julilili42/papers huggingface dataset:
The effect of a short oxygen exposure period on algal biomass degradation and methane release from eutrophic and oligotrophic lake sediments
2025-01-16

Abstract. Algal blooms in lakes result in large amounts of labile carbon being transported down the water column towards the sediments, often resulting in temporary water column hypoxia. The algal biomass is deposited at the surface sediments, where it is degraded by the microbial community. Negative effects of algal blooms and biomass depositions are sometimes mitigated by pumping air or oxygen into the bottom waters of lakes. The fate of the algal biomass, in terms of greenhouse gas release, is however often unknown. We investigated methane emissions from sediments originating from both a eutrophic and oligotrophic lake and tested the effect of additional algal C inputs. Additionally, we investigated the effect of a pulse supply of oxygen, a mediating measure that is currently being used in the investigated eutrophic lake. Our results show a difference in the control experiments based on the state of eutrophication, but the methane release from new algal biomass additions was the same, although the process proceeded more rapidly in the eutrophic sediments. A 3-week pulse of oxygen lowered the emitted methane from both types of sediments by 50 %, not only reducing the emissions of algal biomass additions, but also reducing methane emissions from the experiments without fresh organic matter inputs. This effect was relatively long-lasting: its effects were visible for several weeks after anoxic conditions were re-established, making it a potentially interesting measure to lower methane emissions over a longer period.
Dipole Determination by Polarimetric Spectroscopy Yielding the Orientation of Gold Nanorods
2025-01-16

Plasmonic nanorods and other colloidal nanoparticles are widely used probes for enhanced spectromicroscopies. Precise knowledge of the angular orientation of individual nanostructures, respectively of their resonant modes, is required for purposes such as chiroptical spectroscopy or metasurfaces. However, noninvasive measurements of structures below the diffraction limit prove to be challenging. In this article, dark‐field spectroscopy requiring only four spectra in a simple microscope setup with a polarizer and an analyzer is employed in combination with an analytical dipole model to extract the orientation of the longitudinal dipolar mode of exemplary gold nanorods. This mode coincides with the azimuthal orientation of the colloid, and for irregularly shaped particles it can help to determine their dominant axis. The technique is demonstrated on multiple nanorods with varying aspect ratios. The spectroscopically determined orientations are compared to orientations extracted from electron microscopy images, resulting in standard deviations as low as ±2.4°. The method can be generalized to nanostructures with 3D orientations or multiple resonances.
On-Surface Synthesis and Characterization of Pentadecacene and Its Gold Complexes
2025-01-17

Acenes are an important class of polycyclic aromatic hydrocarbons that have gained considerable attention from chemists, physicists, and material scientists, due to their exceptional potential for organic electronics. They serve as an ideal platform for studying the physical and chemical properties of sp<sup>2</sup> carbon frameworks in the one-dimensional limit and also provide a fertile playground to explore magnetism in graphenic nanostructures due to their zigzag edge topology. While higher acenes up to tridecacene have been successfully generated by means of on-surface synthesis, it is imperative to extend their synthesis toward even longer homologues to comprehensively understand the evolution of their electronic ground state. Here, we demonstrate the on-surface synthesis of pentadecacene (<b>15ac</b>) from a trietheno-bridged precursor via the atom-manipulation-induced dissociation of protecting groups or the elimination of adatoms in a gold-pentadecacene complex. The generated <b>15ac</b> was investigated by scanning tunneling microscopy (STM)/spectroscopy (STS) and noncontact atomic force microscopy (nc-AFM), in combination with first-principles spin-polarized density functional theory (DFT) calculations. We found that <b>15ac</b> exhibits an open-shell singlet ground state with an experimental singlet-triplet gap of 124 meV and an STS transport gap of ∼1.12 eV. The formation of Au-pentadecacene complexes suggested a considerable contribution of polyradical character to the electronic ground state of <b>15ac</b>. Our work contributes to a fundamental understanding of the electronic properties of long acenes and to the development of a versatile STM tip-assisted methodology for the synthesis of elusive compounds.
UV Hyperspectral Imaging and Chemometrics for Honeydew Detection: Enhancing Cotton Fiber Quality
2025-01-17

Cotton, the most widely produced natural fiber, is integral to the textile industry and sustains the livelihoods of millions worldwide. However, its quality is frequently compromised by contamination, particularly from honeydew, a substance secreted by insects that leads to the formation of sticky fibers, thereby impeding textile processing. This study investigates ultraviolet (UV) hyperspectral imaging (230–380 nm) combined with multivariate data analysis to detect and quantify honeydew contaminations in real cotton samples. Reference cotton samples were sprayed multiple times with honey solutions to replicate the natural composition of honeydew. Comparisons were made with an alternative method where samples were soaked in sugar solutions of varying concentrations. Principal component analysis (PCA) and quadratic discriminant analysis (QDA) effectively differentiated and classified samples based on honey spraying times. Additionally, partial least squares regression (PLS-R) was utilized to predict the honeydew content for each pixel in hyperspectral images, achieving a cross-validation coefficient of determination R2 = 0.75 and root mean square error of RMSE = 0.8 for the honey model. By employing a realistic spraying method that closely mimics natural contamination, this study refines sample preparation techniques for improved evaluation of honeydew levels. In conclusion, the integration of hyperspectral imaging with multivariate analysis represents a robust, non-destructive, and rapid approach for real-time detection of honeydew contamination in cotton, offering significant potential for industrial applications.
After a Hand Was Lent: Sporadically Experiencing Multisensory Interference During the Rubber Hand Illusion Does Not Shield Against Disembodiment
2025-01-17

Observations from multisensory body illusions indicate that the body representation can be adapted to changing task demands, e.g., it can be expanded to integrate external objects based on current sensorimotor experience (embodiment). While the mechanisms that promote embodiment have been studied extensively in earlier work, the opposite phenomenon of, removing an embodied entity from the body representation (i.e., disembodiment) has received little attention yet. The current study addressed this phenomenon and drew inspiration from the partial reinforcement extinction effect in instrumental learning which suggests that behavior is more resistant to extinction when reinforcement is delivered irregularly. In analogy to this, we investigated whether experiencing occasional visuo-motor mismatches during the induction phase of the moving rubber hand illusion (intermittent condition) would result in slower disembodiment as compared to a regular induction phase where motor and visual signals always match (continuous condition). However, we did not find an effect of reinforcement schedule on disembodiment. Keeping a recently embodied entity in the body schema, therefore, requires constant updating through correlated perceptual and motor signals.
Interrogating artificial agency
2025-01-17

Can artificial systems act? In the literature we find two camps: sceptics and believers. But the issue of whether artificial systems can act and, if so, how, has not been systematically discussed. This is a foundational question for the philosophy of AI. I sketch a methodological approach to investigating the agency of artificial systems from architectural and behavioural perspectives.
Associations between epilepsy-related polygenic risk and brain morphology in childhood
2025-01-17

A bstract Temporal lobe epilepsy with hippocampal sclerosis (TLE-HS) is associated with a complex genetic architecture, but the translation from genetic risk factors to brain vulnerability remains unclear. Here, we examined associations between epilepsy-related polygenic risk scores for HS (PRS-HS) and brain structure in a large sample of neurotypical children, and correlated these signatures with case-control findings in in multicentric cohorts of patients with TLE-HS. Imaging-genetic analyses revealed PRS-related cortical thinning in temporo-parietal and fronto-central regions, strongly anchored to distinct functional and structural network epicentres. Compared to disease-related effects derived from epilepsy case-control cohorts, structural correlates of PRS-HS mirrored atrophy and epicentre patterns in patients with TLE-HS. By identifying a potential pathway between genetic vulnerability and disease mechanisms, our findings provide new insights into the genetic underpinnings of structural alterations in TLE-HS and highlight potential imaging-genetic biomarkers for early risk stratification and personalized interventions.
From Decay of Correlations to Locality and Stability of the Gibbs State
2025-01-18

Abstract We show that whenever the Gibbs state of a quantum spin system satisfies decay of correlations, then it is stable, in the sense that local perturbations affect the Gibbs state only locally, and it satisfies local indistinguishability, i.e. it exhibits local insensitivity to system size. These implications hold in any dimension, require only locality of the Hamiltonian, and are based on Lieb–Robinson bounds and on a detailed analysis of the locality properties of the quantum belief propagation for Gibbs states. To demonstrate the versatility of our approach, we explicitly apply our results to several physically relevant models in which the decay of correlations is either known to hold or is proved by us. These include Gibbs states of one-dimensional spin chains with polynomially decaying interactions at any temperature, and high-temperature Gibbs states of quantum spin systems with finite-range interactions in any dimension. We also prove exponential decay of correlations above a threshold temperature for Gibbs states of one-dimensional finite spin chains with translation-invariant and exponentially decaying interactions, and then apply our general results.
Lymphoid-tissue-on-chip recapitulates human antibody responses in vitro
2025-01-18

ABSTRACT In the past decades, vaccine development has made great strides. Nevertheless, more often than not, vaccine candidates fail in advanced stages of development and clinical trials. A key reason is the poor predictive value of non-clinical in vivo and in vitro models, due to either species-specific differences in the immune response or insufficient reflection of physiological vaccine mechanisms. Reliable modeling of human adaptive immune responses is a prerequisite to understand processes leading to vaccine-induced protective immunization and to drive informed decisions in vaccine development pipelines. Here, we present a centrifugal microfluidics based organ-on-chip approach to generate an organotypic high density lymphoid tissue on-chip. The model enables long-term culture of lymphoid tissue and raised antigen-specific antibody responses against influenza vaccines even after four weeks on-chip. Antibody response of different magnitude and quality could be induced both by direct antigen exposure as well as by recruitment of antigen-presenting cells from the periphery. The model represents an attractive approach to evaluate the impact of the mode of antigen delivery on adaptive immune responses. Beyond applications in vaccine development, the lymphoid-tissue-on-chip provides a platform to study cellular interactions during homeostasis, immune responses and long-term impact of immunomodulators over several weeks.
Following the Mixtures of Organic Micropollutants with In Vitro Bioassays in a Large Lowland River from Source to Sea
2025-01-19

Human-impacted rivers often contain a complex mixture of organic micropollutants, including pesticides, pharmaceuticals and industrial compounds, along with their transformation products. Combining chemical target analysis for exposure with <i>in vitro</i> bioassays for effect assessment offers a holistic view of water quality. This study targeted the River Elbe in Central Europe, known for its anthropogenic pollution exposure, to obtain an inventory of micropollutant contamination during base flow and to identify hotspots of contamination. We identified tributaries as sources of chemicals activating the aryl hydrocarbon receptor quantified with the AhR-CALUX assay, including historically contaminated tributaries and a newly identified Czech tributary. Increased neurotoxicity, detected by differentiated SH-SY5Y neurons' cytotoxicity and shortened neurite length, was noted in some Czech tributaries. A hotspot for chemicals activating the oxidative stress response in the AREc32 assay was found in the middle Elbe in Germany. An increase in oxidative stress inducing chemicals was observed in the lower Elbe. While effect-based trigger values (EBT) for oxidative stress response, xenobiotic metabolism and neurotoxicity were not exceeded, estrogenicity levels surpassed the EBT in 14% of surface water samples, posing a potential threat to fish reproduction. Target analysis of 713 chemicals resulted in the quantification of 487 micropollutants, of which 133 were active in at least one bioassay. Despite this large number of bioactive quantified chemicals, the mixture effects predicted by the concentrations of the quantified bioactive chemicals and their relative effect potency explained only 0.002-1.2% of the effects observed in the surface water extracts, highlighting a significant unknown fraction in the chemical mixtures. This case study established a baseline for understanding pollution dynamics and spatial variations in the Elbe River, offering a comprehensive view of potential chemical effects in the water and guiding further water quality monitoring in European rivers.
How do intellectually curious and interested people learn and attain knowledge? A focus on behavioral traces of information seeking
2025-01-19

Intellectual curiosity and personal interest are both believed to spark information seeking and facilitate learning. In two preregistered studies (Study 1: exploratory lab study, N = 312; Study 2: online conceptual replication study, N = 960), we investigated effects of curiosity and interest on participants’ information seeking as they studied a hypertext on a historical topic. We captured their behavioral traces with log files. We also examined effects of curiosity, interest, and information-seeking behaviors on knowledge attainment. In both studies, latent profile analyses based on behavioral trace data revealed that some information-seeking profiles were more adaptive (e.g., broad and deep-diving information seeking, Study 1; broad information seeking, Study 2) and some were less adaptive (e.g., disengaged). More adaptive profiles were consistently related to better knowledge test performance. Curiosity and interest positively predicted more adaptive information seeking (Study 1) and knowledge test performance (Study 2); however, these effects were inconsistent across study contexts. Furthermore, curiosity and interest did not interact in predicting information seeking or knowledge attainment (Studies 1 and 2). Overall, our work extends the understanding of how intellectually curious and interested individuals learn and attain knowledge and underscores the promise of using behavioral trace data to study interindividual differences.
Mass rabies exposure of veterinary health care workers in Germany: Management, immune response, and tolerability of post exposure-prophylaxis
2025-01-19

This case highlights challenges in rabies mass exposure management and emphasizes needs for continued preparedness, resource allocation and education about rabies, even in regions considered rabies-free.
Reconstructing the Map: A Neopragmatist Perspective on Cartography in the Context of Artificial Intelligence (AI)
2025-01-20

Abstract The present article explores possibilities for a new theoretical framework in cartography based on a neopragmatist approach. Starting with an outline of Traditional and Critical Cartography, a neopragmatist perspective is developed that promotes inclusivity and problem-solving orientation. This approach draws on the analytical framework of Karl Popper’s Three Worlds Theory, specifically the Theory of Three Spaces. Neopragmatism emphasizes the production of useful knowledge over absolute truth and acknowledges the contingency and flexible interpretability of cartographic representations. In this context, Artificial Intelligence (AI) is described as a dynamic tool for problem-solving, capable of supporting continuous learning and application-oriented adaptation. By employing AI within a neopragmatist framework in cartography, new possibilities emerge for integrating and utilizing diverse social perspectives and (geospatial) data. This approach enables an expansion of the theoretical and practical applicability of cartography. Finally, the article illustrates that the deconstruction—building on J. B. Harley’s influential article Deconstructing the Map (1989)—and reconstruction of maps must exist in a recursive relationship to enable a context- and solution-oriented cartography.
Antiplasmodial Activity of a New Chemotype of Croton sylvaticus Hochst. Ex C. Krauss Essential Oil
2025-01-20

Croton sylvaticus, a tropical African plant, is traditionally used to treat several diseases, including fever, inflammation, and malaria. Essential oils (EOs) from the plant’s leaves, roots, and trunk bark were obtained by hydrodistillation, and their chemical composition was analyzed by gas chromatography–mass spectrometry (GC-MS). The major constituents identified were virdiflorene (18.13 ± 0.46%) in root EO, (E)-β-caryophyllene (18.40 ± 0.60%) in trunk bark EO, and farnesyl acetone (15.26 ± 0.25%) in leaf EO. Notably, Cameroonian C. sylvaticus leaf EO exhibited a distinct and newly described chemotype with high levels of farnesyl acetone, β-copaene-4-α-ol, β-cadinene, α-humulene, and trans-longipinocarveol. In vitro testing revealed significant antiplasmodial activity against Plasmodium falciparum asexual (Pf3D7) and sexual (NF-54 strain) stages, with trunk bark EO showing the highest potency (IC50: 9.06 ± 2.15 μg/mL for Pf3D7 and 0.56 μg/mL for gametocytes). These findings support the traditional antimalarial use of C. sylvaticus and represent the first chemical profile and antiplasmodial efficacy report for its root and trunk bark EOs against both parasite stages. To the best of our knowledge, we also report for the first time the antiplasmodial activity of an EO that exerts significant activity against both the asexual and sexual forms of P. falciparum.
Left ventricular function improvement during angiotensin receptor–neprilysin inhibitor treatment in a cohort of HFrEF/HFmrEF patients
2025-01-20

Abstract Aims Heart failure (HF) patients may lack improvement of left ventricular (LV) ejection fraction (LVEF) despite optimal HF medication comprising an angiotensin receptor–neprilysin inhibitor (ARNI). Therefore, we aimed to identify key predictors for LV functional enhancement and prognostic reverse cardiac remodelling in HF patients on ARNI treatment. Methods We retrospectively analysed 294 consecutive patients with HF with reduced (HFrEF) or mildly reduced (HFmrEF) ejection fraction in our ‘EnTruth’ patient registry. LVEF was determined by echocardiography at initiation of ARNI and at 12 months of follow‐up. We assessed the predictive value of clinically relevant patient‐, HF‐ and treatment‐related parameters in regard to changes in LVEF and all‐cause mortality using medoid clustering and the XGBoost machine learning algorithm. Results Cluster analysis integrating clinically relevant patient characteristics unveiled four characteristic sub‐phenotypes of patients with HFrEF and HFmrEF, respectively. Distinct clusters exhibit a strong ( P &lt; 0.05) therapeutic response to ARNI treatment and enhanced LV function. Key patient criteria, such as duration and aetiology of HF, renal function and de novo ARNI treatment, were significantly ( P &lt; 0.05) associated with change of LVEF and independently predicted cardiac remodelling. By training various machine learning models on relevant clinical parameters, stratification of LVEF improvement by XGBoost resulted in a high prediction accuracy. The stratification of patients with HFrEF [area under the receiver operating characteristic curve (AUC) = 0.77] and HFmrEF (AUC = 0.70) led to an increased diagnostic accuracy of LVEF improvement in the validation cohort. Using machine learning, the likelihood of cardiac remodelling following ARNI treatment, as indicated by our newly established EnTruth score, was directly associated with absolute LVEF improvement in both HFrEF ( r = 0.51, P &lt; 0.0001) and HFmrEF ( r = 0.42, P = 0.001). Ultimately, patients with HFrEF and a high EnTruth score have a lower risk of all‐cause mortality ( P &lt; 0.05 in survival analysis). Conclusions Recognition of essential clinical factors by integrating machine learning and cluster analyses may help to identify HF patients benefiting from improvement of LVEF following ARNI treatment. Early identification of those patients with a high response to ARNI treatment may allow a more refined selection of patients benefiting from an early escalation of HF treatment or interventional therapy.
Targeted and untargeted urinary metabolomics of alkaptonuria patients using ultra high-performance liquid chromatography-tandem mass spectrometry
2025-01-20

Alkaptonuria (AKU) is a rare autosomal-recessive disease which is characterized through black urine and ochronosis. It is caused by deficiency of the enzyme Homogentisate 1,2-dioxygenase in the Phenylalanine/Tyrosine degradation pathway which leads to the accumulation of Homogentisic acid (HGA). Urine was provided by AKU patients and healthy controls. Several different methods were developed in this study each with a specific goal. Firstly, a simple and inexpensive RP-UHPLC-UV method for routine monitoring of HGA as a key metabolite employing a Phenylhexyl stationary phase chemistry. Validation was performed in accordance to FDA guidelines and method selectivity was further evaluated via on-line high-resolution sampling 2D-LC-QToF-MS, coupling the Phenylhexyl phase in the first dimension with a C18 phase in the second dimension. Secondly, a targeted and accurate RP-UHPLC-MRM-QTRAP assay, providing quantitative analysis of the relevant pathway metabolites based on a Phenylhexyl stationary phase, and lastly an untargeted HILIC-UHPLC-QToF-MS/MS method with SWATH (sequential window acquisition of all theoretical mass spectra) acquisition employing a sulfobetaine-type HILIC-Z superficially porous particle column, with the aim of uncovering more details about the metabolic profile of this genetic disorder. By untargeted analysis 204 metabolites could be detected and annotated in positive and negative ESI mode in total. Two separate LC methods were employed, differing in their conditions depending on the ionization mode (20 mM ammonium formate as buffer additive adjusted to a pH = 3.5 with formic acid in ESI<sup>+</sup> mode and 20 mM ammonium acetate adjusted to a pH = 7.5 with acetic acid in ESI<sup>-</sup> mode). By effectively combining the aforementioned methods, a comprehensive workflow was developed, allowing the effective analysis of both patient and control urine samples.