julilili42/papers huggingface dataset:
Fever-like temperature impacts on Staphylococcus aureus and Pseudomonas aeruginosa interaction, physiology, and virulence both in vitro and in vivo
2024-02-05

Abstract Background Staphylococcus aureus (SA) and Pseudomonas aeruginosa (PA) cause a wide variety of bacterial infections and coinfections, showing a complex interaction that involves the production of different metabolites and metabolic changes. Temperature is a key factor for bacterial survival and virulence and within the host, bacteria could be exposed to an increment in temperature during fever development. We analyzed the previously unexplored effect of fever-like temperatures (39 °C) on S. aureus USA300 and P. aeruginosa PAO1 microaerobic mono- and co-cultures compared with 37 °C, by using RNAseq and physiological assays including in vivo experiments. Results In general terms both temperature and co-culturing had a strong impact on both PA and SA with the exception of the temperature response of monocultured PA. We studied metabolic and virulence changes in both species. Altered metabolic features at 39 °C included arginine biosynthesis and the periplasmic glucose oxidation in S. aureus and P. aeruginosa monocultures respectively. When PA co-cultures were exposed at 39 °C, they upregulated ethanol oxidation-related genes along with an increment in organic acid accumulation. Regarding virulence factors, monocultured SA showed an increase in the mRNA expression of the agr operon and hld , pmsα , and pmsβ genes at 39 °C. Supported by mRNA data, we performed physiological experiments and detected and increment in hemolysis, staphyloxantin production, and a decrease in biofilm formation at 39 °C. On the side of PA monocultures, we observed an increase in extracellular lipase and protease and biofilm formation at 39 °C along with a decrease in the motility in correlation with changes observed at mRNA abundance. Additionally, we assessed host–pathogen interaction both in vitro and in vivo. S. aureus monocultured at 39 ο C showed a decrease in cellular invasion and an increase in IL-8—but not in IL-6—production by A549 cell line. PA also decreased its cellular invasion when monocultured at 39 °C and did not induce any change in IL-8 or IL-6 production. PA strongly increased cellular invasion when co-cultured at 37 and 39 °C. Finally, we observed increased lethality in mice intranasally inoculated with S. aureus monocultures pre-incubated at 39 °C and even higher levels when inoculated with co-cultures. The bacterial burden for P. aeruginosa was higher in liver when the mice were infected with co-cultures previously incubated at 39 °C comparing with 37 °C. Conclusions Our results highlight a relevant change in the virulence of bacterial opportunistic pathogens exposed to fever-like temperatures in presence of competitors, opening new questions related to bacteria-bacteria and host–pathogen interactions and coevolution.
Comparison of the accuracy of commercial two-point and multi-echo Dixon MRI for quantification of fat in liver, paravertebral muscles, and vertebral bone marrow
2024-02-05

While no significant differences were observed for liver and PVM, systematic errors in BM FF estimation using two-point Dixon imaging were observed. These discrepancies - mainly resulting from organ-specific T2* times - have to be considered when applying two-point Dixon approaches for assessment of fat content. As suitable correction tools, linear models could provide added value in large-scale epidemiological cohort studies. Sex-specific differences in T2* should be considered.
Trained recurrent neural networks develop phase-locked limit cycles in a working memory task
2024-02-05

Neural oscillations are ubiquitously observed in many brain areas. One proposed functional role of these oscillations is that they serve as an internal clock, or ‘frame of reference’. Information can be encoded by the timing of neural activity relative to the phase of such oscillations. In line with this hypothesis, there have been multiple empirical observations of such phase codes in the brain. Here we ask: What kind of neural dynamics support phase coding of information with neural oscillations? We tackled this question by analyzing recurrent neural networks (RNNs) that were trained on a working memory task. The networks were given access to an external reference oscillation and tasked to produce an oscillation, such that the phase difference between the reference and output oscillation maintains the identity of transient stimuli. We found that networks converged to stable oscillatory dynamics. Reverse engineering these networks revealed that each phase-coded memory corresponds to a separate limit cycle attractor. We characterized how the stability of the attractor dynamics depends on both reference oscillation amplitude and frequency, properties that can be experimentally observed. To understand the connectivity structures that underlie these dynamics, we showed that trained networks can be described as two phase-coupled oscillators. Using this insight, we condensed our trained networks to a reduced model consisting of two functional modules: One that generates an oscillation and one that implements a coupling function between the internal oscillation and external reference. In summary, by reverse engineering the dynamics and connectivity of trained RNNs, we propose a mechanism by which neural networks can harness reference oscillations for working memory. Specifically, we propose that a phase-coding network generates autonomous oscillations which it couples to an external reference oscillation in a multi-stable fashion.
Prognostic Value of Gut Microbiome for Conversion from Mild Cognitive Impairment to Alzheimer’s Disease Dementia within 4 Years: Results from the AlzBiom Study
2024-02-05

Alterations in the gut microbiome are associated with the pathogenesis of Alzheimer’s disease (AD) and can be used as a diagnostic measure. However, longitudinal data of the gut microbiome and knowledge about its prognostic significance for the development and progression of AD are limited. The aim of the present study was to develop a reliable predictive model based on gut microbiome data for AD development. In this longitudinal study, we investigated the intestinal microbiome in 49 mild cognitive impairment (MCI) patients over a mean (SD) follow-up of 3.7 (0.6) years, using shotgun metagenomics. At the end of the 4-year follow-up (4yFU), 27 MCI patients converted to AD dementia and 22 MCI patients remained stable. The best taxonomic model for the discrimination of AD dementia converters from stable MCI patients included 24 genera, yielding an area under the receiver operating characteristic curve (AUROC) of 0.87 at BL, 0.92 at 1yFU and 0.95 at 4yFU. The best models with functional data were obtained via analyzing 25 GO (Gene Ontology) features with an AUROC of 0.87 at BL, 0.85 at 1yFU and 0.81 at 4yFU and 33 KO [Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog] features with an AUROC of 0.79 at BL, 0.88 at 1yFU and 0.82 at 4yFU. Using ensemble learning for these three models, including a clinical model with the four parameters of age, gender, body mass index (BMI) and Apolipoprotein E (ApoE) genotype, yielded an AUROC of 0.96 at BL, 0.96 at 1yFU and 0.97 at 4yFU. In conclusion, we identified novel and timely stable gut microbiome algorithms that accurately predict progression to AD dementia in individuals with MCI over a 4yFU period.
Microbial strategies for phosphorus acquisition in rice paddies under contrasting water regimes: Multiple source tracing by 32P and 33P
2024-02-05

Microbial acquisition and utilization of organic and mineral phosphorus (P) sources in paddy soils are strongly dependent on redox environment and remain the key to understand P turnover and allocation for cell compound synthesis. Using double <sup>32/33</sup>P labeling, we traced the P from three sources in a P-limited paddy soil: ferric iron-bound phosphate (Fe-P), wheat straw P (Straw-P), and soil P (Soil-P) in microbial biomass P (MBP) and phospholipids (Phospholipid-P) of individual microbial groups depending on water regimes: (i) continuous flooding or (ii) alternate wetting and drying. <sup>32/33</sup>P labeling combined with phospholipid fatty acid analysis allowed to trace P utilization by functional microbial groups. Microbial P nutrition was mainly covered by Soil-P, whereas microorganisms preferred to take up P from mineralized Straw-P than from Fe-P dissolution. The main Straw-P mobilizing agents were Actinobacteria under alternating wetting and drying and other Gram-positive bacteria under continuous flooding. Actinobacteria and arbuscular mycorrhiza increased P incorporation into cell membranes by 1.4-5.8 times under alternate wetting and drying compared to continuous flooding. The Fe-P contribution to MBP was 4-5 times larger in bulk than in rooted soil because (i) rice roots outcompeted microorganisms for P uptake from Fe-P and (ii) rhizodeposits stimulated microbial activity, e.g. phosphomonoesterase production and Straw-P mineralization. Higher phosphomonoesterase activities during slow soil drying compensated for the decreased reductive dissolution of Fe-P. Concluding, microbial P acquisition strategies depend on (i) Soil-P, especially organic P, availability, (ii) the activity of phosphomonoesterases produced by microorganisms and roots, and (iii) P sources - all of which depend on the redox conditions. Maximizing legacy P utilization in the soil as a function of the water regime is one potential way to reduce competition between roots and microbes for P in rice cultivation.
Complex dental wear analysis reveals dietary shift in Triassic placodonts (Sauropsida, Sauropterygia)
2024-02-05

Abstract Placodonts were durophagous reptiles of the Triassic seas with robust skulls, jaws, and enlarged, flat, pebble-like teeth. During their evolution, they underwent gradual craniodental changes from the Early Anisian to the Rhaetian, such as a reduction in the number of teeth, an increase in the size of the posterior palatal teeth, an elongation of the premaxilla/rostrum, and a widening of the temporal region. These changes are presumably related to changes in dietary habits, which, we hypothesise, are due to changes in the type and quality of food they consumed. In the present study, the dental wear pattern of a total of nine European Middle to Late Triassic placodont species were investigated using 2D and 3D microwear analyses to demonstrate whether there could have been a dietary shift or grouping among the different species and, whether the possible changes could be correlated with environmental changes affecting their habitats. The 3D analysis shows overlap between species with high variance between values and there is no distinct separation. The 2D analysis has distinguished two main groups. The first is characterised by low number of wear features and high percentage of large pits. The other group have a high feature number, but low percentage of small pits. The 2D analysis showed a correlation between the wear data and the size of the enlarged posterior crushing teeth. Teeth with larger sizes showed less wear feature (with higher pit ratio) but larger individual features. In contrast, the dental wear facet of smaller crushing teeth shows more but smaller wear features (with higher scratch number). This observation may be related to the size of the food consumed, i.e., the wider the crown, the larger food it could crush, producing larger features. Comparison with marine mammals suggests that the dietary preference of Placochelys , Psephoderma and Paraplacodus was not exclusively hard, thick-shelled food. They may have had a more mixed diet, similar to that of modern sea otters. The diet of Henodus may have included plant food, similar to the modern herbivore marine mammals and lizards.
Cytocompatible Triblock Copolymers with Controlled Microstructure Enabling Orthogonally Functionalized Bio-polymer Conjugates
2024-02-06

α,ω-Functionalized block copolymers create various opportunities across myriads of applications such as linkers for targeted drug delivery systems. Combining them with the exceptional properties of polyvinyl phosphonates, such as high control over polymer architecture and biocompatibility, further reinforces their benefits. This study focuses on synthesizing the α-allyl-ω-TMSpropargyl-block-co-polymer P(DAlVP-DEVP-DPrTMSVP) by rare-earth metal-mediated group transfer polymerization. The monomers involved in this process are functionalized diallyl vinyl phosphonate (DAlVP) and dipropargyl vinyl phosphonate (DPrTMSVP), as well as hydrophilic diethyl vinyl phosphonate (DEVP), enabling the incorporation of diverse functionalities into the polymer structure. Click chemistry, including azide-alkyne cycloaddition (AAC) and thiol-ene reactions, facilitates specific and controlled modifications of polymer side chains. Various model substrates, such as benzyl azide, 3-azido-7-hydroxycoumarin, and cysteamine, show the scope of these modifications. The potential in (bio)medical applications is proven with the polymer–biomolecule conjugate α-cholesteryl-ω-folate-block-co-polyvinyl phosphonate, exhibiting remarkable biocompatibility. Our versatile approach also establishes a synthetic platform for drug delivery systems, for instance, in targeted therapy.
(p)ppGpp-mediated GTP homeostasis ensures the survival and antibiotic tolerance ofStaphylococcus aureusduring starvation by preserving the proton motive force
2024-02-06

Abstract Upon nutrient limitation bacteria enter a nongrowing state, which allow bacterial survival and antibiotic tolerance. The mechanisms whether and how the messenger molecule (p)ppGpp contributes to the transition in Firmicutes is debated. Here we show for Staphylococcus aureus that (p)ppGpp-dependent restriction of the GTP pool is essential for the culturability of starved cells and for antibiotic tolerance. Elevated GTP levels in a starving (p)ppGpp-deficient mutant lead to a division-incompetent, dormant state characterized by reduced metabolic activity and alterations in membrane function and architecture. GTP level control of nucleotide sensitive promoters result in transcriptional downregulation of gene of the TCA cycle and electron transport chain. Increasing transcription of qoxABCD , a terminal oxidase of the respiratory chain, through mutation of the transcriptional start site partially restored the culturability of the (p)ppGpp-deficient mutant. Furthermore, we showed that the maintenance of proton motive force under nutritional stress contributes to antibiotic tolerance, supporting the idea of applying (p)ppGpp or PMF inhibitors to combat antibiotic-tolerant bacteria.
Tracing Truth Through Conceptual Scaling: Mapping People’s Understanding of Abstract Concepts
2024-02-06

Traditionally, the investigation of truth has been anchored in a priori reasoning. Cognitive science deviates from this tradition by adding empirical data on how people understand and use concepts. Building on psychophysics and machine learning methods, we introduce conceptual scaling, an approach to map people's understanding of abstract concepts. This approach allows computing participant-specific conceptual maps from obtained ordinal comparison data, thereby quantifying perceived similarities among abstract concepts. Using this approach, we investigated individual's alignment with philosophical theories on truth and the predictive capacity of conceptual maps. Obtained results indicated that, while people's understanding of truth is multifaceted and encapsulates notions of coherence and authenticity, alignment is best for the correspondence theory of truth. Furthermore, conceptual maps allowed predicting individual outcomes with an accuracy of approximately 70%. This research demonstrates that conceptual scaling offers accurate descriptions of individual's understanding of abstract concepts, behavioral predictions, and quantification of alignment with theoretical perspectives.
A Preliminary Report on the Late 13th- to Early 14th-Century Bontosikuyu Shipwreck Site, Selayar Island, South Sulawesi, Indonesia: A Case Study for Regional Capacity Building and Research
2024-02-06

Between 2013 and 2015, the Republic of Indonesia’s Directorate of Preservation of Cultural Heritage and Museums held a series of capacity-building workshops at Selayar Island in South Sulawesi, Indonesia. Maritime archaeologists and practitioners from various government and research institutions attended the training program, including foreign delegates from ASEAN (Association of Southeast Asian Nations) countries. The program’s field school centred on the Bontosikuyu shipwreck site. This shipwreck is dated to the late 13th to early 14th century CE based on 14C dating of organic remains and ceramics analysis. It is considered one of the earliest shipwreck sites around the South Sulawesi region and is significant for understanding further the maritime trade of the eastern Indonesia area.
To understand my decisions, you must understand my task: Expertise effects in theory of mind
2024-02-06

Human behavior is frequently constrained by the behavior of other agents (increasingly artificial agents like machines and software). In a cooperative setting, each individual needs to understand the partners’ intentions and corresponding actions to plan their actions adequately. Misunderstandings have adverse effects and diminish the efficiency of cooperation. We created a game-based experiment to study the effects of understanding a partner’s actions in a cooperative setting. In this game, the players depend on each other’s ability to make good decisions to succeed. In two studies (N = 87, N = 281), we collected data on the understanding of an artificial agent, operationalized as the ability to predict its actions and the skill at the task itself. The participants improve at predicting the agent’s actions and at their subtasks in the game over time. Following a misunderstanding, the participants’ performance at their subtask was worse, as measured by their actions’ quality, speed, and efficiency. Results of Study 2 suggest that the improvements in predicting the agent’s actions are likely the result of an improved understanding of the game rather than an improved understanding of the agent.
The Problem of Evil in the Early Modern Ottoman Period: ʿAbd al-Ghanī al-Nābulusī’s Synthetic Metaphysics of Faith and Disbelief
2024-02-06

Abstract The early modern Muslim world witnessed unparalleled development in theological discussion, of which the problem of evil is a part. This paper aims to uncover a new discourse on the problem of evil in the Ottoman period, by examining the eleventh/ seventeenth-century polymath ʿAbd al-Ghanī al-Nābulusī’s (d. 1143/1731) synthetic theology of evil. More specifically, the study will analyze the way al-Nābulusī discusses the issue of faith ( īmān ) and disbelief ( kufr ) in his Ashʿarī kalām and Akbarian Sufism. Looking first at al-Nābulusī’s kalām metaphysics of īmān and kufr and then his mystical metaphysics, the paper corroborates how between the two sciences, there is a coherent logic in al-Nābulusī’s concordia theology.
A Water-Stable Boronate Ester Cage
2024-02-07

The reversible condensation of catechols and boronic acids to boronate esters is a paradigm reaction in dynamic covalent chemistry. However, facile backward hydrolysis is detrimental for stability and has so far prevented applications for boronate-based materials. Here, we introduce cubic boronate ester cages <b>6</b> derived from hexahydroxy tribenzotriquinacenes and phenylene diboronic acids with <i>ortho</i>-<i>t</i>-butyl substituents. Due to steric shielding, dynamic exchange at the Lewis acidic boron sites is feasible only under acid or base catalysis but fully prevented at neutral conditions. For the first time, boronate ester cages <b>6</b> tolerate substantial amounts of water or alcohols both in solution and solid state. The unprecedented applicability of these materials under ambient and aqueous conditions is showcased by efficient encapsulation and on-demand release of β-carotene dyes and heterogeneous water oxidation catalysis after the encapsulation of ruthenium catalysts.
Systemic inflammation relates to neuroaxonal damage associated with long-term cognitive dysfunction in COVID-19 patients
2024-02-07

Prolonged systemic inflammation in critically ill COVID-19 patients is related to neuroaxonal damage and subsequent long-term cognitive impairment. Moreover, our findings suggest that plasma NfL concentrations during ICU stay may possess prognostic value in predicting future long-term cognitive impairment in patients that survived severe COVID-19.
Occupational health literacy and work ability: a moderation analysis including interpersonal and organizational factors in healthy organizations
2024-02-07

Introduction Healthy organizations approach to occupational safety and health should holistically include individual, interpersonal, and organizational levels. There is an empirical research gap in considering different levels in organizations for health promotion in the context of maximizing work ability. This study aims to investigate the association of (1) occupational health literacy (on an individual level), (2) health-oriented leadership (interpersonal level), (3) participation possibilities in health, and (4) values of health in companies (both organizational levels) on work ability. Additionally, we examined the potentially moderating role of health-oriented leadership, participation possibilities in health, and values of health between occupational health literacy and work ability. Methods Cross-sectional data were obtained from 828 employers and employees in small and medium-sized enterprises. Self-report measures included occupational health literacy, health-oriented leadership, work ability, participation possibilities in health at work, and values of health in the company. Occupational health literacy comprises two factors: a knowledge-/skill-based approach to occupational health and a willingness/responsibility for occupational health. Participation possibilities in health are measured regarding participatory opportunities and co-creation of health at work. Values of health in the company capture the importance of health in the workplace and the scope for improving employees’ health. Data were analyzed using latent regression and latent moderation analyses controlling for age, gender, and educational level. Results Occupational health literacy (knowledge-/skill-based), health-oriented leadership, participation possibilities in health, and values of health in companies showed positive associations with work ability. Health-oriented leadership on an interpersonal level was found to moderate the positive relationship between (knowledge-/skill-based) occupational health literacy and work ability. Participation possibilities in health on an organizational level acted as a moderator on the relationship between both occupational health literacy factors and work ability. Discussion Individual, interpersonal, and organizational factors play important roles in maintaining work ability in healthy organizations. This study highlights the importance of promoting occupational health literacy among employees and leaders, creating a healthy workplace through health-oriented leadership, and providing participatory opportunities for co-creation in health promotion at work. Future research should further explore these factors’ roles in different industries and contexts and how they may be addressed effectively in tailored workplace interventions.