julilili42/papers huggingface dataset:
Studying the mechanisms of bacterial mobility in the rhizosphere using soil model systems
2025-03-14

The mobility of soil bacteria plays a crucial role in rhizosphere colonisation, as exemplified by the complex chemotactic machinery required for effective biofilm formation on growing roots [1]. However, the nature of soil bacterial movements in the soil pore space is poorly characterised. It is difficult to observe the trajectories of individual cells, and the complexity of soil structure makes any observation difficult to replicate. To overcome these difficulties, we have developed a range of microcosm systems that allow live observation of bacterial movement in porous media with precisely controlled physical or chemical properties. Paper-based microfluidic systems have been developed for the in situ extraction of root exudates, which act as a potent chemoattractant for bacteria [2]. Microfluidic devices made of semi-permeable materials allowed the construction of pores through which nutrient release can be controlled, and transparent soil and custom-made microscopes were used to observe bacterial movements when co-cultured with plants [3]. Using Bacillus subtilis as a model organism, we observed that the bacterium occupies very specific regions of pore space in relation to distance from the root [4] or the presence of nutrients, and that movements can be coordinated at a population level [3]. Future work will focus on understanding the conditions under which collective movements of bacteria occur in soil.References[1] Allard-Massicotte, R, et al (2016) &amp;#8220;Bacillus subtilis early colonization of Arabidopsis thaliana roots involves multiple chemotaxis receptors&amp;#8221; MBio, 7(6), 10-1128. [2] Patko, D, et al (2024) "Spatial and temporal detection of root exudates with a paper-based microfluidic device" Soil Biology and Biochemistry 195 (2024): 109456. [3] Liu, Y, et al (2021) "Plant&amp;#8211;environment microscopy tracks interactions of Bacillus subtilis with plant roots across the entire rhizosphere" Proceedings of the National Academy of Sciences 118.48: e2109176118. [3] Engelhardt, I C, et al (2022) "Novel form of collective movement by soil bacteria" The ISME Journal 16.10: 2337-2347. [4] Engelhardt, I C, et al (2024) &amp;#8220;Mobility and growth in confined spaces are important mechanisms for the establishment of Bacillus subtilis in the rhizosphere&amp;#8221; Microbiology, 170(8), 001477.
Testing the top-down feedback in the central visual field using the reversed depth illusion
2025-03-15

In a new framework to understand vision, an information bottleneck impoverishes visual input information downstream of the primary visual cortex along the visual pathway; to aid ongoing visual recognition given the bottleneck, feedback from downstream to upstream visual stages queries for additional information. According to the central-peripheral dichotomy theory, this feedback is primarily directed to the central, rather than the peripheral, visual field. Counterintuitively, this theory predicts illusions visible only in the peripheral visual field, which lacks the feedback query to veto the illusions arising from misleading and impoverished feedforward signals. A paradigmatic example is the predicted and confirmed reversed depth illusion in random-dot stereograms. This theory further predicts that disrupting the feedback renders this illusion visible in the central visual field. We test and confirm this prediction using visual backward masking to disrupt the feedback. This feedback privilege for the central visual field underpins visual understanding through analysis-by-synthesis.
First steps towards paleoclimate constraints for climate prediction and projections with the ICON model
2025-03-15

Anthropogenic emissions are changing Earth&amp;#8217;s global mean temperature towards levels unseen over the observational period. During the Last Interglacial (LIG) warm period, 129-116 thousand years ago, global mean temperature reached up to 1-2 degrees above preindustrial conditions, forced primarily by changes in Earth&amp;#8217;s orbit. Both the Greenland and Antarctic Ice sheet were smaller, with sea level at least 5m, potentially up to 10m, above present levels. The seasonal distribution of solar insolation during the LIG was characterized by higher eccentricity, obliquity, and precession leading to increased Northern, and decreased Southern Hemisphere summer insolation. Most Earth System Models included in the Palaeoclimate Model Intercomparison Project phases 3 and 4 have shown a temperature anomaly of -0.5 up to around 0.5 degrees, far lower than what has been suggested from reconstructions [Otto-Bliesner et al., 2021]. Here, we show first results from idealized equilibrium simulations with a configuration of ICON for climate prediction and projections [ICON-xpp, M&amp;#252;ller et al 2025], varying the planetary orbit using Kepler&amp;#8217;s solutions [Roeckner et al 2003]. We investigate the impact of different orbital forcing on global and regional temperature and precipitation mean state and variability, and discuss the impact of the choice of the land model (JSBACH vs. TERRA). Simulating climate conditions during past warm periods, and evaluating how they compare to palaeoclimate reconstructions, improves our understanding of the Earth System, and can enhance the robustness of future projections. Our initial characterization and evaluation of orbital impacts on climate variability in ICON-xpp is therefore a crucial step towards simulating and then evaluating model performance for longer timescales, or deeper-time periods such as the Eocene, Miocene or Pliocene warmth. Moreover, using higher-resolution ICON paleoclimate simulations could provide a better basis for upcoming model-proxy data comparisons and forward modeling approaches on regional-to-local scales. &amp;#160; References Otto-Bliesner, Bette L., et al. &amp;#8220;The PMIP4 Contribution to CMIP6 - Part 2: Two Interglacials, Scientific Objective and Experimental Design for Holocene and Last Interglacial Simulations.&amp;#8221; Geoscientific Model Development 10, no. 11 (2017): 3979&amp;#8211;4003. https://doi.org/10.5194/gmd-10-3979-2017. Roeckner, E., B&amp;#228;uml, G., Bonaventura, L., Brokopf, R., Esch, M., Giorgetta, M., et al.&amp;#160;(2003).The atmospheric general circulation model ECHAM 5. PART I: Model description.&amp;#160;Report / Max-Planck-Institut f&amp;#252;r Meteorologie,&amp;#160;349. M&amp;#252;ller, W.; Lorenz, S., 2024, "Source code and scripts for publication 'The ICON-based coupled Earth System Model for Climate Predictions and Projections (ICON XPP)'", https://doi.org/10.17617/3.UUIIZ8
And yet they move: microbial movement in soil habitats
2025-03-15

Movement of organisms plays a crucial role in microbial ecology, yet little is known about how, when and at what speeds soil microorganisms move. Literature offers conflicting lines of evidence, even regarding whether single-celled organisms can move at all under typical soil conditions. We review the literature on microbial movement in the context of soil physicochemical complexity, to establish its likelihood and its prerequisite conditions. Our focus is on movement at the spatial and temporal scales relevant for microbiota (&amp;#181;m to cm, seconds to days), with particular attention to bacteria and fungi. We synthesize experimental data for bacteria to show that unicellular movement can occur in moderately moist soils, although it is suppressed under dry conditions. By integrating current knowledge of microbial physiology and soil physics, we propose underlying mechanisms that may overcome the challenging conditions of soil, including non-flagellar surface movements (pili, in particular) and the role of biosurfactants. Our energetic analysis also shows that movement is possible, even under moderately oligotrophic conditions. Movement modes are entirely different for filamentous microorganisms like fungi, however, which are not restricted by water connectivity, grow much slower than prokaryotic movement, and must contend with the great tortuosity of the soil habitat. However, once a fungal network is established, cytoplasmic streaming can translocate resources and even the entire fungal cytoplasm at speeds comparable to bacteria (5 &amp;#181;m/s). Fungal hyphae also provide physical connections and favorable conditions to support prokaryotic movement along their surfaces. Hitchhiking, in which one organism is transported by the movement and energy of another, is also likely to be important in soil. A diverse array of movement possibilities emerges from our analysis, suggesting that soil microorganisms may be much more mobile than often appreciated. These also indicate substantial implications of movement for the ecology and ecological functions of soil microbiota. However, many key unknowns remain to be addressed and hypotheses experimentally tested, and we propose an ambitious roadmap to a comprehensive understanding of microbial movement in soil, and its relevance for biogeochemical cycling.
Fungal necromass composition highlights the ecological significance of microbial death pathways in soil
2025-03-15

Microbial activity drives soil carbon mineralization, while microbial necromass along with other residues contributes to the stable soil organic carbon pool. Still, precise quantification and characterization of microbial residues remains methodologically challenging in complex soil systems, requiring controlled microbial experiments. We have recently presented the conceptual framework of microbial death pathways in soil, where we hypothesized that different agents of death would lead to varying chemical properties of microbial necromass, with consequences for the fate of microbial necromass carbon in soil.In the studies presented here, we have now tested these hypotheses experimentally and analysed fungal mycelial residues exposed to diverse agents of death. We investigated the composition of mycelial residues by (i) microscopic live/dead staining, (ii) measurements of carbon, nitrogen and melanin contents, (iii) Raman spectroscopy and (iv) Nanoscale Secondary Ion Mass Spectrometer (NanoSIMS). Using fungal isolates in a controlled experimental design, we found that heat or fungicide exposure led to rapid hyphal death with less chemical transformation of necromass compared to biomass. By contrast, starvation or senescence (ageing of hyphae) allowed mycelia to internally recycle cytosolic components, leading to residues reduced in cytosolic compounds and characterized by wider C:N ratios and increased melanin contents. A litterbag experiment in soil showed that mycelia resembling the chemical properties of biomass are mineralized more rapidly than chemically altered fungal necromass.We further tested the impact of nitrogen availability on residue formation. Necromass nitrogen contents affect mineralization rates, but also stabilization due to preferential binding of nitrogen-rich compounds to mineral surfaces. Here, fungal residues from nitrogen depleted media showed wide C:N ratios (50-90), resulting from internal recycling of cytosolic compounds but also differential cell wall composition (as indicated by Raman spectroscopy and NanoSIMS analyses). Interestingly, independent of medium nitrogen supply, fungal residues in contact with mineral surfaces (goethite) were strongly nitrogen enriched, indicating preferential binding of nitrogen-rich compounds independent of overall mycelial C:N ratios.In conclusion, specific microbial death pathways may alter the composition of microbial residues in soil, with consequences for carbon mineralization and stabilization processes. These results further highlight the interaction of carbon and nitrogen cycling via microbial turnover and stabilization, mechanisms that must be integrated in future conceptual and experimental approaches.
First-line checkpoint inhibitor therapy in metastatic acral lentiginous melanoma compared to other types of cutaneous melanoma: A multicenter study from the prospective skin cancer registry ADOREG
2025-03-15

Analysis of this real-world cohort of patients with metastatic melanoma showed a trend towards poorer survival outcomes upon first-line treatment with CPI in ALM compared to cutaneous melanoma of other subtypes.
Approach to Myoclonus Dystonia Syndrome: A European Reference Network Survey
2025-03-15

Abstract Background Myoclonus‐dystonia syndrome (MDS) is a genetic movement disorder with childhood‐onset, most frequently caused by SGCE defects. Objective To evaluate the diagnostic and treatment strategies in MDS used by experts from the European Reference Network for rare neurological diseases (ERN‐RND), and to assess the diagnosis and management experience in patients with MDS. Methods Two different questionnaires were distributed: one among neurologists from ERN‐RND, and another among patients and families with SGCE ‐related MDS. Results Twenty‐nine adult and child neurologists from 14 countries, and 84 patients and caregivers from 12 countries, replied to the surveys. All the patients included in the analysis had SGCE ‐related MDS. The mean age was 30.8 years (SD 19,9; range 3–75). Sixty‐nine percent of patients were diagnosed in childhood and 70% had a positive family history. Most participants suffered from predominant upper body myoclonus and focal/segmental dystonia, hindering daily activities in 80% of patients, such as handwriting, drinking, feeding, walking and speech. Botulinum toxin and DBS were effective options for managing movement disorders compared to pharmacological treatments. However, neither of these therapies were applied optimally. We found deficiencies in recognition and management of academic difficulties, and a high unemployment rate. Despite all but one patient reported psychiatric symptoms such as anxiety, depression or OCD, there was a lack of formal psychiatric evaluations. Conclusions SGCE ‐MDS is a well‐known neurological disorder among movement disorder specialists in Europe. Offering a multidisciplinary approach that tackles both movement disorders and neuropsychiatric comorbidities could enhance the diagnosis and treatment of patients with SGCE ‐MDS.
C9orf72 Repeat Expansion Induces Metabolic Dysfunction in Human iPSC-Derived Microglia and Modulates Glial–Neuronal Crosstalk
2025-03-15

Abstract The C9orf72 hexanucleotide repeat expansion mutation is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia, but its cell type-specific effects on energy metabolism and immune pathways remain poorly understood. Using induced pluripotent stem cell (iPSC)-derived motor neurons, astrocytes and microglia from C9orf72 patients and their isogenic controls, we investigated metabolic changes at the single-cell level under basal and inflammatory conditions. Our results showed that microglia are particularly susceptible to metabolic disturbances. While C9orf72 motor neurons exhibited impaired mitochondrial respiration and reduced ATP production, C9orf72 microglia presented pronounced increases in glycolytic activity and oxidative stress, accompanied by the upregulation of the expression of key metabolic enzymes. These metabolic changes in microglia were exacerbated by inflammatory stimuli. To investigate how these changes affect the broader cellular environment, we developed a human iPSC-derived triculture system comprising motor neurons, astrocytes and microglia. This model revealed increased metabolic activity in all cell types and highlighted that microglia-driven metabolic reprogramming in astrocytes contributes to the vulnerability of motor neurons under inflammatory conditions. Our findings highlight the central role of microglia in driving metabolic dysregulation and intercellular crosstalk in ALS pathogenesis and suggest that targeting metabolic pathways in immune cells may provide new therapeutic avenues.
Influence of insulin sensitivity on food cue evoked functional brain connectivity in children
2025-03-16

In response to food cues, children with lower peripheral insulin sensitivity exhibited distinctive patterns of neural connectivity, notably in the insula's functional connections, when contrasted with their counterparts with higher peripheral insulin sensitivity. These differences might influence eating behavior and future risk of developing diabetes.
DIE ARBEIT DES ÜBERSETZENS: RILKE UND MICHELANGELO („SE ’L MIE ROZZO MARTELLO‘‘)
2025-03-16

ABSTRACT This essay examines Rainer Maria Rilke's reception of the sculptor and poet Michelangelo in the context of interest in the Renaissance around 1900, focusing first on the Stundenbuch , the Florenzer Tagebuch and the story ʻVon einem, der die Steine belauschtʼ (from the prose collection: Geschichten vom lieben Gott ). Drawing on Friedrich Nietzsche and his concept of Artistenmetaphysik, Rilke portrays Michelangelo as a ‘superman’ (ʻÜbermenschenʼ) and a desperate seeker for God. Rilke's translation of ʻSe ʼl mie rozzo martelloʼ then shows how he uses Michelangelo's poetic self‐reflection to express a poetics of transformation (‘Verwandlung’) that focuses on the concept of ‘work’. Thus, Michelangelo becomes a figure of identification and reflection for Rilke in two respects: as a poet, he refers back to Rilke himself, as a sculptor to Auguste Rodin, who in his time was often perceived as a new Michelangelo.
Applying Corporate Well‐Being Strategies to Medical Practice: Addressing Physician Burnout and Overwork
2025-03-16

ABSTRACT In August 2023, a tragic case in Kobe City, Japan, highlighted the severe working conditions faced by resident physicians. A resident specialising in internal medicine died by suicide after experiencing extraordinary workloads, including 236 h of overtime in the month before his death. This case underscores the broader systemic issue of excessive working hours in Japan's medical profession, exacerbated by the country's ‘ passion pay ’ culture, which exploits young physicians' dedication. Surveys indicate that 28% of residents experience burnout, with long hours, inefficient task allocation and poor workplace communication as key stressors. Addressing excessive workloads requires restructuring physician responsibilities. Research shows that full‐time physicians under 50 spend significant time on non‐medical tasks that could be delegated to other professionals. The primary physician model, which holds doctors responsible for patients beyond their shifts, further extends work hours. Transitioning to a time‐based task allocation system and implementing task‐shifting strategies could alleviate these burdens. Workplace communication also requires improvement. Limited supervisory support and hierarchical barriers prevent open discussions about well‐being. We underscore that drawing insights from corporate strategies, such as Marui Group's task optimisation policies and TOYOTA's anonymous feedback system, hospitals could implement structured well‐being initiatives for physicians. Physician well‐being directly correlates with patient satisfaction and treatment adherence. Addressing burnout through workload reduction and improved communication is essential for maintaining both doctor and patient health. Hospitals must prioritise physician well‐being alongside patient care, fostering a sustainable working environment for medical professionals.
Disparate X-linked retinoschisis phenotypes in fraternal twins with the same pathogenic variant in the RS1 gene
2025-03-16

Family members with the same pathogenic variant and of the same age can present with significantly different XLRS phenotypes. This highlights the importance of other factors, such as genetic modifiers, epigenetic regulatory events, and environmental influences, in contributing to phenotypic heterogeneity in XLRS patients.
Day-to-day fluctuations in motivation drive effort-based decision-making
2025-03-17

Internal states like motivation fluctuate substantially over time. However, studies of the neurocomputational mechanims of motivated behavior have failed to capture this. Here, we examined how naturalistic ups and downs in state motivation influence the subjective value of reward and effort. In a microlongitudinal design (N = 155, state timepoints = 3,344, decision-making tasks = 845), we captured fluctuations in state and effort-based decision-making using smartphone-based momentary assessments as people went about their daily lives. We found that both state and trait have independent and multiplicative effects on decision-making. State–behavior coupling was particularly pronounced in individuals with higher trait apathy, meaning that their choices were even more state dependent. Using computational modeling, we demonstrate that state motivation prospectively boosted reward sensitivity, making people more willing to exert effort in future. Our results show that day-to-day fluctuations in state and cognition are tightly linked and critical for understanding fundamental human behaviors and mental ill-health.
Microbial transcriptome patterns highlight increased pedogenesis-related activity in arid soils under simulated humid conditions
2025-03-17

Abstract Background In arid and semiarid environments, microbial activity is restricted by low water availability and high evapotranspiration rates, and soil development is limited. Under humid conditions, such limitations can be overcome, accelerating pedogenesis by microbial processes. Our study aims to broaden our understanding of soil development under a climate change scenario toward humid conditions and to identify the microorganisms that help transform initial soils from arid and semiarid sites. We characterized pedogenetic microbial processes and how their gene expression differs between soils from arid and semiarid sites under a sixteen-week climate simulation experiment using metagenomic and metatranscriptomic approaches. Results We found that an intense functional response is triggered under humid climate conditions in the arid site compared to the semiarid site, which showed greater resilience. The arid site undergoes higher transcription of genes involved in soil aggregate formation, phosphorus metabolism, and weathering, potentially adapting the development of arid sites to climate change. Additionally, a transcriptional reconfiguration linked to soil carbon and nitrogen dynamics suggests that soil microorganisms use available organic resources alongside autotrophy in response to increased moisture. Pseudomonadota and Actinomycetota dominated the overall transcriptional profile and specific functions associated with the early stages of soil development in both sites. Conclusions Our findings highlight the rapid activation of pathways related to pedogenesis under humid conditions in arid sites, potentially driven by their metabolic requirements and environmental stressors, influencing soil development dynamics under global climate change.