julilili42/papers huggingface dataset:
NOD1 cooperates with HAX‐1 to promote cell migration in a RIPK2‐ and NF‐ĸB‐independent manner
2023-07-25

The human Nod‐like receptor protein NOD1 is a well‐described pattern‐recognition receptor (PRR) with diverse functions. NOD1 associates with F‐actin and its protein levels are upregulated in metastatic cancer cells. A hallmark of cancer cells is their ability to migrate, which involves actin remodelling. Using chemotaxis and wound healing assays, we show that NOD1 expression correlated with the migration rate and chemotactic index in the cervical carcinoma cell line HeLa. The effect of NOD1 in cell migration was independent of the downstream kinase RIPK2 and NF‐ĸB activity. Additionally, NOD1 negatively regulated the phosphorylation status of cofilin, which inhibits actin turnover. Co‐immunoprecipitation assays identified HCLS1‐associated protein X‐1 (HAX‐1) as a previously unknown interaction partner of NOD1. Silencing of HAX‐1 expression reduced the migration behaviour to similar levels as NOD1 knockdown, and simultaneous knockdown of NOD1 and HAX‐1 showed no additive effect, suggesting that both proteins act in the same pathway. In conclusion, our data revealed an important role of the PRR NOD1 in regulating cell migration as well as chemotaxis in human cervical cancer cells and identified HAX‐1 as a protein that interacts with NOD1 and is involved in this signalling pathway.
Experimental exposure assessment for in vitro cell-based bioassays in 96- and 384-well plates
2023-07-25

In vitro cell-based bioassays have great potential for applications in the human health risk assessment of chemicals. The quantification of freely dissolved concentrations ( C free ) in in vitro assays is essential to generate reliable data for in vitro -to- in vivo extrapolation. Existing methods for the quantification of C free are limited to low-throughput microtiter plates. The present study is a proof of principle for the applicability of a solid-phase microextraction (SPME) method for the determination of C free in the peroxisome proliferator-activated receptor gamma (PPARγ) bioassay run in 384-well plates with 80 μL medium per well. The effect concentrations obtained from 384-well plates were compared with those obtained from 96-well plates in a previous study. Nominal effect concentrations obtained using 96- and 384-well plates agreed with each other within a factor of three, and freely dissolved effect concentrations agreed within a factor of 6.5. The good degree of agreement in the results from both plate formats proves the general applicability of the SPME method for the determination of C free for bioassays in 384-well plates, making the present study a first step toward exposure assessment in high-throughput bioassays.
Ambient Awareness of Who Knows What: Spontaneous Inferences of Domain Expertise
2023-07-25

Being aware of others' expertise is essential for knowledge exchange. Browsing social media has been shown to foster such awareness, often referred to as "ambient awareness". However, the underlying psychological mechanism has not yet been established. In a series of three preregistered experiments (total N = 445), we tested the notions that individuals make inferences about others' domains of expertise when being exposed to domain-implying social media posts, and that they do so spontaneously – that is, unintentionally and efficiently. Regardless of whether individuals were carefully reading, browsing through, or memorizing domain-implying posts, and whether they had an explicit goal to form an impression or not, we found consistent evidence that they made inferences about others' expertise domains, as evidenced by responses in a (false) probe recognition paradigm and explicit domain identification (Experiments 1 − 3). We also showed that they did so unintentionally (Experiment 2) and efficiently (Experiment 3). Spontaneous domain inferences are a plausible psychological mechanism for how ambient awareness of who knows what is achieved through regular social media use. Our findings provide causal evidence for the proposed mechanism underlying the link between social media use and expertise localization and highlight the role of social media posts in this process.
H.E.S.S. realtime follow-ups of IceCube high-energy neutrino alerts
2023-07-25

The evidence for multi-messenger photon and neutrino emission from the blazar TXS 0506+056 has demonstrated the importance of realtime follow-up of neutrino events by various ground- and space-based facilities. The effort of H.E.S.S. and other experiments in coordinating observations to obtain quasi-simultaneous multiwavelength flux and spectrum measurements has been critical in measuring the chance coincidence with the high-energy neutrino event IC-170922A and constraining theoretical models. For about a decade, the H.E.S.S. transient program has included a search for gamma-ray emission associated with high-energy neutrino alerts, looking for gamma-ray activity from known sources and newly detected emitters consistent with the neutrino location. In this contribution, we present an overview of follow-up activities for realtime neutrino alerts with H.E.S.S. in 2021 and 2022. Our analysis includes both public IceCube neutrino alerts and alerts exchanged as part of a joint H.E.S.S.--IceCube program. We focus on interesting coincidences observed with gamma-ray sources, particularly highlighting the significant detection of PKS 0625-35, an AGN previously detected by H.E.S.S., and three IceCube neutrinos.
Direct Spectroscopic Identification of BN-Arynes and Subtle Steric Effects on Nitrogen Fixation
2023-07-25

1,2-Azaborinines are the BN analogues of arynes through exchange of the formal CC triple bond by an isoelectronic BN bond. The BN-arynes are an underexplored class of reactive intermediates. Dibenzo[c,e][1,2]azaborinine (10,9-BN-phenanthryne) 1 was inferred as reactive intermediate by trapping reactions. Here it is shown that 1 can be generated in the gas phase by thermolysis from the pyridine adduct of 9-azido-9-borafluorene by cleavage of the dative bond with pyridine and dinitrogen extrusion. The ionization energy of 1 is 8.2 eV with ionization resulting from the π HOMO. Under cryogenic matrix isolation conditions, 9-azido-9-borafluorene photolysis results in isomerization to the dinitrogen adduct of 1 without involvement of a triplet borylnitrene intermediate. Photochemical nitrogen extrusion from 1•N2 is not possible and nitrogen fixation is irreversible under cryogenic conditions. In contrast, 2,4,7,9-tetra-tert-butyldibenzo[c,e][1,2]azaborinine can be photogenerated from the corresponding azidoborole precursor under cryogenic matrix isolation conditions, and nitrogen fixation is precluded due to steric hindrance. The BN stretching vibration at 1751 cm-1 is much weaker than in typical linear diaryl iminoboranes.
Abundance of radioactive technetium in Przybylski's star revisited
2023-07-25

Abstract We have searched for lines of the radioactive element technetium (Tc) in the spectrum of Przybylski's star (HD 101065). The nuclei of this chemical element are formed in the slow process of capturing thermalized neutrons. The possible lines of Tc I are heavily blended. We have synthesized the profile of one resonance line at 4297.06 Å , which is also a part of the complex blend, and we arrived at a decision that it is not visible in the spectrum (as was first noted by Ryabchikova), casting doubt on the existence of technetium in the atmosphere of the Przybylski's star. Therefore, based on our calculated combined profile, which has been adjusted to the observed blend profile at 4297.2 Å (that may possibly contain the resonance technetium line 4297.06 Å), we reduce the maximum technetium abundance to (Tc/H) = 2.5. This value can be considered only as an upper limit of the technetium abundance in the Przybylski's star.
A fungal pathogen manipulates phytocytokine signaling for plant infection
2023-07-25

<title>Abstract</title> <italic>Phytocytokines are hormone-like plant peptides that modulate immune homeostasis and development. Phytosulfokine (PSK) mediates plant growth and attenuates activation of plant pattern-triggered immunity (PTI). We show that the small cysteine-containing effector VdSCP8 from Verticillium dahliae (Vd) is a virulence-promoting protein that suppresses PTI in Arabidopsis thaliana and Nicotiana benthamiana. Apoplastic SCP8 suppresses immune activation through leucine-rich repeat ectodomain pattern recognition receptors. SCP8 virulence and immunosuppressive activities require PHYTOSULFOKINE RECEPTOR 1 (PSKR1), which binds PSK and forms a complex with co-receptor BAK1 for PTI suppression. We find that PSK, like SCP8, suppresses PTI, SCP8 stimulates PSKR1-BAK1 complex formation, and that Vd requires PSK signaling for host infection. SCP8 interacts with an apoplastic subtilase, and co-expression of SCP8 and subtilase inhibitors reduces PTI suppression. Our findings suggest that a multi-host plant pathogen manipulates PTI by enhancing immunosuppressive PSK signaling, likely through plant subtilase activity.</italic>
New insights into ischaemic complications after thoracic endovascular aneurysm repair
2023-07-25

Journal Article New insights into ischaemic complications after thoracic endovascular aneurysm repair Get access Mario Lescan Mario Lescan Department of Thoracic and Cardiovascular Surgery, University Medical Centre Tübingen, Tübingen, Germany Corresponding author. Department of Thoracic and Cardiovascular Surgery, University Medical Center Tübingen, Hoppe-Seyler Strasse 3, 72076 Tübingen, Germany. Tel: +49-7071-29-68194; fax: +49-7071-29-4047; e-mail: mario.lescan@med.uni-tuebingen.de (M. Lescan). https://orcid.org/0000-0002-3124-4994 Search for other works by this author on: Oxford Academic PubMed Google Scholar European Journal of Cardio-Thoracic Surgery, Volume 64, Issue 2, August 2023, ezad264, https://doi.org/10.1093/ejcts/ezad264 Published: 26 July 2023 Article history Published: 26 July 2023 Corrected and typeset: 01 August 2023
MERF: Memory-Efficient Radiance Fields for Real-time View Synthesis in Unbounded Scenes
2023-07-26

Neural radiance fields enable state-of-the-art photorealistic view synthesis. However, existing radiance field representations are either too compute-intensive for real-time rendering or require too much memory to scale to large scenes. We present a Memory-Efficient Radiance Field (MERF) representation that achieves real-time rendering of large-scale scenes in a browser. MERF reduces the memory consumption of prior sparse volumetric radiance fields using a combination of a sparse feature grid and high-resolution 2D feature planes. To support large-scale unbounded scenes, we introduce a novel contraction function that maps scene coordinates into a bounded volume while still allowing for efficient ray-box intersection. We design a lossless procedure for baking the parameterization used during training into a model that achieves real-time rendering while still preserving the photorealistic view synthesis quality of a volumetric radiance field.
Extensive pedigrees reveal the social organization of a Neolithic community
2023-07-26

Abstract Social anthropology and ethnographic studies have described kinship systems and networks of contact and exchange in extant populations 1–4 . However, for prehistoric societies, these systems can be studied only indirectly from biological and cultural remains. Stable isotope data, sex and age at death can provide insights into the demographic structure of a burial community and identify local versus non-local childhood signatures, archaeogenetic data can reconstruct the biological relationships between individuals, which enables the reconstruction of pedigrees, and combined evidence informs on kinship practices and residence patterns in prehistoric societies. Here we report ancient DNA, strontium isotope and contextual data from more than 100 individuals from the site Gurgy ‘les Noisats’ (France), dated to the western European Neolithic around 4850–4500 bc . We find that this burial community was genetically connected by two main pedigrees, spanning seven generations, that were patrilocal and patrilineal, with evidence for female exogamy and exchange with genetically close neighbouring groups. The microdemographic structure of individuals linked and unlinked to the pedigrees reveals additional information about the social structure, living conditions and site occupation. The absence of half-siblings and the high number of adult full siblings suggest that there were stable health conditions and a supportive social network, facilitating high fertility and low mortality 5 . Age-structure differences and strontium isotope results by generation indicate that the site was used for just a few decades, providing new insights into shifting sedentary farming practices during the European Neolithic.
A review on deep learning applications in highly multiplexed tissue imaging data analysis
2023-07-26

Since its introduction into the field of oncology, deep learning (DL) has impacted clinical discoveries and biomarker predictions. DL-driven discoveries and predictions in oncology are based on a variety of biological data such as genomics, proteomics, and imaging data. DL-based computational frameworks can predict genetic variant effects on gene expression, as well as protein structures based on amino acid sequences. Furthermore, DL algorithms can capture valuable mechanistic biological information from several spatial “omics” technologies, such as spatial transcriptomics and spatial proteomics. Here, we review the impact that the combination of artificial intelligence (AI) with spatial omics technologies has had on oncology, focusing on DL and its applications in biomedical image analysis, encompassing cell segmentation, cell phenotype identification, cancer prognostication, and therapy prediction. We highlight the advantages of using highly multiplexed images (spatial proteomics data) compared to single-stained, conventional histopathological (“simple”) images, as the former can provide deep mechanistic insights that cannot be obtained by the latter, even with the aid of explainable AI. Furthermore, we provide the reader with the advantages/disadvantages of DL-based pipelines used in preprocessing highly multiplexed images (cell segmentation, cell type annotation). Therefore, this review also guides the reader to choose the DL-based pipeline that best fits their data. In conclusion, DL continues to be established as an essential tool in discovering novel biological mechanisms when combined with technologies such as highly multiplexed tissue imaging data. In balance with conventional medical data, its role in clinical routine will become more important, supporting diagnosis and prognosis in oncology, enhancing clinical decision-making, and improving the quality of care for patients.
Protein target highlights in CASP15: Analysis of models by structure providers
2023-07-26

Abstract We present an in‐depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three‐dimensional protein structures continues to impress, reproducing uncommon features not previously observed in experimental structures is still a challenge. Furthermore, instances with conformational flexibility and large multimeric complexes highlight the need for novel scoring strategies to better emphasize biologically relevant structural regions. Looking ahead, closer integration of computational and experimental techniques will play a key role in determining the next challenges to be unraveled in the field of structural molecular biology.
Dictionary Fields: Learning a Neural Basis Decomposition
2023-07-26

We present Dictionary Fields, a novel neural representation which decomposes a signal into a product of factors, each represented by a classical or neural field representation, operating on transformed input coordinates. More specifically, we factorize a signal into a coefficient field and a basis field, and exploit periodic coordinate transformations to apply the same basis functions across multiple locations and scales. Our experiments show that Dictionary Fields lead to improvements in approximation quality, compactness, and training time when compared to previous fast reconstruction methods. Experimentally, our representation achieves better image approximation quality on 2D image regression tasks, higher geometric quality when reconstructing 3D signed distance fields, and higher compactness for radiance field reconstruction tasks. Furthermore, Dictionary Fields enable generalization to unseen images/3D scenes by sharing bases across signals during training which greatly benefits use cases such as image regression from partial observations and few-shot radiance field reconstruction.
Epistemic virtue in higher education: testing the mechanisms of intellectual character development
2023-07-26

Abstract Epistemic virtues are character traits conducive to principled ways of thinking, leading to a life of flourishing. Recent years have witnessed an emergence of theoretical accounts describing how they develop. However, few if any studies have conducted rigorous empirical investigation into the mechanisms of intellectual virtue development. In this study, we review several significant frameworks before utilizing a randomized, pretest/posttest control trial design to understand the impacts of a novel thinking disposition intervention on intellectual virtue growth. We ascertain the direct and indirect effects of the intervention on four key intellectual virtues: curiosity, humility, integrity, and tenacity. Additionally, we test theoretical mediators of virtue learning. Clear evidence favoring a theory-inspired mediator is observed, though we observe weaker signals of direct effects, with nuances across the virtues. For instance, tenacity and curiosity variables appear to respond more to the intervention than do humility and integrity. Findings are discussed in light of contemporary theoretical perspectives.
Open innovation networks: a driver for knowledge mobilisation in schools?
2023-07-26

Purpose In organisational and innovation research, the term “open innovation” refers to the inflow and outflow of knowledge to and from organisations: with open innovation theory suggesting active exchanges of knowledge with external actors leads to the development of exploitable new ideas. In the field of education, however, the exchange of knowledge with external parties represents a paradigm shift. In response, this article presents findings from research design to explore the nature and composition of school innovation networks, and the effects of such these networks on knowledge mobilisation. Design/methodology/approach The study draws on data from a representative random sample of 411 German school leaders. Respondents were asked to detail their engagement in open and closed innovation activity and their school's external collaborations during the last 12 months. A latent class distal outcome model was developed to examine whether different types of collaboration associate with different knowledge mobilisation processes. Findings The study findings suggest that schools in Germany mainly use internal knowledge for innovation, with external knowledge exchange taking place on a very limited basis. Knowledge mobilisation varies depending on the innovation network. The authors use the findings to indicate new insights for how schools can further innovate learning and teaching in future. Originality/value Although there is increasing discussion on Professional Learning Networks in schools, the discourse on knowledge mobilisation within educational networks is limited, making concept of open innovation so far completely absent from discourses on school improvement. This paper initiates the population of this new research space.
The first evidence of tidally induced activity in a brown dwarf-M dwarf pair: a Chandra study of the NLTT 41135/41136 system
2023-07-26

ABSTRACT The magnetic activity of low-mass stars changes as they age. The primary process decreasing the stellar activity level is the angular momentum loss via magnetized stellar wind. However, processes like tidal interactions between stars and their close companions may slow down the braking effect and the subsequent decrease of the activity level. Until now, the tidal impact of substellar objects like brown dwarfs on the evolution of their central stars has not been quantified. Here, we analyse the X-ray properties of NLTT 41135, an M dwarf tightly orbited by a brown dwarf, to determine the impact of tidal interactions between them. We find that NLTT 41135 is more than an order of magnitude brighter in the X-ray regime than its stellar companion, NLTT 41136, also an M dwarf star, with whom it forms a wide binary system. To characterize the typical intrinsic activity scatter between coeval M dwarf stars, we analyse a control sample of 25 M dwarf wide binary systems observed with the XMM–Newton and Chandra telescopes and the eROSITA instrument onboard the Spectrum Röntgen Gamma satellite. The activity difference in the NLTT 41135/41136 system is a 3.44σ outlier compared to the intrinsic activity scatter of the control systems. Therefore, the most convincing explanation for the observed activity discrepancy is tidal interactions between the M dwarf and its brown dwarf. This shows that tidal interactions between a star and a substellar companion can moderately alter the expected angular-momentum evolution of the star, making standard observational proxies for its age, such as X-ray emission, unreliable.
The capsular polysaccharide obstructs wall teichoic acid functions inStaphylococcus aureus
2023-07-26

Abstract Background The cell envelope of Staphylococcus aureus contains two major secondary cell wall glycopolymers: capsular polysaccharide (CP) and wall teichoic acid (WTA). Both the CP and the WTA are attached to the cell wall and play distinct roles in S. aureus colonization, pathogenesis, and bacterial evasion of host immune defenses. Objective We aimed to investigate whether CP interferes with WTA-mediated properties. Methods Strains with natural heterogeneous expression of CP, strains with homogeneous high CP expression and CP-deficient strains were compared to WTA deficient controls regarding WTA dependent phage binding, cell adhesion, IgG deposition, and virulence in vivo . Results WTA-mediated phage adsorption, specific antibody deposition and cell adhesion were negatively correlated with CP expression. WTA, but not CP, enhanced the bacterial burden in a mouse abscess model, while CP overexpression resulted in intermediate virulence in vivo . Conclusions CP protects the bacteria from WTA-dependent opsonization and phage binding. This protection comes at the cost of diminished adhesion to host cells. The highly complex regulation and mostly heterogeneous expression of CP has probably evolved to ensure the survival and optimal physiological adaptation of the bacterial population as a whole.
The Language of 21st Century Skills: Next Directions for Closing the Skills Gap Between Employers and Postsecondary Graduates
2023-07-26

The onus of preparing skilled employees for the modern workforce is largely placed on institutions of higher education. However, recent surveys consistently show a skills gap between what employers’ desire and what graduates possess. This review engages this discussion in the context of measuring and assessing 21st century skills. We begin by succinctly reviewing literature pertaining to the skills gap, including what types of skills are commonly referenced, before moving to examine literature indicating the relations between current 21st century skills and job-related outcomes. Finally, we conclude with recommendations for higher education researchers examining skill development. Our recommendations cover three key corresponding areas: theories of cognitive development, intervention design, measurement and assessment.