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An improved value for the lifetime of the (anti-)hypertriton has been obtained using the data sample of Pb-Pb collisions at sNN−−−√= 5.02 TeV collected by the ALICE experiment at the LHC. The (anti-)hypertriton has been reconstructed via its charged two-body mesonic decay channel and the lifetime has been determined from an exponential fit to the dN/d(ct) spectrum. The measured value, τ = 242+34−38 (stat.) ± 17 (syst.) ps, is compatible with all the available theoretical predictions, thus contributing to the solution of the longstanding hypertriton lifetime puzzle.
5-iodotubercidin sensitizes cells to RIPK1-dependent necroptosis by interfering with NFκB signaling
(2023)
Receptor-interacting protein kinases (RIPK) −1 and −3 are master regulators of cell fate decisions in response to diverse stimuli and are subjected to multiple checkpoint controls. Earlier studies have established the presence of distinct IKK1/2 and p38/MK2-dependent checkpoints which suppress RIPK1 activation by directly phosphorylating it at different residues. In the present study, we investigated TNF-induced death in MAPK-activated protein kinase 2 (MK2)-deficient cells and show that MK2-deficiency or inactivation predominantly results in necroptotic cell death, even in the absence of caspase inhibition. While MK2-deficient cells can be rescued from necroptosis by RIPK1 inhibitors, RIPK3 inhibition seems to revert the process triggering apoptosis. To understand the mechanism of this necroptosis switch, we screened a 149-compound kinase inhibitor library for compounds which preferentially sensitize MK2-deficient MEFs to TNF-induced cell death. The most potent inhibitor identified was 5-Iodotubericidin, an adenosine analogue acting as adenosine kinase and protein kinase inhibitor. 5-ITu also potentiated LPS-induced necroptosis when combined with MK2 inhibition in RAW264.7 macrophages. Further mechanistic studies revealed that 5-Iodotubericidin induces RIPK1-dependent necroptosis in the absence of MK2 activity by suppressing IKK signaling. The identification of this role for the multitarget kinase inhibitor 5-ITu in TNF-, LPS- and chemotherapeutics-induced necroptosis will have potential implications in RIPK1-targeted therapies.
We tested 6–7-year-olds, 18–22-year-olds, and 67–74-year-olds on an associative memory task that consisted of knowledge-congruent and knowledge-incongruent object–scene pairs that were highly familiar to all age groups. We compared the three age groups on their memory congruency effect (i.e., better memory for knowledge-congruent associations) and on a schema bias score, which measures the participants’ tendency to commit knowledge-congruent memory errors. We found that prior knowledge similarly benefited memory for items encoded in a congruent context in all age groups. However, for associative memory, older adults and, to a lesser extent, children overrelied on their prior knowledge, as indicated by both an enhanced congruency effect and schema bias. Functional Magnetic Resonance Imaging (fMRI) performed during memory encoding revealed an age-independent memory x congruency interaction in the ventromedial prefrontal cortex (vmPFC). Furthermore, the magnitude of vmPFC recruitment correlated positively with the schema bias. These findings suggest that older adults are most prone to rely on their prior knowledge for episodic memory decisions, but that children can also rely heavily on prior knowledge that they are well acquainted with. Furthermore, the fMRI results suggest that the vmPFC plays a key role in the assimilation of new information into existing knowledge structures across the entire lifespan. vmPFC recruitment leads to better memory for knowledge-congruent information but also to a heightened susceptibility to commit knowledge-congruent memory errors, in particular in children and older adults.
A candidate gene cluster for the bioactive natural product gyrophoric acid in lichen-forming fungi
(2022)
Natural products of lichen-forming fungi are structurally diverse and have a variety of medicinal properties. Despite this, they a have limited implementation in industry, because the corresponding genes remain unknown for most of the natural products. Here we implement a long-read sequencing and bioinformatic approach to identify the biosynthetic gene cluster of the bioactive natural product gyrophoric acid (GA). Using 15 high-quality genomes representing nine GA-producing species of the lichen-forming fungal genus Umbilicaria, we identify the most likely GA cluster and investigate cluster gene organization and composition across the nine species. Our results show that GA clusters are promiscuous within Umbilicaria, with only three genes that are conserved across species, including the PKS gene. In addition, our results suggest that the same cluster codes for different but structurally similar NPs, i.e., GA, umbilicaric acid and hiascic acid, bringing new evidence that lichen metabolite diversity is also generated through regulatory mechanisms at the molecular level. Ours is the first study to identify the most likely GA cluster, and thus provides essential information to open new avenues for biotechnological approaches to producing and modifying GA and similar lichen-derived compounds. We show that bioinformatics approaches are useful in linking genes and potentially associated natural products. Genome analyses help unlocking the pharmaceutical potential of organisms such as lichens, which are biosynthetically diverse but slow growing, and difficult to cultivate due to their symbiotic nature.
The European Beech is the dominant climax tree in most regions of Central Europe and valued for its ecological versatility and hardwood timber. Even though a draft genome has been published recently, higher resolution is required for studying aspects of genome architecture and recombination. Here we present a chromosome-level assembly of the more than 300 year-old reference individual, Bhaga, from the Kellerwald-Edersee National Park (Germany). Its nuclear genome of 541 Mb was resolved into 12 chromosomes varying in length between 28 Mb and 73 Mb. Multiple nuclear insertions of parts of the chloroplast genome were observed, with one region on chromosome 11 spanning more than 2 Mb of the genome in which fragments up to 54,784 bp long and covering the whole chloroplast genome were inserted randomly. Unlike in Arabidopsis thaliana, ribosomal cistrons are present in Fagus sylvatica only in four major regions, in line with FISH studies. On most assembled chromosomes, telomeric repeats were found at both ends, while centromeric repeats were found to be scattered throughout the genome apart from their main occurrence per chromosome. The genome- wide distribution of SNPs was evaluated using a second individual from Jamy Nature Reserve (Poland). SNPs, repeat elements and duplicated genes were unevenly distributed in the genomes, with one major anomaly on chromosome 4. The genome presented here adds to the available highly resolved plant genomes and we hope it will serve as a valuable basis for future research on genome architecture and for understanding the past and future of European Beech populations in a changing climate.
Treatments for amblyopia focus on vision therapy and patching of one eye. Predicting the success of these methods remains difficult, however. Recent research has used binocular rivalry to monitor visual cortical plasticity during occlusion therapy, leading to a successful prediction of the recovery rate of the amblyopic eye. The underlying mechanisms and their relation to neural homeostatic plasticity are not known. Here we propose a spiking neural network to explain the effect of short-term monocular deprivation on binocular rivalry. The model reproduces perceptual switches as observed experimentally. When one eye is occluded, inhibitory plasticity changes the balance between the eyes and leads to longer dominance periods for the eye that has been deprived. The model suggests that homeostatic inhibitory plasticity is a critical component of the observed effects and might play an important role in the recovery from amblyopia.
In this paper, we investigate the usefulness of a wide range of features for their usefulness in the resolution of nominal coreference, both as hard constraints (i.e. completely removing elements from the list of possible candidates) as well as soft constraints (where a cumulation of violations of soft constraints will make it less likely that a candidate is chosen as the antecedent). We present a state of the art system based on such constraints and weights estimated with a maximum entropy model, using lexical information to resolve cases of coreferent bridging.
Based on the quadratic residuosity assumption we present a non-interactive crypto-computing protocol for the greater-than function, i.e., a non-interactive procedure between two parties such that only the relation of the parties' inputs is revealed. In comparison to previous solutions our protocol reduces the number of modular multiplications significantly. We also discuss applications to conditional oblivious transfer, private bidding and the millionaires' problem.
Multicomponent Tree Adjoining Grammars (MCTAGs) are a formalism that has been shown to be useful for many natural language applications. The definition of non-local MCTAG however is problematic since it refers to the process of the derivation itself: a simultaneity constraint must be respected concerning the way the members of the elementary tree sets are added. Looking only at the result of a derivation (i.e., the derived tree and the derivation tree), this simultaneity is no longer visible and therefore cannot be checked. I.e., this way of characterizing MCTAG does not allow to abstract away from the concrete order of derivation. In this paper, we propose an alternative definition of MCTAG that characterizes the trees in the tree language of an MCTAG via the properties of the derivation trees (in the underlying TAG) the MCTAG licences. We provide similar characterizations for various types of MCTAG. These characterizations give a better understanding of the formalisms, they allow a more systematic comparison of different types of MCTAG, and, furthermore, they can be exploited for parsing.
Multicomponent Tree Adjoining Grammars (MCTAG) is a formalism that has been shown to be useful for many natural language applications. The definition of MCTAG however is problematic since it refers to the process of the derivation itself: a simultaneity constraint must be respected concerning the way the members of the elementary tree sets are added. This way of characterizing MCTAG does not allow to abstract away from the concrete order of derivation. In this paper, we propose an alternative definition of MCTAG that characterizes the trees in the tree language of an MCTAG via the properties of the derivation trees (in the underlying TAG) the MCTAG licences. This definition gives a better understanding of the formalism, it allows a more systematic comparison of different types of MCTAG, and, furthermore, it can be exploited for parsing.