Miracle-dz/UniFAR-FTUs huggingface dataset:
SHIP1 modulates antimalarial immunity by bridging the crosstalk between type I IFN signaling and autophagy

ABSTRACT Stringent control of the type I interferon (IFN-I) signaling is critical for host immune defense against infectious diseases, yet the molecular mechanisms that regulate this pathway remain elusive. Here, we show that Src homology 2 containing inositol phosphatase 1 (SHIP1) suppresses IFN-I signaling by promoting IRF3 degradation during malaria infection. Genetic ablation of Ship1 in mice leads to high levels of IFN-I and confers resistance to Plasmodium yoelii nigeriensis (P.y.) N67 infection. Mechanistically, SHIP1 promotes the selective autophagic degradation of IRF3 by enhancing K63-linked ubiquitination of IRF3 at lysine 313, which serves as a recognition signal for NDP52-mediated selective autophagic degradation. In addition, SHIP1 is downregulated by IFN-I-induced miR-155-5p upon P.y. N67 infection and severs as a feedback loop of the signaling crosstalk. This study reveals a regulatory mechanism between IFN-I signaling and autophagy, and verifies SHIP1 can be a potential target for therapeutic intervention against malaria and other infectious diseases. IMPORTANCE Malaria remains a serious disease affecting millions of people worldwide. Malaria parasite infection triggers tightly controlled type I interferon (IFN-I) signaling that plays a critical role in host innate immunity; however, the molecular mechanisms underlying the immune responses are still elusive. Here, we discover a host gene [Src homology 2-containing inositol phosphatase 1 (SHIP1)] that can regulate IFN-I signaling by modulating NDP52-mediated selective autophagic degradation of IRF3 and significantly affect parasitemia and resistance of Plasmodium-infected mice. This study identifies SHIP1 as a potential target for immunotherapies in malaria and highlights the crosstalk between IFN-I signaling and autophagy in preventing related infectious diseases. SHIP1 functions as a negative regulator during malaria infection by targeting IRF3 for autophagic degradation. Malaria remains a serious disease affecting millions of people worldwide. Malaria parasite infection triggers tightly controlled type I interferon (IFN-I) signaling that plays a critical role in host innate immunity; however, the molecular mechanisms underlying the immune responses are still elusive. Here, we discover a host gene [Src homology 2-containing inositol phosphatase 1 (SHIP1)] that can regulate IFN-I signaling by modulating NDP52-mediated selective autophagic degradation of IRF3 and significantly affect parasitemia and resistance of Plasmodium-infected mice. This study identifies SHIP1 as a potential target for immunotherapies in malaria and highlights the crosstalk between IFN-I signaling and autophagy in preventing related infectious diseases. SHIP1 functions as a negative regulator during malaria infection by targeting IRF3 for autophagic degradation.
A Cre Driver Line for Genetic Targeting of Kappa Opioid Receptor Expressing Cells

Abstract Here we describe the generation and characterization of a Cre knock-in mouse line that harbors a Cre insertion in the 3′UTR of the κ opioid receptor gene (Oprk1) locus and provides genetic access to populations of κ opioid receptor (KOR)-expressing neurons throughout the brain. Using a combination of techniques including RNA in situ hybridization and immunohistochemistry, we report that Cre is expressed with high fidelity in KOR-expressing cells throughout the brain in this mouse line. We also provide evidence that Cre insertion does not alter basal KOR function. Baseline anxiety-like behaviors and nociceptive thresholds are unaltered in Oprk1-Cre mice. Chemogenetic activation of KOR-expressing cells in the basolateral amygdala (BLAKOR cells) resulted in several sex-specific effects on anxiety-like and aversive behaviors. Activation led to decreased anxiety-like behavior on the elevated plus maze and increased sociability in female but not in male Oprk1-Cre mice. Activation of BLAKOR cells also attenuated KOR agonist-induced conditioned place aversion (CPA) in male Oprk1-Cre mice. Overall, these results suggest a potential role for BLAKOR cells in regulating anxiety-like behaviors and KOR-agonist mediated CPA. In summary, these results provide evidence for the utility of the newly generated Oprk1-Cre mice in assessing localization, anatomy, and function of KOR circuits throughout the brain.
Infinitely many solutions for Kirchhoff type problems

This paper is devoted to the study of infinitely many solutions for a class of Kirchhoff type problems on a bounded domain. Based on the Fountain Theorem of Bartsch, we obtain the multiplicity results, which unify and sharply improve the recent results of He and Zou [X. He, W. Zou, Multiplicity of solutions for a class of Kirchhoff type problems, Acta Math. Appl. Sin. (Engl. Ser.) 26 (2010) 387-394]. Mathematics subject classification (2010): 35J60, 35J25.
A STIM dependent dopamine-neuropeptide axis maintains the larval drive to feed and grow in Drosophila

Appropriate nutritional intake is essential for organismal survival. In holometabolous insects such as Drosophila melanogaster, the quality and quantity of food ingested as larvae determines adult size and fecundity. Here we have identified a subset of dopaminergic neurons (THD’) that maintain the larval motivation to feed. Dopamine release from these neurons requires the ER Ca2+ sensor STIM. Larvae with loss of STIM stop feeding and growing, whereas expression of STIM in THD’ neurons rescues feeding, growth and viability of STIM null mutants to a significant extent. Moreover STIM is essential for maintaining excitability and release of dopamine from THD’ neurons. Optogenetic stimulation of THD’ neurons activated neuropeptidergic cells, including median neuro secretory cells that secrete insulin-like peptides. Loss of STIM in THD’ cells alters the developmental profile of specific insulin-like peptides including ilp3. Loss of ilp3 partially rescues STIM null mutants and inappropriate expression of ilp3 in larvae affects development and growth. In summary we have identified a novel STIM-dependent function of dopamine neurons that modulates developmental changes in larval feeding behaviour and growth.
Staphylococcus aureus Detection in Milk Using a Thickness Shear Mode Acoustic Aptasensor with an Antifouling Probe Linker

Contamination of food by pathogens can pose a serious risk to health. Therefore, monitoring for the presence of pathogens is critical to identify and regulate microbiological contamination of food. In this work, an aptasensor based on a thickness shear mode acoustic method (TSM) with dissipation monitoring was developed to detect and quantify Staphylococcus aureus directly in whole UHT cow’s milk. The frequency variation and dissipation data demonstrated the correct immobilization of the components. The analysis of viscoelastic properties suggests that DNA aptamers bind to the surface in a non-dense manner, which favors the binding with bacteria. The aptasensor demonstrated high sensitivity and was able to detect S. aureus in milk with a 33 CFU/mL limit of detection. Analysis was successful in milk due to the sensor’s antifouling properties, which is based on 3-dithiothreitol propanoic acid (DTTCOOH) antifouling thiol linker. Compared to bare and modified (dithiothreitol (DTT), 11-mercaptoundecanoic acid (MUA), and 1-undecanethiol (UDT)) quartz crystals, the sensitivity of the sensor’s antifouling in milk improved by about 82–96%. The excellent sensitivity and ability to detect and quantify S. aureus in whole UHT cow’s milk demonstrates that the system is applicable for rapid and efficient analysis of milk safety.
Impacts of Sex Ratio Meiotic Drive on Genome Structure and Function in a Stalk-Eyed Fly

Abstract Stalk-eyed flies in the genus Teleopsis carry selfish genetic elements that induce sex ratio (SR) meiotic drive and impact the fitness of male and female carriers. Here, we assemble and describe a chromosome-level genome assembly of the stalk-eyed fly, Teleopsis dalmanni, to elucidate patterns of divergence associated with SR. The genome contains tens of thousands of transposable element (TE) insertions and hundreds of transcriptionally and insertionally active TE families. By resequencing pools of SR and ST males using short and long reads, we find widespread differentiation and divergence between XSR and XST associated with multiple nested inversions involving most of the SR haplotype. Examination of genomic coverage and gene expression data revealed seven X-linked genes with elevated expression and coverage in SR males. The most extreme and likely drive candidate involves an XSR-specific expansion of an array of partial copies of JASPer, a gene necessary for maintenance of euchromatin and associated with regulation of TE expression. In addition, we find evidence for rapid protein evolution between XSR and XST for testis expressed and novel genes, that is, either recent duplicates or lacking a Dipteran ortholog, including an X-linked duplicate of maelstrom, which is also involved in TE silencing. Overall, the evidence suggests that this ancient XSR polymorphism has had a variety of impacts on repetitive DNA and its regulation in this species.
Planification Evolutionnaire par Décomposition

Ce rapport presente l'approche Divide-and-Evolve pour la resolution generique des problemes de planification temporelle par decomposition. L'idee principale de l'approche est la recherche des solutions dans l'espace des decompositions en etats intermediaires a l'aide d'un algorithme evolutionnaire: les solutions candidates sont des sequences d'etats intermediaires qui definissent successivement les plans partiels du probleme initial. Nous nous sommes interesses a la resolution des problemes de type "simple temporal planning problems". La resolution des sequences d'etats intermediaires et la determination d'une solution globale se font a l'aide du planificateur CPT. Ce rapport formalise l'approche, definit l'algorithme Divide-and-Evolve et compare les resultats obtenus a ceux trouves par les meilleurs planificateurs existants a notre connaissance.
The chloride antiporter CLCN7 is a modifier of lysosome dysfunction in FIG4 and VAC14 mutants

The phosphatase FIG4 and the scaffold protein VAC14 function in the biosynthesis of PI(3,5)P2, a signaling lipid that inhibits the lysosomal chloride transporter ClC-7. Loss-of-function mutations of FIG4 and VAC14 reduce PI(3,5)P2 and result in lysosomal disorders characterized by accumulation of enlarged lysosomes and neurodegeneration. Similarly, a gain of function mutation of CLCN7 encoding ClC-7 also results in enlarged lysosomes. We therefore tested the ability of reduced CLCN7 expression to compensate for loss of FIG4 or VAC14. Knock-out of CLCN7 corrected lysosomal swelling and partially corrected lysosomal hyperacidification in FIG4 null cell cultures. Knockout of the related transporter CLCN6 (ClC-6) in FIG4 null cells did not affect the lysosome phenotype. In the Fig4 null mouse, reduction of ClC-7 by expression of the dominant negative CLCN7 variant p.Gly215Arg improved growth and neurological function and increased lifespan by 20%. These observations demonstrate a role for the CLCN7 chloride transporter in pathogenesis of FIG4 and VAC14 disorders. Reduction of CLCN7 provides a new target for treatment of FIG4 and VAC14 deficiencies that lack specific therapies, such as Charcot-Marie-Tooth Type 4J and Yunis-Varón syndrome.
Tropical dry woodland loss occurs disproportionately in areas of highest conservation value

Tropical and subtropical dry woodlands are rich in biodiversity and carbon. Yet, many of these woodlands are under high deforestation pressure and remain weakly protected. Here, we assessed how deforestation dynamics relate to areas of woodland protection and to conservation priorities across the world's tropical dry woodlands. Specifically, we characterized different types of deforestation frontier from 2000 to 2020 and compared them to protected areas (PAs), Indigenous Peoples' lands and conservation areas for biodiversity, carbon and water. We found that global conservation priorities were always overrepresented in tropical dry woodlands compared to the rest of the globe (between 4% and 96% more than expected, depending on the type of conservation priority). Moreover, about 41% of all dry woodlands were characterized as deforestation frontiers, and these frontiers have been falling disproportionately in areas with important regional (i.e. tropical dry woodland) conservation assets. While deforestation frontiers were identified within all tropical dry woodland classes of woodland protection, they were lower than the average within protected areas coinciding with Indigenous Peoples' lands (23%), and within other PAs (28%). However, within PAs, deforestation frontiers have also been disproportionately affecting regional conservation assets. Many emerging deforestation frontiers were identified outside but close to PAs, highlighting a growing threat that the conserved areas of dry woodland will become isolated. Understanding how deforestation frontiers coincide with major types of current woodland protection can help target context‐specific conservation policies and interventions to tropical dry woodland conservation assets (e.g. PAs in which deforestation is rampant require stronger enforcement, inactive deforestation frontiers could benefit from restoration). Our analyses also identify recurring patterns that can be used to test the transferability of governance approaches and promote learning across social–ecological contexts.
5-Aminolevulinic acid bypasses mitochondrial complex I deficiency and corrects physiological dysfunctions in Drosophila

Abstract Complex I (CI) deficiency in mitochondrial oxidative phosphorylation (OXPHOS) is the most common cause of mitochondrial diseases, and limited evidence-based treatment options exist. Although CI provides the most electrons to OXPHOS, complex II (CII) is another entry point of electrons. Enhancement of this pathway may compensate for a loss of CI; however, the effects of boosting CII activity on CI deficiency are unclear at the animal level. 5-Aminolevulinic acid (5-ALA) is a crucial precursor of heme, which is essential for CII, complex III, complex IV (CIV) and cytochrome c activities. Here, we show that feeding a combination of 5-ALA hydrochloride and sodium ferrous citrate (5-ALA-HCl + SFC) increases ATP production and suppresses defective phenotypes in Drosophila with CI deficiency. Knockdown of sicily, a Drosophila homolog of the critical CI assembly protein NDUFAF6, caused CI deficiency, accumulation of lactate and pyruvate and detrimental phenotypes such as abnormal neuromuscular junction development, locomotor dysfunctions and premature death. 5-ALA-HCl + SFC feeding increased ATP levels without recovery of CI activity. The activities of CII and CIV were upregulated, and accumulation of lactate and pyruvate was suppressed. 5-ALA-HCl + SFC feeding improved neuromuscular junction development and locomotor functions in sicily-knockdown flies. These results suggest that 5-ALA-HCl + SFC shifts metabolic programs to cope with CI deficiency. Bullet outline 5-Aminolevulinic acid (5-ALA-HCl + SFC) increases ATP production in flies with complex I deficiency. 5-ALA-HCl + SFC increases the activities of complexes II and IV. 5-ALA-HCl + SFC corrects metabolic abnormalities and suppresses the detrimental phenotypes caused by complex I deficiency.
Association between psoriasis and thyroid function: results from the Brazilian Longitudinal Study of Adults Health (ELSA-Brasil)

ABSTRACT Objective: To determine the relationship between psoriasis, thyroid-stimulating hormone (TSH), free thyroxine (FT4), free triodothyronine (FT3), thyroid peroxidase antibodies (TPOAb), and subclinical thyroid dysfunctions in middle-aged and older adults. Materials and methods: Cross-sectional analyses included a self-reported medical diagnosis of psoriasis and thyroid function from the 3rd visit (2017-2019) of the Brazilian Longitudinal Study of Adult Health (ELSA-Brasil). TSH, FT4, and FT3 levels were analyzed as continuous variables and quintiles, and TPOAb positivity and subclinical hypothyroidism as a yes/no variable. Logistic regression models were built as crude and adjusted by main confounders (age, sex, education level, race/ethnicity, and smoking). Results: From 9,649 participants (52.3% women; 59.2 ± 8.7 years old), the prevalence of psoriasis was 2.8% (n = 270). TSH, FT4, TPOAb positivity, and subclinical hypothyroidism were not associated with psoriasis in the main analyses. In the stratified analysis, our findings showed positive associations of the lowest (OR = 2.01; 95% CI 1.05-3.84; p = 0.036) and the highest (OR = 2.13; 95% CI 1.12-4.05; p = 0.022) quintiles of FT4 and a protective association of TPOAb positivity (OR = 0.43; 95% CI 0.19-0.98; p = 0.046) with prevalent psoriasis in women. In the logistic regression for FT3, participants in the 1st quintile showed a statistically significant association with psoriasis for the whole sample (OR = 1.66; 95% CI 1.11-2.46; p = 0.013) and for men (OR = 2.25; 95% CI 1.25-4.04; p = 0.007) in the sex-stratified analysis. Conclusions: The present study showed that the association of FT4 levels with psoriasis are different according to sex, with a possible U-shaped curve in women but not in men. Although there were some associations of FT3 with psoriasis, they may be a consequence of non-thyroidal illness syndrome. Further prospective data may clarify the association of thyroid function and psoriasis.
Estimation of Limited Dependent Variable Habit Persistence Models on Panel Data with an Application to the Dynamics of Self-employment in the former East Germany

Not available in German. The paper suggests two multi-step estimation methods for dynamic limited dependent variable models with random effects on panel data. The estimated coefficients are consistent, in the sense that the number of individuals tends to infinity and the number of time periods is fixed. The error terms are assumed to be independently and identical distributed across individuals, but otherwise unrestricted. The estimators have the advantages that they are asymptotically efficient in their proposed class, and that the vast literature on parametric and semi-parametric estimators of limited dependent variable models for cross-sections as well as the resulting software can be utilised. The small sample behaviour of the methods is investigated using a Monte Carlo study. The preferred method is applied to the analysis of the dynamics of self-employment in the former East Germany after unification.
Adaptive Safe Reinforcement Learning With Full-State Constraints and Constrained Adaptation for Autonomous Vehicles

High-performance learning-based control for the typical safety-critical autonomous vehicles invariably requires that the full-state variables are constrained within the safety region even during the learning process. To solve this technically critical and challenging problem, this work proposes an adaptive safe reinforcement learning (RL) algorithm that invokes innovative safety-related RL methods with the consideration of constraining the full-state variables within the safety region with adaptation. These are developed toward assuring the attainment of the specified requirements on the full-state variables with two notable aspects. First, thus, an appropriately optimized backstepping technique and the asymmetric barrier Lyapunov function (BLF) methodology are used to establish the safe learning framework to ensure system full-state constraints requirements. More specifically, each subsystem’s control and partial derivative of the value function are decomposed with asymmetric BLF-related items and an independent learning part. Then, the independent learning part is updated to solve the Hamilton–Jacobi–Bellman equation through an adaptive learning implementation to attain the desired performance in system control. Second, with further Lyapunov-based analysis, it is demonstrated that safety performance is effectively doubly assured via a methodology of a constrained adaptation algorithm during optimization (which incorporates the projection operator and can deal with the conflict between safety and optimization). Therefore, this algorithm optimizes system control and ensures that the full set of state variables involved is always constrained within the safety region during the whole learning process. Comparison simulations and ablation studies are carried out on motion control problems for autonomous vehicles, which have verified superior performance with smaller variance and better convergence performance under uncertain circumstances. The effectiveness of the safe performance of overall system control with the proposed method accordingly has been verified.
Lead Monoxide Nanostructures for Nanophotonics: A Review

Black-phosphorus-analog lead monoxide (PbO), as a new emerging 2D material, has rapidly gained popularity in recent years due to its unique optical and electronic properties. Recently, both theoretical prediction and experimental confirmation have revealed that PbO exhibits excellent semiconductor properties, including a tunable bandgap, high carrier mobility, and excellent photoresponse performance, which is undoubtedly of great interest to explore its practical application in a variety of fields, especially in nanophotonics. In this minireview, we firstly summarize the synthesis of PbO nanostructures with different dimensionalities, then highlight the recent progress in the optoelectronics/photonics applications based on PbO nanostructures, and present some personal insights on the current challenges and future opportunities in this research area. It is anticipated that this minireview can pave the way to fundamental research on functional black-phosphorus-analog PbO-nanostructure-based devices to meet the growing demands for next-generation systems.
Controlled release of adeno‐associated virus from alginate hydrogel microbeads with enhanced sensitivity to ultrasound

Adeno‐associated virus (AAV)‐based gene therapy holds promise as a fundamental treatment for genetic disorders. For clinical applications, it is necessary to control AAV release timing to avoid an immune response to AAV. Here we propose an ultrasound (US)‐triggered on‐demand AAV release system using alginate hydrogel microbeads (AHMs) with a release enhancer. By using a centrifuge‐based microdroplet shooting device, the AHMs encapsulating AAV with tungsten microparticles (W‐MPs) are fabricated. Since W‐MPs work as release enhancers, the AHMs have high sensitivity to the US with localized variation in acoustic impedance for improving the release of AAV. Furthermore, AHMs were coated with poly‐l‐lysine (PLL) to adjust the release of AAV. By applying US to the AAV encapsulating AHMs with W‐MPs, the AAV was released on demand, and gene transfection to cells by AAV was confirmed without loss of AAV activity. This proposed US‐triggered AAV release system expands methodological possibilities in gene therapy.