuals (the "click" in Muller's Ratchet). Here we report on the genomic divergence and distribution of mutations across eight sympatric pairs of sexual and apomictic (asexual) Boechera (Brassicaceae) genotypes. We show that apomicts harbor a greater number of derived mutations than sympatric sexual genotypes. Furthermore, in phylogenetically constrained sites that are subject to contemporary purifying selection, the ancestral, conserved allele is more likely to be retained in sexuals than apomicts. These results indicate that apomictic lineages accumulate mutations at otherwise conserved sites more often than sexuals, and support the conclusion that deleterious mutation accumulation can be a powerful force in the evolution of asexual higher plants.

Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris.

Whole-genome duplication (WGD) events have occurred repeatedly during flowering plant evolution, and there is growing evidence for predictable patterns of gene retention and loss following polyploidization. Despite these important insights, the rate and processes governing the earliest stages of diploidization remain poorly understood, and the relative importance of genetic drift, positive selection, and relaxed purifying selection in the process of gene degeneration and loss is unclear. Here, we conduct whole-genome resequencing in Capsella bursa-pastoris, a recently formed tetraploid with one of the most widespread species distributions of any angiosperm. Whole-genome data provide strong support for recent hybrid origins of the tetraploid species within the past 100,000-300,000 y from two diploid progenitors in the Capsella genus. Major-effect inactivating mutations are frequent, but many were inherited from the parental species and show no evidence of being fixed by positive selection. Despite a lack of large-scale gene loss, we observe a decrease in the efficacy of natural selection genome-wide due to the combined effects of demography, selfing, and genome redundancy from WGD. Our results suggest that the earliest stages of diploidization are associated with quantitative genome-wide decreases in the strength and efficacy of selection rather than rapid gene loss, and that nonfunctionalization can receive a "head start" through a legacy of deleterious variants and differential expression originating in parental diploid populations.

Using Lean to Rapidly and Sustainably Transform a Behavioral Health Crisis Program: Impact on Throughput and Safety.

BACKGROUND: Lean has been increasingly applied in health care to reduce waste and improve quality, particularly in fast-paced and high-acuity clinical settings such as emergency departments. In addition, Lean's focus on engagement of frontline staff in problem solving can be a catalyst for organizational change. In this study, ConnectionsAZ demonstrates how they applied Lean principles to rapidly and sustainably transform clinical operations in a behavioral health crisis facility. METHODS: A multidisciplinary team of management and frontline staff defined values-based outcome measures, mapped the current and ideal processes, and developed new processes to achieve the ideal. Phase I was implemented within three months of assuming management of the facility and involved a redesign of flow, space utilization, and clinical protocols. Phase II was implemented three months later and improved the provider staffing model. Organizational changes such as the development of shift leads and daily huddles were implemented to sustain change and create an environment supportive of future improvements. RESULTS: Post-Phase I, there were significant decreases (pre vs. post and one-year post) in median door-to-door dwell time (343 min vs. 118 and 99), calls to security for behavioral emergencies (13.5 per month vs. 4.3 and 4.8), and staff injuries (3.3 per month vs. 1.2 and 1.2). Post-Phase II, there were decreases in median door-to-doctor time (8.2 hours vs. 1.6 and 1.4) and hours on diversion (90% vs. 17% and 34%). CONCLUSIONS: Lean methods can positively affect safety and throughput and are complementary to patient-centered clinical goals in a behavioral health setting.

Evidence for widespread positive and negative selection in coding and conserved noncoding regions of Capsella grandiflora.

The extent that both positive and negative selection vary across different portions of plant genomes remains poorly understood. Here, we sequence whole genomes of 13 Capsella grandiflora individuals and quantify the amount of selection across the genome. Using an estimate of the distribution of fitness effects, we show that selection is strong in coding regions, but weak in most noncoding regions, with the exception of 5' and 3' untranslated regions (UTRs). However, estimates of selection on noncoding regions conserved across the Brassicaceae family show strong signals of selection. Additionally, we see reductions in neutral diversity around functional substitutions in both coding and conserved noncoding regions, indicating recent selective sweeps at these sites. Finally, using expression data from leaf tissue we show that genes that are more highly expressed experience stronger negative selection but comparable levels of positive selection to lowly expressed genes. Overall, we observe widespread positive and negative selection in coding and regulatory regions, but our results also suggest that both positive and negative selection on plant noncoding sequence are considerably rarer than in animal genomes.

Southern Ocean deep-water carbon export enhanced by natural iron fertilization.

The addition of iron to high-nutrient, low-chlorophyll regions induces phytoplankton blooms that take up carbon. Carbon export from the surface layer and, in particular, the ability of the ocean and sediments to sequester carbon for many years remains, however, poorly quantified. Here we report data from the CROZEX experiment in the Southern Ocean, which was conducted to test the hypothesis that the observed north-south gradient in phytoplankton concentrations in the vicinity of the Crozet Islands is induced by natural iron fertilization that results in enhanced organic carbon flux to the deep ocean. We report annual particulate carbon fluxes out of the surface layer, at three kilometres below the ocean surface and to the ocean floor. We find that carbon fluxes from a highly productive, naturally iron-fertilized region of the sub-Antarctic Southern Ocean are two to three times larger than the carbon fluxes from an adjacent high-nutrient, low-chlorophyll area not fertilized by iron. Our findings support the hypothesis that increased iron supply to the glacial sub-Antarctic may have directly enhanced carbon export to the deep ocean. The CROZEX sequestration efficiency (the amount of carbon sequestered below the depth of winter mixing for a given iron supply) of 8,600 mol mol(-1) was 18 times greater than that of a phytoplankton bloom induced artificially by adding iron, but 77 times smaller than that of another bloom initiated, like CROZEX, by a natural supply of iron. Large losses of purposefully added iron can explain the lower efficiency of the induced bloom(6). The discrepancy between the blooms naturally supplied with iron may result in part from an underestimate of horizontal iron supply.

Pollen-specific, but not sperm-specific, genes show stronger purifying selection and higher rates of positive selection than sporophytic genes in Capsella grandiflora.

Selection on the gametophyte can be a major force shaping plant genomes as 7-11% of genes are expressed only in that phase and 60% of genes are expressed in both the gametophytic and sporophytic phases. The efficacy of selection on gametophytic tissues is likely to be influenced by sexual selection acting on male and female functions of hermaphroditic plants. Moreover, the haploid nature of the gametophytic phase allows selection to be efficient in removing recessive deleterious mutations and fixing recessive beneficial mutations. To assess the importance of gametophytic selection, we compared the strength of purifying selection and extent of positive selection on gametophyte- and sporophyte-specific genes in the highly outcrossing plant Capsella grandiflora. We found that pollen-exclusive genes had a larger fraction of sites under strong purifying selection, a greater proportion of adaptive substitutions, and faster protein evolution compared with seedling-exclusive genes. In contrast, sperm cell-exclusive genes had a smaller fraction of sites under strong purifying selection, a lower proportion of adaptive substitutions, and slower protein evolution compared with seedling-exclusive genes. Observations of strong selection acting on pollen-expressed genes are likely explained by sexual selection resulting from pollen competition aided by the haploid nature of that tissue. The relaxation of selection in sperm might be due to the reduced influence of intrasexual competition, but reduced gene expression may also be playing an important role.

Pure in-phase heteronuclear correlation NMR experiments.

A general NMR approach to provide pure in-phase (PIP) multiplets in heteronuclear correlation experiments is described. The implementation of a zero-quantum filter efficiently suppresses any unwanted anti-phase contributions that usually distort the multiplet pattern of cross-peaks and can hamper their analysis. The clean pattern obtained in PIP-HSQMBC experiments is suitable for a direct extraction of coupling constants in resolved signals, for a peak-fitting process from a reference signal, and for the application of the IPAP technique in non-resolved multiplets.

k-mer-based approaches to bridging pangenomics and population genetics.

Many commonly studied species now have more than one chromosome-scale genome assembly, revealing a large amount of genetic diversity previously missed by approaches that map short reads to a single reference. However, many species still lack multiple reference genomes and correctly aligning references to build pangenomes is challenging, limiting our ability to study this missing genomic variation in population genetics. Here, we argue that $k$-mers are a crucial stepping stone to bridging the reference-focused paradigms of population genetics with the reference-free paradigms of pangenomics. We review current literature on the uses of $k$-mers for performing three core components of most population genetics analyses: identifying, measuring, and explaining patterns of genetic variation. We also demonstrate how different $k$-mer-based measures of genetic variation behave in population genetic simulations according to the choice of $k$, depth of sequencing coverage, and degree of data compression. Overall, we find that $k$-mer-based measures of genetic diversity scale consistently with pairwise nucleotide diversity ($\pi$) up to values of about $\pi = 0.025$ ($R^2 = 0.97$) for neutrally evolving populations. For populations with even more variation, using shorter $k$-mers will maintain the scalability up to at least $\pi = 0.1$. Furthermore, in our simulated populations, $k$-mer dissimilarity values can be reliably approximated from counting bloom filters, highlighting a potential avenue to decreasing the memory burden of $k$-mer based genomic dissimilarity analyses. For future studies, there is a great opportunity to further develop methods to identifying selected loci using $k$-mers.

Integrated Time Nanosecond Pulse Irreversible Electroporation (INSPIRE): Assessment of Dose, Temperature, and Voltage on Experimental and Clinical Treatment Outcomes.

OBJECTIVE: This study sought to investigate a novel strategy using temperature-controlled delivery of nanosecond pulsed electric fields as an alternative to the 50-100 microsecond pulses used for irreversible electroporation. METHODS: INSPIRE treatments were carried out at two temperatures in 3D tumor models using doses between 0.001 s and 0.1 s. The resulting treatment zones were quantified using viability staining and lethal electric field intensities were determined numerically. Computational modeling was then used to determine parameters necessary for INSPIRE treatments to achieve equivalent treatment zones to clinical electroporation treatments and evaluate the potential for these treatments to induce deleterious thermal damage. RESULTS: Lethal thresholds between 1109 and 709 V/cm were found for nominal 0.01 s treatments with pulses between 350 ns and 2000 ns at physiological temperatures. Further increases in dose resulted in significant decreases in lethal thresholds. Given these experimental results, treatment zones comparable to clinical electroporation are possible by increasing the dose and voltage used with nanosecond duration pulses. Temperature-controlled simulations indicate minimal thermal cell death while achieving equivalent treatment volumes to clinical electroporation. CONCLUSION: Nanosecond electrical pulses can achieve comparable outcomes to traditional electroporation provided sufficient electrical doses or voltages are applied. The use of temperature-controlled delivery may minimize thermal damage during treatment. SIGNIFICANCE: Intense muscle stimulation and the need for cardiac gating have limited irreversible electroporation. Nanosecond pulses can alleviate these challenges, but traditionally have produced significantly smaller treatment zones. This study suggests that larger ablation volumes may be possible with the INSPIRE approach and that future in vivo studies are warranted.

Treatment of Spontaneous Tumors With Algorithmically Controlled Electroporation.

OBJECTIVE: To study the safety and efficacy of algorithmically controlled electroporation (ACE) against spontaneous equine melanoma. METHODS: A custom temperature sensing coaxial electrode was paired with a high voltage pulse generation system with integrated temperature feedback controls. Computational modeling and ex vivo studies were conducted to evaluate the system's ability to achieve and maintain target temperatures. Twenty-five equine melanoma tumors were treated with a 2000 V protocol consisting of a 2-5-2 waveform, 45 °C temperature set point, and integrated energized times of 0.005 s, 0.01 s, or 0.02 s (2500x, 5000x, and 10000x 2 µs pulses, respectively). Patients returned 20-50 days post treatment to determine the efficacy of the treatment. RESULTS: ACE temperature control algorithms successfully achieved and maintained target temperatures in a diverse population of spontaneous tumors with significant variation in tissue impedance. All treatments were completed successfully without and without adverse events. Complete response rates greater than 93% were achieved in all treatment groups. CONCLUSION: ACE is a safe and effective treatment for spontaneous equine melanoma. The temperature control algorithm enabled rapid delivery of electroporation treatments without prior knowledge of tissue electrical or thermal properties and could adjust to real time changes in tissue properties. SIGNIFICANCE: Real time temperature control in electroporation procedures enables treatments near critical structures where thermal damage is contraindicated. Unlike standard approaches, ACE protocols do not require extensive pretreatment planning or knowledge of tissue properties to determine an optimal energy delivery rate and they can account for changes in tissue state (e.g., perfusion) in real time to simultaneously minimize treatment time and potential for thermal damage.

Video self-modeling in children with autism: a pilot study validating prerequisite skills and extending the utilization of VSM across skill sets.

Given the recent interest in the use of video self-modeling (VSM) to provide instruction within iPod apps and other pieces of handheld mobile assistive technologies, investigating appropriate prerequisite skills for effective use of this intervention is particularly timely and relevant. To provide additional information regarding the efficacy of VSM for students with autism and to provide insights into any possible prerequisite skills students may require for such efficacy, the authors investigated the use of VSM in increasing the instances of effective initiations of interpersonal greetings for three students with autism that exhibited different pre-intervention abilities. Results showed that only one of the three participants showed an increase in self-initiated greetings following the viewing of videos edited to show each participant self-modeling a greeting when entering his or her classroom. Due to the differences in initial skill sets between the three children, this finding supports anecdotally observed student prerequisite abilities mentioned in previous studies that may be required to effectively utilize video based teaching methods.

Splint Quality Assessment and Improvement Among Emergency Department Staff.

The purpose of this quality improvement project is to assess and improve the quality of splint application in the emergency department (ED), as well as the splint application confidence level of the ED staff. Consistent and high-quality splint application is critical in fracture stabilization and prevention of further injury. Significantly high turnover and a lack of formal training of ED staff has led to poor splint application, and in some cases, patient injuries related to the splints themselves. These injuries include pain, edema, and skin complications (A. P. Carino, 2017). A random, Likert-based analysis was performed on 20 ED-applied splints. Once analysis was complete, training courses were implemented to improve splint application techniques. Using the same Likert-based tool, applications of 20 posttraining splints were analyzed. In addition, ED staff confidence levels were scored before and after the training courses. Overall, statistically significant improvement was achieved in splint application quality and staff confidence. Correct splint applications increased from 50% to 95% after the educational sessions. Staff confidence in splint application also increased, from 35% to 77.1%. Quality splint application affects all patients. The higher risk population is more likely to suffer the consequences of poor splint application. This project had a positive impact on the region's marginalized patient population. These patients have limited resources, including lack of transportation, financial limitations, and typically are at higher risk for complications due to comorbidities.

High-yielding synthesis of cyclometallated iridium complexes with hydrogen bond-rich ligands.

A library of cyclometallated iridium(III) complexes with a strong H-bonding motif in their ancillary ligand was synthesized, characterized and their photophysical properties measured. Demonstrated herein is a general synthetic high yield procedure for these compounds. We ascribe these yields to the use of an intermediary primer ligand. This de novo strategy circumnavigates the standard synthetic issues of H-bond rich ligand precursors (self-aggregation and poor solubility in organic solvents).

Bayesian analysis of molecular variance in pyrosequences quantifies population genetic structure across the genome of Lycaeides butterflies.

The distribution of genetic variation within and among populations is commonly used to infer their demographic and evolutionary histories. This endeavour has the potential to benefit substantially from high-throughput next-generation sequencing technologies through a rapid increase in the amount of data available and a corresponding increase in the precision of parameter estimation. Here we report the results of a phylogeographic study of the North American butterfly genus Lycaeides using 454 sequence data. This study serves the dual purpose of demonstrating novel molecular and analytical methods for population genetic analyses with 454 sequence data and expanding our knowledge of the phylogeographic history of Lycaeides. We obtained 341,045 sequence reads from 12 populations that we were able to assemble into 15,262 contigs (most of which were variable), representing one of the largest population genetic data sets for a non-model organism to date. We examined patterns of genetic variation using a hierarchical Bayesian analysis of molecular variance model, which provides precise estimates of genome-level phi(ST) while appropriately modelling uncertainty in locus-specific phi(ST). We found that approximately 36% of sequence variation was partitioned among populations, suggesting historical or current isolation among the sampled populations. Estimates of pairwise genome-level phi(ST) were largely consistent with a previous phylogeographic model for Lycaeides, suggesting fragmentation into two to three refugia during Pleistocene glacial cycles followed by post-Pleistocene range expansion and secondary contact leading to introgressive hybridization. This study demonstrates the potential of using genome-level data to better understand the phylogeographic history of populations.

Absolute configurations of tubulin inhibitors taltobulin (HTI-286) and HTI-042 characterized by X-ray diffraction analysis and NMR studies.

The stereochemistry of the tubulin inhibitors taltobulin HTI-286 (2) and HTI-042 (3) was determined by utilizing the DPFGSE 1D NOE experiment. Single crystal X-ray diffraction analysis further confirmed the absolute configuration of these two compounds, which carry the (S,S,S)-configuration necessary for biological activity.

Males optimally balance selfish and kin-selected strategies of sexual competition in the guppy.

Resolving the strategies by which organisms compete for limited resources is key to understanding behavioural and social evolution. When competing for matings, males in many species allocate mating effort preferentially towards higher-quality females. How males balance this against avoiding competition with rival males, who should also prefer high-quality females, is poorly understood. Kin selection theory further complicates these dynamics: males should avoid competition with close relatives especially because of added, indirect fitness costs. However, whether between-male relatedness modulates the intensity of intrasexual competition is equivocal. Here, we develop and test an analytical model describing how males should optimally allocate their mating efforts in response to information about differences in female quality, competitor presence/absence and competitor relatedness. Using freely interacting groups of Trinidadian guppies (Poecilia reticulata), we show concordance between observed and predicted mating effort allocation across all combinations of these factors. Thus, male mating effort is sensitive to variation in female quality, competitor presence and competitor relatedness, which is consistent with a kin-selected strategy of male-male competition. The fit of our model's predictions demonstrates that males integrate assessments of female quality and competitive context in a quantitatively meaningful way, implicating a competitive strategy that has been fine-tuned to maximize inclusive fitness gains.