julilili42/papers huggingface dataset:
Magnetic equilibria of relativistic axisymmetric stars: The impact of flow constants
2023-10-03

Symmetries and conservation laws associated with the ideal Einstein-Euler system, for stationary and axisymmetric stars, can be utilized to define a set of flow constants. These quantities are conserved along flow lines in the sense that their gradients are orthogonal to the four-velocity. They are also conserved along surfaces of constant magnetic flux, making them powerful tools to identify general features of neutron star equilibria. One important corollary of their existence is that mixed poloidal-toroidal fields are inconsistent with the absence of meridional flows except in some singular sense, a surprising but powerful result first proven by Bekenstein and Oron. In this work, we revisit the flow constant formalism to rederive this result together with several new ones concerning both nonlinear and perturbative magnetic equilibria. Our investigation is supplemented by some numerical solutions for multipolar magnetic fields on top of a Tolman-VII background, where strict power-counting of the flow constants is used to ensure a self-consistent treatment.
Establishing an online resource to facilitate global collaboration and inclusion of underrepresented populations: Experience from the MJFF Global Genetic Parkinson’s Disease Project
2023-10-03

Parkinson’s disease (PD) is the fastest-growing neurodegenerative disorder, currently affecting ~7 million people worldwide. PD is clinically and genetically heterogeneous, with at least 10% of all cases explained by a monogenic cause or strong genetic risk factor. However, the vast majority of our present data on monogenic PD is based on the investigation of patients of European White ancestry, leaving a large knowledge gap on monogenic PD in underrepresented populations. Gene-targeted therapies are being developed at a fast pace and have started entering clinical trials. In light of these developments, building a global network of centers working on monogenic PD, fostering collaborative research, and establishing a clinical trial-ready cohort is imperative. Based on a systematic review of the English literature on monogenic PD and a successful team science approach, we have built up a network of 59 sites worldwide and have collected information on the availability of data, biomaterials, and facilities. To enable access to this resource and to foster collaboration across centers, as well as between academia and industry, we have developed an interactive map and online tool allowing for a quick overview of available resources, along with an option to filter for specific items of interest. This initiative is currently being merged with the Global Parkinson’s Genetics Program (GP2), which will attract additional centers with a focus on underrepresented sites. This growing resource and tool will facilitate collaborative research and impact the development and testing of new therapies for monogenic and potentially for idiopathic PD patients.
TopDownApp: An open and modular platform for analysis and visualisation of top‐down proteomics data
2023-10-03

Abstract Although Top‐down (TD) proteomics techniques, aimed at the analysis of intact proteins and proteoforms, are becoming increasingly popular, efforts are needed at different levels to generalise their adoption. In this context, there are numerous improvements that are possible in the area of open science practices, including a greater application of the FAIR (Findable, Accessible, Interoperable, and Reusable) data principles. These include, for example, increased data sharing practices and readily available open data standards. Additionally, the field would benefit from the development of open data analysis workflows that can enable data reuse of public datasets, something that is increasingly common in other proteomics fields.
De-suppression of mesenchymal cell identities and variable phenotypic outcomes associated with knockout ofBbs1
2023-10-03

Abstract Bardet-Biedl syndrome (BBS) is an archetypal ciliopathy caused by dysfunction of primary cilia. BBS affects multiple tissues, including the kidney, eye and hypothalamic satiety response. Understanding pan-tissue mechanisms of pathogenesis versus those which are tissue specific, and gauging their associated inter-individual variation owing to genetic background and stochastic processes, is of paramount importance in syndromology. The BBSome is a membrane trafficking and intraflagellar transport (IFT) adaptor protein complex formed by 8 BBS proteins, including BBS1, which is the most commonly mutated gene in BBS. To investigate disease pathogenesis we generated a series of clonal renal collecting duct IMCD3 cell lines carrying defined biallelic nonsense or frameshift mutations in Bbs1 , as well as a panel of matching wild-type CRISPR control clones. Using a phenotypic screen and an unbiased multi-omics approach we note significant clonal variability for all assays, emphasising the importance of analysing panels of genetically-defined clones. Our results suggest that BBS1 is required for suppression of mesenchymal cell identities as IMCD3 cell passage number increases. This was associated with a failure to express epithelial cell markers and tight junction formation, which was variable amongst clones. Transcriptomic analysis of hypothalamic preparations from BBS mutant mice, and BBS patient fibroblasts, suggested that dysregulation of epithelial-to-mesenchymal transition (EMT) genes is a general predisposing feature of BBS across tissues. Collectively this work suggests that the dynamic stability of the BBSome is essential for suppression of mesenchymal cell identities as epithelial cells differentiate.
Species identification and drug susceptibility testing of non-tuberculous mycobacteria by Line Probe Assay in Lambaréné, Gabon—a cross-sectional study
2023-10-03

Abstract Background Non-tuberculous mycobacteria (NTM) are a group of bacteria that cause rare lung infections and are increasingly recognized as causative agents of opportunistic and device-associated infections in humans. In Gabon, there is a lack of data on NTM species identification and drug susceptibility. The aim of this study was to identify the frequency of NTM species and their genotypic susceptibility pattern to commonly used antibiotics for NTM infections in Gabon. Methods A cross-sectional study was conducted at the CERMEL TB laboratory from January 2020 to December 2022, NTM subspecies identification and drug susceptibility testing to macrolides and aminoglycosides were performed using the genotype NTM-DR kit. Results The study found that out of 524 culture-positive specimens, 146 (28%) were NTM, with the predominant group being Mycobacterium avium complex (MAC) and Mycobacterium abscessus complex (MABC). All MAC isolates were fully susceptible to macrolides and aminoglycosides, while five MABC isolates carried mutations indicative of reduced susceptibility to macrolide and aminoglycoside drugs. Conclusions These findings suggest that clinicians may use macrolides and aminoglycosides to manage NTM infections caused by MAC, but further investigation is required to determine MABC drug susceptibility.
Longitudinal national evidence that social media use did not drive climate skepticism and polarization in the 2010s
2023-10-03

The global rise of social media has profoundly changed the ways in which citizens search for information; yet there is still uncertainty regarding the extent to which this societal transformation should be a cause for concern. One popular notion holds that the rise of social media in the 2010s contributed to the proliferation of climate skeptic and polarized beliefs. However, extant evidence relies predominantly on (repeated and one-shot) cross-sectional studies. Here, we leverage a longitudinal national panel survey unique to New Zealand that tracked social media use and climate change beliefs consistently among the same citizens (N=3.611) across four annual waves (2011-2014; wave-to-wave retention rates: &amp;gt; 80%). Results revealed that first, climate change belief trajectories were consistently positive (becoming less skeptical), regardless of whether citizens were Facebook users or non-users; speaking against the notion that social media use fostered climate skeptic beliefs. Second, Facebook users who were initially more skeptical tended to increase more in their climate change beliefs compared to Facebook users who were initially less skeptic; effectively reducing (vs. exacerbating) polarization. These results were robust for both beliefs in the reality, and the human cause of climate change; across different operationalizations of social media use; and held despite consistent evidence for the politicization of climate change in New Zealand during the study period. This evidence challenges the notion that the global rise of social media in the 2010s exacerbated climate skepticism and polarization.
EuCARE-HOSPITALISED Study Protocol: A Cohort Study of Patients Hospitalised with COVID-19 in the EuCARE Project
2023-10-03

Abstract Background. Severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19), can lead to hospitalisation, particularly in elderly, immunocompromised, and non-vaccinated or partially vaccinated individuals. Although vaccination provides protection, the duration of this protection wanes over time. Additional doses can restore immunity, but the influence of viral variants, specific sequences, and vaccine-induced immune responses on disease severity remains unclear. Moreover, the efficacy of therapeutic interventions during hospitalisation requires further investigation. The study aims to analyse the clinical course of COVID-19 in hospitalised patients, taking into account SARS-CoV-2 variants, viral sequences, and the impact of different vaccines. The primary outcome is all-cause in-hospital mortality, while secondary outcomes include admission to intensive care unit and length of stay, duration of hospitalisation, and the level of respiratory support required. Methods. This ongoing multicentre study observes hospitalised adult patients with confirmed SARS-CoV-2 infection, utilising a combination of retrospective and prospective data collection. It aims to gather clinical and laboratory variables from around 35,000 patients, with potential for a larger sample size. Data analysis will involve biostatistical and machine-learning techniques. Selected patients will provide biological material. The study started on October 14, 2021 and is scheduled to end on October 13, 2026. Discussion. The analysis of a large sample of retrospective and prospective data about the acute phase of SARS CoV-2 infection in hospitalised patients, viral variants and vaccination in several European and non-European countries will help us to better understand risk factors for disease severity and the interplay between SARS CoV-2 variants, immune responses and vaccine efficacy. The main strengths of this study are the large sample size, the long study duration covering different waves of COVID-19 and the collection of biological samples that allows future research. Registration . The trial has been registered on ClinicalTrials.gov. The unique identifier assigned to this trial is NCT05463380.
Multimodal profiling of peripheral blood identifies proliferating circulating effector CD4+T cells as predictors for response to integrin α4β7-blocking therapy in patients with inflammatory bowel disease
2023-10-03

ABSTRACT Despite the success of biological therapies in inflammatory bowel disease (IBD), patient management remains challenging due to a lack of therapy response predictors. Here we prospectively sampled two cohorts of IBD patient cohorts receiving the anti-integrin α4β7 antibody vedolizumab. Samples were subjected to mass cytometry, single-cell RNA sequencing, single-cell V(D)J sequencing, serum proteomics, and multidimensional flow cytometry to comprehensively assess vedolizumab-induced immunological changes in the peripheral blood and their potential associations with treatment response. Vedolizumab induced changes in the abundance of both circulating innate and adaptive immune cell compartments and modified the T cell receptor diversity of circulating gut-homing CD4 + memory T cells. Through integration of multimodal parameters and machine learning, we identify that pretreatment activated proliferating CD4 + memory T cell abundance is associated with treatment failure, independent of clinical variables, thereby providing a reliable predictive classifier with significant implications for the personalized management of IBD patients.
On a Derivation of the Absorbing Boundary Rule
2023-10-03

Consider detectors waiting for a quantum particle to arrive at a surface in 3-space. For predicting the probability distribution of the time and place of detection, a rule was proposed in [arXiv:1601.03715], called the absorbing boundary rule (ABR) and involving a 1-particle Schrödinger equation with an absorbing boundary condition on . While plausibility arguments for the ABR were given there, it would be desirable to derive the ABR from a microscopic model of a detector. We outline here such a derivation by putting together known results from the literature. Our derivation is non-rigorous, and it would still be desirable to have a rigorous version of it in the future.
Jasmonates and salicylic acid: Evolution of defense hormones in land plants
2023-10-04

The emergence of plant hormone signaling pathways is deeply intertwined with land plant evolution. In angiosperms, two plant hormones, salicylic Acid (SA) and Jasmonates (JAs), play a key role in plant defense, where JAs-mediated defenses are typically activated in response to herbivores and necrotrophic pathogens, whereas SA is prioritized against hemi/biotrophic pathogens. Thus, studying the evolution of SA and JAs and their crosstalk is essential to understand the evolution of molecular plant-microbe interactions (EvoMPMI) in land plants. Recent advances in the evolution of SA and JAs biosynthesis, signaling, and crosstalk in land plants illustrated that the insight gained in angiosperms does not necessarily apply to non-seed plant lineages, where the receptors perceive different ligands and the hormones activate pathways independently on the canonical receptors. In this review, recent findings on the two main defense hormones (JAs and SA) in non-seed plants, including functional studies in the bryophyte model Marchantia polymorpha, will be discussed.
Ballistic macroscopic fluctuation theory
2023-10-04

We introduce a new universal framework describing fluctuations and correlations in quantum and classical many-body systems, at the Euler hydrodynamic scale of space and time. The framework adapts the ideas of the conventional macroscopic fluctuation theory (MFT) to systems that support ballistic transport. The resulting “ballistic MFT” (BMFT) is solely based on the Euler hydrodynamics data of the many-body system. Within this framework, mesoscopic observables are classical random variables depending only on the fluctuating conserved densities, and Euler-scale fluctuations are obtained by deterministically transporting thermodynamic fluctuations via the Euler hydrodynamics. Using the BMFT, we show that long-range correlations in space generically develop over time from long-wavelength inhomogeneous initial states in interacting models. This result, which we verify by numerical calculations, challenges the long-held paradigm that at the Euler scale, fluid cells may be considered uncorrelated. We also show that the Gallavotti-Cohen fluctuation theorem for non-equilibrium ballistic transport follows purely from time-reversal invariance of the Euler hydrodynamics. We check the validity of the BMFT by applying it to integrable systems, and in particular the hard-rod gas, with extensive simulations that confirm our analytical results.
The geoeconomics of infrastructures: viewing globalization and global rivalry through a lens of infrastructural competition
2023-10-04

ABSTRACTIn the current triad competition between the US, the EU, and China, globalization-relevant infrastructures serve both as the means and ends of conflicts. This paper asks how this historical constellation of geoeconomic competition has changed the infrastructure policy of its centers. Its political-economic perspective discusses infrastructures not just in terms of their strategic instrumentalization, but also of their role in global production and geoeconomic competition. It underlines how infrastructures serve as fixes that counteract internal crisis dynamics and allow for an expansion of productive activity. The paper undertakes an empirical comparison of the triad centers' central infrastructural measures and flagship projects. The results highlight a shared reorientation towards infrastructure policy that is driven by internal crisis dynamics and external competition over contested markets. Yet, it also reveals the varieties of infrastructural approaches as regards political objectives, modes of policy-making, and the role of national businesses.KEYWORDS: BRIglobalizationinfrastructuregeoeconomicsgeopoliticsGlobal Gateway Disclosure statementNo potential conflict of interest was reported by the author(s).Additional informationNotes on contributorsJoscha AbelsJoscha Abels is researcher and lecturer at the Institute of Political Science, University of Tübingen. His main focus is on topics of International Political Economy and European Integration. Specific research interests lie in the fields of geoeconomics, infrastructure policy, international institutions, and the political economy of the Economic and Monetary Union. He has contributed to journals such as Competition & Change, Comparative European Politics, and European Politics and Society.Hans-Jürgen BielingHans-Jürgen Bieling is Professor of Political Economy at the Institute of Political Science, University of Tübingen. His main focus is on topics of International Political Economy and European Integration. Specific research interests lie in the fields of financial markets, labour relations, right-wing populism, geoeconomics, and infrastructure policy. He has contributed to journals such as Journal of Common Market Studies, Journal of European Public Policy, and New Political Economy.
Noninvasive and invasive imaging of lower-extremity acute and chronic venous thrombotic disease
2023-10-04

The spectrum of venous thromboembolic (VTE) disease encompasses both acute deep venous thrombosis (DVT) and chronic postthrombotic changes (CPC). A large percentage of acute DVT patients experience recurrent VTE despite adequate anticoagulation, and may progress to CPC. Further, the role of iliocaval venous obstruction (ICVO) in lower-extremity VTE has been increasingly recognized in recent years. Imaging continues to play an important role in both acute and chronic venous disease. Venous duplex ultrasound remains the gold standard for diagnosing acute VTE. However, imaging of CPC is more complex and may involve computed tomography, magnetic resonance, contrast-enhanced ultrasound, or intravascular ultrasound. In this narrative review, we aim to discuss the full spectrum of venous disease imaging for both acute and chronic venous thrombotic disease.
Braincase and neuroanatomy of the lagerpetid Dromomeron gregorii (Archosauria, Pterosauromorpha) with comments on the early evolution of the braincase and associated soft tissues in Avemetatarsalia
2023-10-04

Abstract The anatomy of the braincase and associated soft tissues of the lagerpetid Dromomeron gregorii (Archosauria: Avemetatarsalia) from the Late Triassic of the United States is here described. This corresponds to the first detailed description of cranial materials of Lagerpetidae, an enigmatic group of Late Triassic (c. 236–200 Million years ago) animals that are the closest known relatives of pterosaurs, the flying reptiles. The braincase of D. gregorii is characterized by the presence of an anteriorly elongated laterosphenoid and a postparietal, features observed in stem‐archosaurs but that were still unknown in early members of the avian lineage of archosaurs. Using micro‐computed tomography (CT‐scan data), we present digital reconstructions of the brain and endosseous labyrinth of D. gregorii . The brain of D. gregorii exhibits a floccular lobe of the cerebellum that projects within the space of the semicircular canals. The semicircular canals are relatively large when compared to other archosauromorphs, with the anterior canal exhibiting a circular shape. These features of the sensory structures of D. gregorii are more similar to those of pterosaurs than to those of other early avemetatarsalians. In sum, the braincase anatomy of D. gregorii shows a combination of plesiomorphic and apomorphic features in the phylogenetic context of Archosauria and suggests that the still poorly understood early evolution of the braincase in avemetatarsalians is complex, with a scenario of independent acquisitions and losses of character states.
Distribution of corpora amylacea in the human midbrain: using synchrotron radiation phase-contrast microtomography, high-field magnetic resonance imaging, and histology
2023-10-04

Corpora amylacea (CA) are polyglucosan aggregated granules that accumulate in the human body throughout aging. In the cerebrum, CA have been found in proximity to ventricular walls, pial surfaces, and blood vessels. However, studies showing their three-dimensional spatial distribution are sparse. In this study, volumetric images of four human brain stems were obtained with MRI and phase-contrast X-ray microtomography, followed up by Periodic acid Schiff stain for validation. CA appeared as hyperintense spheroid structures with diameters up to 30 μm. An automatic pipeline was developed to segment the CA, and the spatial distribution of over 200,000 individual corpora amylacea could be investigated. A threefold—or higher—density of CA was detected in the dorsomedial column of the periaqueductal gray (860–4,200 CA count/mm 3 ) than in the superior colliculus (150–340 CA count/mm 3 ). We estimated that about 2% of the CA were located in the immediate vicinity of the vessels or in the peri-vascular space. While CA in the ependymal lining of the cerebral aqueduct was rare, the sub-pial tissue of the anterior and posterior midbrain contained several CA. In the sample with the highest CA density, quantitative maps obtained with MRI revealed high R2 * values and a diamagnetic shift in a region which spatially coincided with the CA dense region.