Model-implied simulation-based power estimation for correctly specified and distributionally misspecified models: Applications to nonlinear and linear structural equation models.

Closed-form (asymptotic) analytical power estimation is only available for limited classes of models, requiring correct model specification for most applications. Simulation-based power estimation can be applied in almost all scenarios where data following the model can be estimated. However, a general framework for calculating the required sample sizes for given power rates is still lacking. We propose a new model-implied simulation-based power estimation (MSPE) method for the z-test that makes use of the asymptotic normality property of estimates of a wide class of estimators, the M-estimators, and give theoretical justification for the approach. M-estimators include maximum-likelihood, least squares estimates and limited information estimators, but also estimators used for misspecified models, hence, the new simulation-based power modeling method is widely applicable. The MSPE employs a parametric model to describe the relationship between power and sample size, which can then be used to determine the required sample size for a specified power rate. We highlight its performance in linear and nonlinear structural equation models (SEM) for correctly specified models and models under distributional misspecification. Simulation results suggest that the new power modeling method is unbiased and shows good performance with regard to root mean squared error and type I error rates for the predicted required sample sizes and predicted power rates, outperforming alternative approaches, such as the naïve approach of selecting a discrete selection of sample sizes with linear interpolation of power or simple logistic regression approaches. The MSPE appears to be a valuable tool to estimate power for models without an (asymptotic) analytical power estimation.

Comparative analysis reveals assortative mate preferences in darters independent of sympatry and sex.

A preference for mating with conspecifics over heterospecifics is fundamental to the maintenance of species diversity in sexually reproducing organisms. This type of positive assortative preference results in sexual isolation, and a reduction in gene flow between species due to differences in mate choice. The proximate and ultimate causes of sexual isolation therefore constitute active areas of research in evolutionary biology. Sexual isolation is often stronger between closely related sympatric species as compared to allopatric species because of processes such as reinforcement. In addition, traditional theories of sexual selection suggest that because reproduction is more costly to females, they should be the choosier sex and play a more central role in sexual isolation. We conducted a comparative analysis of assortative mate preferences in males and females of sympatric and allopatric species pairs of darters (fish genus Etheostoma). We performed a meta-analysis of 17 studies, encompassing 21 species, in which assortative preference was measured when fish were (in most cases) allowed only visual information. As expected, we found stronger preferences for conspecifics over heterospecifics across studies and species. However, we did not find an effect of sympatry or sex on the strength of preference for conspecifics, but rather remarkable variation across species. We offer several testable hypotheses to explain the variation we observed in the strength of assortative preference.

Catalytic and noncatalytic functions of DNA polymerase κ in translesion DNA synthesis.

Translesion DNA synthesis (TLS) is a cellular process that enables the bypass of DNA lesions encountered during DNA replication and is emerging as a primary target of chemotherapy. Among vertebrate DNA polymerases, polymerase κ (Polκ) has the distinctive ability to bypass minor groove DNA adducts in vitro. However, Polκ is also required for cells to overcome major groove DNA adducts but the basis of this requirement is unclear. Here, we combine CRISPR base-editor screening technology in human cells with TLS analysis of defined DNA lesions in Xenopus egg extracts to unravel the functions and regulations of Polκ during lesion bypass. Strikingly, we show that Polκ has two main functions during TLS, which are differentially regulated by Rev1 binding. On the one hand, Polκ is essential to replicate across a minor groove DNA lesion in a process that depends on PCNA ubiquitylation but is independent of Rev1. On the other hand, through its cooperative interaction with Rev1 and ubiquitylated PCNA, Polκ appears to stabilize the Rev1-Polζ extension complex on DNA to allow extension past major groove DNA lesions and abasic sites, in a process that is independent of Polκ's catalytic activity. Together, our work identifies catalytic and noncatalytic functions of Polκ in TLS and reveals important regulatory mechanisms underlying the unique domain architecture present at the C-terminal end of Y-family TLS polymerases.

Estimating power in complex nonlinear structural equation modeling including moderation effects: The powerNLSEM R-package.

The model-implied simulation-based power estimation (MSPE) approach is a new general method for power estimation (Irmer et al., 2024). MSPE was developed especially for power estimation of non-linear structural equation models (SEM), but it also can be applied to linear SEM and manifest models using the R package powerNLSEM. After first providing some information about MSPE and the new adaptive algorithm that automatically selects sample sizes for the best prediction of power using simulation, a tutorial on how to conduct the MSPE for quadratic and interaction SEM (QISEM) using the powerNLSEM package is provided. Power estimation is demonstrated for four methods, latent moderated structural equations (LMS), the unconstrained product indicator (UPI), a simple factor score regression (FSR), and a scale regression (SR) approach to QISEM. In two simulation studies, we highlight the performance of the MSPE for all four methods applied to two QISEM with varying complexity and reliability. Further, we justify the settings of the newly developed adaptive search algorithm via performance evaluations using simulation. Overall, the MSPE using the adaptive approach performs well in terms of bias and Type I error rates.

PARP1-dependent DNA-protein crosslink repair.

DNA-protein crosslinks (DPCs) are toxic lesions that inhibit DNA related processes. Post-translational modifications (PTMs), including SUMOylation and ubiquitylation, play a central role in DPC resolution, but whether other PTMs are also involved remains elusive. Here, we identify a DPC repair pathway orchestrated by poly-ADP-ribosylation (PARylation). Using Xenopus egg extracts, we show that DPCs on single-stranded DNA gaps can be targeted for degradation via a replication-independent mechanism. During this process, DPCs are initially PARylated by PARP1 and subsequently ubiquitylated and degraded by the proteasome. Notably, PARP1-mediated DPC resolution is required for resolving topoisomerase 1-DNA cleavage complexes (TOP1ccs) induced by camptothecin. Using the Flp-nick system, we further reveal that in the absence of PARP1 activity, the TOP1cc-like lesion persists and induces replisome disassembly when encountered by a DNA replication fork. In summary, our work uncovers a PARP1-mediated DPC repair pathway that may underlie the synergistic toxicity between TOP1 poisons and PARP inhibitors.

Ketamine alleviates NMDA receptor hypofunction through synaptic trapping.

Activity-dependent modulations of N-methyl-D-aspartate glutamate receptor (NMDAR) trapping at synapses regulate excitatory neurotransmission and shape cognitive functions. Although NMDAR synaptic destabilization has been associated with severe neurological and psychiatric conditions, tuning NMDAR synaptic trapping to assess its clinical relevance for the treatment of brain conditions remains a challenge. Here, we report that ketamine (KET) and other clinically relevant NMDAR open channel blockers (OCBs) promote interactions between NMDAR and PDZ-domain-containing scaffolding proteins and enhance NMDAR trapping at synapses. We further show that KET-elicited trapping enhancement compensates for depletion in synaptic receptors triggered by autoantibodies from patients with anti-NMDAR encephalitis. Preventing synaptic depletion mitigates impairments in NMDAR-mediated CaMKII signaling and alleviates anxiety- and sensorimotor-gating-related behavioral deficits provoked by autoantibodies. Altogether, these findings reveal an unexpected dimension of OCB action and stress the potential of targeting receptor anchoring in NMDAR-related synaptopathies.

What are the DNA lesions underlying formaldehyde toxicity?

Formaldehyde is a highly reactive organic compound. Humans can be exposed to exogenous sources of formaldehyde, but formaldehyde is also produced endogenously as a byproduct of cellular metabolism. Because formaldehyde can react with DNA, it is considered a major endogenous source of DNA damage. However, the nature of the lesions underlying formaldehyde toxicity in cells remains vastly unknown. Here, we review the current knowledge of the different types of nucleic acid lesions that are induced by formaldehyde and describe the repair pathways known to counteract formaldehyde toxicity. Taking this knowledge together, we discuss and speculate on the predominant lesions generated by formaldehyde, which underly its natural toxicity.

Flow-controlled ventilation decreases mechanical power in postoperative ICU patients.

BACKGROUND: Mechanical power (MP) is the energy delivered by the ventilator to the respiratory system and combines factors related to the development of ventilator-induced lung injury (VILI). Flow-controlled ventilation (FCV) is a new ventilation mode using a constant low flow during both inspiration and expiration, which is hypothesized to lower the MP and to improve ventilation homogeneity. Data demonstrating these effects are scarce, since previous studies comparing FCV with conventional controlled ventilation modes in ICU patients suffer from important methodological concerns. OBJECTIVES: This study aims to assess the difference in MP between FCV and pressure-controlled ventilation (PCV). Secondary aims were to explore the effect of FCV in terms of minute volume, ventilation distribution and homogeneity, and gas exchange. METHODS: This is a physiological study in post-cardiothoracic surgery patients requiring mechanical ventilation in the ICU. During PCV at baseline and 90 min of FCV, intratracheal pressure, airway flow and electrical impedance tomography (EIT) were measured continuously, and hemodynamics and venous and arterial blood gases were obtained repeatedly. Pressure-volume loops were constructed for the calculation of the MP. RESULTS: In 10 patients, optimized FCV versus PCV resulted in a lower MP (7.7 vs. 11.0 J/min; p = 0.004). Although FCV did not increase overall ventilation homogeneity, it did lead to an improved ventilation of the dependent lung regions. A stable gas exchange at lower minute volumes was obtained. CONCLUSIONS: FCV resulted in a lower MP and improved ventilation of the dependent lung regions in post-cardiothoracic surgery patients on the ICU. Trial registration Clinicaltrials.gov identifier: NCT05644418. Registered 1 December 2022, retrospectively registered.

VCF1 is a p97/VCP cofactor promoting recognition of ubiquitylated p97-UFD1-NPL4 substrates.

The hexameric AAA+ ATPase p97/VCP functions as an essential mediator of ubiquitin-dependent cellular processes, extracting ubiquitylated proteins from macromolecular complexes or membranes by catalyzing their unfolding. p97 is directed to ubiquitylated client proteins via multiple cofactors, most of which interact with the p97 N-domain. Here, we discover that FAM104A, a protein of unknown function also named VCF1 (VCP/p97 nuclear Cofactor Family member 1), acts as a p97 cofactor in human cells. Detailed structure-function studies reveal that VCF1 directly binds p97 via a conserved α-helical motif that recognizes the p97 N-domain with unusually high affinity, exceeding that of other cofactors. We show that VCF1 engages in joint p97 complex formation with the heterodimeric primary p97 cofactor UFD1-NPL4 and promotes p97-UFD1-NPL4-dependent proteasomal degradation of ubiquitylated substrates in cells. Mechanistically, VCF1 indirectly stimulates UFD1-NPL4 interactions with ubiquitin conjugates via its binding to p97 but has no intrinsic affinity for ubiquitin. Collectively, our findings establish VCF1 as an unconventional p97 cofactor that promotes p97-dependent protein turnover by facilitating p97-UFD1-NPL4 recruitment to ubiquitylated targets.

The Fanconi anemia pathway repairs colibactin-induced DNA interstrand cross-links.

Colibactin is a secondary metabolite produced by bacteria present in the human gut and is implicated in the progression of colorectal cancer and inflammatory bowel disease. This genotoxin alkylates deoxyadenosines on opposite strands of host cell DNA to produce DNA interstrand cross-links (ICLs) that block DNA replication. While cells have evolved multiple mechanisms to resolve ("unhook") ICLs encountered by the replication machinery, little is known about which of these pathways promote resistance to colibactin-induced ICLs. Here, we use Xenopus egg extracts to investigate replication-coupled repair of plasmids engineered to contain site-specific colibactin-ICLs. We show that replication fork stalling at a colibactin-ICL leads to replisome disassembly and activation of the Fanconi anemia ICL repair pathway, which unhooks the colibactin-ICL through nucleolytic incisions. These incisions generate a DNA double-strand break intermediate in one sister chromatid, which can be repaired by homologous recombination, and a monoadduct ("ICL remnant") in the other. Our data indicate that translesion synthesis past the colibactin-ICL remnant depends on Polη and a Polκ-REV1-Polζ polymerase complex. Although translesion synthesis past colibactin-induced DNA damage is frequently error-free, it can introduce T>N point mutations that partially recapitulate the mutation signature associated with colibactin exposure in vivo. Taken together, our work provides a biochemical framework for understanding how cells tolerate a naturally-occurring and clinically-relevant ICL.

Discovery of Darovasertib (NVP-LXS196), a Pan-PKC Inhibitor for the Treatment of Metastatic Uveal Melanoma.

Uveal melanoma (UM) is the most common primary intraocular malignancy in the adult eye. Despite the aggressive local management of primary UM, the development of metastases is common with no effective treatment options for metastatic disease. Genetic analysis of UM samples reveals the presence of mutually exclusive activating mutations in the Gq alpha subunits GNAQ and GNA11. One of the key downstream targets of the constitutively active Gq alpha subunits is the protein kinase C (PKC) signaling pathway. Herein, we describe the discovery of darovasertib (NVP-LXS196), a potent pan-PKC inhibitor with high whole kinome selectivity. The lead series was optimized for kinase and off target selectivity to afford a compound that is rapidly absorbed and well tolerated in preclinical species. LXS196 is being investigated in the clinic as a monotherapy and in combination with other agents for the treatment of uveal melanoma (UM), including primary UM and metastatic uveal melanoma (MUM).

Sparsity in an artificial neural network predicts beauty: Towards a model of processing-based aesthetics.

Generations of scientists have pursued the goal of defining beauty. While early scientists initially focused on objective criteria of beauty ('feature-based aesthetics'), philosophers and artists alike have since proposed that beauty arises from the interaction between the object and the individual who perceives it. The aesthetic theory of fluency formalizes this idea of interaction by proposing that beauty is determined by the efficiency of information processing in the perceiver's brain ('processing-based aesthetics'), and that efficient processing induces a positive aesthetic experience. The theory is supported by numerous psychological results, however, to date there is no quantitative predictive model to test it on a large scale. In this work, we propose to leverage the capacity of deep convolutional neural networks (DCNN) to model the processing of information in the brain by studying the link between beauty and neuronal sparsity, a measure of information processing efficiency. Whether analyzing pictures of faces, figurative or abstract art paintings, neuronal sparsity explains up to 28% of variance in beauty scores, and up to 47% when combined with a feature-based metric. However, we also found that sparsity is either positively or negatively correlated with beauty across the multiple layers of the DCNN. Our quantitative model stresses the importance of considering how information is processed, in addition to the content of that information, when predicting beauty, but also suggests an unexpectedly complex relationship between fluency and beauty.

Profiling ubiquitin signalling with UBIMAX reveals DNA damage- and SCFß-Trcp1-dependent ubiquitylation of the actin-organizing protein Dbn1.

Ubiquitin widely modifies proteins, thereby regulating most cellular functions. The complexity of ubiquitin signalling necessitates unbiased methods enabling global detection of dynamic protein ubiquitylation. Here, we describe UBIMAX (UBiquitin target Identification by Mass spectrometry in Xenopus egg extracts), which enriches ubiquitin-conjugated proteins and quantifies regulation of protein ubiquitylation under precise and adaptable conditions. We benchmark UBIMAX by investigating DNA double-strand break-responsive ubiquitylation events, identifying previously known targets and revealing the actin-organizing protein Dbn1 as a major target of DNA damage-induced ubiquitylation. We find that Dbn1 is targeted for proteasomal degradation by the SCFß-Trcp1 ubiquitin ligase, in a conserved mechanism driven by ATM-mediated phosphorylation of a previously uncharacterized ß-Trcp1 degron containing an SQ motif. We further show that this degron is sufficient to induce DNA damage-dependent protein degradation of a model substrate. Collectively, we demonstrate UBIMAX's ability to identify targets of stimulus-regulated ubiquitylation and reveal an SCFß-Trcp1-mediated ubiquitylation mechanism controlled directly by the apical DNA damage response kinases.

Ocular Pharmacology and Toxicology of TRPV1 Antagonist SAF312 (Libvatrep).

Purpose: To evaluate the pharmacology and toxicology of SAF312, a transient receptor potential vanilloid 1 (TRPV1) antagonist. Methods: TRPV1 expression in human ocular tissues was evaluated with immunohistochemistry. Inhibition of calcium influx in Chinese hamster ovary (CHO) cells expressing human TRPV1 (hTRPV1) and selectivity of SAF312 were assessed by a fluorescent imaging plate reader assay. Ocular tissue and plasma pharmacokinetics (PK) were assessed following a single topical ocular dose of SAF312 (0.5%, 1.0%, 1.5%, 2.5%) in rabbits. Safety and tolerability of SAF312 were evaluated in rabbits and dogs. Effects of SAF312 on corneal wound healing after photorefractive keratectomy (PRK) surgery were assessed in rabbits. Results: TRPV1 expression was noted in human cornea and conjunctiva. SAF312 inhibited calcium influx in CHO-hTRPV1 cells induced by pH 5.5 (2-[N-morpholino] ethanesulfonic acid), N-arachidonoylethanolamine, capsaicin, and N-arachidonoyl dopamine, with IC50 values of 5, 10, 12, and 27 nM, respectively, and inhibition appeared noncompetitive. SAF312 demonstrated high selectivity for TRPV1 (>149-fold) over other TRP channels. PK analysis showed highest concentrations of SAF312 in cornea and conjunctiva. SAF312 was found to be safe and well tolerated in rabbits and dogs up to the highest feasible concentration of 2.5%. No delay in wound healing after PRK was observed. Conclusions: SAF312 is a potent, selective, and noncompetitive antagonist of hTRPV1 with an acceptable preclinical safety profile for use in future clinical trials. Translational Relevance: SAF312, which was safe and well tolerated without causing delay in wound healing after PRK in rabbits, may be a potential therapeutic agent for ocular surface pain.

Social and sexual consequences of facial femininity in a non-human primate.

In humans, femininity shapes women's interactions with both genders, but its influence on animals remains unknown. Using 10 years of data on a wild primate, we developed an artificial intelligence-based method to estimate facial femininity from naturalistic portraits. Our method explains up to 30% of the variance in perceived femininity in humans, competing with classical methods using standardized pictures taken under laboratory conditions. We then showed that femininity estimated on 95 female mandrills significantly correlated with various socio-sexual behaviors. Unexpectedly, less feminine female mandrills were approached and aggressed more frequently by both sexes and received more male copulations, suggesting a positive valuation of masculinity attributes rather than a perception bias. This study contributes to understand the role of femininity on animal's sociality and offers a framework for non-invasive research on visual communication in behavioral ecology.

Loose Tumor Cells in Pulmonary Arteries of Lung Adenocarcinoma Resection Specimen: No Correlation With Survival, Despite High Prevalence.

CONTEXT.­: Loose tumor cells and tumor cell clusters can be recognized in the lumen of intratumoral pulmonary arteries of resected non-small cell lung cancer specimens. It is unclear whether these should be considered tumor-emboli, and as such could predict a worsened prognosis. OBJECTIVE.­: To investigate the nature and prognostic impact of pulmonary artery intraluminal tumor cells. DESIGN.­: This multicenter study involved an exploratory pilot study and a validation study from 3 institutions. For the exploratory pilot, a retrospective pulmonary resection cohort of primary adenocarcinomas, diagnosed between November 2007 and November 2010, were scored for the presence of tumor cells, as well as potentially other cells in the intravascular spaces using hematoxylin-eosin, and cytokeratin 7 (CK7) stains. In the validation part, 2 retrospective cohorts of resected pulmonary adenocarcinomas, between January 2011 and December 2016, were included. Recurrence-free survival (RFS) and overall survival (OS) data were collected. RESULTS.­: In the pilot study, CK7+ intravascular cells, mainly tumor cells, were present in 23 of 33 patients (69.7%). The 5-year OS for patients with intravascular tumor cells was 61%, compared with 40% for patients without intravascular tumor cells (P = .19). In the validation study, CK7+ intravascular tumor cells were present in 41 of 70 patients (58.6%). The 5-year RFS for patients with intravascular tumor cells was 80.0%, compared with 80.6% in patients without intravascular tumor cells (P = .52). The 5-year OS rates were, respectively, 82.8% and 71.6% (P = .16). CONCLUSIONS.­: Loose tumor cells in pulmonary arterial lumina were found in most non-small cell lung cancer resection specimens and were not associated with a worse RFS or OS. Therefore, most probably they represent an artifact.

NMDA receptor functions in health and disease: Old actor, new dimensions.

N-Methyl-D-aspartate ionotropic glutamate receptors (NMDARs) play key roles in synaptogenesis, synaptic maturation, long-term plasticity, neuronal network activity, and cognition. Mirroring this wide range of instrumental functions, abnormalities in NMDAR-mediated signaling have been associated with numerous neurological and psychiatric disorders. Thus, identifying the molecular mechanisms underpinning the physiological and pathological contributions of NMDAR has been a major area of investigation. Over the past decades, a large body of literature has flourished, revealing that the physiology of ionotropic glutamate receptors cannot be restricted to fluxing ions, and involves additional facets controlling synaptic transmissions in health and disease. Here, we review newly discovered dimensions of postsynaptic NMDAR signaling supporting neural plasticity and cognition, such as the nanoscale organization of NMDAR complexes, their activity-dependent redistributions, and non-ionotropic signaling capacities. We also discuss how dysregulations of these processes may directly contribute to NMDAR-dysfunction-related brain diseases.

The Mandrillus Face Database: A portrait image database for individual and sex recognition, and age prediction in a non-human primate.

The Mandrillus Project is a long-term field research project in ecology and evolutionary biology, monitoring, since 2012, a natural population of mandrills (Mandrillus sphinx; primate) located in Southern Gabon. The Mandrillus Face Database was launched at the beginning of the project and now contains 29,495 photographic portraits collected on 397 individuals from this population, from birth to death for some of them. Portrait images have been obtained by manually processing images taken in the field with DSLR cameras: faces have been cropped to remove the ears and rotated to align the eyes horizontally. The database provides portrait images resized to 224 × 224 pixels associated with several manually annotated labels: individual identity, sex, age, face view, and image quality. Labels are stored within the image metadata and in a table accompanying the image database. This database will allow training and comparing methods on individual and sex recognition, and age prediction in a non-human animal.