julilili42/papers huggingface dataset:
Dust production through collisions between small bodies: an application to the G-ring arc
2025-02-27

The G-ring arc of Saturn, confined by the 7:6 corotation eccentric resonance with Mimas, is primarily composed of micrometric particles. These particles, significantly influenced by the solar radiation pressure, are subject to rapid depletion. This study investigates a mechanism for dust replenishment in the arc, specifically analysing collisions between macroscopic bodies and the satellite Aegaeon. Utilizing N-body and smoothed particle hydrodynamics simulations, we assess the dust generation from these impacts, with a focus on the most likely collision parameters derived from the N-body simulations. Our findings indicate that, while collisions among macroscopic bodies are inefficient for dust production, impacts involving Aegaeon are substantially more effective, providing conservative lower limits for dust generation. This mechanism, in conjunction with the natural decay processes and continuous dust generation from impacts, potentially keeps the arc population over thousands of years with a possible variation in brightness. This article is part of the theme issue ‘Major advances in planetary sciences thanks to stellar occultations’.
Efficacy of integrated social cognitive remediation vs neurocognitive remediation in schizophrenia: Results from the multicenter randomized controlled ISST (Integrated Social Cognition And Social Skills Therapy) study
2025-02-27

Both therapies differentially improved measures of the cognitive domains they were designed for. Moreover, they both improved social functioning with high effect sizes (d = 0.8-1.0), underlining the important role of CRT in recovery-oriented schizophrenia treatment. However, the absence of a third group without an active intervention limits the interpretability of the results.
Improved Isolation of Ultra-High-Molecular-Weight Genomic DNA Suitable for Third-Generation Sequencing
2025-02-27

Although a variety of protocols to isolate high-molecular-weight genomic DNA exist, the isolation and preservation of ultra-high-molecular-weight genomic DNA of sufficient quality and length for error-free third-generation sequencing remains challenging. Inspired by the isolation of high-molecular-weight DNA in agarose plugs suitable to be separated by pulsed-field gel electrophoresis, we report the construction of an incubation chamber for DNA isolation. The chamber is flanked by semi-permeable polycarbonate membranes of variable pore size for the selective diffusion of compounds and components, which allows efficient cell lysis and the subsequent isolation of ultra-high-molecular-weight genomic DNA without shearing. The designed experimental approach is simple, but effective in isolating high-quality ultra-long genomic DNA that is suitable for third-generation sequencing by Oxford Nanopore Technology from challenging bacterial samples. We envisage that genomic DNA isolation using the incubation chamber, or variations thereof, will facilitate the regular sequencing of megabasepair-long DNA fragments, with a multitude of applications in microbiology, immunology, oncology, paleontology and forensic science.
Pion nuclear fragmentation functions revisited
2025-02-27

We revisit the notion of nuclear parton-to-pion fragmentation functions at next-to-leading order accuracy as an effective description of hadroproduction in nuclear environments such as in semi-inclusive lepton-nucleus deep-inelastic scattering and in single inclusive proton-nucleus collisions. We assess their viability in the face of very precise data collected for the latter at the CERN-LHC over the past decade as well as recent measurements of the former carried out by the CLAS experiment at JLab.
Differential risk assessment in persons at risk of type 2 diabetes using urinary peptidomics
2025-02-27

Urinary peptidome classifiers support the increased risk of CKD and suggest an elevated risk of heart failure and coronary artery disease in the high-risk prediabetes cluster 6. Urine peptidomics show promising potential as a tool for identifying high-risk prediabetes individuals and guiding early preventive interventions.
Characterization and host range prediction of Staphylococcus aureus phages through receptor-binding protein analysis
2025-02-28

Bacteriophages are crucial in bacterial communities and can be used for therapy of multidrug-resistant pathogens such as Staphylococcusaureus. However, the host range of new phages remains difficult to predict. We identified the receptor-binding proteins (RBPs) of 335 S. aureus-infecting phages, yielding 8 distinct RBP clusters. Recombinant representative RBPs of all clusters, including several subclusters, were analyzed for binding to S. aureus strains differing in potential phage receptor structures. Notably, most of the phages encoded two separate RBPs, and all RBPs used S. aureus wall teichoic acid (WTA) polymers as receptors, albeit with varying preference for WTA glycosylation patterns and backbone structures. Based on these findings, a sequence-based tool for predicting the adsorption of new phages was developed. Moreover, one of the RBPs proved useful for identifying S. aureus-type WTA in other bacterial species. These findings facilitate the characterization of phage and bacterial isolates and the development of phage therapies.
Assessment of PFAS contamination in agricultural soils: Non-target identification of precursors, fluorine mass balance and microcosm studies
2025-02-28

Biodegradation of PFAS is examined in eight PFAS precursor-contaminated topsoil samples in order to determine generation rate constants for perfluorocarboxyl acids (PFCA) and to elucidate soil properties affecting these. PFAS were analyzed via both target (HPLC-MS/MS) and non-target (HPLC-QTOF) (semi)quantification. FTMAPs, diPAPs, and diSAmPAP were identified and accounted for > 80 % of the total PFAS burden, which ranged from ∼ 280-9700 ng g<sup>-1</sup>. These levels were confirmed by chemical oxidation of precursors (TOP assay) which allowed to close the fluorine mass balance against extractable organic fluorine (EOF). Notably, in some organic carbon rich samples, repeated oxidation was needed to achieve a complete fluorine mass balance. Batch microcosm incubations and total precursor quantification allowed to determine production rate constants of short-chain PFCA, which ranged from 0.02 to 0.50 year<sup>-1</sup> depending on PFAS and soil physicochemical properties. Principal component analysis (PCA) indicated that both acid phosphomonoesterase and, to some extent, microbial biomass influences the production rates of short-chain PFAS in soils. This allowed to assess contamination time scales, indicating that production and thus release of PFAS from precursor decay will continue for years to decades. This bears the risk of contamination of adjacent environmental compartments such as groundwater and surface water bodies.
pyOpenMS-viz: Streamlining Mass Spectrometry Data Visualization with pandas
2025-02-28

Mass spectrometry data visualization is essential for a wide range of applications, such as validation of workflows and results, benchmarking new algorithms, and creating comprehensive quality control reports. Python offers a popular and powerful framework for analyzing and visualizing multidimensional data; however, generating commonly used mass spectrometry plots in Python can be cumbersome. Here we present pyOpenMS-viz, a versatile, unified framework for generating mass spectrometry plots. pyOpenMS-viz directly extends pandas DataFrame plotting for generating figures in a single line of code. This implementation enables easy integration across various Python-based mass spectrometry tools that already use pandas DataFrames to store MS data. pyOpenMS-viz is open-source under a BSD 3-Clause license and freely available at https://github.com/OpenMS/pyopenms_viz.
Precision oncology – Guideline of the Austrian, German and Swiss Societies for hematology and medical oncology
2025-02-28

Precision oncology is a multi-step process including patient selection, tumor profiling, molecular tumor board discussion and personalized cancer management. So far, it remains largely unstandardized. The implementation of precision oncology can be beneficial for patients but implementation differs widely between tumor types and local practices. A working group was established by the Austrian, German and Swiss societies for Hematology and Medical Oncology to establish an expert consensus on evidence-based standards and implementation of precision oncology. Herein, we present a summary of this guideline. The full documents are available at www.onkopedia-guidelines.info.
Regulation of PVT‐CeA Circuit in Deoxynivalenol‐Induced Anorexia and Aversive‐Like Emotions
2025-02-28

Abstract Neuronal plasticity in the central amygdala (CeA) is essential for modulating feeding behaviors and emotional responses, potentially influencing reactions to Deoxynivalenol (DON). Acute oral administration of DON elicits a dose‐responsive reduction in food intake, accompanied by pronounced alterations in locomotor activity and feeding frequency. This study investigates circuitry adaptations that mediate DON's effects on feeding, by targeting of GABA neurons in the CeA. Following exposure to DON, an increase in connectivity between the paraventricular nucleus of the thalamus (PVT) and CeA GABA neurons is observed, suggesting the involvement of this pathway in DON's adverse effects on feeding and emotional states. Chemogenetic and optogenetic manipulations of CeA GABA neurons resulted in substantial alterations in mice's feeding and overall activity. These findings suggest that CeA GABA neurons are involved in DON‐induced anorexia and aversive‐like emotional responses. Additionally, the administration of the SCN10A antagonist (A‐803467) effectively mitigated DON‐induced anorexia and aversive‐like emotions, highlighting the pivotal role of the PVT‐CeA circuit and CeA GABA neurons in regulating the physiological and emotional impacts of DON. These findings have significant implications for public health and clinical interventions, offering potential therapeutic strategies to mitigate DON's adverse effects on human health.
Tuberculosis Visualized With the Ultrasound Probe: A Systematic Review of Sonographic Pattern Descriptions and an Analysis of Common Sonographic Features
2025-02-28

Abstract Evidence on tuberculosis (TB) ultrasound patterns is scarce. We systematically reviewed the literature aiming to identify common TB ultrasound features. Sources included PubMed, Cochrane Library, and others (1 January 2000 through 30 August 2021). Any article type (retrospective, prospective, cases, trials) with verbal ultrasound descriptions of TB were included; those with &amp;lt;2 ultrasound features were excluded. We adapted Murad et al (2018) for quality assessment. The outcome was a descriptive frequency ranking of ultrasound features and patterns (combinations) per organ. From 388 publications, 613 ultrasound descriptions across 23 organs from 2167 individuals (465 single cases, 1702 from case series/studies) were extracted. The most commonly described sonographic patterns related to the female breast (n = 45), the liver (n = 40), and the pancreas (n = 37). The synthesis reveals sonographic TB patterns, but is constrained by limited representativeness of studies and the partly subjective analysis. Our review may serve as a clinical or research resource. Clinical Trials Registration PROSPERO (CRD42021283319)
Admixture as a source for HLA variation in Neolithic European farming communities
2025-02-28

Abstract Background The northern European Neolithic is characterized by two major demographic events: immigration of early farmers from Anatolia at 7500 years before present, and their admixture with local western hunter-gatherers forming late farmers, from around 6200 years before present. The influence of this admixture event on variation in the immune-relevant human leukocyte antigen (HLA) region is understudied. Results We analyzed genome-wide data of 125 individuals from seven archeological early farmer and late farmer sites located in present-day Germany. The late farmer group studied here is associated with the Wartberg culture, from around 5500–4800 years before present. We note that late farmers resulted from sex-biased admixture from male western hunter-gatherers. In addition, we observe Y-chromosome haplogroup I as the dominant lineage in late farmers, with site-specific sub-lineages. We analyze true HLA genotypes from 135 Neolithic individuals, the majority of which were produced in this study. We observe significant shifts in HLA allele frequencies from early farmers to late farmers, likely due to admixture with western hunter-gatherers. Especially for the haplotype DQB1*04:01-DRB1*08:01, there is evidence for a western hunter-gatherer origin. The HLA diversity increased from early farmers to late farmers. However, it is considerably lower than in modern populations. Conclusions Both early farmers and late farmers exhibit a relatively narrow HLA allele spectrum compared to today. This coincides with sparse traces of pathogen DNA, potentially indicating a lower pathogen pressure at the time.
Mapping the global distribution and conservation status of oases—ecosystems of pivotal biocultural relevance
2025-02-28

Background Oases are azonal, highly productive, densely vegetated areas within drylands, often converted to agriculture, and characterized by significant biocultural diversity. Despite their importance, comprehensive information on the global distribution and biocultural diversity of oases has been lacking. Methods To address this gap, a detailed bibliographic search and random forest modeling were combined to create a global map of oases, with a focus on Asia and North Africa (ANA). Results In the ANA region, oases cover 1.5% of the dryland area and are populated by 150 million people, with an additional 268 million people living nearby and most likely being dependent on them. Globally, oases contain more than 8,200 vertebrate species, of which 13% are classified as threatened. However, less than 0.5% of their total area is currently under protection, making oases one of the least conserved ecosystems worldwide. These findings highlight the distinct biocultural, ecological, and geopolitical importance of oases, which are increasingly threatened by climate change and direct human impacts. Despite their significance, oases remain undervalued, emphasizing an urgent need for developing adaptative strategies to sustainably manage these pivotal ecosystems.
Spin Self-Organization in an Optical Cavity Facilitated by Inhomogeneous Broadening
2025-02-28

We study the onset of collective spin self-organization in a thermal ensemble of driven two-level atoms confined in an optical cavity. The atoms spontaneously form a spin pattern above a critical driving strength that sets a threshold and is determined by the cavity parameters, the initial temperature, and the transition frequency of the atomic spin. Remarkably, we find that inhomogeneous Doppler broadening facilitates the onset of spin self-organization. In particular, the threshold is nonmonotonic when increasing the spin transition frequency and reaches a minimum when the Doppler broadening is of similar magnitude. This feature emerges due to Doppler-induced resonances. Above the threshold, we find cooperative dynamics of spin, spatial, and momentum degrees of freedom leading to density modulations, fast reduction of kinetic energy, and the emergence of nonthermal states. More broadly, our work demonstrates how broadening can facilitate strong light-matter interactions in many-body systems.
Atmospheric and Oceanic Pathways Drive Separate Modes of Southern Hemisphere Climate in Simulations of Spontaneous Dansgaard‐Oeschger‐Type Oscillations
2025-02-28

Abstract Dansgaard‐Oeschger (DO) events are a dominant mode of millennial‐scale climate variability during the last glacial period with most pronounced impacts in the North Atlantic region. In Antarctica, they manifest primarily as a muted and phase‐shifted temperature signal, but recent studies suggest an additional in‐phase component. Here, we analyze the Southern Hemisphere (SH) response to spontaneous DO‐type oscillations in a general circulation model. The dominant Antarctic temperature mode is phase‐shifted compared to Greenland temperature variations and consistent with the oceanic pathway described by the bipolar seesaw model. However, the leading SH atmospheric circulation mode varies synchronously with Greenland temperatures. A westward‐shifted Walker circulation and strengthened Hadley cell during Greenland temperature maxima cause zonally heterogeneous jet stream anomalies differing from the Southern Annular Mode pattern. Comparison of simulated O with speleothems and ice cores indicates a good agreement in the tropics and SH mid‐latitudes but deviations in Antarctica warrant further research.
Endovascular treatment for isolated cervical internal carotid artery occlusion: ETIICA study
2025-02-28

Introduction: Evidence regarding the benefit of endovascular therapy (EVT) in patients with acute ischemic stroke (AIS) due to isolated cervical internal carotid artery occlusion (c-ICA-O) is lacking. We assessed the outcomes and safety of EVT in patients with isolated c-ICA-O. Methods: Retrospective multicenter cohort study of patients with an AIS due to isolated c-ICA-O, within 24-h since last-seen-well. Comparisons were made between EVT and best medical therapy (BMT). The primary outcome was 3-months modified Rankin Scale (mRS) ordinal shift. Secondary outcomes included 3-month favorable outcome (mRS 0–2, or return to pre-stroke mRS), symptomatic intracranial hemorrhage (sICH) and any parenchymal hemorrhage. Outcomes were compared combining inverse probability of treatment weighting with regression models and propensity score matching (PSM) as sensitivity analysis. Results: We analyzed 998 patients (66.2% male, mean age 71.1 ± 13.2 years). 487 (48.8%) patients received EVT and 511 (51.2%) received BMT. Patients receiving EVT had a higher admission NIHSS [13 (7–18) vs 5 (2–13)] compared to BMT. There was no difference between EVT and BMT groups in 3-month mRS shift (adjusted common odds ratio [OR], 1.01 [95% CI 0.76–1.34]) and favorable outcome (adjusted OR [aOR] 1.16 [95% CI 0.84–1.60]). No patient (0%) in the BMT group had sICH versus 1.6% in the EVT group. Parenchymal hemorrhage was numerically higher in EVT patients (2.7% vs 0.6%; aOR 3.85 [95% CI 0.98–15.23]). PSM analysis revealed similar results. Discussion and conclusion: In patients with isolated c-ICA-O, EVT was associated with similar odds of disability and intracranial bleeding compared to BMT. Randomized-controlled clinical trials in patients with isolated c-ICA-O are warranted.
Benchmarking deep learning for automated peak detection on GIWAXS data
2025-02-28

Recent advancements in X-ray sources and detectors have dramatically increased data generation, leading to a greater demand for automated data processing. This is particularly relevant for real-time grazing-incidence wide-angle X-ray scattering (GIWAXS) experiments which can produce hundreds of thousands of diffraction images in a single day at a synchrotron beamline. Deep learning (DL)-based peak-detection techniques are becoming prominent in this field, but rigorous benchmarking is essential to evaluate their reliability, identify potential problems, explore avenues for improvement and build confidence among researchers for seamless integration into their workflows. However, the systematic evaluation of these techniques has been hampered by the lack of annotated GIWAXS datasets, standardized metrics and baseline models. To address these challenges, we introduce a comprehensive framework comprising an annotated experimental dataset, physics-informed metrics adapted to the GIWAXS geometry and a competitive baseline – a classical, non-DL peak-detection algorithm optimized on our dataset. Furthermore, we apply our framework to benchmark a recent DL solution trained on simulated data and discover its superior performance compared with our baseline. This analysis not only highlights the effectiveness of DL methods for identifying diffraction peaks but also provides insights for further development of these solutions.
LITURGICAL POLITICS IN THE POETRY OF PAUL CELAN*
2025-02-28

ABSTRACT Drawing on Celan's conception of poetry as a means of orienting the individual towards the ‘completely Other’, this paper emphasises poetry's ability to create community without reproducing exclusionary group identities. The analysis reveals a latent politics in Celan's poetry, emphasising its ability to gather disparate individuals into a community. Through close readings of each poem, I argue that in ‘Tenebrae’ and ‘Psalm’, Celan's use of inversion empties religious imagery of positive religious claims while preserving its form and structure. In ‘Tenebrae’, for example, the poem instructs the ‘Lord’ to pray to the anonymous collective ‘us’, implicitly constituting a community by using the collective pronoun. Similarly, in ‘Psalm’, Celan's inversion of traditional liturgical form creates a space for collective mourning and also subverts the positive religious content. Engaging with previous scholarship on Celan's poetics, the article offers a new perspective on the political dimensions of his work, arguing that religious imagery plays a significant role in forming political imagination through his poetry. I conclude by emphasising the importance of Celan's poetry in bringing about a community of readers, thereby suggesting that poetry can bind individuals into a collective endowed with political agency.
The Upper Sedimentary Sequence of Grotta di Fumane, Northern Italy: A Micromorphological Approach to Study Imprints of Human Occupation and Paleoclimate Change
2025-03-01

ABSTRACT Fumane Cave contains a sequence of natural and anthropogenic deposits documenting key transitions in the Paleolithic of Northern Italy. Open questions remain concerning the stratigraphic integrity, the formation processes, postdepositional alterations, and paleoclimatic implications of the sedimentary record. We examine these aspects through an extensive investigation based on field descriptions and micromorphological analysis of thin sections sampled during the last 25 years of excavations. Major components of the sediments are carbonate sands and limestone rubble originating from the physical breakdown of the cave roof and walls. Limited amounts of mica and quartz grains attest to weak eolian inputs. Sediments contain anthropogenic features and variable amounts of charcoal, bone, and lithic artifacts reflecting different uses of the site. Cryoturbation features observed in the field suggest an increased intensity of frost mainly after the accumulation of unit A2. This unit as well as unit A6 also show increased abundance of silt and clay cappings under the microscope, probably reflecting higher rates of snowfall and percolating meltwater during colder periods of the Last Glacial. However, limited expression of micromorphological features related to frost suggests rather modest changes in climate during the accumulation of the sequence. Overall, field descriptions and the micromorphological approach mostly corroborate the stratigraphic integrity of the sequence, underlining the high value of Fumane Cave as an archive of the late Middle to early Upper Paleolithic in Southern Europe.