julilili42/papers huggingface dataset:
Shear-Wave-Elastography in Neurofibromatosis Type I
2022-01-31

Ultrasound shear wave elastography (SWE) is an increasingly used imaging modality that expands clinical ultrasound by measuring the elasticity of various tissues, such as the altered elasticity of tumors. Peripheral nerve tumors are rare, have been well-characterized by B-mode-ultrasound, but have not yet been investigated with SWE. Given the lack of studies, a first step would be to investigate homogeneous peripheral nerve tumors (PNTs), histologically neurofibromas or schwannomas, which can occur in multiple in neurofibromatosis type 1 and 2 (NF1 and 2), respectively. Hence, we measured shear wave velocity (SWV) in 30 PNTs of 11 patients with NF1 within the median nerve. The SWV in PNTs ranged between 2.8 ± 0.8 m/s and correlated with their width and approximate volume but not with their length or height. Furthermore, we determined the extent to which PNTs alter the SWV of the median nerve for three positions of the wrist joint: neutral (zero-degree), individual maximal flexion and maximal extension. Here, SWV was decreased in NF1 patients compared to age- and sex-matched controls (p = 0.029) during maximal wrist extension. We speculate that the presence of PNTs may have a biomechanical impact on peripheral nerves which has not been demonstrated yet.
Spatial Venomics - Cobra Venom System Reveals Spatial Differentiation of Snake Toxins by Mass Spectrometry Imaging
2022-01-31

Abstract Among venomous animals, toxic secretions have evolved as biochemical weapons associated with various highly specialized delivery systems on many occasions. Despite extensive research, there is still limited knowledge of the functional biology of most animal toxins, including their venom production and storage, as well as the morphological structures within sophisticated venom producing tissues that might underpin venom modulation. Here we report on the spatial exploration of a snake venom gland system by matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI), in combination with standard proteotranscriptomic approaches, to enable in situ toxin mapping in spatial intensity maps across a venom gland sourced from the Egyptian cobra ( Naja haje ). MALDI-MSI toxin visualization on the elapid venom gland reveals high spatial heterogeneity of different toxin classes at the proteoform level, which may be the result of physiological constraints on venom production and/or storage that reflects the potential for venom modulation under diverse stimuli.
Modeling Dynamic Personality Theories in a Continuous-time Framework: An Illustration
2022-01-31

Personality psychology has traditionally focused on stable between-person differences. Yet, recent theoretical developments and empirical insights have led to a new conceptualization of personality as a dynamic system (e.g., Cybernetic Big Five Theory). Such dynamic systems comprise several components that need to be conceptually distinguished and mapped to a statistical model for estimation. In the current work, we illustrate how common components from these new dynamic personality theories may be implemented in a continuous-time modeling framework. As an empirical example, we use experience sampling data from N = 180 persons (with on average T = 40 [SD = 8] measurement occasions) to investigate four different effects between momentary happiness, momentary extraverted behavior, and the perception of a situation as social: (1) between-person effects, (2) contemporaneous effects, (3) autoregressive effects, and (4) cross-lagged effects. We highlight that these four effects must not necessarily point in the same direction, which is in line with assumptions from dynamic personality theories.
Young Exoplanet Transit Initiative follow-up observations of the T Tauri star CVSO 30 with transit-like dips
2022-01-31

ABSTRACT The T Tauri star CVSO 30, also known as PTFO 8-8695, was studied intensively with ground-based telescopes as well as with satellites over the last decade. It showed a variable light curve with additional repeating planetary transit-like dips every ∼10.8 h. However, these dimming events changed in depth and duration since their discovery and from autumn 2018 on, they were not even present or near the predicted observing times. As reason for the detected dips and their changes within the complex light curve, e.g. a disintegrating planet, a circumstellar dust clump, stellar spots, possible multiplicity, and orbiting clouds at a Keplerian co-rotating radius were discussed and are still under debate. In this paper, we present additional optical monitoring of CVSO 30 with the meter class telescopes of the Young Exoplanet Transit Initiative in Asia and Europe over the last 7 yr and characterize CVSO 30 with the new Early Data Release 3 of the European Space Agency-Gaia mission. As a result, we describe the evolution of the dimming events in the optical wavelength range since 2014 and present explanatory approaches for the observed variabilities. We conclude that orbiting clouds of gas at a Keplerian co-rotating radius are the most promising scenario to explain most changes in CVSO 30’s light curve.
Osvaldo Cavallar / Julius Kirshner, Jurists and Jurisprudence in Medieval Italy. Texts and Contexts. (Toronto Studies in Medieval Law.) Toronto, ON, University of Toronto Press 2020
2022-01-31

Article Osvaldo Cavallar / Julius Kirshner, Jurists and Jurisprudence in Medieval Italy. Texts and Contexts. (Toronto Studies in Medieval Law.) Toronto, ON, University of Toronto Press 2020 was published on February 1, 2022 in the journal Historische Zeitschrift (volume 314, issue 1).
Genetic and epigenetic differentiation across intertidal gradients in the foundation plant Spartina alterniflora
2022-01-31

This record contains supplementary information for the article "Genetic and epigenetic differentiation across intertidal gradients in the foundation plant Spartina alterniflora". It contains the barcodes (barcodes.txt), the reference contigs (contigs.fasta.gz), the annotation of the reference contigs (mergedAnnot.csv.gz), the SNPs (snps.vcf.gz), the methylation data (methylation.txt.gz), and the experimental design (design.txt). All data are unfiltered. All reads are available on SRA (PRJNA798549). Note that the barcode sequences and the control nucleotide were already removed from the demultiplexed files (hence, for each sample, reads are also split into "watson" and "crick" based on the control nucleotide).
Eryptosis: Programmed Death of Nucleus-Free, Iron-Filled Blood Cells
2022-02-01

Human erythrocytes are organelle-free cells packaged with iron-containing hemoglobin, specializing in the transport of oxygen. With a total number of approximately 25 trillion cells per individual, the erythrocyte is the most abundant cell type not only in blood but in the whole organism. Despite their low complexity and their inability to transcriptionally upregulate antioxidant defense mechanisms, they display a relatively long life time, of 120 days. This ensures the maintenance of tissue homeostasis where the clearance of old or damaged erythrocytes is kept in balance with erythropoiesis. Whereas the regulatory mechanisms of erythropoiesis have been elucidated over decades of intensive research, the understanding of the mechanisms of erythrocyte clearance still requires some refinement. Here, we present the main pathways leading to eryptosis, the programmed death of erythrocytes, with special emphasis on Ca2+ influx, the generation of ceramide, oxidative stress, kinase activation, and iron metabolism. We also compare stress-induced erythrocyte death with erythrocyte ageing and clearance, and discuss the similarities between eryptosis and ferroptosis, the iron-dependent regulated death of nucleated blood cells. Finally, we focus on the pathologic consequences of deranged eryptosis, and discuss eryptosis in the context of different infectious diseases, e.g., viral or parasitic infections, and hematologic disorders.
Four-color single-molecule imaging with engineered tags resolves the molecular architecture of signaling complexes in the plasma membrane
2022-02-01

Localization and tracking of individual receptors by single-molecule imaging opens unique possibilities to unravel the assembly and dynamics of signaling complexes in the plasma membrane. We present a comprehensive workflow for imaging and analyzing receptor diffusion and interaction in live cells at single molecule level with up to four colors. Two engineered, monomeric GFP variants, which are orthogonally recognized by anti-GFP nanobodies, are employed for efficient and selective labeling of target proteins in the plasma membrane with photostable fluorescence dyes. This labeling technique enables us to quantitatively resolve the stoichiometry and dynamics of the interferon-γ (IFNγ) receptor signaling complex in the plasma membrane of living cells by multicolor single-molecule imaging. Based on versatile spatial and spatiotemporal correlation analyses, we identify ligand-induced receptor homo- and heterodimerization. Multicolor single-molecule co-tracking and quantitative single-molecule Förster resonance energy transfer moreover reveals transient assembly of IFNγ receptor heterotetramers and confirms its structural architecture.
A Review of the EUSO-Balloon Pathfinder for the JEM-EUSO Program
2022-02-01

Abstract EUSO-Balloon is a pathfinder for JEM-EUSO , the mission concept of a spaceborne observatory which is designed to observe Ultra-High Energy Cosmic Ray (UHECR)-induced Extensive Air Showers (EAS) by detecting their UltraViolet (UV) light tracks “from above.” On August 25, 2014, EUSO-Balloon was launched from Timmins Stratospheric Balloon Base (Ontario, Canada) by the balloon division of the French Space Agency CNES. After reaching a floating altitude of 38 km, EUSO-Balloon imaged the UV light in the wavelength range ∼290–500 nm for more than 5 hours using the key technologies of JEM-EUSO . The flight allowed a good understanding of the performance of the detector to be developed, giving insights into possible improvements to be applied to future missions. A detailed measurement of the photoelectron counts in different atmospheric and ground conditions was achieved. By means of the simulation of the instrument response and by assuming atmospheric models, the absolute intensity of diffuse light was estimated. The instrument detected hundreds of laser tracks with similar characteristics to EASs shot by a helicopter flying underneath. These are the first recorded laser tracks measured from a fluorescence detector looking down on the atmosphere. The reconstruction of the direction of the laser tracks was performed. In this work, a review of the main results obtained by EUSO-Balloon is presented as well as implications for future space-based observations of UHECRs.
The impact of molecular data on the phylogenetic position of the putative oldest crown crocodilian and the age of the clade
2022-02-01

The use of molecular data for living groups is vital for interpreting fossils, especially when morphology-only analyses retrieve problematic phylogenies for living forms. These topological discrepancies impact on the inferred phylogenetic position of many fossil taxa. In Crocodylia, morphology-based phylogenetic inferences differ fundamentally in placing Gavialis basal to all other living forms, whereas molecular data consistently unite it with crocodylids. The Cenomanian Portugalosuchus azenhae was recently described as the oldest crown crocodilian, with affinities to Gavialis , based on morphology-only analyses, thus representing a potentially important new molecular clock calibration . Here, we performed analyses incorporating DNA data into these morphological datasets, using scaffold and supermatrix (total evidence) approaches, in order to evaluate the position of basal crocodylians, including Portugalosuchus . Our analyses incorporating DNA data robustly recovered Portugalosuchus outside Crocodylia (as well as thoracosaurs, planocraniids and Borealosuchus spp.), questioning the status of Portugalosuchus as crown crocodilian and any future use as a node calibration in molecular clock studies. Finally, we discuss the impact of ambiguous fossil calibration and how, with the increasing size of phylogenomic datasets, the molecular scaffold might be an efficient (though imperfect) approximation of more rigorous but demanding supermatrix analyses.
Looking through the windows: a study about the dependency of phase-coupling estimates on the data length
2022-02-01

Abstract Objective . Being able to characterize functional connectivity (FC) state dynamics in a real-time setting, such as in brain–computer interface, neurofeedback or closed-loop neurostimulation frameworks, requires the rapid detection of the statistical dependencies that quantify FC in short windows of data. The aim of this study is to characterize, through extensive realistic simulations, the reliability of FC estimation as a function of the data length. In particular, we focused on FC as measured by phase-coupling (PC) of neuronal oscillations, one of the most functionally relevant neural coupling modes. Approach . We generated synthetic data corresponding to different scenarios by varying the data length, the signal-to-noise ratio (SNR), the phase difference value, the spectral analysis approach (Hilbert or Fourier) and the fractional bandwidth. We compared seven PC metrics, i.e. imaginary part of phase locking value (iPLV), PLV of orthogonalized signals, phase lag index (PLI), debiased weighted PLI, imaginary part of coherency, coherence of orthogonalized signals and lagged coherence. Main results . Our findings show that, for a SNR of at least 10 dB, a data window that contains 5–8 cycles of the oscillation of interest (e.g. a 500–800 ms window at 10 Hz) is generally required to achieve reliable PC estimates. In general, Hilbert-based approaches were associated with higher performance than Fourier-based approaches. Furthermore, the results suggest that, when the analysis is performed in a narrow frequency range, a larger window is required. Significance . The achieved results pave the way to the introduction of best-practice guidelines to be followed when a real-time frequency-specific PC assessment is at target.
The Paracaspase MALT1 in Cancer
2022-02-01

Almost twenty years ago, the importance of the paracaspase MALT1 in antigen receptor-induced NF-κB activation was first described. Since then, several other immune receptors, G-protein-coupled receptors, and receptor tyrosine kinases were identified as relying on MALT1 to induce NF-κB activation. In various hematological malignancies and solid tumors, MALT1 is constitutively activated and drives chronic NF-κB target gene expression. Deregulated MALT1 activity in cancer thus promotes tumor cell survival, proliferation, and metastasis. Since the molecular function of MALT1 partially requires its protease activity, pharmacological targeting of MALT1 may represent a promising anti-cancer strategy. Here, we review the molecular features of MALT1 activation and function as well as the therapeutic potential of MALT1 inhibition in hematological malignancies and solid tumors.
Platelets subvert antitumor efficacy of T cell-recruiting bispecific antibodies
2022-02-01

T cell-based immunotherapy, for example, with T cell-recruiting bispecific antibody (bsAb), has revolutionized oncological treatment. However, many patients do not respond to treatment, and long-term remissions are still rare. Several tumor immune evasion mechanisms have been reported to counteract efficiency of T cell-engaging therapeutics. Platelets largely affect cancer pathophysiology by mediating tumor invasion, metastasis, and immune evasion. On treatment of patients in a clinical trial with a PSMA×CD3 bsAb ( NCT04104607 ), we observed profound treatment-associated platelet activation, mirrored by a decrease of total platelet count. On modeling the treatment setting, we found that platelet activation significantly reduced bsAb-mediated CD4 + and CD8 + T-cell reactivity as revealed by impaired T-cell degranulation, secretion of perforin, and ultimately, inhibition of target cell lysis. This effect occurred in a transforming growth factor beta (TGF-β)-dependent manner and was not restricted to PSMA×CD3 bsAb, but rather observed with various CD3-directed bispecific constructs, including the approved CD19×CD3 bsAb blinatumomab. BsAb-mediated T-cell reactivity could be restored by platelet inhibition and specifically by blocking the TGF-β axis. Together, our findings demonstrate that platelets undermine the efficacy of T cell-recruiting bsAb and identify modulation of platelet function as a means to reinforce the effectiveness of bsAb treatment.
Dynamical Taxonomy: Some Taxonomic Ranks to Systematically Classify Every Chaotic Attractor
2022-02-01

Characterizing accurately chaotic behaviors is not a trivial problem and must allow to determine the properties that two given chaotic invariant sets share or not. The underlying problem is the classification of chaotic regimes, and their labeling. Addressing these problems corresponds to the development of a dynamical taxonomy, exhibiting the key properties discriminating the variety of chaotic behaviors discussed in the abundant literature. Starting from the hierarchy of chaos initially proposed by one of us, we systematized the description of chaotic regimes observed in three- and four-dimensional spaces, which cover a large variety of known (and less known) examples of chaos. Starting with the spectrum of Lyapunov exponents as the first taxonomic ranks, we extended the description to higher ranks with some concepts inherited from topology (bounding torus, surface of section, first-return map, ...). By treating extensively the Rössler and the Lorenz attractors, we extended the description of branched manifold — the highest known taxonomic rank for classifying chaotic attractor — by a linking matrix (or linker) to multicomponent attractors (bounded by a torus whose genus [Formula: see text]).
Feasibility, psychological outcomes and practical use of a stress-preventive leadership intervention in the workplace hospital: the results of a mixed-method phase-II study
2022-02-01

Objectives Hospitals are psychologically demanding workplaces with a need for context-specific stress-preventive leadership interventions. A stress-preventive interprofessional leadership intervention for middle management has been developed. This phase-II study investigates its feasibility and outcomes, including work-related stress, well-being and transformational leadership. Design This is a mixed-methods study with three measure points (T0: baseline, T1: after the last training session, T2: 3-month follow-up). Additionally, focus groups were conducted to assess participants’ change in everyday work. Setting A tertiary hospital in Germany. Participants N=93 leaders of different professions. Intervention An interactive group setting intervention divided in five separate sessions ((1) self-care as a leader, (2) leadership attitudes and behaviour, (3) motives, needs and stressors of employees, (4) strengthen the resource ‘team’, (5) reflection and focus groups). The intervention was conducted between June 2018 and March 2020 in k=5 runs of the intervention. Outcome measures Feasibility and acceptance were measured with a self-developed intervention specific questionnaire. Psychological outcomes were assessed with the following scales: work-related strain with the Irritation Scale, well-being with the WHO-5 Well-being Index and transformational leadership with the Questionnaire of Integrative Leadership. Results After the intervention at T2, over 90% of participants reported that they would recommend the intervention to another coworker (92.1%, n=59) and all participants (n=64) were satisfied with the intervention and rated the intervention as practical relevant for their everyday work. Participants’ self-rated cognitive irritation was reduced, whereas their well-being and transformational leadership behaviour were improved over time. Focus group discussions revealed that participants implemented intervention contents successfully in their everyday work. Conclusions This intervention was feasible and showed first promising intraindividual changes in psychological outcomes. Participants confirmed its practical relevance. As a next step, the intervention will be evaluated as part of a multicentre—randomised controlled trial within the project SEEGEN (SEElische GEsundheit am Arbeitsplatz KrankeNhaus).
Toxicity and Efficacy of Local Ablative, Image-guided Radiotherapy in Gallium-68 Prostate-specific Membrane Antigen Targeted Positron Emission Tomography-staged, Castration-sensitive Oligometastatic Prostate Cancer: The OLI-P Phase 2 Clinical Trial.
2022-02-01

In this clinical trial, 63 patients with up to five metastases of prostate cancer without androgen deprivation therapy were included. We showed that local ablative radiotherapy is safe and that one in five patients had no recurrent prostate-specific antigen value after 3 yr. Local ablative radiotherapy might be an option to avoid systemic therapy in selected patients.
Scalar leptoquark pair production at the LHC: precision predictions in the era of flavour anomalies
2022-02-01

A bstract We comprehensively examine precision predictions for scalar leptoquark pair production at the LHC. In particular, we investigate the impact of lepton t -channel exchange diagrams that are potentially relevant in the context of leptoquark scenarios providing an explanation for the flavour anomalies. We also evaluate the corresponding total rates at the next-to-leading order in QCD. Moreover, we complement this calculation with the resummation of soft-gluon radiation at the next-to-next-to-leading logarithmic accuracy, hence providing the most precise predictions for leptoquark pair production at the LHC to date. Relying on a variety of benchmark scenarios favoured by the anomalies, our results exhibit an interesting interplay between the t -channel diagram contributions, the flavour texture satisfied by the leptoquark Yukawa couplings, the leptoquark masses and their representations under the Standard Model gauge group, as well as the chosen set of parton densities used for the numerical evaluations. The net effect on a cross section turns out to be very non-generic and ranges up to about 60% with respect to the usual next-to-leading-order predictions in QCD (i.e. without any t -channel contribution) for some scenarios considered. Dedicated calculations are thus required for any individual leptoquark model that could be considered in a collider analysis in order to assess the size of the studied corrections. In order to facilitate such calculations we provide dedicated public numerical packages.
Diagnosis of Platelet Function Disorders: A Challenge for Laboratories
2022-02-01

Abstract In patients with normal plasmatic coagulation and bleeding tendency, platelet function defect can be assumed. Congenital platelet function defects are rare. Much more commonly they are acquired. The clinical bleeding tendency of platelet function defects is heterogeneous, which makes diagnostic approaches difficult. During the years, a large variety of tests for morphological phenotyping and functional analysis have been developed. The diagnosis of platelet function defects is based on standardized bleeding assessment tools followed by a profound morphological evaluation of the platelets. Platelet function assays like light transmission aggregation, luminoaggregometry, and impedance aggregometry followed by flow cytometry are commonly used to establish the diagnosis in these patients. Nevertheless, despite great efforts, standardization of these tests is poor and in most cases, quality control is lacking. In addition, these tests are still limited to specialized laboratories. This review summarizes the approaches to morphologic phenotyping and platelet testing in patients with suspected platelet dysfunction, beginning with a standardized bleeding score and ending with flow cytometry testing. The diagnosis of a functional defect requires a good collaboration between the laboratory and the clinician.