julilili42/papers huggingface dataset:
VOLUMETRIC ANALYSIS OF LAMELLAR MACULAR HOLE
2023-01-25

Background: To investigate the cavity of lamellar macular holes (LMH-CV) by using volumetric analysis of optical coherence tomography images. Methods: Single-center, retrospective, observational case series. The volume of the LMH-CV and epiretinal proliferation was determined. Best-corrected visual acuity, central macular thickness, maximum horizontal diameter and minimum horizontal diameter, and the presence of foveal bump and ellipsoid zone defect were noted. Results: Forty-nine eyes of 46 patients (20 women) were included in the baseline analysis. The natural course group consisted of 25 patients (27 eyes) with a mean follow-up of 19.2 ± 15.7 months. The volume of LMH-CV was found to be a predictive factor for baseline best-corrected visual acuity ( P = 0.038, ß-coefficient = 0.338, 95% CI: 0.275–8.893). Whereas no significant change at the last visit was observed in central macular thickness, minimum horizontal diameter, and maximum horizontal diameter, the LMH-CV and epiretinal proliferation volume increased significantly ( P = 0.036, P &lt; 0.001, respectively). Eyes with foveal bump had larger minimum horizontal diameter, maximum horizontal diameter, and LMH-CV volume ( P = 0.008, P &lt; 0.001, P = 0.024, respectively). Eyes with ellipsoid zone defect showed larger LMH-CV and epiretinal proliferation volume, but thinner central macular thickness ( P = 0.038, P = 0.004, P = 0.012, respectively). Conclusion: Volumetric analysis of LMH-CV detects changes in the natural course of lamellar macular hole earlier than the measurement of horizontal diameters. Further studies will clarify whether volumetric analysis of the lamellar macular hole is useful as an additional biomarker in the management of lamellar macular hole.
Image analysis of retinal images in eye safety evaluations for optical systems
2023-01-25

Optical systems that emit radiation between the visible and near-infrared wavelength region pose a potential hazard to human vision as the radiation is imaged on the retina. The radiation interacts with the retinal tissue in a photomechanical, photothermal, and photochemical manner that can result in irreversible injuries. To ensure an eye safe system, it is important to correctly apply the laser safety standard IEC 60825-1:2014 or the lamp safety standard IEC 62471:2006. We aim to provide a general calculation procedure for both coherent and incoherent sources, which are compliant with the respective safety standards. An air-equivalent eye model generates retinal images. Two software-based calculation methods are introduced, which are referred to as image analysis. The first method calculates the angular subtense of the apparent source needed for photomechanical and photothermal limits. The second method applies to photochemical limits. Using exemplary optical systems, the image analysis is investigated. The proposed image analysis gives guidance for missing aspects in the standards and reduces ambiguity and complexity. The proposed method can be used for eye safety evaluations since it follows the concept of the safety standards with conservative approaches.
Functional MRI to quantify perfusion changes of a renal allograft after embolization of an arteriovenous fistula
2023-01-25

Abstract Acute allograft injury was observed in a 37-year-old woman within a few weeks after kidney transplantation. Neither renal ultrasound nor computerized tomography (CT) and magnetic resonance (MR) angiography revealed any anomaly. An MR protocol was then performed including arterial spin labeling and intravoxel incoherent motion diffusion weighted imaging. Both arterial spin labeling and the perfusion fraction in the diffusion weighted imaging showed decreased perfusion compared to reference values. The patient subsequently underwent angiography, where an arteriovenous fistula in the upper calix of the transplant kidney was detected and immediate embolization was performed. A second functional MR, performed one week later, demonstrated a 40% increase in organ perfusion. We conclude that functional MR with arterial spin labeling and intravoxel incoherent motion have the potential to provide complementary information of clinical value to conventional imaging for monitoring renal allografts.
Theory Ambrosia
2023-01-25

The "Theory Ambrosia" summarizes essential findings on happiness, mental health and the way to it and condenses them into an all-encompassing theory. This paper describes the elements of the theory and explains how it came about. If we want world peace, there is probably no way around this theory.
Dose accumulation for MR-guided adaptive radiotherapy: From practical considerations to state-of-the-art clinical implementation
2023-01-26

MRI-linear accelerator (MR-linac) devices have been introduced into clinical practice in recent years and have enabled MR-guided adaptive radiation therapy (MRgART). However, by accounting for anatomical changes throughout radiation therapy (RT) and delivering different treatment plans at each fraction, adaptive radiation therapy (ART) highlights several challenges in terms of calculating the total delivered dose. Dose accumulation strategies—which typically involve deformable image registration between planning images, deformable dose mapping, and voxel-wise dose summation—can be employed for ART to estimate the delivered dose. In MRgART, plan adaptation on MRI instead of CT necessitates additional considerations in the dose accumulation process because MRI pixel values do not contain the quantitative information used for dose calculation. In this review, we discuss considerations for dose accumulation specific to MRgART and in relation to current MR-linac clinical workflows. We present a general dose accumulation framework for MRgART and discuss relevant quality assurance criteria. Finally, we highlight the clinical importance of dose accumulation in the ART era as well as the possible ways in which dose accumulation can transform clinical practice and improve our ability to deliver personalized RT.
A targeted multi-proteomics approach generates a blueprint of the ciliary ubiquitinome
2023-01-26

Establishment and maintenance of the primary cilium as a signaling-competent organelle requires a high degree of fine tuning, which is at least in part achieved by a variety of post-translational modifications. One such modification is ubiquitination. The small and highly conserved ubiquitin protein possesses a unique versatility in regulating protein function via its ability to build mono and polyubiquitin chains onto target proteins. We aimed to take an unbiased approach to generate a comprehensive blueprint of the ciliary ubiquitinome by deploying a multi-proteomics approach using both ciliary-targeted ubiquitin affinity proteomics, as well as ubiquitin-binding domain-based proximity labelling in two different mammalian cell lines. This resulted in the identification of several key proteins involved in signaling, cytoskeletal remodeling and membrane and protein trafficking. Interestingly, using two different approaches in IMCD3 and RPE1 cells, respectively, we uncovered several novel mechanisms that regulate cilia function. In our IMCD3 proximity labeling cell line model, we found a highly enriched group of ESCRT-dependent clathrin-mediated endocytosis-related proteins, suggesting an important and novel role for this pathway in the regulation of ciliary homeostasis and function. In contrast, in RPE1 cells we found that several structural components of caveolae (CAV1, CAVIN1, and EHD2) were highly enriched in our cilia affinity proteomics screen. Consistently, the presence of caveolae at the ciliary pocket and ubiquitination of CAV1 specifically, were found likely to play a role in the regulation of ciliary length in these cells. Cilia length measurements demonstrated increased ciliary length in RPE1 cells stably expressing a ubiquitination impaired CAV1 mutant protein. Furthermore, live cell imaging in the same cells revealed decreased CAV1 protein turnover at the cilium as the possible cause for this phenotype. In conclusion, we have generated a comprehensive list of cilia-specific proteins that are subject to regulation via ubiquitination which can serve to further our understanding of cilia biology in health and disease.
Radiolabeled GPVI-Fc for PET Imaging of Multiple Extracellular Matrix Fibers: A New Look into Pulmonary Fibrosis Progression
2023-01-26

Invariably fatal and with a particularly fast progression, pulmonary fibrosis (PF) is currently devoid of curative treatment options. Routine clinical diagnosis relies on breathing tests and visualizing the changes in lung structure by CT, but anatomic information is often not sufficient to identify early signs of progressive PF. For more efficient diagnosis, additional imaging techniques were investigated in combination with CT, such as <sup>18</sup>F-FDG PET, although with limited success because of lack of disease specificity. Therefore, novel molecular targets enabling specific diagnosis are investigated, in particular for molecular imaging techniques. <b>Methods:</b> In this study, we used a <sup>64</sup>Cu-radiolabeled platelet glycoprotein VI fusion protein (<sup>64</sup>Cu-GPVI-Fc) targeting extracellular matrix (ECM) fibers as a PET tracer to observe longitudinal ECM remodeling in a bleomycin-induced PF mouse model. <b>Results:</b> <sup>64</sup>Cu-GPVI-Fc showed significant uptake in fibrotic lungs, matching histology results. Contrary to <sup>18</sup>F-FDG PET measurements, <sup>64</sup>Cu-GPVI-Fc uptake was linked entirely to the fibrotic activity of tissue and not was susceptible to inflammation. <b>Conclusion:</b> Our study highlights <sup>64</sup>Cu-GPVI-Fc as a specific tracer for ECM remodeling in PF, with clear therapy-monitoring and clinical translation potential.
Sulfur Monoxide Release and Capture: A Computational Study
2023-01-26

Abstract Thermolysis of thiirane oxide leads to production of highly reactive sulfur monoxide. The liberated SO can in turn be trapped with a diene scavenger forming dihydrothiophene oxide. Since the intermediate diatomic possesses a triplet ground state, the SO transfer can proceed on two spin‐state surfaces. Here, we study the competition between singlet concerted and stepwise triplet diradical mechanisms utilizing the M06‐2X density functional as well as CCSD(T) and MRCI+Q wavefunction theories. We find that the decomposition of thiirane oxide prefers to pass through a triplet diradical intermediate that becomes accessible from a nearby minimum energy crossing point (MECP). Hence, the thermolysis of thiirane oxide is expected to predominantly release triplet ground state sulfur monoxide in agreement with previous experimental reports. The addition of 3 SO to 1,3‐butadiene initially generates an allylic diradical, that ring‐closes to a thiirane oxide through another MECP, and a subsequent rearrangement gives access to the final product.
Kinase Activity Is Not Required for G Protein–Coupled Receptor Kinase 4 Restraining mTOR Signaling during Cilia and Kidney Development
2023-01-26

Significance Statement G protein–coupled receptor kinase 4 (GRK4) regulates renal sodium and water reabsorption. Although GRK4 variants with elevated kinase activity have been associated with salt-sensitive or essential hypertension, this association has been inconsistent among different study populations. In addition, studies elucidating how GRK4 may modulate cellular signaling are sparse. In an analysis of how GRK4 affects the developing kidney, the authors found that GRK4 modulates mammalian target of rapamycin (mTOR) signaling. Loss of GRK4 in embryonic zebrafish causes kidney dysfunction and glomerular cysts. Moreover, GRK4 depletion in zebrafish and cellular mammalian models results in elongated cilia. Rescue experiments suggest that hypertension in carriers of GRK4 variants may not be explained solely by kinase hyperactivity; instead, elevated mTOR signaling may be the underlying cause. Background G protein–coupled receptor kinase 4 (GRK4) is considered a central regulator of blood pressure through phosphorylation of renal dopaminergic receptors and subsequent modulation of sodium excretion. Several nonsynonymous genetic variants of GRK4 have been only partially linked to hypertension, although these variants demonstrate elevated kinase activity. However, some evidence suggests that function of GRK4 variants may involve more than regulation of dopaminergic receptors alone. Little is known about the effects of GRK4 on cellular signaling, and it is also unclear whether or how altered GRK4 function might affect kidney development. Methods To better understand the effect of GRK4 variants on the functionality of GRK4 and GRK4's actions in cellular signaling during kidney development, we studied zebrafish, human cells, and a murine kidney spheroid model. Results Zebrafish depleted of Grk4 develop impaired glomerular filtration, generalized edema, glomerular cysts, pronephric dilatation, and expansion of kidney cilia. In human fibroblasts and in a kidney spheroid model, GRK4 knockdown produced elongated primary cilia. Reconstitution with human wild-type GRK4 partially rescues these phenotypes. We found that kinase activity is dispensable because kinase-dead GRK4 (altered GRK4 that cannot result in phosphorylation of the targeted protein) prevented cyst formation and restored normal ciliogenesis in all tested models. Hypertension-associated genetic variants of GRK4 fail to rescue any of the observed phenotypes, suggesting a receptor-independent mechanism. Instead, we discovered unrestrained mammalian target of rapamycin signaling as an underlying cause. Conclusions These findings identify GRK4 as novel regulator of cilia and of kidney development independent of GRK4's kinase function and provide evidence that the GRK4 variants believed to act as hyperactive kinases are dysfunctional for normal ciliogenesis.
Optical characterisation of spectacle lenses for myopia control
2023-01-26

Myopia is the most common ocular disorder worldwide and the leading cause of visual impairment in children. Its progression affects the normal retinal development, increasing the risk of suffering severe ocular pathologies that lead to irreversible blindness. Although the mechanism for myopia progression is not completely elucidated yet, it is suggested that the quality of the peripheral retinal images may play a role. This produced an enormous interest in using spectacle lenses with different focusing properties for foveal and peripheral vision as a treatment to slow myopia progression. In this work, we developed a novel instrument to optically characterise spectacle lenses designed for myopia control under realistic viewing conditions. First, the testing beam impinges the spectacle under test with different eccentricities. For each eccentricity, a steering mirror guides the beam towards a liquid crystal spatial light modulator (SLM). The SLM allows for reproducing several pupil sizes, shaping the pupil according to the eccentricity, reproducing ocular aberrations for different levels of myopia, and acquiring the through-focus point spread functions (PSFs). An electrically tunable liquid lens, conjugated to the SLM, compensates the base power of the tested lens and focuses the beam into a camera's sensor. Three spectacle lenses were tested, and different optical metrics were calculated from the PSF and the modulation transfer function.
The actin depolymerizing factor StADF2 alters StREM1.3 plasma membrane nanodomains to inhibit thePotato Virus X
2023-01-26

ABSTRACT The dynamic regulation of the plasma membrane (PM) organization at the nanoscale emerged as a key element shaping the outcome of host-microbe interactions. Protein organization into nanodomains (ND) is often assumed to be linked to the activation of cellular processes. In contrast, we have previously shown that the phosphorylation of the Solanum tuberosum REM1.3 (StREM1.3) N-terminal domain disperses its native ND organization and promotes its inhibitory effect on Potato Virus X (PVX) cell-to-cell movement. Here, we show that the phosphorylation of StREM1.3 modify the chemical environment of numerous residues in its intrinsically-disordered N-terminal domain. We leveraged exploratory screens to identify potential phosphorylation-dependent interactors of StREM1.3. Herewith, we uncovered uncharacterized regulators of PVX cell-to-cell movement, linking StREM1.3 to autophagy, water channels and the actin cytoskeleton. We show that the Solanum tuberosum actin depolymerizing factors 2 (StADF2) alters StREM1.3 NDs and limits PVX cell-to-cell movement in a REMORIN-dependent manner. Mutating a conserved single residue reported to affect ADFs affinity to actin inhibits StADF2 effect on StREM1.3 ND organization and PVX cell-to-cell movement. These observations provide functional links between the organization of plant PM and the actin cytoskeleton and suggests that the alteration of StREM1.3 ND organization promotes plant anti-viral responses. We envision that analogous PM re-organization applies for additional signaling pathways in plants and in other organisms.
Error- and inhibitory-related brain activity associated with political ideology: A multi-site replication study
2023-01-26

The relationship between political ideology and brain activity has captured the fascination of scientists and the public alike. Using approaches from cognitive neuroscience to provide insights into deeply held and personal beliefs requires careful navigation, with the application of robust methods that generate replicable results. A hallmark study in this area from Amodio et al. (2007) reported that brain components reflective of conflict monitoring and inhibition (namely the ERN [error-related negativity] and N2) are heightened in individuals who self-identify as liberal compared to conservative. While the study is highly influential and well-cited in the scientific literature, no direct replications of their findings exist and as such, this work was selected as a target replication for the #EEGManyLabs initiative. This cross-cultural multi-site study (N=320) will conduct a thorough replication of the Amodio et al. (2007) study, strictly adhering to the original protocol, namely by administering a Go/No-Go task with simultaneous EEG recording and a one-item scale asking participants to rate the extent to which they are liberal or conservative. We will supplement the original study with new measures that may better correspond to political identity in non-US contexts, such as religiosity, dogmatism, and traditionalism. In line with the original study, we will conduct correlational analyses between self-identified liberalism and ERN/N2 amplitudes. In addition, Bayesian linear regressions will be used to provide robust estimates of the strength of association between other components of political ideology and electrophysiological signals.
The Unique Character of Vatican II’s Teaching
2023-01-26

Abstract Since the end of Vatican II, there has been an ongoing battle on the normativity of this council, the interpretation of its texts, and its peculiar character. This chapter explores the qualitative uniqueness of the council reflected in the events and the documents it produced, from the papal invitation and throughout all the sessions. It argues that Immanuel Kant and his notions of transcendental logic and of the related transcendental form of reflection provide a way to understand the council’s peculiar character and uniqueness and to demonstrate how the epistemological presuppositions of Vatican II are not to be confused with those of Vatican I.
Report on scipost_202210_00023v1
2023-01-26

The CRESST-III experiment aims at the direct detection of dark matter particles via their elastic scattering off nuclei in a scintillating CaWO 4 target crystal.For many years CaWO 4 crystals have successfully been produced in-house at Technische Universität München with a focus on high radiopurity.To further improve the CaWO 4 crystals, an extensive chemical purification of the raw materials has been performed and the crystal TUM93
Follicular Lymphoma in the 5th Edition of the WHO-Classification of Haematolymphoid Neoplasms—Updated Classification and New Biological Data
2023-01-27

The conceptual description of Follicular lymphoma (FL) in the 5th edition of the World Health Organization (WHO) classification of haematolymphoid tumors (WHO-HAEM5) has undergone significant revision. The vast majority of FL (85%) with a follicular growth pattern are composed of centrocytes and centroblasts, harbor the t(14;18)(q32;q21) translocation and are now termed classic FL (cFL). They are set apart from three related subtypes, FL with predominantly follicular growth pattern, FL with unusual cytological features (uFL) and follicular large B-cell lymphoma (FLBCL). In contrast to the revised 4th edition of the WHO classification of haematolymphoid tumors (WHO-HAEM4R), grading of cFL is no longer mandatory. FL with a predominantly diffuse growth pattern had been previously recognized in WHO-HAEM4R. It frequently occurs as a large tumor in the inguinal region and is associated with CD23 expression. An absence of the IGH::BCL2 fusion and frequent STAT6 mutations along with 1p36 deletion or TNFRSF14 mutation is typical. The newly introduced subtype of uFL includes two subsets that significantly diverge from cFL: one with “blastoid” and one with “large centrocyte” variant cytological features. uFL more frequently displays variant immunophenotypic and genotypic features. FLBCL is largely identical to WHO-HAEM4R FL grade 3B and renaming was done for reasons of consistency throughout the classification. In-situ follicular B-cell neoplasm, pediatric-type FL, duodenal-type FL and primary cutaneous follicle center lymphoma are categorized as discrete entities. In addition, novel findings concerning underlying biological mechanisms in the pathogenesis of early and systemic follicular lymphoma will be presented.
Chiral and trace anomalies in deeply virtual Compton scattering
2023-01-27

Inspired by recent work by Tarasov and Venugopalan, we calculate the one-loop quark box diagrams relevant to polarized and unpolarized deep inelastic scattering (DIS) by introducing off-forward momentum l&lt;sup&gt;μ&lt;/sup&gt; as an infrared regulator. In the polarized case, we rederive the pole 1/l&lt;sup&gt;2&lt;/sup&gt; related to the axial (chiral) anomaly. In addition, we obtain the usual logarithmic term and the DIS coefficient function. We interpret the result in terms of the generalized parton distributions (GPDs) and and discuss the possible violation of QCD factorization for the Compton scattering amplitude. Remarkably, we also find poles in the unpolarized case which are remnants of the trace anomaly. We argue that these poles are canceled by the would-be massless glueball poles in the GPDs H and E as well as in their moments, the nucleon gravitational form factors A, B and D. This mechanism sheds light on the connection between the gravitational form factors and the gluon condensate operator F&lt;sup&gt;μν&lt;/sup&gt;F&lt;sub&gt;μν&lt;/sub&gt;.
Testing the influence of QUDs on the occurrence of Conditional Perfection
2023-01-27

In natural language conversations, speakers often communicate ‘if and only if’ when they say ‘if’. The reasons why in some circumstances, yet not all, conditionals receive a biconditional interpretation remain under investigation. Von Fintel (2001) proposed an account where the interpretation of a conditional (“if p, then q”) is predicted to depend on the focus of the conversation which may either lie on the conditions that make the consequent, q, true or on the consequences following when the antecedent, p, is true. To test this account, we present two novel behavioral experiments with non-text based stimuli that take advantage of participants’ intuitive understanding of physics. We find some supporting evidence for the tested account that is not conclusive but suggests that other aspects, like the nature of potential alternative causes for the consequent to become true (e.g., with or w/o the influence of an external variable), also play a role for the interpretation of the conditional.