Miracle-dz/UniFAR-FTUs huggingface dataset:
People and plant interaction at the Houli Culture Yuezhuang site in Shandong Province, China

Palaeoethnobotanical research at the Yuezhuang site, a Houli Culture settlement in Jinan, Shandong Province, China, dating to 8000–7700 cal. BP, documents human–environment interaction and the local subsistence economy soon after the initiation of food production in the region. This economy supported a sizeable community that occupied a kilometer stretch of floodplain along the Nandasha River. The research explores plant domestication, the extent to which the Yuezhuang population had developed a food production niche, and, to a lesser extent, the development of agriculture in the lower Yellow River valley. In order to do so, charred seeds from a variety of plant taxa were recovered by flotation of sediment from pits and cultural strata. Just over 30% of the seed assemblage is rice (Oryza sativa), broomcorn/common millet (Panicum miliaceum), and foxtail millet (Setaria italica subsp. italica). The status of several other plants such as soybean (Glycine max subsp. max or G. max subsp. soja), perilla (Perilla sp.), and chenopod (Chenopodium sp.) that are also cultivated in East Asia is also assessed. Most of the plant taxa are from open, sunlit, and anthropogenic, disrupted habitats. Diverse grasses similar to those found at later sites indicate that the farming niche documented at the late Neolithic Longshan Culture in Shandong Province was being established by 8000–7700 cal. BP. The plant remains assemblage is compared with three assemblages, two belonging to the Houli Culture and one from the late Neolithic Longshan Culture. Anthropogenic habitats and their formation, maintenance and use, wetland exploitation, cultivation, hunting–gathering–fishing, and animal management characterize the mature (late) Houli Culture niche.
The end of the reign of a “master regulator’’? A defect in function of the LasR quorum sensing regulator is a common feature of Pseudomonas aeruginosa isolates

ABSTRACT Pseudomonas aeruginosa, a bacterium causing infections in immunocompromised individuals, regulates several of its virulence functions using three interlinked quorum sensing (QS) systems (las, rhl, and pqs). Despite its presumed importance in regulating virulence, dysfunction of the las system regulator LasR occurs frequently in strains isolated from various environments, including clinical infections. This newfound abundance of LasR-defective strains calls into question existing hypotheses regarding their selection. Indeed, current assumptions concerning factors driving the emergence of LasR-deficient isolates and the role of LasR in the QS hierarchy must be reconsidered. Here, we propose that LasR is not the primary master regulator of QS in all P. aeruginosa genetic backgrounds, even though it remains ecologically significant. We also revisit and complement current knowledge on the ecology of LasR-dependent QS in P. aeruginosa, discuss the hypotheses explaining the putative adaptive benefits of selecting against LasR function, and consider the implications of this renewed understanding.
Heightened response to positive facial cues as a potential marker of resilience following childhood adversity

ABSTRACT Background: Childhood maltreatment profoundly influences social and emotional development, increasing psychiatric risk. Alterations in the implicit processing of threat-related cues following early abuse and neglect represent a marker of mental health vulnerability. Less is known about how early adversity influences the perception of positive social cues, despite their central role in establishing and maintaining social interactions and their association with better mental health outcomes. Methods: The sample consisted of 42 children and adolescents with substantiated childhood maltreatment experiences and 32 peers (mean age 13.3), matched on age, pubertal status, gender, socioeconomic status, ethnicity, and cognitive ability. A computerised experimental task assessed the perceived emotional intensity of positive (happy) and negative (fearful) facial expressions. Mental health symptoms were measured via self- and parental reports, and perceived social support was self-reported. Results: The experience of abuse and neglect was associated with heightened perceived intensity of positive facial cues. Cross-sectional post-hoc moderation and mediation analyses, employing a model-building approach, revealed that in maltreatment-exposed participants: (i) their increased response to positive facial cues was associated with lower symptoms; (ii) the presence of social support accounted for their heightened perceived intensity of positive facial cues; (iii) the presence of social support putatively contributed to lower symptoms by increasing the perceived intensity of positive facial cues. No group differences in perceived intensity of negative expressions were observed. Conclusions: These findings provide fresh insight into how positive faces are processed following maltreatment experience in childhood. Maltreatment experience was found to be associated with heightened perceived intensity of happy faces, which in turn was associated with better mental health and greater levels of social support. This suggests that heightened saliency of positive emotions acts protectively in children with maltreatment experience.
KPC-2 allelic variants in Klebsiella pneumoniae isolates resistant to ceftazidime-avibactam from Argentina: blaKPC-80, blaKPC-81, blaKPC-96 and blaKPC-97

ABSTRACT Ceftazidime-avibactam (CZA) therapy has significantly improved survival rates for patients infected by carbapenem-resistant bacteria, including KPC producers. However, resistance to CZA is a growing concern, attributed to multiple mechanisms. In this study, we characterized four clinical CZA-resistant Klebsiella pneumoniae isolates obtained between July 2019 and December 2020. These isolates expressed novel allelic variants of blaKPC-2 resulting from changes in hotspots of the mature protein, particularly in loops surrounding the active site of KPC. Notably, KPC-80 had an K269_D270insPNK mutation near the Lys270-loop, KPC-81 had a del_I173 mutation within the Ω-loop, KPC-96 showed a Y241N substitution within the Val240-loop and KPC-97 had an V277_I278insNSEAV mutation within the Lys270-loop. Three of the four isolates exhibited low-level resistance to imipenem (4 µg/mL), while all remained susceptible to meropenem. Avibactam and relebactam effectively restored carbapenem susceptibility in resistant isolates. Cloning mutant blaKPC genes into pMBLe increased imipenem MICs in recipient Escherichia coli TOP10 for blaKPC-80, blaKPC-96, and blaKPC-97 by two dilutions; again, these MICs were restored by avibactam and relebactam. Frameshift mutations disrupted ompK35 in three isolates. Additional resistance genes, including blaTEM-1, blaOXA-18 and blaOXA-1, were also identified. Interestingly, three isolates belonged to clonal complex 11 (ST258 and ST11) and one to ST629. This study highlights the emergence of CZA resistance including unique allelic variants of blaKPC-2 and impermeability. Comprehensive epidemiological surveillance and in-depth molecular studies are imperative for understanding and monitoring these complex resistance mechanisms, crucial for effective antimicrobial treatment strategies. IMPORTANCE The emergence of ceftazidime-avibactam (CZA) resistance poses a significant threat to the efficacy of this life-saving therapy against carbapenem-resistant bacteria, particularly Klebsiella pneumoniae-producing KPC enzymes. This study investigates four clinical isolates exhibiting resistance to CZA, revealing novel allelic variants of the key resistance gene, blaKPC-2. The mutations identified in hotspots surrounding the active site of KPC, such as K269_D270insPNK, del_I173, Y241N and V277_I278insNSEAV, prove the adaptability of these pathogens. Intriguingly, low-level resistance to imipenem and disruptions in porin genes were observed, emphasizing the complexity of the resistance mechanisms. Interestingly, three of four isolates belonged to clonal complex 11. This research not only sheds light on the clinical significance of CZA resistance but also shows the urgency for comprehensive surveillance and molecular studies to inform effective antimicrobial treatment strategies in the face of evolving bacterial resistance.
Prevalence and variability of siderophore production in the Achromobacter genus

ABSTRACT Achromobacter spp. are opportunistic pathogens of environmental origin increasingly isolated in patients with underlying conditions like cystic fibrosis (CF). Despite recent advances, their virulence factors remain incompletely studied, and siderophore production has not yet been investigated in this genus. The aim of this study was to evaluate the production of siderophores in a large collection of Achromobacter spp. and evaluate the variability according to the origin of the strain and species. A total of 163 strains were studied, including 128 clinical strains (CF and non-CF patients) and 35 strains of environmental origin. Siderophores were quantified by the liquid chrome azurol-sulphonate assay. Species were identified by nrdA gene-based phylogeny. Strains were assigned to 20 species, with Achromobacter xylosoxidans being the most represented (51.5% of strains). Siderophore production was observed in 72.4% of the strains, with amounts ranging from 10.1% to 90% siderophore units. A significantly higher prevalence of siderophore-producing strains and greater production of siderophores were observed for clinical strains compared with strains of environmental origin. Highly variable observations were made according to species: A. xylosoxidans presented unique characteristics (one of the highest prevalence of producing strains and highest amounts produced, particularly by CF strains). Siderophores are important factors for bacterial growth commonly produced by members of the Achromobacter genus. The significance of the observations made during this study must be further investigated. Indeed, the differences observed according to species and the origin of strains suggest that siderophores may represent important determinants of the pathophysiology of Achromobacter spp. infections and also contribute to the particular epidemiological success of A. xylosoxidans in human infections. IMPORTANCE Achromobacter spp. are recognized as emerging opportunistic pathogens in humans with various underlying diseases, including cystic fibrosis (CF). Although their pathophysiological traits are increasingly studied, their virulence factors remain incompletely described. Particularly, siderophores that represent important factors of bacterial growth have not yet been studied in this genus. A population-based study was performed to explore the ability of members of the Achromobacter genus to produce siderophores, both overall and in relevant subgroups (Achromobacter species; strain origin, either clinical—from CF or non-CF patients—or environmental). This study provides original data showing that siderophore production is a common trait of Achromobacter strains, particularly observed among clinical strains. The major species, Achromobacter xylosoxidans, encompassed both one of the highest prevalence of siderophore-producing strains and strains producing the largest amounts of siderophores, particularly observed for CF strains. These observations may represent additional advantages accounting for the epidemiological success of this species.
Typologie de l'érosion interne et érosion interne des digues fluviales : une courte revue bibliographique

L'article est une analyse de cas d'erosion interne de digues fluviales (digues du Mississippi et digues du Danube). Ces deux cas, bien documentes, permettent de mettre en avant le role de la profondeur du substratumet des anciens lits dans le developpement des erosions internes en fondation.
Interleukin-22 Contributes to Blood–Brain Barrier Disruption via STAT3/VEGFA Activation in Escherichia coli Meningitis

Escherichia coli continues to be the predominant Gram-negative pathogen causing neonatal meningitis worldwide. Inflammatory mediators have been implicated in the pathogenesis of meningitis and are key therapeutic targets. The role of interleukin-22 (IL-22) in various diseases is diverse, with both protective and pathogenic effects. However, little is understood about the mechanisms underlying the damaging effects of IL-22 on the blood–brain barrier (BBB) in E. coli meningitis. We observed that meningitic E. coli infection induced IL-22 expression in the serum and brain of mice. The tight junction proteins (TJPs) components ZO-1, Occludin, and Claudin-5 were degraded in the mouse brain and human brain microvascular endothelial cells (hBMEC) following IL-22 administration. Moreover, the meningitic E. coli-caused increase in BBB permeability in wild-type mice was restored by knocking out IL-22. Mechanistically, IL-22 activated the STAT3-VEGFA signaling cascade in E. coli meningitis, thus eliciting the degradation of TJPs to induce BBB disruption. Our data indicated that IL-22 is an essential host accomplice during E. coli-caused BBB disruption and could be targeted for the therapy of bacterial meningitis.
Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA and in situ sequencing

Mapping the connectivity of diverse neuronal types provides the foundation for understanding the structure and function of neural circuits. High-throughput and low-cost neuroanatomical techniques based on RNA barcode sequencing have the potential to map circuits at cellular resolution and a brain-wide scale, but existing Sindbis virus-based techniques can only map long-range projections using anterograde tracing approaches. Rabies virus can complement anterograde tracing approaches by enabling either retrograde labeling of projection neurons or monosynaptic tracing of direct inputs to genetically targeted postsynaptic neurons. However, barcoded rabies virus has so far been only used to map non-neuronal cellular interactions in vivo and synaptic connectivity of cultured neurons. Here we combine barcoded rabies virus with single-cell and in situ sequencing to perform retrograde labeling and transsynaptic labeling in the mouse brain. We sequenced 96 retrogradely labeled cells and 295 transsynaptically labeled cells using single-cell RNA-seq, and 4130 retrogradely labeled cells and 2914 transsynaptically labeled cells in situ. We found that the transcriptomic identities of rabies virus-infected cells can be robustly identified using both single-cell RNA-seq and in situ sequencing. By associating gene expression with connectivity inferred from barcode sequencing, we distinguished long-range projecting cortical cell types from multiple cortical areas and identified cell types with converging or diverging synaptic connectivity. Combining in situ sequencing with barcoded rabies virus complements existing sequencing-based neuroanatomical techniques and provides a potential path for mapping synaptic connectivity of neuronal types at scale.
On the Weak Contractibility of the Space of Pure States

We prove that the space $\mathscr{P}(\mathfrak{A})$ of pure states of a nonelementary, simple, separable, real rank zero $C^*$-algebra $\mathfrak{A}$ has trivial homotopy groups of all orders when $\mathscr{P}(\mathfrak{A})$ is equipped with the weak* topology. The convex-valued and finite-dimensional selection theorems of Michael are used to deform a family of pure states via the action of a homotopy of unitaries so that the entire family evaluates to one on a given projection $P \in \mathfrak{A}$. Then, the excision theorem of Akemann, Anderson, and Pedersen is used to iterate this deformation for a sequence of projections in $\mathfrak{A}$ excising a base point of the family of pure states, thereby contracting the family to the base point. Finally, we compare our weak contractibility result to the spaces of pure states of commutative $C^*$-algebras and rational rotation algebras, and compute the homotopy groups of the latter in terms of the homotopy groups of spheres.
TopoNav: Topological Navigation for Efficient Exploration in Sparse Reward Environments

Autonomous robots exploring unknown environments face a significant challenge: navigating effectively without prior maps and with limited external feedback. This challenge intensifies in sparse reward environments, where traditional exploration techniques often fail. In this paper, we present TopoNav, a novel topological navigation framework that integrates active mapping, hierarchical reinforcement learning, and intrinsic motivation to enable efficient goal-oriented exploration and navigation in sparse-reward settings. TopoNav dynamically constructs a topological map of the environment, capturing key locations and pathways. A two-level hierarchical policy architecture, comprising a high-level graph traversal policy and low-level motion control policies, enables effective navigation and obstacle avoidance while maintaining focus on the overall goal. Additionally, TopoNav incorporates intrinsic motivation to guide exploration toward relevant regions and frontier nodes in the topological map, addressing the challenges of sparse extrinsic rewards. We evaluate TopoNav both in the simulated and real-world off-road environments using a Clearpath Jackal robot, across three challenging navigation scenarios: goal-reaching, feature-based navigation, and navigation in complex terrains. We observe an increase in exploration coverage by 7- 20%, in success rates by 9-19%, and reductions in navigation times by 15-36% across various scenarios, compared to state-of-the-art methods
Milnor fibrations of arrangements with trivial algebraic monodromy

Each complex hyperplane arrangement gives rise to a Milnor fibration of its complement. Although the Betti numbers of the Milnor fiber $F$ can be expressed in terms of the jump loci for rank 1 local systems on the complement, explicit formulas are still lacking in full generality, even for $b_1(F)$. We study here the"generic"case (in which $b_1(F)$ is as small as possible), and look deeper into the algebraic topology of such Milnor fibrations with trivial algebraic monodromy. Our main focus is on the cohomology jump loci and the lower central series quotients of $\pi_1(F)$. In the process, we produce a pair of arrangements for which the respective Milnor fibers have the same Betti numbers, yet non-isomorphic fundamental groups: the difference is picked by the higher-depth characteristic varieties and by the Schur multipliers of the second nilpotent quotients.
Uniform error bounds of the ensemble transform Kalman filter for infinite-dimensional dynamics with multiplicative covariance inflation

Data assimilation is a method of uncertainty quantification to estimate the hidden true state by updating the prediction owing to model dynamics with observation data. As a prediction model, we consider a class of nonlinear dynamical systems on Hilbert spaces including the two-dimensional Navier-Stokes equations and the Lorenz '63 and '96 equations. For nonlinear model dynamics, the ensemble Kalman filter (EnKF) is often used to approximate the mean and covariance of the probability distribution with a set of particles called an ensemble. In this paper, we consider a deterministic version of the EnKF known as the ensemble transform Kalman filter (ETKF), performing well even with limited ensemble sizes in comparison to other stochastic implementations of the EnKF. When the ETKF is applied to large-scale systems, an ad-hoc numerical technique called a covariance inflation is often employed to reduce approximation errors. Despite the practical effectiveness of the ETKF, little is theoretically known. The present study aims to establish the theoretical analysis of the ETKF. We obtain that the estimation error of the ETKF with and without the covariance inflation is bounded for any finite time. In particular, the uniform-in-time error bound is obtained when an inflation parameter is chosen appropriately, justifying the effectiveness of the covariance inflation in the ETKF.
Enhanced sampling of robust molecular datasets with uncertainty-based collective variables

Generating a data set that is representative of the accessible configuration space of a molecular system is crucial for the robustness of machine learned interatomic potentials (MLIP). However, the complexity of molecular systems, characterized by intricate potential energy surfaces (PESs) with numerous local minima and energy barriers, presents a significant challenge. Traditional methods of data generation, such as random sampling or exhaustive exploration, are either intractable or may not capture rare, but highly informative configurations. In this study, we propose a method that leverages uncertainty as the collective variable (CV) to guide the acquisition of chemically-relevant data points, focusing on regions of the configuration space where ML model predictions are most uncertain. This approach employs a Gaussian Mixture Model-based uncertainty metric from a single model as the CV for biased molecular dynamics simulations. The effectiveness of our approach in overcoming energy barriers and exploring unseen energy minima, thereby enhancing the data set in an active learning framework, is demonstrated on the alanine dipeptide benchmark system.
On Convergence of Adam for Stochastic Optimization under Relaxed Assumptions

The Adaptive Momentum Estimation (Adam) algorithm is highly effective in training various deep learning tasks. Despite this, there's limited theoretical understanding for Adam, especially when focusing on its vanilla form in non-convex smooth scenarios with potential unbounded gradients and affine variance noise. In this paper, we study vanilla Adam under these challenging conditions. We introduce a comprehensive noise model which governs affine variance noise, bounded noise and sub-Gaussian noise. We show that Adam can find a stationary point with a $\mathcal{O}(\text{poly}(\log T)/\sqrt{T})$ rate in high probability under this general noise model where $T$ denotes total number iterations, matching the lower rate of stochastic first-order algorithms up to logarithm factors. More importantly, we reveal that Adam is free of tuning step-sizes with any problem-parameters, yielding a better adaptation property than the Stochastic Gradient Descent under the same conditions. We also provide a probabilistic convergence result for Adam under a generalized smooth condition which allows unbounded smoothness parameters and has been illustrated empirically to more accurately capture the smooth property of many practical objective functions.