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The adaptive immune system holds invaluable information on past and present immune responses in the form of B and T cell receptor sequences, but we are limited in our ability to decode this information. Machine learning approaches are under active investigation for a range of tasks relevant to understanding and manipulating the adaptive immune receptor repertoire, including matching receptors to the antigens they bind, generating antibodies or T cell receptors for use as therapeutics, and diagnosing disease based on patient repertoires. Progress on these tasks has the potential to substantially improve the development of vaccines, therapeutics, and diagnostics, as well as advance our understanding of fundamental immunological principles. We outline key challenges for the field, highlighting the need for software benchmarking, targeted large-scale data generation, and coordinated research efforts., Competing Interests: Declaration of interests V.G. declares advisory board positions in aiNET GmbH, Enpicom B.V., Absci, Omniscope, and Diagonal Therapeutics. V.G. is a consultant for Adaptive Biosystems, Specifica Inc., Roche/Genentech, immunai, LabGenius, and FairJourney Biologics. T.J.O., G.I., J.P.L., R.A.B., R.A.A., and V.G. are employees of Imprint LLC. T.J.O is a consultant for CDI Labs., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

This study introduces a novel approach to enhance surface plasmon resonance (SPR) sensing using Kramers-Kronig (K-K) relations for phase extraction from reflection spectra. By applying the K-K relations, a phase shift sensitivity of 3400°/RIU is achieved improving SPR detection limits to 9 × 10 -6 RIU, which is four times more sensitive than conventional methods for determining SPR peak shifts. This advancement enables more precise detection of refractive index changes in aqueous solutions, making it valuable for biosensing and environmental monitoring with spectrometers.

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., (© 2024. The Author(s).)

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., (© 2024. The Author(s).)

Fatty acids play many critical roles in brain function but have not been investigated in essential tremor (ET), a frequent movement disorder suspected to involve cerebellar dysfunction. Here, we report a postmortem comparative analysis of fatty acid profiles by gas chromatography in the cerebellar cortex from ET patients (n = 15), Parkinson's disease (PD) patients (n = 15) and Controls (n = 17). Phosphatidylcholine (PC), phosphatidylethanolamine (PE) and phosphatidylinositol (PI)/ phosphatidylserine (PS) were separated by thin-layer chromatography and analyzed separately. First, the total amounts of fatty acids retrieved from the cerebellar cortex were lower in ET patients compared with PD patients, including monounsaturated (MUFA) and polyunsaturated fatty acids (PUFA). The diagnosis of ET was associated with lower cerebellar levels of saturated fatty acids (SFA) and PUFA (DHA and ARA) in the PE fraction specifically, but with a higher relative content of dihomo-γ-linolenic acid (DGLA; 20:3 ω-6) in the PC fraction. In contrast, a diagnosis of PD was associated with higher absolute concentrations of SFA, MUFA and ω-6 PUFA in the PI + PS fractions. However, relative PI + PS contents of ω-6 PUFA were lower in both PD and ET patients. Finally, linear regression analyses showed that the ω-3:ω-6 PUFA ratio was positively associated with age of death, but inversely associated with insoluble α-synuclein. Although it remains unclear how these FA changes in the cerebellum are implicated in ET or PD pathophysiology, they may be related to an ongoing neurodegenerative process or to dietary intake differences. The present findings provide a window of opportunity for lipid-based therapeutic nutritional intervention., Competing Interests: Declarations. Ethics Approval and Consent to Participate: All human brain samples included in the present study were from patients or a family member who had filled out a consent form. Competing Interests: The authors declare no competing interests., (© 2024. The Author(s).)

Researchers have shown growing interest in using deep neural networks (DNNs) to efficiently test the effects of perceptual processes on the evolution of color patterns and morphologies. Whether this is a valid approach remains unclear, as it is unknown whether the relative detectability of ecologically relevant stimuli to DNNs actually matches that of biological neural networks. To test this, we compare image classification performance by humans and six DNNs (AlexNet, VGG-16, VGG-19, ResNet-18, SqueezeNet, and GoogLeNet) trained to detect artificial moths on tree trunks. Moths varied in their degree of crypsis, conferred by different sizes and spatial configurations of transparent wing elements. Like humans, four of six DNN architectures found moths with larger transparent elements harder to detect. However, humans and only one DNN architecture (GoogLeNet) found moths with transparent elements touching one side of the moth's outline harder to detect than moths with untouched outlines. When moths were small, the camouflaging effect of transparent elements touching the moth's outline was reduced for DNNs but enhanced for humans. Prey size can thus interact with camouflage type in opposing directions in humans and DNNs, which warrants a deeper investigation of size interactions with a broader range of stimuli. Overall, our results suggest that humans and DNNs responses had some similarities, but not enough to justify the widespread use of DNNs for studies of camouflage., (© The Author(s) 2024. Published by Oxford University Press on behalf of the European Society of Evolutionary Biology. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Purpose of Review: To summarize basic physiological concepts of breathing effort and outline various methods for monitoring effort of inspiratory and expiratory muscles., Recent Findings: Esophageal pressure (Pes) measurement is the reference standard for respiratory muscle effort quantification, but various noninvasive screening tools have been proposed. Expiratory occlusion pressures (P0.1 and Pocc) could inform about low and high effort and the resulting lung stress, with Pocc outperforming P0.1 in identifying high effort. The pressure muscle index during an inspiratory hold could unveil inspiratory muscle effort, however obtaining a reliable inspiratory plateau can be difficult. Surface electromyography has the potential for inspiratory effort estimation, yet this is technically challenging for real-time assessment. Expiratory muscle activation is common in the critically ill warranting their assessment, that is, via gastric pressure monitoring. Expiratory muscle activation also impacts inspiratory effort interpretation which could result in both under- and overestimation of the resulting lung stress. There is likely a future role for machine learning applications to automate breathing effort monitoring at the bedside., Summary: Different tools are available for monitoring the respiratory muscles' effort during mechanical ventilation - from noninvasive screening tools to more invasive quantification methods. This could facilitate a lung and respiratory muscle-protective ventilation approach., (Copyright © 2024 The Author(s). Published by Wolters Kluwer Health, Inc.)

JOURNAL/nrgr/04.03/01300535-202502000-00033/figure1/v/2024-05-28T214302Z/r/image-tiff There is a need to develop interventions to slow or reverse the degeneration of dopamine neurons in Parkinson's disease after diagnosis. Given that preclinical and clinical studies suggest benefits of dietary n-3 polyunsaturated fatty acids, such as docosahexaenoic acid, and exercise in Parkinson's disease, we investigated whether both could synergistically interact to induce recovery of the dopaminergic pathway. First, mice received a unilateral stereotactic injection of 6-hydroxydopamine into the striatum to establish an animal model of nigrostriatal denervation. Four weeks after lesion, animals were fed a docosahexaenoic acid-enriched or a control diet for the next 8 weeks. During this period, the animals had access to a running wheel, which they could use or not. Docosahexaenoic acid treatment, voluntary exercise, or the combination of both had no effect on (i) distance traveled in the open field test, (ii) the percentage of contraversive rotations in the apomorphine-induction test or (iii) the number of tyrosine-hydroxylase-positive cells in the substantia nigra pars compacta. However, the docosahexaenoic acid diet increased the number of tyrosine-hydroxylase-positive terminals and induced a rise in dopamine concentrations in the lesioned striatum. Compared to docosahexaenoic acid treatment or exercise alone, the combination of docosahexaenoic acid and exercise (i) improved forelimb balance in the stepping test, (ii) decreased the striatal DOPAC/dopamine ratio and (iii) led to increased dopamine transporter levels in the lesioned striatum. The present results suggest that the combination of exercise and docosahexaenoic acid may act synergistically in the striatum of mice with a unilateral lesion of the dopaminergic system and provide support for clinical trials combining nutrition and physical exercise in the treatment of Parkinson's disease., (Copyright © 2025 Copyright: © 2025 Neural Regeneration Research.)

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., Competing Interests: Declaration of interests The authors declare that they have no competing interests., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

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., Competing Interests: None., (© 2024 The Author(s). Ecology and Evolution published by John Wiley & Sons Ltd.)

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., (© 2024. The Author(s).)

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., (© 2024. The Author(s).)

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., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

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 study, 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., Competing Interests: The authors have no relevant financial interest in the products or companies described in this article., (© 2024 College of American Pathologists.)

Background: High prostate eicosapentaenoic fatty acid (EPA) levels were associated with a significant reduction of upgrading to grade group (GG) ≥ 2 prostate cancer in men under active surveillance. We aimed to evaluate the effect of MAG-EPA long-chain omega-3 fatty acid dietary supplement on prostate cancer proliferation., Methods: A phase II double-blind randomized placebo-controlled trial was conducted in 130 men diagnosed with GG ≥ 2 prostate cancer and undergoing radical prostatectomy between 2015-2017 (Clinicaltrials.gov: NCT02333435). Participants were randomized to receive 3 g daily of either MAG-EPA (n = 65) or placebo (n = 65) for 7 weeks (range 4-10) prior to radical prostatectomy. The primary outcome was the cancer proliferation index quantified by automated image analysis of tumor nuclear Ki-67 expression using standardized prostatectomy tissue microarrays. Additional planned outcomes at surgery are reported including plasma levels of 27 inflammatory cytokines and fatty acid profiles in circulating red blood cells membranes and prostate tissue., Results: Cancer proliferation index measured by Ki-67 expression was not statistically different between the intervention (3.10%) and placebo (2.85%) groups (p = 0.64). In the per protocol analyses, the adjusted estimated effect of MAG-EPA was greater but remained non-significant. Secondary outcome was the changes in plasma levels of 27 cytokines, of which only IL-7 was higher in MAG-EPA group compared to placebo (p = 0.026). Men randomized to MAG-EPA prior to surgery had four-fold higher EPA levels in prostate tissue compared to those on placebo., Conclusions: This MAG-EPA intervention did not affect the primary outcome of prostate cancer proliferation according to nuclear Ki-67 expression. More studies are needed to decipher the effects of long-chain omega-3 fatty acid dietary supplementation in men with prostate cancer., (© 2024. The Author(s).)

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., (© 2024. The Author(s).)

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., (© 2024. The Author(s).)

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.

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).

Background and Purpose: The only validated treatment to prevent brain damage associated with hypoxia-ischemia (HI) encephalopathy of the newborn is controlled hypothermia with limited benefits. Additional putative neuroprotective drug candidates include sildenafil citrate, a phosphodiesterase-type 5 inhibitor. The main objective of this preclinical study is to assess its ability to reduce HI-induced neuroinflammation, in particular through its potential effect on microglial activation., Methods: HI was induced in P10 Sprague-Dawley rats by unilateral carotid permanent artery occlusion and hypoxia (HI) and treated by either hypothermia (HT) alone, Sildenafil (Sild) alone or combined treatment (SildHT). Lesion size and glial activation were analyzed by immunohistochemistry, qRT-PCR, and proteomic analyses performed at P13., Results: None of the treatments was associated with a significant early reduction in lesion size 72h after HI, despite significant changes in tissue loss distribution. Significant reductions in both Iba1 + (within the ipsilateral hemisphere) and GFAP + cells (within the ipsilateral hippocampus) were observed in SildHT group, but not in the other treatment groups. In microglia-sorted cells, pro-inflammatory markers, i.e. Il1b, Il6, Nos2, and CD86 were significantly downregulated in SildHT treatment group only. These changes were restricted to the ipsilateral hemisphere, were not evidenced in sorted astrocytes, and were not sex dependent. Proteomic analyses in sorted microglia refined the pro-inflammatory effect of HI and confirmed a biologically relevant impact of SildHT on specific molecular pathways including genes related to neutrophilic functions., Conclusions: Our findings suggest that Sildenafil combined with controlled hypothermia produces maximum effect in mitigating microglial activation induced by HI through complex proteomic regulation. The reduction of neuroinflammation induced by Sildenafil may represent an interesting therapeutic strategy for neonatal neuroprotection., (© 2024. The Author(s).)

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 SCF β-Trcp1 ubiquitin ligase, in a conserved mechanism driven by ATM-mediated phosphorylation of a previously uncharacterized β-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 SCF β-Trcp1 -mediated ubiquitylation mechanism controlled directly by the apical DNA damage response kinases., (© 2023. The Author(s).)

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., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Dibot et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: In the general population, a higher omega-3 polyunsaturated fatty acids intake is associated with lower levels of several psychological symptoms, especially depression. However, the existing evidence in cancer is equivocal., Methods: This phase IIB double-blind, placebo-controlled trial was aimed at comparing the effects of eicosapentaenoic acid monoacylglyceride (MAG-EPA) supplementation and high oleic acid sunflower oil (HOSO; placebo) on depression levels (primary outcome) and other symptoms (anxiety, fear of cancer recurrence, fatigue, insomnia, perceived cognitive impairments; secondary outcomes). Participants, recruited in a prostate cancer clinic, were randomized to MAG-EPA (3.75 g daily; n = 65) or HOSO (3.75 g daily; n = 65) for 1 year post-radical prostatectomy (RP), starting 4-10 weeks before surgery. Patients completed self-report scales at baseline (before RP) and 3, 6, 9, and 12 months after: Hospital Anxiety and Depression Scale (HADS), Fear of Cancer Recurrence Inventory (FCRI), Insomnia Severity Index (ISI), Fatigue Symptom Inventory (FSI), and Functional Assessment of Cancer Therapy-Cognitive Function (FACT-Cog)., Results: Analyses showed significant reductions in HADS-depression, HADS-anxiety, FCRI, ISI, FSI-number of days, and FACT-Cog-impact scores over time. A significant group-by-time interaction was obtained on FACT-Cog-Impact scores only; yet, the temporal change was significant in HOSO patients only., Conclusions: Several symptoms significantly decreased over time, mainly within the first months of the study. However, MAG-EPA did not produce greater reductions than HOSO. Omega-3 supplementation does not seem to improve psychological symptoms of men treated with RP., (© 2023 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.)

Psoriasis is a skin disease characterized by epidermal hyperplasia and an inappropriate activation of the adaptive immunity. A dysregulation of the skin's lipid mediators is reported in the disease with a predominance of the inflammatory cascade derived from n-6 polyunsaturated fatty acids (n-6 PUFAs). Bioactive lipid mediators derived from arachidonic acid (AA) are involved in the inflammatory functions of T cells in psoriasis, whereas n-3 PUFAs' derivatives are anti-inflammatory metabolites. Here, we sought to evaluate the influence of a supplementation of the culture media with eicosapentaenoic acid (EPA) on the lipid profile of a psoriatic skin model produced with polarized T cells. Healthy and psoriatic skin substitutes were produced following the auto-assembly technique. Psoriatic skin substitutes produced with or without T cells presented increased epidermal and dermal linolenic acid (LA) and AA levels. N-6 PUFA lipid mediators were strongly measured in psoriatic substitutes, namely, 13-hydroxyoctadecadienoic acid (13-HODE), prostaglandin E 2 (PGE 2 ) and 12-hydroxyeicosatetraenoic acid (12-HETE). The added EPA elevated the amounts of EPA, n-3 docosapentaenoic acid (DPA) and docosahexaenoic acid (DHA) in the epidermal and dermal phospholipids. The EPA supplementation balanced the production of epidermal lipid mediators, with an increase in prostaglandin E 3 (PGE 3 ), 12-hydroxyeicosapentaenoic acid (12-HEPE) and N -eicosapentaenoyl-ethanolamine (EPEA) levels. These findings show that EPA modulates the lipid composition of psoriatic skin substitutes by encouraging the return to a cutaneous homeostatic state.

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., Competing Interests: The authors declare no competing interests., (© 2023 The Authors.)

Objective: We aimed to evaluate the effectiveness of utilizing artificial intelligence (AI) to quantify the extent of pneumonia from chest CT scans, and to determine its ability to predict clinical deterioration or mortality in patients admitted to the hospital with COVID-19 in comparison to semi-quantitative visual scoring systems., Methods: A deep-learning algorithm was utilized to quantify the pneumonia burden, while semi-quantitative pneumonia severity scores were estimated through visual means. The primary outcome was clinical deterioration, the composite end point including admission to the intensive care unit, need for invasive mechanical ventilation, or vasopressor therapy, as well as in-hospital death., Results: The final population comprised 743 patients (mean age 65  ±  17 years, 55% men), of whom 175 (23.5%) experienced clinical deterioration or death. The area under the receiver operating characteristic curve (AUC) for predicting the primary outcome was significantly higher for AI-assisted quantitative pneumonia burden (0.739, p = 0.021) compared with the visual lobar severity score (0.711, p < 0.001) and visual segmental severity score (0.722, p = 0.042). AI-assisted pneumonia assessment exhibited lower performance when applied for calculation of the lobar severity score (AUC of 0.723, p = 0.021). Time taken for AI-assisted quantification of pneumonia burden was lower (38 ± 10 s) compared to that of visual lobar (328 ± 54 s, p < 0.001) and segmental (698 ± 147 s, p < 0.001) severity scores., Conclusion: Utilizing AI-assisted quantification of pneumonia burden from chest CT scans offers a more accurate prediction of clinical deterioration in patients with COVID-19 compared to semi-quantitative severity scores, while requiring only a fraction of the analysis time., Advances in Knowledge: Quantitative pneumonia burden assessed using AI demonstrated higher performance for predicting clinical deterioration compared to current semi-quantitative scoring systems. Such an AI system has the potential to be applied for image-based triage of COVID-19 patients in clinical practice.

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.

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., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Aim: To assess whether small-for-gestational-age (SGA) - an indicator of poor fetal growth, may affect metabolic health biomarkers in infancy and explore the predictors., Methods: This was a nested matched (1:2) prospective observational study of 65 SGA (birth weight < 10th percentile) and 130 optimal-for-gestational-age (OGA, birth weight 25th-75th percentiles, control) infants in the 3D birth cohort with subjects recruited in Canada from 1 May 2010 to 31 August 2012. The outcomes included homeostasis model assessment of insulin resistance (HOMA-IR) and beta-cell function (HOMA-β), circulating leptin and adiponectin concentrations at age 2 years., Results: HOMA-IR, HOMA-β, leptin and adiponectin concentrations were similar in SGA versus OGA infants. Female sex and accelerated growth in length during mid-infancy (3-12 months) were associated with higher HOMA-IR. Caucasian ethnicity and decelerated growth in weight during late infancy (12-24 months) were associated with lower HOMA-IR. Current BMI was positively associated with circulating adiponectin in SGA infants only (+13.4% [4.0%-23.7%] per BMI z score increment)., Conclusion: Insulin resistance and secretion, circulating leptin and adiponectin levels were normal in SGA subjects in infancy at age 2 years. The novel observation in SGA-specific positive association between current BMI and circulating adiponectin suggests dysfunctional adiposity-adiponectin negative feedback loop development during infancy in SGA subjects., (© 2023 Foundation Acta Paediatrica. Published by John Wiley & Sons Ltd.)

Prostate cancer (PCa) and associated treatments incur symptoms that may impact patients' quality of life. Studies have shown beneficial relationships between diet, especially omega-3 fatty acids, and these symptoms. Unfortunately, only few data describing the relationship between long-chain omega-3 fatty acids (LCn3) and PCa-related symptoms in patients are available. The purpose of this study was to evaluate the effects of LCn3 supplementation on PCa-specific quality of life in 130 men treated by radical prostatectomy. Men were randomized to receive a daily dose of either 3.75 g of fish oil or a placebo starting 7 weeks before surgery and for up to one-year post-surgery. Quality of life was assessed using the validated EPIC-26 and IPSS questionnaires at randomization, at surgery, and every 3 months following surgery. Between-group differences were assessed using linear mixed models. Intention-to-treat analyses showed no significant difference between the two groups. However, at 12-month follow-up, per-protocol analyses showed a significantly greater increase in the urinary irritation function score (better urinary function) (MD = 5.5, p = 0.03) for the LCn3 group compared to placebo. These results suggest that LCn3 supplementation may improve the urinary irritation function in men with PCa treated by radical prostatectomy and support to conduct of larger-scale studies.

In recent years, computer science has made major advances in understanding drawing behavior. Artificial intelligence, and more precisely deep learning, has displayed unprecedented performance in the automatic recognition and classification of large databases of sketches and drawings collected through touchpad devices. Although deep learning can perform these tasks with high accuracy, the way they are performed by the algorithms remains largely unexplored. Improving the interpretability of deep neural networks is a very active research area, with promising recent advances in understanding human cognition. Deep learning thus offers a powerful framework to study drawing behavior and the underlying cognitive processes, particularly in children and non-human animals, on whom knowledge is incomplete. In this literature review, we first explore the history of deep learning as applied to the study of drawing along with the main discoveries in this area, while proposing open challenges. Second, multiple ideas are discussed to understand the inherent structure of deep learning models. A non-exhaustive list of drawing datasets relevant to deep learning approaches is further provided. Finally, the potential benefits of coupling deep learning with comparative cultural analyses are discussed., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Beltzung, Pelé, Renoult and Sueur.)

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., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. The authors declare the following financial interests/personal relationships which may be considered as potential competing interests:, (© 2023 The Authors.)

Fanconi Anemia (FA) is a rare, genome instability-associated disease characterized by a deficiency in repairing DNA crosslinks, which are known to perturb several cellular processes, including DNA transcription, replication, and repair. Formaldehyde, a by-product of metabolism, is thought to drive FA by generating DNA interstrand crosslinks (ICLs) and DNA-protein crosslinks (DPCs). However, the impact of formaldehyde on global cellular pathways has not been investigated thoroughly. Herein, using a pangenomic CRISPR-Cas9 screen, we identify EXO1 as a critical regulator of formaldehyde-induced DNA lesions. We show that EXO1 knockout cell lines exhibit formaldehyde sensitivity leading to the accumulation of replicative stress, DNA double-strand breaks, and quadriradial chromosomes, a typical feature of FA. After formaldehyde exposure, EXO1 is recruited to chromatin, protects DNA replication forks from degradation, and functions in parallel with the FA pathway to promote cell survival. In vitro, EXO1-mediated exonuclease activity is proficient in removing DPCs. Collectively, we show that EXO1 limits replication stress and DNA damage to counteract formaldehyde-induced genome instability., (© 2023. The Author(s).)

Behavioral discrimination of kin is a key process structuring social relationships in animals. In this study, we provide evidence for discrimination towards non-kin by third-parties through a mechanism of phenotype matching. In mandrills, we recently demonstrated increased facial resemblance among paternally related juvenile and adult females indicating adaptive opportunities for paternal kin recognition. Here, we hypothesize that mandrill mothers use offspring's facial resemblance with other infants to guide offspring's social opportunities towards similar-looking ones. Using deep learning for face recognition in 80 wild mandrill infants, we first show that infants sired by the same father resemble each other the most, independently of their age, sex or maternal origin, extending previous results to the youngest age class. Using long-term behavioral observations on association patterns, and controlling for matrilineal origin, maternal relatedness and infant age and sex, we then show, as predicted, that mothers are spatially closer to infants that resemble their own offspring more, and that this maternal behavior leads to similar-looking infants being spatially associated. We then discuss the different scenarios explaining this result, arguing that an adaptive maternal behavior is a likely explanation. In support of this mechanism and using theoretical modeling, we finally describe a plausible evolutionary process whereby mothers gain fitness benefits by promoting nepotism among paternally related infants. This mechanism, that we call 'second-order kin selection', may extend beyond mother-infant interactions and has the potential to explain cooperative behaviors among non-kin in other social species, including humans., Competing Interests: MC, CP, BR, PA, EW, PK, FR, JR No competing interests declared, (© 2022, Charpentier, Poirotte et al.)

Gobius ater Bellotti, 1888 is the Mediterranean gobiid species whose live appearance has remained unknown the longest since its description. A goby observed in southern France in 2021 is here identified as G. ater based on a diagnosis of morphological characters visible on high-quality underwater photographs. Then, the authors provide the first description of colouration in live G. ater and a species diagnosis based on colouration. This diagnosis allows the authors to validate a previous photographic record, also from France. Reviewing all claims of G. ater, they argue that only seven records are unambiguously valid, including the two photographic records presented here., (© 2022 Fisheries Society of the British Isles.)

Drawings have been widely used as a window to the mind; as such, they can reveal some aspects of the cognitive and emotional worlds of other animals that can produce them. The study of non-human drawings, however, is limited by human perception, which can bias the methodology and interpretation of the results. Artificial intelligence can circumvent this issue by allowing automated, objective selection of features used to analyze drawings. In this study, we use artificial intelligence to investigate seasonal variations in drawings made by Molly, a female orangutan who produced more than 1299 drawings between 2006 and 2011 at the Tama Zoological Park in Japan. We train the VGG19 model to first classify the drawings according to the season in which they are produced. The results show that deep learning is able to identify subtle but significant seasonal variations in Molly's drawings, with a classification accuracy of 41.6%. We use VGG19 to investigate the features that influence this seasonal variation. We analyze separate features, both simple and complex, related to color and patterning, and to drawing content and style. Content and style classification show maximum performance for moderately complex, highly complex, and holistic features, respectively. We also show that both color and patterning drive seasonal variation, with the latter being more important than the former. This study demonstrates how deep learning can be used to objectively analyze non-figurative drawings and calls for applications to non-primate species and scribbles made by human toddlers.

Purpose: Quantitative lung measures derived from computed tomography (CT) have been demonstrated to improve prognostication in coronavirus disease 2019 (COVID-19) patients but are not part of clinical routine because the required manual segmentation of lung lesions is prohibitively time consuming. We aim to automatically segment ground-glass opacities and high opacities (comprising consolidation and pleural effusion). Approach: We propose a new fully automated deep-learning framework for fast multi-class segmentation of lung lesions in COVID-19 pneumonia from both contrast and non-contrast CT images using convolutional long short-term memory (ConvLSTM) networks. Utilizing the expert annotations, model training was performed using five-fold cross-validation to segment COVID-19 lesions. The performance of the method was evaluated on CT datasets from 197 patients with a positive reverse transcription polymerase chain reaction test result for SARS-CoV-2, 68 unseen test cases, and 695 independent controls. Results: Strong agreement between expert manual and automatic segmentation was obtained for lung lesions with a Dice score of 0.89 ± 0.07 ; excellent correlations of 0.93 and 0.98 for ground-glass opacity (GGO) and high opacity volumes, respectively, were obtained. In the external testing set of 68 patients, we observed a Dice score of 0.89 ± 0.06 as well as excellent correlations of 0.99 and 0.98 for GGO and high opacity volumes, respectively. Computations for a CT scan comprising 120 slices were performed under 3 s on a computer equipped with an NVIDIA TITAN RTX GPU. Diagnostically, the automated quantification of the lung burden % discriminate COVID-19 patients from controls with an area under the receiver operating curve of 0.96 (0.95-0.98). Conclusions: Our method allows for the rapid fully automated quantitative measurement of the pneumonia burden from CT, which can be used to rapidly assess the severity of COVID-19 pneumonia on chest CT., (© 2022 Society of Photo-Optical Instrumentation Engineers (SPIE).)

Covalent binding of proteins to DNA forms DNA-protein crosslinks (DPCs), which represent cytotoxic DNA lesions that interfere with essential processes such as DNA replication and transcription. Cells possess different enzymatic activities to counteract DPCs. These include enzymes that degrade the adducted proteins, resolve the crosslinks, or incise the DNA to remove the crosslinked proteins. An important question is how DPCs are sensed and targeted for removal via the most suited pathway. Recent advances have shown the inherent role of DNA replication in triggering DPC removal by proteolysis. However, DPCs are also efficiently sensed and removed in the absence of DNA replication. In either scenario, post-translational modifications (PTMs) on DPCs play essential and versatile roles in orchestrating the repair routes. In this review, we summarize the current knowledge of the mechanisms that trigger DPC removal via PTMs, focusing on ubiquitylation, small ubiquitin-related modifier (SUMO) conjugation (SUMOylation), and poly (ADP-ribosyl)ation (PARylation). We also briefly discuss the current knowledge gaps and emerging hypotheses in the field., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Leng and Duxin.)

Reef fishes are closely connected to many human populations, yet their contributions to society are mostly considered through their economic and ecological values. Cultural and intrinsic values of reef fishes to the public can be critical drivers of conservation investment and success, but remain challenging to quantify. Aesthetic value represents one of the most immediate and direct means by which human societies engage with biodiversity, and can be evaluated from species to ecosystems. Here, we provide the aesthetic value of 2,417 ray-finned reef fish species by combining intensive evaluation of photographs of fishes by humans with predicted values from machine learning. We identified important biases in species' aesthetic value relating to evolutionary history, ecological traits, and International Union for Conservation of Nature (IUCN) threat status. The most beautiful fishes are tightly packed into small parts of both the phylogenetic tree and the ecological trait space. In contrast, the less attractive fishes are the most ecologically and evolutionary distinct species and those recognized as threatened. Our study highlights likely important mismatches between potential public support for conservation and the species most in need of this support. It also provides a pathway for scaling-up our understanding of what are both an important nonmaterial facet of biodiversity and a key component of nature's contribution to people, which could help better anticipate consequences of species loss and assist in developing appropriate communication strategies., Competing Interests: The authors have declared that no competing interests exist.

Numerous photographs of live fishes posted by anglers and divers on social media and citizen science databases are important sources of information for ichthyological research. However, validating records that extend the known ecology and bathymetric or geographic distribution of species should rely on a rigorous identification process. The family Gobiidae, with their small size, superficial resemblance among species and high species richness are particularly difficult to identify. Therefore, the identification from photographs of live individuals of Mediterranean marine gobies from the continental shelf was studied. A dichotomous identification key is provided based on photographs of live individuals, allowing positive identification of 41 out of the 66 species reviewed in this publication. Then, for all 66 species we provide a brief description of important characters, which can be used for provisional identification for those species that could not be positively identified using the key. Pending further progress in identification of live individuals, we suggest that records extending the known geographic and ecological species distribution be taken into account only if they could be validated using the dichotomous identification key.

Psoriasis is an autoimmune skin disease with an increased number of leukocytes infiltrating the dermal and epidermal compartments compared with normal skin. N-3 polyunsaturated fatty acids (n-3 PUFAs) are frequently used in the clinic in order to attenuate the symptoms of psoriasis. For psoriatic patients, a supplementation of the diet with alpha-linolenic acid (ALA) reduces the activation of T cell signaling pathways, leading to a significant reduction in inflammatory cytokine secretion. However, the precise mechanism of action of n-3 PUFAs in psoriasis is still not understood. In the present study, we elucidated the bioaction of ALA on the adaptive immune component of psoriasis by using a psoriatic skin model produced with the addition of activated T cells. Healthy and psoriatic skin substitutes were produced according to the self-assembly method, using culture media supplemented with 10 μM of ALA. T cells were isolated from blood samples using a negative selection isolation method. ALA supplementation regulated the hyperproliferation and abnormal cell differentiation of psoriatic keratinocytes stimulated by T cells. Additionally, the exogenous ALA was correctly incorporated into the phospholipids of keratinocytes, which resulted in increased levels of ALA, eicosapentaenoic acid (EPA) and n-3 docosapentaenoic acid (n-3 DPA). The infiltration of T cells into the epidermis was reduced when ALA was added to the culture medium, and significant decreases in the levels of inflammatory cytokines and chemokines such as CXCL1, interleukin-6 (IL-6) and interleukin-8 (IL-8) were consequently measured in psoriatic substitutes supplemented with this n-3 PUFA. Altogether, our results showed that in this psoriatic skin model enriched with T cells, ALA exerted its beneficial effect by decreasing the quantities of inflammatory mediators released by T cells.

DNA interstrand crosslinks (ICLs) are cytotoxic lesions that threaten genome integrity. The Fanconi anemia (FA) pathway orchestrates ICL repair during DNA replication, with ubiquitylated FANCI-FANCD2 (ID2) marking the activation step that triggers incisions on DNA to unhook the ICL. Restoration of intact DNA requires the coordinated actions of polymerase ζ (Polζ)-mediated translesion synthesis (TLS) and homologous recombination (HR). While the proteins mediating FA pathway activation have been well characterized, the effectors regulating repair pathway choice to promote error-free ICL resolution remain poorly defined. Here, we uncover an indispensable role of SCAI in ensuring error-free ICL repair upon activation of the FA pathway. We show that SCAI forms a complex with Polζ and localizes to ICLs during DNA replication. SCAI-deficient cells are exquisitely sensitive to ICL-inducing drugs and display major hallmarks of FA gene inactivation. In the absence of SCAI, HR-mediated ICL repair is defective, and breaks are instead re-ligated by polymerase θ-dependent microhomology-mediated end-joining, generating deletions spanning the ICL site and radial chromosomes. Our work establishes SCAI as an integral FA pathway component, acting at the interface between TLS and HR to promote error-free ICL repair., (© 2022 The Authors. Published under the terms of the CC BY NC ND 4.0 license.)

The explanatory power of Hamilton's rule, the main explanatory principle of social evolution theory, is an ongoing subject of controversy. In this paper, we reinforce the case for the considerable value of the regression-based version of the rule in explaining the evolution of social traits. Although we agree that the rule can have an organizing role in social evolution research, we maintain that it does not explain in virtue of citing causes or providing an organizing framework. Instead, we argue it either provides an explanation by constraint or a non-causal counterfactual explanation., (Copyright © 2021 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Single molecule localization (SML) and tracking (SPT) techniques, such as (spt)PALM, (u/DNA)PAINT and quantum dot tracking, have given unprecedented insight into the nanoscale molecular organization and dynamics in living cells. They allow monitoring individual proteins with millisecond temporal resolution and high spatial resolution (<30 nm) by precisely localizing the point spread function (PSF) of individual emitters and tracking their position over time. While SPT methods have been extended to study the temporal dynamics and co-organization of multiple proteins, conventional experimental setups are restricted in the number of proteins they can probe simultaneously and usually have to tradeoff between the number of colors, the spatio-temporal resolution, and the field of view. Yet, localizing and tracking several proteins simultaneously at high spatial and temporal resolution within large field of views can provide important biological insights. By employing a dual-objective spectral imaging configuration compatible with live cell imaging combined with dedicated computation tools, we demonstrate simultaneous 3D single particle localization and tracking of multiple distinct species over large field of views to be feasible without compromising spatio-temporal resolution. The dispersive element introduced into the second optical path induces a spectrally dependent displacement, which we used to analytically separate up to five different fluorescent species of single emitters based on their emission spectra. We used commercially available microscope bodies aligned one on top of the other, offering biologists with a very ergonomic and flexible instrument covering a broad range of SMLM applications. Finally, we developed a powerful freely available software, called PALMTracer, which allows to quantitatively assess 3D + t + λ SMLM data. We illustrate the capacity of our approach by performing multi-color 3D DNA-PAINT of fixed samples, and demonstrate simultaneous tracking of multiple receptors in live fibroblast and neuron cultures., Competing Interests: Author CB was employed by the company Imagine Optic under a PhD Cifre contract. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Butler, Saraceno, Kechkar, Bénac, Studer, Dupuis, Groc, Galland and Sibarita.)

Conventional breeding efforts for iron (Fe) and zinc (Zn) biofortification of bread wheat (Triticum aestivum L.) have been hindered by a lack of genetic variation for these traits and a negative correlation between grain Fe and Zn concentrations and yield. We have employed genetic engineering to constitutively express (CE) the rice (Oryza sativa) nicotianamine synthase 2 (OsNAS2) gene and upregulate biosynthesis of two metal chelators - nicotianamine (NA) and 2'-deoxymugineic acid (DMA) - in bread wheat, resulting in increased Fe and Zn concentrations in wholemeal and white flour. Here we describe multi-location confined field trial (CFT) evaluation of a low-copy transgenic CE-OsNAS2 wheat event (CE-1) over 3 years and demonstrate higher concentrations of NA, DMA, Fe, and Zn in CE-1 wholemeal flour, white flour, and white bread and higher Fe bioavailability in CE-1 white flour relative to a null segregant (NS) control. Multi-environment models of agronomic and grain nutrition traits revealed a negative correlation between grain yield and grain Fe, Zn, and total protein concentrations, yet no correlation between grain yield and grain NA and DMA concentrations. White flour Fe bioavailability was positively correlated with white flour NA concentration, suggesting that NA-chelated Fe should be targeted in wheat Fe biofortification efforts., (© 2021 Society for Experimental Biology and John Wiley & Sons Ltd.)

Polyunsaturated fatty acids (PUFAs) play an important role in the establishment and the maintenance of the skin barrier function. However, the impact of their derived lipid mediators remains unclear. Skin substitutes were engineered according to the self-assembly method with a culture medium supplemented with 10 μM of both α-linolenic acid (ALA) and linoleic acid (LA). The supplementation with ALA and LA decreased testosterone absorption through a tissue-engineered reconstructed skin model, thus indicating an improved skin barrier function following supplementation. The exogenously provided fatty acids were incorporated into the phospholipid and triglyceride fractions of the skin substitutes. Indeed, the dual supplementation increased the levels of eicosapentaenoic acid (EPA) (15-fold), docosapentaenoic acid (DPA) (3-fold), and LA (1.5-fold) in the epidermal phospholipids while it increased the levels of ALA (>20-fold), DPA (3-fold) and LA (1.5-fold) in the epidermal triglycerides. The bioactive lipid mediator profile of the skin substitutes, including prostaglandins, hydroxy-fatty acids, N-acylethanolamines and monoacylglycerols, was next analyzed using liquid chromatography-tandem mass spectrometry. The lipid supplementation further modulated bioactive lipid mediator levels of the reconstructed skin substitutes, leading to a lipid mediator profile more representative of the one found in normal human skin. These findings show that an optimized supply of PUFAs via culture media is essential for the establishment of improved barrier function in vitro. STATEMENT OF SIGNIFICANCE: Supplementation of the culture medium with 10 μM of both α-linolenic acid (ALA) and linoleic acid (LA) improved the skin barrier function of a tissue-engineered skin model. The exogenously provided fatty acids were incorporated into the phospholipid and triglyceride fractions of the skin substitutes and further modulated bioactive lipid mediator levels, including prostaglandins, hydroxy-fatty acids, N-acylethanolamines and monoacylglycerols. These findings highlight the important role of ALA and LA in skin homeostasis and show that an optimized supply of polyunsaturated fatty acids via culture media is essential for the establishment of improved barrier function in vitro., Competing Interests: Declaration of Competing Interest The authors declare no competing interests, (Copyright © 2021. Published by Elsevier Ltd.)

Context: Fetal overgrowth "programs" an elevated risk of obesity and type 2 diabetes in adulthood. Plausibly, adipokines may be involved in programming metabolic health., Objective: This work aimed to evaluate whether large-for-gestational-age (LGA), an indicator of fetal overgrowth, is associated with altered circulating leptin and adiponectin levels in infancy, and assess the determinants., Methods: In the Canadian 3D birth cohort, we studied 70 LGA (birth weight > 90th percentile) and 140 optimal-for-gestational-age (OGA, 25th-75th percentiles) infants matched by maternal ethnicity, smoking, and gestational age at delivery. The primary outcomes were fasting leptin, and total and high-molecular-weight (HMW) adiponectin concentrations at age 2 years., Results: LGA infants had higher body mass index (BMI) than OGA infants. However, there were no significant differences in leptin, and total and HMW adiponectin concentrations. Leptin concentrations were positively associated with female sex, weight (z score) gain 0 to 24 months, current BMI, and the sum of triceps and subscapular skinfold thickness, and negatively associated with maternal age and White ethnicity. Female sex was associated with lower total and HMW adiponectin concentrations. Weight (z score) gain 0 to 24 months and current BMI were positively correlated with total and HMW adiponectin concentrations in LGA infants only., Conclusion: This study is the first to demonstrate that LGA does not matter for circulating leptin and adiponectin concentrations in infancy, and there may be LGA-specific positive associations between weight gain or current BMI and adiponectin concentrations in infancy, suggesting dysfunction in establishing the adiposity-adiponectin negative feedback loop in LGA individuals., (© The Author(s) 2021. Published by Oxford University Press on behalf of the Endocrine Society. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

We previously identified matrix metalloproteinase 2 (MMP2) and MMP9 plasma levels as candidate biomarkers of bevacizumab activity in patients with recurrent glioblastoma. The aim of this study was to assess the predictive value of MMP2 and MMP9 in a randomized phase III trial in patients with newly diagnosed glioblastoma and to explore their tumor source. In this post hoc analysis of the AVAglio trial (AVAGlio/NCT00943826), plasma samples from 577 patients (bevacizumab, n = 283; placebo, n = 294) were analyzed for plasma MMP9 and MMP2 levels by enzyme-linked immunosorbent assay. A prospective local cohort of 38 patients with newly diagnosed glioblastoma was developed for analysis of tumor characteristics by magnetic resonance imaging and measurement of plasma and tumor levels of MMP9 and MMP2. In this AVAglio study, MMP9, but not MMP2, was correlated with bevacizumab efficacy. Patients with low MMP9 derived a significant 5.2-month overall survival (OS) benefit with bevacizumab (HR 0.51, 95% CI 0.34-0.76, p = 0.0009; median 13.6 vs. 18.8 months). In multivariate analysis, a significant interaction was seen between treatment and MMP9 (p = 0.03) for OS. In the local cohort, we showed that preoperative MMP9 plasma levels decreased after tumor resection and were correlated with tumor levels of MMP9 mRNA (p = 0.03). However, plasma MMP9 was not correlated with tumor size, invasive pattern, or angiogenesis. Using immunohistochemistry, we showed that MMP9 was expressed by inflammatory cells but not by tumor cells. After cell sorting, we showed that MMP9 was expressed by CD45+ immune cells. Finally, using flow cytometry, we showed that MMP9 was expressed by tumor-infiltrating neutrophils. In conclusion, circulating MMP9 is predictive of bevacizumab efficacy and is released by tumor-infiltrating neutrophils., (© 2021. The Author(s).)