Embedded Complexity of Evolutionary Sequences.

Multiple pathways and outcomes are common in evolutionary sequences for biological and other environmental systems due to nonlinear complexity, historical contingency, and disturbances. From any starting point, multiple evolutionary pathways are possible. From an endpoint or observed state, multiple possibilities exist for the sequence of events that created it. However, for any observed historical sequence-e.g., ecological or soil chronosequences, stratigraphic records, or lineages-only one historical sequence actually occurred. Here, a measure of the embedded complexity of historical sequences based on algebraic graph theory is introduced. Sequences are represented as system states S(t), such that S(t - 1) ≠ S(t) ≠ S(t + 1). Each sequence of N states contains nested subgraph sequences of length 2, 3, …, N - 1. The embedded complexity index (which can also be interpreted in terms of embedded information) compares the complexity (based on the spectral radius λ1) of the entire sequence to the cumulative complexity of the constituent subsequences. The spectral radius is closely linked to graph entropy, so the index also reflects information in the sequence. The analysis is also applied to ecological state-and-transition models (STM), which represent observed transitions, along with information on their causes or triggers. As historical sequences are lengthened (by the passage of time and additional transitions or by improved resolutions or new observations of historical changes), the overall complexity asymptotically approaches λ1 = 2, while the embedded complexity increases as N2.6. Four case studies are presented, representing coastal benthic community shifts determined from biostratigraphy, ecological succession on glacial forelands, vegetation community changes in longleaf pine woodlands, and habitat changes in a delta.

Assembling a Hippo: the evolutionary emergence of an animal developmental signaling pathway.

Decades of work in developmental genetics has given us a deep mechanistic understanding of the fundamental signaling pathways underlying animal development. However, little is known about how these pathways emerged and changed over evolutionary time. Here, we review our current understanding of the evolutionary emergence of the Hippo pathway, a conserved signaling pathway that regulates tissue size in animals. This pathway has deep evolutionary roots, emerging piece by piece in the unicellular ancestors of animals, with a complete core pathway predating the origin of animals. Recent functional studies in close unicellular relatives of animals and early-branching animals suggest an ancestral function Hippo pathway of cytoskeletal regulation, which was subsequently co-opted to regulate proliferation and animal tissue size.

Does arthroscopic or open washout in native knee septic arthritis result in superior post-operative function? A systematic review and meta-analysis of randomised controlled trials and observational studies.

AIMS: Septic arthritis (SA) of the native knee joint is associated with significant morbidity. This review compared post-operative functional outcomes (patient-reported outcome measures (PROMs) and range of movement (ROM)) following arthroscopic washout (AW) and open washout (OW) amongst adult patients with SA of the native knee. The need for further operative intervention was also considered. METHODS: Electronic databases of PubMed, MEDLINE, Embase, Cochrane, Web of Science and Scopus were searched between 16 February 2023 and 18 March 2023. Randomised controlled trials (RCTs) and comparative observational analytic studies comparing function (reflected in PROMs or ROM) at latest follow-up following AW and OW were included. A narrative summary was provided concerning post-operative PROMs. Pooled estimates for mean ROM and re-operation rates were conducted using the random-effects model. The risk of bias was assessed using the Cochrane risk-of-bias assessment tool-2 for RCTs and the Risk of Bias in Non-Randomized Studies of Interventions tool for observational analytic studies. RESULTS: Of 2580 retrieved citations, 7 articles (1 RCT and 6 cohort studies) met the inclusion criteria. Of these, five had some concerns/moderate risk of bias, and two had serious risk. There was a slight tendency for superior mean PROMs following AW compared with OW, but due to small effect sizes, this was unlikely clinically relevant. Additionally, the use of four different PROMs scales made direct comparisons impossible. AW was associated with superior ROM (mean difference 20.18° (95% CI 14.35, 26.02; p < 0.00001)), whilst there was a tendency for lower re-operation requirements following AW (OR 0.64, 95% CI 0.26, 1.57, p = 0.44). CONCLUSIONS: AW was associated with equivalent to superior post-operative function and lower requirement for further intervention compared with OW. Results need to be interpreted cautiously, taking into consideration the methodological and clinical heterogeneity of the included studies. SYSTEMATIC REVIEW REGISTRATION: PROSPERO 2022, CRD42022364062.

Improved Detection of Tryptic Peptides from Tissue Sections Using Desorption Electrospray Ionization Mass Spectrometry Imaging.

DESI-MSI is an ambient ionization technique used frequently for the detection of lipids, small molecules, and drug targets. Until recently, DESI had only limited use for the detection of proteins and peptides due to the setup and needs around deconvolution of data resulting in a small number of species being detected at lower spatial resolution. There are known differences in the ion species detected using DESI and MALDI for nonpeptide molecules, and here, we identify that this extends to proteomic species. DESI MS images were obtained for tissue sections of mouse and rat brain using a precommercial heated inlet (approximately 450 °C) to the mass spectrometer. Ion mobility separation resolved spectral overlap of peptide ions and significantly improved the detection of multiply charged species. The images acquired were of pixel size 100 µm (rat brain) and 50 µm (mouse brain), respectively. Observed tryptic peptides were filtered against proteomic target lists, generated by LC-MS, enabling tentative protein assignment for each peptide ion image. Precise localizations of peptide ions identified by DESI and MALDI were found to be comparable. Some spatially localized peptides ions were observed in DESI that were not found in the MALDI replicates, typically, multiply charged species with a low mass to charge ratio. This method demonstrates the potential of DESI-MSI to detect large numbers of tryptic peptides from tissue sections with enhanced spatial resolution when compared to previous DESI-MSI studies.

Sensorineural correlates of failed functional recovery after natural regeneration of vestibular hair cells in adult mice.

Vestibular hair cells (HCs) are mechanoreceptors that sense head motions by modulating the firing rate of vestibular ganglion neurons (VGNs), whose central processes project to vestibular nucleus neurons (VNNs) and cerebellar neurons. We explored vestibular function after HC destruction in adult Pou4f3+/DTR (DTR) mice, in which injections of high-dose (50 ng/g) diphtheria toxin (DT) destroyed most vestibular HCs within 2 weeks. At that time, DTR mice had lost the horizontal vestibulo-ocular reflex (aVORH), and their VNNs failed to upregulate nuclear cFos expression in response to a vestibular stimulus (centrifugation). Five months later, 21 and 14% of HCs were regenerated in utricles and horizontal ampullae, respectively. The vast majority of HCs present were type II. This degree of HC regeneration did not restore the aVORH or centrifugation-evoked cFos expression in VNNs. The failure to regain vestibular pathway function was not due to degeneration of VGNs or VNNs because normal neuron numbers were maintained after HC destruction. Furthermore, sinusoidal galvanic stimulation at the mastoid process evoked cFos protein expression in VNNs, indicating that VGNs were able to regulate VNN activity after HC loss. aVORH and cFos responses in VNNs were robust after low-dose (25 ng/g) DT, which compared to high-dose DT resulted in a similar degree of type II HC death and regeneration but spared more type I HCs in both organs. These findings demonstrate that having more type I HCs is correlated with stronger responses to vestibular stimulation and suggest that regenerating type I HCs may improve vestibular function after HC loss.

The Hippo kinase cascade regulates a contractile cell behavior and cell density in a close unicellular relative of animals.

The genomes of close unicellular relatives of animals encode orthologs of many genes that regulate animal development. However, little is known about the function of such genes in unicellular organisms or the evolutionary process by which these genes came to function in multicellular development. The Hippo pathway, which regulates cell proliferation and tissue size in animals, is present in some of the closest unicellular relatives of animals, including the amoeboid organism Capsaspora owczarzaki. We previously showed that the Capsaspora ortholog of the Hippo pathway nuclear effector Yorkie/YAP/TAZ (coYki) regulates actin dynamics and the three-dimensional morphology of Capsaspora cell aggregates, but is dispensable for cell proliferation control (Phillips et al., 2022). However, the function of upstream Hippo pathway components, and whether and how they regulate coYki in Capsaspora, remained unknown. Here, we analyze the function of the upstream Hippo pathway kinases coHpo and coWts in Capsaspora by generating mutant lines for each gene. Loss of either kinase results in increased nuclear localization of coYki, indicating an ancient, premetazoan origin of this Hippo pathway regulatory mechanism. Strikingly, we find that loss of either kinase causes a contractile cell behavior and increased density of cell packing within Capsaspora aggregates. We further show that this increased cell density is not due to differences in proliferation, but rather actomyosin-dependent changes in the multicellular architecture of aggregates. Given its well-established role in cell density-regulated proliferation in animals, the increased density of cell packing in coHpo and coWts mutants suggests a shared and possibly ancient and conserved function of the Hippo pathway in cell density control. Together, these results implicate cytoskeletal regulation but not proliferation as an ancestral function of the Hippo pathway kinase cascade and uncover a novel role for Hippo signaling in regulating cell density in a proliferation-independent manner.

Social Determinants of Health and Cancer Care: An ASCO Policy Statement.

ASCO's new policy statement on SDOH supports practices that sustain and advance cancer health equity.

Practical Considerations in Dose Extrapolation from Animals to Humans.

Animal studies are an important component of drug product development and the regulatory review process since modern practices have been in place, for almost a century. A variety of experimental systems are available to generate aerosols for delivery to animals in both liquid and solid forms. The extrapolation of deposited dose in the lungs from laboratory animals to humans is challenging because of genetic, anatomical, physiological, pharmacological, and other biological differences between species. Inhaled drug delivery extrapolation requires scrutiny as the aerodynamic behavior, and its role in lung deposition is influenced not only by the properties of the drug aerosol but also by the anatomy and pulmonary function of the species in which it is being evaluated. Sources of variability between species include the formulation, delivery system, and species-specific biological factors. It is important to acknowledge the underlying variables that contribute to estimates of dose scaling between species.

The Hippo kinase cascade regulates a contractile cell behavior and cell density in a close unicellular relative of animals.

The genomes of close unicellular relatives of animals encode orthologs of many genes that regulate animal development. However, little is known about the function of such genes in unicellular organisms or the evolutionary process by which these genes came to function in multicellular development. The Hippo pathway, which regulates cell proliferation and tissue size in animals, is present in some of the closest unicellular relatives of animals, including the amoeboid organism Capsaspora owczarzaki. We previously showed that the Capsaspora ortholog of the Hippo pathway nuclear effector Yorkie/YAP/TAZ (coYki) regulates actin dynamics and the three-dimensional morphology of Capsaspora cell aggregates, but is dispensable for cell proliferation control (Phillips et al., 2022). However, the function of upstream Hippo pathway components, and whether and how they regulate coYki in Capsaspora, remained unknown. Here, we analyze the function of the upstream Hippo pathway kinases coHpo and coWts in Capsaspora by generating mutant lines for each gene. Loss of either kinase results in increased nuclear localization of coYki, indicating an ancient, premetazoan origin of this Hippo pathway regulatory mechanism. Strikingly, we find that loss of either kinase causes a contractile cell behavior and increased density of cell packing within Capsaspora aggregates. We further show that this increased cell density is not due to differences in proliferation, but rather actomyosin-dependent changes in the multicellular architecture of aggregates. Given its well-established role in cell density-regulated proliferation in animals, the increased density of cell packing in coHpo and coWts mutants suggests a shared and possibly ancient and conserved function of the Hippo pathway in cell density control. Together, these results implicate cytoskeletal regulation but not proliferation as an ancestral function of the Hippo pathway kinase cascade and uncover a novel role for Hippo signaling in regulating cell density in a proliferation-independent manner.

Transient Structural Dynamics of Glycogen Phosphorylase from Nonequilibrium Hydrogen/Deuterium-Exchange Mass Spectrometry.

It remains a major challenge to ascertain the specific structurally dynamic changes that underpin protein functional switching. There is a growing need in molecular biology and drug discovery to complement structural models with the ability to determine the dynamic structural changes that occur as these proteins are regulated and function. The archetypal allosteric enzyme glycogen phosphorylase is a clinical target of great interest to treat type II diabetes and metastatic cancers. Here, we developed a time-resolved nonequilibrium millisecond hydrogen/deuterium-exchange mass spectrometry (HDX-MS) approach capable of precisely locating dynamic structural changes during allosteric activation and inhibition of glycogen phosphorylase. We resolved obligate transient changes in the localized structure that are absent when directly comparing active/inactive states of the enzyme and show that they are common to allosteric activation by AMP and inhibition by caffeine, operating at different sites. This indicates that opposing allosteric regulation by inhibitor and activator ligands is mediated by pathways that intersect with a common structurally dynamic motif. This mass spectrometry approach uniquely stands to discover local transient structural dynamics and could be used broadly to identify features that influence the structural transitions of proteins.

Randomised trial of genetic testing and targeted intervention to prevent the development and progression of Paget's disease of bone.

INTRODUCTION: Paget's disease of bone (PDB) frequently presents at an advanced stage with irreversible skeletal damage. Clinical outcomes might be improved by earlier diagnosis and prophylactic treatment. METHODS: We randomised 222 individuals at increased risk of PDB because of pathogenic SQSTM1 variants to receive 5 mg zoledronic acid (ZA) or placebo. The primary outcome was new bone lesions assessed by radionuclide bone scan. Secondary outcomes included change in existing lesions, biochemical markers of bone turnover and skeletal events related to PDB. RESULTS: The median duration of follow-up was 84 months (range 0-127) and 180 participants (81%) completed the study. At baseline, 9 (8.1%) of the ZA group had PDB lesions vs 12 (10.8%) of the placebo group. Two of the placebo group developed new lesions versus none in the ZA group (OR 0.41, 95% CI 0.00 to 3.43, p=0.25). Eight of the placebo group had a poor outcome (lesions which were new, unchanged or progressing) compared with none of the ZA group (OR 0.08, 95% CI 0.00 to 0.42, p=0.003). At the study end, 1 participant in the ZA group had lesions compared with 11 in the placebo group. Biochemical markers of bone turnover were significantly reduced in the ZA group. One participant allocated to placebo required rescue therapy with ZA because of symptomatic disease. The number and severity of adverse events did not differ between groups. CONCLUSIONS: Genetic testing for pathogenic SQSTM1 variants coupled with intervention with ZA is well tolerated and has favourable effects on the progression of early PDB. TRIAL REGISTRATION NUMBER: ISRCTN11616770.

Improved stability second harmonic conversion of a diode-pumped Yb:YAG laser at the 0.5 kW level.

We report on efficient and stable, type-I phase-matched second harmonic conversion of a nanosecond high-energy, diode-pumped, Yb:YAG laser. With a frequency-doubling crystal in an enclosed, temperature controller with optical windows, 0.5% energy stability was achieved for approximately half an hour. This resulted in 48.9 J pulses at 10 Hz (489 W) and a conversion efficiency of 73.8%. These results are particularly important for stable and reliable operation of high-energy, frequency-doubled lasers.

Locating what comes to mind in empirically derived representational spaces.

Real-world judgements and decisions often require choosing from an open-ended set of options which cannot be exhaustively considered before a choice is made. Recent work has found that the options people do consider tend to have particular features, such as high historical value. Here, we pursue the idea that option generation during decision making may reflect a more general mechanism for calling things to mind, by which relevant features in a context-appropriate representational space guide what comes to mind. In this paper, we evaluate this proposal primarily based on what comes to mind in different familiar categories. We first introduce an empirical approach for deriving the space of features that people use to represent items in a particular category and for locating the category members that come to mind within that space. We show that in both familiar and ad hoc categories, a category member's location along certain dimensions of the derived feature space predicts its likelihood of coming to mind. Next, we show that category members from these feature space locations come to mind by default in a way that is somewhat impervious to conscious control. We then demonstrate that the extent to which a given dimension is a predictor of what comes to mind within a category is related to how relevant that feature is for representing the category in question, using a novel measure of general feature relevance. Finally, we illustrate the usefulness of this framework in the context of a decision making task. We close with the proposal that people call category members to mind according to their location in representational space, specifically based on the predicted usefulness of considering category members with particular features.

Three-Month Variability of Commonly Evaluated Biomarkers in Clinically Stable COPD.

Introduction: Clinical decisions in chronic obstructive pulmonary disease (COPD) treatment often utilize serially assessed physiologic parameters and biomarkers. To better understand the reliability of these tests, we evaluated changes in commonly assessed biomarkers over 3 months in patients with clinically stable COPD. Methods: We performed an observational prospective cohort study of 89 individuals with clinically stable COPD, defined as no exacerbation history within 3 months of enrollment. Biomarkers included lung function and functional performance status, patient-reported outcomes of symptoms and health status, and blood markers of inflammation. The correlation between testing at baseline and at 3-month follow-up was reported as the intraclass correlation coefficient (ICC). "Outliers" had significant variability between tests, defined as >1.645 standard deviations between the two measurements. Differences in clinical features between outliers and others were compared. Results: Participants with COPD (n = 89) were 70.5 ± 6.7 years old, 54 (61%) male, had a 40 pack-year smoking history with 24.7% being current smokers, and postbronchodilator forced expiratory volume in one second (FEV1) 62.3 ± 22.7% predicted. The biomarkers with excellent agreement between the initial and the follow-up measurements were FEV1 (ICC = 0.96), Saint George's Respiratory Questionnaire (SGRQ) (ICC = 0.98), COPD Assessment Test (CAT) (ICC = 0.93) and C-reactive protein (CRP) (ICC = 0.90). By contrast, parameters showing less robust agreement were 6-minute walking distance (ICC = 0.75), eosinophil count (ICC = 0.77), erythrocyte sedimentation rate (ICC = 0.75) and white blood cell count (ICC = 0.48). Individuals with greater variability in biomarkers reported chronic bronchitis more often and had higher baseline SGRQ and CAT scores. Conclusion: Our study evaluated the stability of commonly assessed biomarkers in clinically stable COPD and showed excellent agreement between baseline and three-month follow-up values for FEV1, SGRQ, CAT and CRP. Individuals with chronic bronchitis and more symptomatic disease at baseline demonstrated greater variability in 3-month interval biomarkers.

Ultrasensitive Surface Plasmon Resonance Sensor with a Feature of Dynamically Tunable Sensitivity and High Figure of Merit for Cancer Detection.

Cancer is one of the leading causes of death worldwide, and it is well known that an early detection of cancer in a human body will provide an opportunity to cure the cancer. Early detection of cancer depends on the sensitivity of the measuring device and method, where the lowest detectable concentration of the cancerous cell in a test sample becomes a matter of high importance. Recently, Surface Plasmon Resonance (SPR) has proven to be a promising method to detect cancerous cells. The SPR method is based on the detection of changes in refractive indices of samples under testing and the sensitivity of such a SPR based sensor is related to the smallest detectable change in the refractive index of the sample. There exist many techniques where different combinations of metals, metal alloys and different configurations have been shown to lead to high sensitivities of the SPR sensors. Based on the difference in the refractive index between a normal healthy cell and a cancerous cell, recently, SPR method has been shown to be applicable to detect different types of cancers. In this work, we propose a new sensor surface configuration that comprises of gold-silver-graphene-black phosphorus to detect different cancerous cells based on the SPR method. Additionally, recently we proposed that the application of electric field across gold-graphene layers that form the SPR sensor surface can provide enhanced sensitivity than that is possible without the application of electrical bias. We utilized the same concept and numerically studied the impact of electrical bias across the gold-graphene layers combined with silver and black Phosphorus layers which forms the SPR sensor surface. Our numerical results have shown that electrical bias across the sensor surface in this new heterostructure can provide enhanced sensitivity compared to the original unbiased sensor surface. Not only that, our results have shown that as the electrical bias increases, the sensitivity increases up to a certain value and stabilizes at a still improved sensitivity value. Such dependence of sensitivity on the applied bias provides a dynamic tunability of the sensitivity and figure-of-merit (FOM) of the sensor to detect different types of cancer. In this work, we used the proposed heterostructure to detect six different types of cancers: Basal, Hela, Jurkat, PC12, MDA-MB-231, and MCF-7. Comparing our results to work published recently, we were able to achieve an enhanced sensitivity ranging from 97.2 to 1851.4 (deg/RIU) and FOM values ranging from 62.13 to 89.81 far above the values presented recently by other researchers.

Clinical Pharmacology and Translational Considerations in the Development of CRISPR-Based Therapies.

Genome editing holds the potential for curative treatments of human disease, however, clinical realization has proven to be a challenging journey with incremental progress made up until recently. Over the last decade, advances in clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) systems have provided the necessary breakthrough for genome editing in the clinic. The progress of investigational CRISPR therapies from bench to bedside reflects the culmination of multiple advances occurring in parallel, several of which intersect with clinical pharmacology and translation. Directing the CRISPR therapy to the intended site of action has necessitated novel delivery platforms, and this has resulted in special considerations for the complete characterization of distribution, metabolism, and excretion, as well as immunogenicity. Once at the site of action, CRISPR therapies aim to make permanent alterations to the genome and achieve therapeutically relevant effects with a single dose. This fundamental aspect of the mechanism of action for CRISPR therapies results in new considerations for clinical translation and dose selection. Early advances in model-informed development of CRISPR therapies have incorporated key facets of the mechanism of action and have captured hallmark features of clinical pharmacokinetics and pharmacodynamics from phase I investigations. Given the recent emergence of CRISPR therapies in clinical development, the landscape continues to evolve rapidly with ample opportunity for continued innovation. Here, we provide a snapshot of selected topics in clinical pharmacology and translation that has supported the advance of systemically administered in vivo and ex vivo CRISPR-based investigational therapies in the clinic.

The intentions of information sources can affect what information people think qualifies as true.

The concept of truth is at the core of science, journalism, law, and many other pillars of modern society. Yet, given the imprecision of natural language, deciding what information should count as true is no easy task, even with access to the ground truth. How do people decide whether a given claim of fact qualifies as true or false? Across two studies (N = 1181; 16,248 observations), participants saw claims of fact alongside the ground truth about those claims. Participants classified each claim as true or false. Although participants knew precisely how accurate the claims were, participants classified claims as false more often when they judged the information source to be intending to deceive (versus inform) their audience, and classified claims as true more often when they judged the information source to be intending to provide an approximate (versus precise) account. These results suggest that, even if people have access to the same set of facts, they might disagree about the truth of claims if they attribute discrepant intentions to information sources. Such findings may shed light on the robust and persistent disagreements over claims of fact that have arisen in the "post-truth era".

Assessing the Potential Efficacy of an Intervention for Incarcerated People With Mental Illness.

OBJECTIVE: This preliminary study tested the efficacy of an evidence-based correctional intervention (Thinking for a Change) with an adapted delivery to incarcerated people with mental illness. METHODS: A small-scale randomized controlled trial (N=47 men) was conducted. Outcomes were changes in aggression, number of behavioral infractions, and days in administrative segregation. Treatment targets were impulsivity, interpersonal problem-solving skills, and attitudes supportive of crime. Linear mixed-effects models were used to examine within-person and between-group differences over time, and nonparametric tests were used to examine between-group differences in criminal legal outcomes postintervention. RESULTS: Statistically significant within-person differences were found for all treatment targets and for one study outcome (aggression). Statistically significant differences in impulsivity were found between the experimental and control groups (B=-7.10, p=0.02). CONCLUSIONS: Existing evidence-based correctional interventions can affect the lives of people with mental illness. Accelerated research in this area may benefit people with mental illness at high risk for criminal legal system involvement.