julilili42/papers huggingface dataset:
Crosstalk between NFAT and NFκB Signaling Regulates NK Cell Immunosurveillance
2023-11-02

One of the major transcriptional regulators in lymphoid cells is NFAT (Nuclear Factor of Activated T Cells), controlling lymphocyte development and activity. The role of NFAT signaling is well defined in T cells, the cytotoxic lymphocytes of the adaptive immunity. However, surprisingly little is known regarding the relevance of this transcription factor family in NK cells as effector cells of the innate immunity. Available data indicate that NFAT activity is dispensable for development of NK cells, whereas effects of the immunosuppressive drugs cyclosporin A and tacrolimus, that inhibit calcineurin and consecutively NFAT, implicate an involvement of the NFAT family in NK cell function. We here employed different genetic mouse models and functional analyses to unravel the role of NFAT1 (NFATc2) and NFAT2 (NFATc1) in NK cell reactivity. In vitro knockout (KO) of NFAT1 (NFATc2) or NFAT2 (NFATc1) enhanced NK cell degranulation and resulted in increased production of granzyme B and perforin upon stimulation of activating receptors like NK1.1 or Nkp46 or upon co-culture with different leukemia and solid tumor cells. In line, cytotoxicity assays revealed increased lysis of YAC-1 and B16F10 tumor cells by both NFAT1- and NFAT2-deficient NK cells as compared to wildtype (WT) controls. The inhibitory effect of NFAT transcription factors on NK cell effector function could also be confirmed in vivo by employing WT and NFAT KO animals in syngeneic B16F10 melanoma, RMA-S lymphoma and LL/2-luc lung carcinoma models, which revealed a significantly reduced tumor burden in NFAT1 and NFAT2 KO mice. Furthermore, we detected higher numbers of tumor infiltrating NK cells in NFAT KO mice, which suggested improved NK cell migration and homing to the tumor side. Comparative analyses with single NFAT as well as NFAT1+NFAT2 double KO and WT animals further confirmed the inhibitory effect of NFAT1 and NFAT2 and pointed to additive effects of NFAT1 and NFAT2 in NK cell tumor immunosurveillance. Proteomics analysis of NK cells from the different NFAT KO strains revealed altered expression of molecules which are regulating chemokine receptor expression as well as a decreased expression of NFκB inhibitory molecules, like NFKBIB (NFKB inhibitor beta) Commd6 (COMM domain containing 6). NFκB signaling was shown to regulate granzyme B and perforin synthesis and expression. Thus, we suggest that NFAT1 and NFAT2 inhibit NFκB signaling in NK cells, and NFAT1 and NFAT2 KO reinforce NFκB induced granzyme B and perforin expression and thereby increase NK cell cytotoxicity. Taken together, our results identify NFAT as a negative regulator of NK cell function. In addition, we provide the first evidence for a direct functional involvement of NFAT1 and NFAT2 in NK cell antitumor reactivity by regulation tumor infiltration and cytotoxicity of NK cell.
Cross‐linked polysiloxane‐coated stable bond O‐9‐(2,6‐diisopropylphenylcarbamoyl)quinine and quinidine chiral stationary phases as well as application in enantioselective cryo‐HPLC
2023-11-02

Abstract In this work, brush‐type chiral stationary phases (CSPs) with O ‐9‐(2,6‐diisopropylphenylcarbamoyl)‐modified quinidine (DIPPCQD‐brush/‐SH) and O ‐9‐(2,6‐diisopropylphenylcarbamoyl)‐modified quinine (DIPPCQN‐brush/‐SH) were prepared as benchmarks for comparison with new corresponding polymeric CSPs with more stable bonding chemistry. These polymeric CSPs were prepared by coating a thin poly(3‐mercaptopropyl)‐methylsiloxane film together with the chiral selector onto vinyl‐modified silica. In a second step, immobilization of the quinine/quinidine derivatives as well as cross‐linking of the polysiloxane film to the vinyl‐silica is achieved by a double thiol‐ene click reaction. The polymeric CSPs exhibited similar enantioselectivity as the corresponding brush phases, but showed lower chromatographic efficiencies. Chiral acidic substances were separated into enantiomers (e.g., N ‐protected amino acids, herbicides like dichlorprop) in accordance with an enantioselective anion‐exchange process. Oxidation of residual thiol groups of the polymer DIPPCQN‐CSP introduced sulfonic acid co‐ligands on the silica surface, which resulted in greatly reduced retention times. Acting as immobilized counterions, they allowed to reduce the concentration of counterions in the mobile phase, which is favorable for liquid chromatography (LC)–electrospray ionization–mass spectrometry application. Ibuprofen showed a single peak under ambient column temperature. However, application of cryogenic cooling of the column enabled to achieve baseline separation at –20°C column temperature. It can be explained by an enthalpically dominated separation, which leads to an increase in separation factors when the temperature is reduced. While it is quite uncommon to work at subzero degree column temperature, this work illustrates the potential to exploit such temperature regime for optimization of LC enantiomer separations.
Coherent spin-phonon scattering in facilitated Rydberg lattices
2023-11-02

We investigate the dynamics of a spin system with facilitation constraint that can be studied using Rydberg atoms in arrays of optical tweezer traps. The elementary degrees of freedom of the system are domains of Rydberg excitations that expand ballistically through the lattice. Due to mechanical forces, Rydberg excited atoms are coupled to vibrations within their traps. At zero temperature and large trap depth, it is known that virtually excited lattice vibrations only renormalize the timescale of the ballistic propagation. However, when vibrational excitations are initially present -- i.e., when the external motion of the atoms is prepared in an excited Fock state, coherent state or thermal state -- resonant scattering between spin domain walls and phonons takes place. This coherent and deterministic process, which is free from disorder, leads to a reduction of the power-law exponent characterizing the expansion of spin domains. Furthermore, the spin domain dynamics is sensitive to the coherence properties of the atoms' vibrational state, such as the relative phase of coherently superimposed Fock states. Even for a translationally invariant initial state the latter manifests macroscopically in a phase-sensitive asymmetric expansion.
Bayesian real-time classification of multi-messenger electromagnetic and gravitational-wave observations
2023-11-02

Because of the electromagnetic radiation produced during the merger, compact binary coalescences with neutron stars may result in multi-messenger observations. In order to follow up on the gravitational-wave signal with electromagnetic telescopes, it is critical to promptly identify the properties of these sources. This identification must rely on the properties of the progenitor source, such as the component masses and spins, as determined by low-latency detection pipelines in real time. The output of these pipelines, however, might be biased, which could decrease the accuracy of parameter recovery. Machine learning algorithms are used to correct this bias. In this work, we revisit this problem and discuss two new implementations of supervised machine learning algorithms, K-Nearest Neighbors and Random Forest, which are able to predict the presence of a neutron star and post-merger matter remnant in low-latency compact binary coalescence searches across different search pipelines and data sets. Additionally, we present a novel approach for calculating the Bayesian probabilities for these two metrics. Instead of metric scores derived from binary machine learning classifiers, our scheme is designed to provide the astronomy community well-defined probabilities. This would deliver a more direct and easily interpretable product to assist electromagnetic telescopes in deciding whether to follow up on gravitational-wave events in real time.
Language in international human resource management: current state of research and future research directions
2023-11-03

Research on language in international business has grown substantially during the last two decades. However, research that links language to human resource management (HRM) has remained scarce. This is unfortunate because attracting, developing, motivating, and retaining a multilingual workforce is essential for the long-term success of organizations in today's global business world. The present special issue on language in international HRM contributes to tackling this gap. We provide an overview of the current state of research on language in nternational HRM and preview the papers in this special issue. Building on and extending current knowledge, we propose future research directions in terms of 1) a nuanced understanding of HRM functions, 2) language as part of multinational diversity management, 3) consideration of different actors and different contexts, 4) robust theorizing at multiple levels, and 5) more diverse methods to capture complex realities of a multilingual workforce.
The effect of thermal winds on the outbursts evolution of LMXB systems
2023-11-03

ABSTRACT Theoretical models of accretion discs and observational data indicate that the X-ray emission from the inner parts of an accretion disc can irradiate its outer regions and induce a thermal wind, which carries away the mass and angular momentum from the disc. Our aim is to investigate the influence of the thermal wind on the outburst light curves of black hole X-ray binary systems. We carry out numerical simulations of a non-stationary disc accretion with wind using upgraded open code freddi. We assume that the wind launches only from the ionized part of the disc and may turn off if the latter shrinks fast enough. Our estimates of the viscosity parameter α are shifted downward compared to a scenario without a wind. Generally, correction of α depends on the spectral hardness of central X-rays and the disc outer radius, but unlikely to exceed a factor of 10 in the case of a black hole low-mass X-ray binary (BH LMXB). We fit 2002 outburst of BH LMXB 4U 1543 − 47 taking into account the thermal wind. The mass-loss in the thermal wind is of order of the accretion rate on the central object at the peak of the outburst. New estimate of the viscosity parameter α for the accretion disc in this system is about two times lower than the previous one. Additionally, we calculate evolution of the number of hydrogen atoms towards 4U 1543 − 47 due to the thermal wind from the hot disc.
1,25(OH)2D3 inhibits Lewis lung cancer cell migration via NHE1‐sensitive metabolic reprograming
2023-11-03

Abstract High prevalence and metastasis rates are characteristics of lung cancer. Glycolysis provides energy for the development and metastasis of cancer cells. The 1,25‐dihydroxy vitamin D3 (1,25(OH) 2 D 3 ) has been linked to reducing cancer risk and regulates various physiological functions. We hypothesized that 1,25(OH) 2 D 3 could be associated with the expression and activity of Na + /H + exchanger isoform 1 (NHE1) of Lewis lung cancer cells, thus regulating glycolysis as well as migration by actin reorganization. Followed by online public data analysis, Vitamin D3 receptor, the receptor of 1,25(OH) 2 D 3 has been proved to be abundant in lung cancers. We demonstrated that 1,25(OH) 2 D 3 treatment suppressed transcript levels, protein levels, and activity of NHE1 in LLC cells. Furthermore, 1,25(OH) 2 D 3 treatment resets the metabolic balance between glycolysis and OXPHOS, mainly including reducing glycolytic enzymes expression and lactate production. In vivo experiments showed the inhibition effects on tumor growth as well. Therefore, we concluded that 1,25(OH) 2 D 3 could amend the NHE1 function, which leads to metabolic reprogramming and cytoskeleton reconstruction, finally inhibits the cell migration.
Stabilization of Colloidal Germanium Nanoparticles: From the Study to the Prospects of the Application in Thin-Film Technology
2023-11-03

We present the stabilization of halide-terminated Ge nanoparticles prepared via a disproportionation reaction of metastable Ge(I)X solutions with well-defined size distribution. Further tailoring of the stability of the Ge nanoparticles was achieved using variations in the substituent. Ge nanoparticles obtained in this way are readily dispersed in organic solvents, long-term colloidally stable, and are perfect prerequisites for thin-film preparation. This gives these nanomaterials a future in surface-dependent optical applications, as shown for the halide-terminated nanoparticles.
Indistinguishable network dynamics can emerge from unalike plasticity rules
2023-11-04

Synaptic plasticity is thought to be critical for building and maintaining brain circuits. Models of plasticity, or plasticity rules, are typically designed by hand, and evaluated based on their ability to elicit similar neuron or circuit properties to ground truth. While this approach has provided crucial insights into plasticity mechanisms, it is limited in its scope by human intuition and cannot identify all plasticity mechanisms that are consistent with the empirical data of interest. In other words, focusing on individual hand-crafted rules ignores the potential degeneracy of plasticity mechanisms that explain the same empirical data, and may thus lead to inaccurate experimental predictions. Here, we use an unsupervised, adversarial approach to infer plasticity rules directly from neural activity recordings. We show that even in a simple, idealised network model, many mechanistically different plasticity rules are equally compatible with empirical data. Our results suggest the need for a shift in the study of plasticity rules, considering as many degenerate plasticity mechanisms consistent with data as possible, before formulating experimental predictions.
Development and Initial Validation of Two Simulation Workflows Using GATE for a Total-Body PET/CT Scanner
2023-11-04

Monte Carlo simulation studies potentially support understanding and characterizing new total-body PET/CT scanners such as the Biograph Vision Quadra (Siemens Healthineers), which enable a broad field of novel applications. This work aims to develop and validate two simulation workflows using the Geant4 Application for Emission Tomography (GATE). Workflow 1 is designed to model the response of the Biograph Vision Quadra as closely as possible by using a custom readout and digitizer modeling tool with an integrated coincidence sorter. Further, the same image reconstruction is performed as for real scan data with the e7 tools (Siemens Healthineers). Workflow 2 is developed for increased flexibility based on open-source software and the Customizable and Advanced Software for Tomographic Reconstruction (CASToR) code for image reconstruction. Phantom simulation studies were performed to validate the workflows against measurement data. Using the normalization matrix of the real scanner with an adapted calibration factor, Workflow 1 demonstrated an excellent quantification accuracy with differences of less than 1% for three different phantoms. Image quality analysis using an IEC phantom simulation with 60 s scan time showed good agreements of contrast recovery coefficients and lung residual error with experimental data. The anthropomorphic XCAT phantom was used for patient-like simulations. The successful NEMA-NU validation of the simulation workflows will enable the investigation of scenarios which practically cannot be tested on patients. Further, the generation of training and validation data sets including simulation ground truth data for machine learning algorithms will be enabled.
Migration in Times of Pandemic: Mark Twain’s “3,000 Years Among the Microbes” and the Prospect of Planetary Health
2023-11-04

Mark Twain’s novel fragment “3, 000 Years Among the Microbes” (1905) tells the story of the formerly human, now microbial protagonist “Huck” Bkshp. Huck reports from the retrospective of three thousand years of microbial time on the challenges of existence as a microbe in the body of the Hungarian immigrant and “tramp” Blitzowski. Migration and epi- and pandemic events enter into an often-fatal relationship. For many migrants, the desolate health care systems of their home countries were often one of the reasons for leaving in the first place. However, both during transit and on arrival at their destinations, they are exposed to no less precarious situations. Moreover, they are often perceived as a threat themselves. Against the backdrop of the lived pandemic experience of nineteenth-century cholera, Twain’s text depicts the hardships of migration in a literary original way and thus can be read as a paradigmatic literary manifest for the meeting point of transnational American studies and the Medical Humanities. In Twain’s novel fragment, the human-microbial protagonist Huck carries cholera, one of the deadliest pandemic threats of the nineteenth century. When immigrating into his host’s immigrant body, Blitzowski, he also becomes a carrier of the disease. That migrants bring fatal diseases is a topos not only in the (hi-)story of American immigration. Border closures and entry bans are often the first measures during disease outbreaks. However, epi- and pandemics cannot be excluded. As the impossibility of containment is a central topic of Twain’s narrative, I argue, it also can be seen as an early imagination of the emerging concept of “Planetary Health,” which, especially by focusing on recent microbiome research, rethinks the entanglements of human and more-than-human migrations in the face of current and future states of crisis.
Cultural use of tropane alkaloids ofBrugmansiaspecies and cultivars in Colombia depends on local plant growth environment rather than genetic diversity
2023-11-04

Abstract Borracheros or Angel Trumpets ( Brugmansia spp.) of the Solanaceae plant family are known for producing scopolamine and other tropane alkaloids and are widely used by indigenous communities in the Andes for medicinal and ritual purposes. Growing different varieties has increased the popularity of Brugmansia species in recent years, leading to the promotion of hybridization to get new morphotypes. However, so far no medical or cultural use of plant extracts could be linked to selected Brugmansia species or cultivars. Moreover, until now there is only limited knowledge about the effect of hybridization on tropane alkaloid contents and/or diversity of Brugmansia species or cultivars. Here, a liquid chromatography-mass spectrometry (LC-MS) approach was applied to identify and characterize secondary metabolite contents in various Brugmansia species and hybrids from different geographic origins in Colombia. The analysis of the metabolic data sets revealed that tropane alkaloids and other secondary metabolites accumulate in a leaf and flower specific manner. Although some minor differences were found between Brugmansia subgroups, the only significant difference exists between plants collected in the Sibundoy Valley, where they have been domesticated by indigenous communities since a long time and those, which so far have not been used by humans at all. The different genetic constitutions of Brugmancia species and cultivars are not the dominating reason for their differences in tropane alkaloid contents and medical and cultural usages, as there is no clear taxonomical signature based on the metabolite properties for species segregation. Instead, their use by indigenous communities during ceremonies and for medical treatment such as wound healing, infection control, rheumatism and arthritis is rather caused by the plasticity of the individual plants to react to the local abiotic and biotic environments by the variation of secondary metabolite composition and by the differences in the bioavailability of the active compounds as result of the extraction method.
SegCODEBRIM:
2023-11-04

&amp;lt;p&amp;gt;&amp;lt;strong&amp;gt;SegCODEBRIM: COncrete DEfect BRidge IMage Dataset for semantic Segmentation of &amp;nbsp;concrete cracks&amp;lt;/strong&amp;gt;. The images were taken from the CODEBRIM (https://zenodo.org/records/2620293) dataset and annotated manually.&amp;nbsp;&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;&amp;nbsp;&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;&amp;nbsp;&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;Dataset is presented and detailed in our WACV 2024 publication: https://arxiv.org/abs/2309.09637v1&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;&amp;nbsp;&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;. If you make use of the dataset &amp;lt;strong&amp;gt;please cite it as follows&amp;lt;/strong&amp;gt;:&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;&amp;lt;strong&amp;gt;"Achref Jaziri, Martin Mundt, Andres Fernandez Rodriguez, Visvanathan Ramesh. Designing a Hybrid Neural System to Learn Real-world Crack Segmentation from Fractal-based Simulation. IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), 2024"&amp;lt;/strong&amp;gt;&amp;lt;/p&amp;gt;&amp;lt;p&amp;gt;This GitHub repository presents the code to reproduce the paper results and data loaders: https://github.com/achrefjaziri/SimCrack&amp;lt;/p&amp;gt;
SegCODEBRIM:
2023-11-05

SegCODEBRIM: COncrete DEfect BRidge IMage Dataset for semantic Segmentation of concrete cracks. The images were taken from the CODEBRIM (https://zenodo.org/records/2620293) dataset and annotated manually. Dataset is presented and detailed in our WACV 2024 publication: https://arxiv.org/abs/2309.09637v1 . If you make use of the dataset please cite it as follows: "Achref Jaziri, Martin Mundt, Andres Fernandez Rodriguez, Visvanathan Ramesh. Designing a Hybrid Neural System to Learn Real-world Crack Segmentation from Fractal-based Simulation. IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), 2024" This GitHub repository presents the code to reproduce the paper results and data loaders: https://github.com/achrefjaziri/SimCrack
Phenotypic similarity-based approach for variant prioritization for unsolved rare disease: a preliminary methodological report
2023-11-06

Abstract Rare diseases (RD) have a prevalence of not more than 1/2000 persons in the European population, and are characterised by the difficulty experienced in obtaining a correct and timely diagnosis. According to Orphanet, 72.5% of RD have a genetic origin although 35% of them do not yet have an identified causative gene. A significant proportion of patients suspected to have a genetic RD receive an inconclusive exome/genome sequencing. Working towards the International Rare Diseases Research Consortium (IRDiRC)’s goal for 2027 to ensure that all people living with a RD receive a diagnosis within one year of coming to medical attention, the Solve-RD project aims to identify the molecular causes underlying undiagnosed RD. As part of this strategy, we developed a phenotypic similarity-based variant prioritization methodology comparing submitted cases with other submitted cases and with known RD in Orphanet. Three complementary approaches based on phenotypic similarity calculations using the Human Phenotype Ontology (HPO), the Orphanet Rare Diseases Ontology (ORDO) and the HPO-ORDO Ontological Module (HOOM) were developed; genomic data reanalysis was performed by the RD-Connect Genome-Phenome Analysis Platform (GPAP). The methodology was tested in 4 exemplary cases discussed with experts from European Reference Networks. Variants of interest (pathogenic or likely pathogenic) were detected in 8.8% of the 725 cases clustered by similarity calculations. Diagnostic hypotheses were validated in 42.1% of them and needed further exploration in another 10.9%. Based on the promising results, we are devising an automated standardized phenotypic-based re-analysis pipeline to be applied to the entire unsolved cases cohort.