julilili42/papers huggingface dataset:
X-Ray Polarized View of the Accretion Geometry in the X-Ray Binary Circinus X-1
2024-01-01

Abstract Cir X-1 is a neutron star X-ray binary characterized by strong variations in flux during its eccentric ∼16.6 day orbit. There are also strong variations in the spectral state, and it has historically shown both atoll and Z state properties. We observed the source with the Imaging X-ray Polarimetry Explorer during two orbital segments, 6 days apart, for a total of 263 ks. We find an X-ray polarization degree in these segments of 1.6% ± 0.3% and 1.4% ± 0.3% at polarization angles of 37° ± 5° and −12° ± 7°, respectively. Thus, we observed a rotation of the polarization angle by 49° ± 8° along the orbit. Because variations of accretion flow, and then of the hardness ratio, are expected during the orbit, we also studied the polarization binned in hardness ratio and found the polarization angle differing by 67° ± 11° between the lowest and highest values of the hardness ratio. We discuss possible interpretations of this result that could indicate a possible misalignment between the symmetry axes of the accretion disk and the Comptonizing region caused by the misalignment of the neutron star’s angular momentum with respect to the orbital one.
Natural Experiments: Missed Opportunities for Causal Inference in Psychology
2024-01-01

Knowledge about causal effects is essential for building useful theories and designing effective interventions. The preferred design for learning about causal effects is randomized experiments (i.e., studies in which the researchers randomly assign units to treatment and control conditions). However, randomized experiments are often unethical or unfeasible. On the other hand, observational studies are usually feasible but lack the random assignment that renders randomized experiments causally informative. Natural experiments can sometimes offer unique opportunities for dealing with this dilemma, allowing causal inference on the basis of events that are not controlled by researchers but that nevertheless establish random or as-if random assignment to treatment and control conditions. Yet psychological researchers have rarely exploited natural experiments. To remedy this shortage, we describe three main types of studies exploiting natural experiments (standard natural experiments, instrumental-variable designs, and regression-discontinuity designs) and provide examples from psychology and economics to illustrate how natural experiments can be harnessed. Natural experiments are challenging to find, provide information about only specific causal effects, and involve assumptions that are difficult to validate empirically. Nevertheless, we argue that natural experiments provide valuable causal-inference opportunities that have not yet been sufficiently exploited by psychologists.
Perspectives on computational modeling of biological systems and the significance of the SysMod community
2024-01-01

Abstract Motivation In recent years, applying computational modeling to systems biology has caused a substantial surge in both discovery and practical applications and a significant shift in our understanding of the complexity inherent in biological systems. Results In this perspective article, we briefly overview computational modeling in biology, highlighting recent advancements such as multi-scale modeling due to the omics revolution, single-cell technology, and integration of artificial intelligence and machine learning approaches. We also discuss the primary challenges faced: integration, standardization, model complexity, scalability, and interdisciplinary collaboration. Lastly, we highlight the contribution made by the Computational Modeling of Biological Systems (SysMod) Community of Special Interest (COSI) associated with the International Society of Computational Biology (ISCB) in driving progress within this rapidly evolving field through community engagement (via both in person and virtual meetings, social media interactions), webinars, and conferences. Availability and implementation Additional information about SysMod is available at https://sysmod.info.
A Guide to Feature Importance Methods for Scientific Inference
2024-01-01

Abstract While machine learning (ML) models are increasingly used due to their high predictive power, their use in understanding the data-generating process (DGP) is limited. Understanding the DGP requires insights into feature-target associations, which many ML models cannot directly provide due to their opaque internal mechanisms. Feature importance (FI) methods provide useful insights into the DGP under certain conditions. Since the results of different FI methods have different interpretations, selecting the correct FI method for a concrete use case is crucial and still requires expert knowledge. This paper serves as a comprehensive guide to help understand the different interpretations of global FI methods. Through an extensive review of FI methods and providing new proofs regarding their interpretation, we facilitate a thorough understanding of these methods and formulate concrete recommendations for scientific inference. We conclude by discussing options for FI uncertainty estimation and point to directions for future research aiming at full statistical inference from black-box ML models.
Nasal commensals reduce Staphylococcus aureus proliferation by restricting siderophore availability
2024-01-01

Abstract The human microbiome is critically associated with human health and disease. One aspect of this is that antibiotic-resistant opportunistic bacterial pathogens, such as methicillin-resistant Staphylococcus aureus, can reside within the nasal microbiota, which increases the risk of infection. Epidemiological studies of the nasal microbiome have revealed positive and negative correlations between non-pathogenic species and S. aureus, but the underlying molecular mechanisms remain poorly understood. The nasal cavity is iron-limited, and bacteria are known to produce iron-scavenging siderophores to proliferate in such environments. Siderophores are public goods that can be consumed by all members of a bacterial community. Accordingly, siderophores are known to mediate bacterial competition and collaboration, but their role in the nasal microbiome is unknown. Here, we show that siderophore acquisition is crucial for S. aureus nasal colonization in vivo. We screened 94 nasal bacterial strains from seven genera for their capacity to produce siderophores as well as to consume the siderophores produced by S. aureus. We found that 80% of the strains engaged in siderophore-mediated interactions with S. aureus. Non-pathogenic corynebacterial species were found to be prominent consumers of S. aureus siderophores. In co-culture experiments, consumption of siderophores by competitors reduced S. aureus growth in an iron-dependent fashion. Our data show a wide network of siderophore-mediated interactions between the species of the human nasal microbiome and provide mechanistic evidence for inter-species competition and collaboration impacting pathogen proliferation. This opens avenues for designing nasal probiotics to displace S. aureus from the nasal cavity of humans.
Electrical-energy storage into chemical-energy carriers by combining or integrating electrochemistry and biology
2024-01-01

Our societies must reconsider current industrial practices and find carbon-neutral alternatives to avoid the detrimental environmental effects that come with the release of greenhouse gases from fossil-energy carriers.
Real-time monitoring for the next core-collapse supernova in JUNO
2024-01-01

Abstract The core-collapse supernova (CCSN) is considered one of the most energetic astrophysical events in the universe. The early and prompt detection of neutrinos before (pre-SN) and during the supernova (SN) burst presents a unique opportunity for multi-messenger observations of CCSN events. In this study, we describe the monitoring concept and present the sensitivity of the system to pre-SN and SN neutrinos at the Jiangmen Underground Neutrino Observatory (JUNO), a 20 kton liquid scintillator detector currently under construction in South China. The real-time monitoring system is designed to ensure both prompt alert speed and comprehensive coverage of progenitor stars. It incorporates prompt monitors on the electronic board as well as online monitors at the data acquisition stage. Assuming a false alert rate of 1 per year, this monitoring system exhibits sensitivity to pre-SN neutrinos up to a distance of approximately 1.6 (0.9) kiloparsecs and SN neutrinos up to about 370 (360) kiloparsecs for a progenitor mass of 30 solar masses, considering both normal and inverted mass ordering scenarios. The pointing ability of the CCSN is evaluated by analyzing the accumulated event anisotropy of inverse beta decay interactions from pre-SN or SN neutrinos. This, along with the early alert, can play a crucial role in facilitating follow-up multi-messenger observations of the next galactic or nearby extragalactic CCSN.
Microphysiological pancreas-on-chip platform with integrated sensors to model endocrine function and metabolism
2024-01-01

Pancreatic in vitro models are crucial for research on diseases such as diabetes mellitus. A novel thermoplastic organ-on-chip with integrated real-time read-outs models the complex microphysiological structure and function of the endocrine pancreas.
Conversational AI facilitates mental health assessments and is associated with improved recovery rates
2024-01-01

Mental health services across the globe are overburdened due to increased patient need for psychological therapies and a shortage of qualified mental health practitioners. This is unlikely to change in the short-to-medium term. Digital support is urgently needed to facilitate access to mental healthcare while creating efficiencies in service delivery. In this paper, we evaluate the use of a conversational artificial intelligence (AI) solution ( Limbic Access ) to assist both patients and mental health practitioners with referral, triage, and clinical assessment of mild-to-moderate adult mental illness. Assessing this solution in the context of England’s National Health Service (NHS) Talking Therapies services, we demonstrate in a cohort study design that deploying such an AI solution is associated with improved recovery rates. We find that those NHS Talking Therapies services that introduced the conversational AI solution improved their recovery rates, while comparable NHS Talking Therapies services across the country reported deteriorating recovery rates during the same time period. Further, we provide an economic analysis indicating that the usage of this AI solution can be highly cost-effective relative to other methods of improving recovery rates. Together, these results highlight the potential of AI solutions to support mental health services in the delivery of quality care in the context of worsening workforce supply and system overburdening. For transparency, the authors of this paper declare our conflict of interest as employees and shareholders of Limbic Access, the AI solution referred to in this paper.
Staphylococcus epidermidis bacteriocin A37 kills natural competitors with a unique mechanism of action
2024-01-01

Abstract Many bacteria produce antimicrobial compounds such as lantibiotics to gain advantage in the competitive natural environments of microbiomes. Epilancins constitute an until now underexplored family of lantibiotics with an unknown ecological role and unresolved mode of action. We discovered production of an epilancin in the nasal isolate Staphylococcus epidermidis A37. Using bioinformatic tools, we found that epilancins are frequently encoded within staphylococcal genomes, highlighting their ecological relevance. We demonstrate that production of epilancin A37 contributes to Staphylococcus epidermidis competition specifically against natural corynebacterial competitors. Combining microbiological approaches with quantitative in vivo and in vitro fluorescence microscopy and cryo-electron tomography, we show that A37 enters the corynebacterial cytoplasm through a partially transmembrane-potential-driven uptake without impairing the cell membrane function. Upon intracellular aggregation, A37 induces the formation of intracellular membrane vesicles, which are heavily loaded with the compound and are essential for the antibacterial activity of the epilancin. Our work sheds light on the ecological role of epilancins for staphylococci mediated by a mode of action previously unknown for lantibiotics.
Histological and functional characterization of 3D human skin models mimicking the inflammatory skin diseases psoriasis and atopic dermatitis
2024-01-01

ABSTRACT Three-dimensional (3D) human skin equivalents have emerged as valuable tools in skin research, replacing animal experimentation and precluding the need for patient biopsies. In this study, we advanced 3D skin equivalents to model the inflammatory skin diseases atopic dermatitis and psoriasis by cytokine stimulation, and were successful in integrating TH1 T cells into skin models to develop an immunocompetent 3D psoriasis model. We performed in-depth histological and functional characterization of 3D skin equivalents and validated them in terms of tissue architecture, pathological changes, expression of antimicrobial peptides and Staphylococcus aureus colonization using 3D reconstruction by multiphoton microscopy and phenotyping by highly multiplexed ‘co-detection by indexing’ (CODEX) microscopy. We show that our skin equivalents have a structural architecture with a well-developed dermis and epidermis, thus resembling human skin. In addition, the skin models of atopic dermatitis and psoriasis show several phenotypic features of inflammatory skin disease, including disturbed epidermal differentiation and alterations in the expression of epidermal barrier genes and antimicrobial peptides, and can be reliably used to test novel treatment strategies. Therefore, these 3D equivalents will be a valuable tool in experimental dermatological research.
‘Better see a doctor?’ Status quo of symptom checker apps in Germany: A cross-sectional survey with a mixed-methods design (CHECK.APP)
2024-01-01

Background Symptom checker apps (SCAs) offer symptom classification and low-threshold self-triage for laypeople. They are already in use despite their poor accuracy and concerns that they may negatively affect primary care. This study assesses the extent to which SCAs are used by medical laypeople in Germany and which software is most popular. We examined associations between satisfaction with the general practitioner (GP) and SCA use as well as the number of GP visits and SCA use. Furthermore, we assessed the reasons for intentional non-use. Methods We conducted a survey comprising standardised and open-ended questions. Quantitative data were weighted, and open-ended responses were examined using thematic analysis. Results This study included 850 participants. The SCA usage rate was 8%, and approximately 50% of SCA non-users were uninterested in trying SCAs. The most commonly used SCAs were NetDoktor and Ada. Surprisingly, SCAs were most frequently used in the age group of 51–55 years. No significant associations were found between SCA usage and satisfaction with the GP or the number of GP visits and SCA usage. Thematic analysis revealed skepticism regarding the results and recommendations of SCAs and discrepancies between users’ requirements and the features of apps. Conclusion SCAs are still widely unknown in the German population and have been sparsely used so far. Many participants were not interested in trying SCAs, and we found no positive or negative associations of SCAs and primary care.
Resistive switching memories with enhanced durability enabled by mixed-dimensional perfluoroarene perovskite heterostructures
2024-01-01

Mixed-dimensional heterostructures of 2D perfluoroarene perovskite phases are used in resistive switching memories based on perovskite solar cells, showing enhanced performance and stability, which highlights the perspective for self-powered memories.
X-Ray Polarization of the Eastern Lobe of SS 433
2024-01-01

Abstract How astrophysical systems translate the kinetic energy of bulk motion into the acceleration of particles to very high energies is a pressing question. SS 433 is a microquasar that emits TeV γ -rays indicating the presence of high-energy particles. A region of hard X-ray emission in the eastern lobe of SS 433 was recently identified as an acceleration site. We observed this region with the Imaging X-ray Polarimetry Explorer and measured a polarization degree in the range 38%–77%. The high polarization degree indicates the magnetic field has a well-ordered component if the X-rays are due to synchrotron emission. The polarization angle is in the range −12° to +10° (east of north), which indicates that the magnetic field is parallel to the jet. Magnetic fields parallel to the bulk flow have also been found in supernova remnants and the jets of powerful radio galaxies. This may be caused by interaction of the flow with the ambient medium.
Nickel catalyzed C–S cross coupling of sterically hindered substrates enabled by flexible bidentate phosphines
2024-01-01

The challenging nickel-catalyzed coupling of ortho -substituted aryl triflates with thiols was accomplished by employing a versatile bidentate ligand, capable of decoordination of one phosphorus atom during the deprotonation of thiol.
Hydrogen–independent CO2 reduction dominates methanogenesis in five temperate lakes that differ in trophic states
2024-01-01

Abstract Emissions of microbially produced methane (CH4) from lake sediments are a major source of this potent greenhouse gas to the atmosphere. The rates of CH4 production and emission are believed to be influenced by electron acceptor distributions and organic carbon contents, which in turn are affected by anthropogenic inputs of nutrients leading to eutrophication. Here, we investigate how eutrophication influences the abundance and community structure of CH4 producing Archaea and methanogenesis pathways across time–resolved sedimentary records of five Swiss lakes with well–characterized trophic histories. Despite higher CH4 concentrations which suggest higher methanogenic activity in sediments of eutrophic lakes, abundances of methanogens were highest in oligotrophic lake sediments. Moreover, while the methanogenic community composition differed significantly at the lowest taxonomic levels (OTU), depending on whether sediment layers had been deposited under oligotrophic or eutrophic conditions, it showed no clear trend in relation to in situ distributions of electron acceptors. Remarkably, even though methanogenesis from CO2-reduction was the dominant pathway in all sediments based on carbon isotope fractionation values, taxonomic identities, and genomes of resident methanogens, CO2-reduction with hydrogen (H2) was thermodynamically unfavorable based on measured reactant and product concentrations. Instead, strong correlations between genomic abundances of CO2-reducing methanogens and anaerobic bacteria with potential for extracellular electron transfer suggest that methanogenic CO2-reduction in lake sediments is largely powered by direct electron transfer from syntrophic bacteria without involvement of H2 as an electron shuttle.
Ag-based coordination polymer-enhanced photocatalytic degradation of ciprofloxacin and nitrophenol
2024-01-01

A novel Ag coordination polymer (Ag-TIPA) was rationally designed, successfully prepared and used for the photodegradation of ciprofloxacin and nitrophenol, showing excellent photocatalytic performance and high reusability.
A novel approach to guide GD2-targeted therapy in pediatric tumors by PET and [64Cu]Cu-NOTA-ch14.18/CHO
2024-01-01

<b>Background:</b> The tumor-associated disialoganglioside GD2 is a <i>bona fide</i> immunotherapy target in neuroblastoma and other childhood tumors, including Ewing sarcoma and osteosarcoma. GD2-targeting antibodies proved to be effective in neuroblastoma and GD2-targeting chimeric antigen receptors (CAR)- expressing T cells as well as natural killer T cells (NKTs) are emerging. However, assessment of intra- and intertumoral heterogeneity has been complicated by ineffective immunohistochemistry as well as sampling bias in disseminated disease. Therefore, a non-invasive approach for the assessment and visualization of GD2 expression <i>in-vivo</i> is of upmost interest and might enable a more appropriate treatment stratification. <b>Methods:</b> Recently, [<sup>64</sup>Cu]Cu-NOTA-ch14.18/CHO (<sup>64</sup>Cu-GD2), a radiolabeled GD2-antibody for imaging with Positron-Emission-Tomography (PET) was developed. We here report our first clinical patients' series (n = 11) in different pediatric tumors assessed with <sup>64</sup>Cu-GD2 PET/MRI. GD2-expression in tumors and tissue uptake in organs was evaluated by semiquantitative measurements of standardized uptake values (SUV) with PET/MRI on day 1 p.i. (n = 11) as well as on day 2 p.i. (n = 6). <b>Results:</b> In 8 of 9 patients with suspicious tumor lesions on PET/MRI at least one metastasis showed an increased <sup>64</sup>Cu-GD2 uptake and a high tracer uptake (SUV<sub>max</sub> > 10) was measured in 4 of those 8 patients. Of note, sufficient image quality with high tumor to background contrast was readily achieved on day 1. In case of <sup>64</sup>Cu-GD2-positive lesions, an excellent tumor to background ratio (at least 6:1) was observed in bones, muscles or lungs, while lower tumor to background contrast was seen in the spleen, liver and kidneys. Furthermore, we demonstrated extensive tumor heterogeneity between patients as well as among different metastatic sites in individual patients. Dosimetry assessment revealed a whole-body dose of only 0.03 mGy/MBq (range 0.02-0.04). <b>Conclusion:</b> <sup>64</sup>Cu-GD2 PET/MRI enables the non-invasive assessment of individual heterogeneity of GD2 expression, which challenges our current clinical practice of patient selection, stratification and immunotherapy application scheme for treatment with anti-GD2 directed therapies.
Evolution of sub-ice-shelf channels reveals changes in ocean-driven melt in West Antarctica
2024-01-01

Abstract Basal channels, which are troughs carved into the undersides of ice shelves by buoyant plumes of water, are modulators of ice-shelf basal melt and structural stability. In this study, we track the evolution of 12 large basal channels beneath ice shelves of the Amundsen and Bellingshausen seas region in West Antarctica using the Landsat record since its start in the 1970s through 2020. We observe examples of channel growth, interactions with ice-shelf features, and systematic changes in sinuosity that give insight into the life cycles of basal channels. We use the last two decades of the record, combined with contemporary ice-flow velocity datasets, to separate channel-path evolution into components related to advection by ice flow and those controlled by other forcings, such as ocean melt or surface accumulation. Our results show that ice-flow-independent lateral channel migration is overwhelmingly to the left when viewed down-flow, suggesting that it is dominated by Coriolis-influenced ocean melt. By applying a model of channel-path evolution dominantly controlled by ice flow and ocean melt, we show that the majority of channels surveyed exhibit non-steady behavior that serves as a novel proxy for increased ocean forcing in West Antarctica starting at least in the early 1970s.