Miracle-dz/UniFAR-FTUs huggingface dataset:
SPASCER: spatial transcriptomics annotation at single-cell resolution

Abstract In recent years, the explosive growth of spatial technologies has enabled the characterization of spatial heterogeneity of tissue architectures. Compared to traditional sequencing, spatial transcriptomics reserves the spatial information of each captured location and provides novel insights into diverse spatially related biological contexts. Even though two spatial transcriptomics databases exist, they provide limited analytical information. Information such as spatial heterogeneity of genes and cells, cell-cell communication activities in space, and the cell type compositions in the microenvironment are critical clues to unveil the mechanism of tumorigenesis and embryo differentiation. Therefore, we constructed a new spatial transcriptomics database, named SPASCER (https://ccsm.uth.edu/SPASCER), designed to help understand the heterogeneity of tissue organizations, region-specific microenvironment, and intercellular interactions across tissue architectures at multiple levels. SPASCER contains datasets from 43 studies, including 1082 sub-datasets from 16 organ types across four species. scRNA-seq was integrated to deconvolve/map spatial transcriptomics, and processed with spatial cell-cell interaction, gene pattern and pathway enrichment analysis. Cell–cell interactions and gene regulation network of scRNA-seq from matched spatial transcriptomics were performed as well. The application of SPASCER will provide new insights into tissue architecture and a solid foundation for the mechanistic understanding of many biological processes in healthy and diseased tissues.
A borderline focused Reflective Functioning measure – Interrater reliability of the Mentalization Breakdown Interview

Abstract Objective Mentalizing difficulties can be considered the core psychopathology of borderline personality disorder (BPD). Typical failures of mentalizing are targets in therapy for BPD. They are related to severe distress, relational problems, self-destructive behaviors, violence, or substance misuse. A major obstacle in BPD treatment research is the lack of suitable and easily administrated methods to assess mentalizing ability during treatment. The Mentalization Breakdown Interview (MBI) is a new method for capturing episodic mentalizing difficulties occurring in close relationships. Interviews are videotaped and scored in accordance with the Reflective Functioning Scale (MBI-RF). In this way the patients’ ability to retrospectively reflect over such episodes are evaluated. This study investigates the interrater reliability of MBI-RF. Methods The study includes videotapes of MBIs from 32 patients with BPD in an outpatient clinic specialized on mentalization-based treatment (MBT). The MBIs were performed by MBT therapists. Three certified raters scored MBI-RF. Results The interrater reliability was good for MBI-RF. Conclusions The MBI is promising as a BPD-focused method for the assessment of Reflective Functioning.
Anti-IL 23 biologics for the treatment of plaque psoriasis

ABSTRACT Introduction Psoriasis is a chronic inflammatory disease that can drastically affect a patient’s quality-of-life and is associated with multiple comorbid conditions. The most common form of psoriasis is plaque psoriasis, commonly presenting as sharply demarcated, erythematous plaques with overlying silvery scale on the trunk, extensor surfaces, limbs, and scalp. Although initially limited to oral therapies, the choices in systemic therapies for moderate-to-severe plaque psoriasis have evolved with biologic immunotherapies being the main focus. Areas covered In this review, we describe the IL-23/Th17 axis and IL-23 inhibitors as targets for a growing family of biologics. This family includes the FDA-approved medications ustekinumab, guselkumab, tildrakizumab, and risankizumab. We will review the safety and efficacy of these medications throughout various Phase 1,2, and 3, trials for moderate-to-severe psoriasis. A literature search of PubMed was utilized for the following terms: ‘psoriasis and IL-23,’ ‘ustekinumab,’ ‘guselkumab,’ ‘tildrakizumab,’ and ‘risankizumab. ’ We also searched for clinical trials involving IL-23 inhibitors registered at ClinicalTrials.gov. Expert opinion Anti-IL 23 therapy, especially anti-p19 monoclonal antibodies, should be considered first-line therapy for moderate-to-severe plaque psoriasis due to their efficacy and relative safety. More research is required to expand the scope of anti-p19 therapy to pediatric populations and additional indications such as psoriatic arthritis.
Self-reported health change in haemodialysis recipients modulates the effect of frailty upon mortality and hospital admissions: outcomes from a large prospective UK cohort.

BACKGROUND Frailty among haemodialysis patients is associated with hospitalisation and mortality, but high frailty prevalence suggests further discrimination of risk is required. We hypothesised that incorporation of self-reported health with frailty measurement may aid risk stratification. METHODS Prospective cohort study of 485 prevalent haemodialysis recipients linked to English national datasets. Frailty Phenotype (FP), Frailty Index (FI), Edmonton Frail Scale (EFS), Clinical Frailty Scale (CFS) and self-reported health change were assessed. Mortality was explored using Fine and Gray regression, and admissions by negative binomial regression. RESULTS Over a median 678 (IQR: 531-812) days, there were 111 deaths, and 1241 hospitalisations. Increasing frailty was associated with mortality on adjusted analyses for FP (SHR 1.26, 95% C.I. 1.05-1.53, P = 0.01), FI (SHR 1.21, 95% C.I. 1.09-1.35, P = 0.001), and CFS (SHR 1.32, 95% C.I. 1.11-1.58, P = 0.002), but not EFS (HR 1.08, 95% C.I. 0.99-1.18, P = 0.1). Health change interacted with frailty tools to modify association with mortality; only those who rated their health as the same or worse experienced increased mortality hazard associated with frailty by FP (Pinteraction = 0.001 and 0.035 respectively), FI (Pinteraction = 0.002 and 0.007 respectively), and CFS (Pinteraction = 0.009 and 0.02 respectively). CFS was the only frailty tool associated with hospitalisation (incidence rate ratio 1.12, 95% CI 1.02-1.23, P = 0.02). CONCLUSIONS We confirm the high burden of hospitalisation and mortality associated with haemodialysis patients regardless of frailty tool utilised and introduce the discriminatory ability of self-reported health to identify the most at-risk frail individuals.
A NEAR-INFRARED CENSUS OF THE MULTICOMPONENT STELLAR STRUCTURE OF EARLY-TYPE DWARF GALAXIES IN THE VIRGO CLUSTER

The fraction of star-forming to quiescent dwarf galaxies varies from almost infinity in the field to zero in the centers of rich galaxy clusters. What is causing this pronounced morphology–density relation? What do quiescent dwarf galaxies look like when studied in detail, and what conclusions can be drawn about their formation mechanism? Here we study a nearly magnitude-complete sample (−19 < Mr < −16 mag) of 121 Virgo cluster early types with deep near-infrared images from the SMAKCED project. We fit two-dimensional models with optional inner and outer components, as well as bar and lens components (in ∼15% of the galaxies), to the galaxy images. While a single Sérsic function may approximate the overall galaxy structure, it does not entirely capture the light distribution of two-thirds of our galaxies, for which multicomponent models provide a better fit. This fraction of complex galaxies shows a strong dependence on luminosity, being larger for brighter objects. We analyze the global and component-specific photometric scaling relations of early-type dwarf galaxies and discuss similarities with bright early and late types. The dwarfs' global galaxy parameters show scaling relations that are similar to those of bright disk galaxies. The inner components are mostly fitted with Sérsic n values close to 1. At a given magnitude, they are systematically larger than the bulges of spirals, suggesting that they are not ordinary bulges. We argue that the multicomponent structures in early-type dwarfs are mostly a phenomenon inherent to the disks and may indeed stem from environmental processing.
HProteome-BSite: predicted binding sites and ligands in human 3D proteome

Abstract Atomic-level knowledge of protein-ligand interactions allows a detailed understanding of protein functions and provides critical clues to discovering molecules regulating the functions. While recent innovative deep learning methods for protein structure prediction dramatically increased the structural coverage of the human proteome, molecular interactions remain largely unknown. A new database, HProteome-BSite, provides predictions of binding sites and ligands in the enlarged 3D human proteome. The model structures for human proteins from the AlphaFold Protein Structure Database were processed to structural domains of high confidence to maximize the coverage and reliability of interaction prediction. For ligand binding site prediction, an updated version of a template-based method GalaxySite was used. A high-level performance of the updated GalaxySite was confirmed. HProteome-BSite covers 80.74% of the UniProt entries in the AlphaFold human 3D proteome. Predicted binding sites and binding poses of potential ligands are provided for effective applications to further functional studies and drug discovery. The HProteome-BSite database is available at https://galaxy.seoklab. org/hproteome-bsite/database and is free and open to all users.
Black strings ending on horizons

We construct an approximate static gravitational solution of the Einstein equations, with negative cosmological constant, describing a test black string stretching from the boundary of the Schwarzschild–AdS5 black brane toward the horizon. The construction builds on a derivative expansion method, assuming that the black brane metric changes slowly along the black string direction. We provide a solution up to second order in derivatives, and it implies, in particular, that the black string must shrink to zero size at the horizon of the black brane. In the near-horizon region of the black brane, where the two horizons intersect, we provide an exact solution of a cone that describes two intersecting horizons at different temperatures. Moreover, we show that this solution equally describes a thin and long black droplet.
Quantum linear least mean squares estimators

In this paper, we consider a class of plants whose internal states are governed by general non-commutative linear quantum stochastic differential equations (QSDEs). The state variables of such plants are supposed to be physically realizable. As a result of physical realizability, the commutation relations are preserved for such systems. We assume that the output signal of plant satisfies a non-commutative linear QSDE. Here, we obtain non-commutative linear least mean squares estimators of the plant's state which are supposed, given as a linear combination of innovation processes similar to Belavkin-Kalman (commutative output) and classical Kalman filtering. However, such estimators are more general than Belavkin-Kalman and classical Kalman filters. Furthermore, we obtain sufficient conditions ensuring physical realizability of such non-commutative least mean squares estimators. Indeed, this paper shows that the physical realizability of such non-commutative least mean square estimator imposes some strict constraints which makes these estimators unusable for many quantum systems.
Utilização de bioestimulante na produção de mudas de alface

Avaliou-se o efeito de bioestimulantes na producao de mudas de alface, no delineamento experimental inteiramente casualizado, com quatro repeticoes, em esquema fatorial 2 x 4. Os tratamentos resultaram da combinacao de dois bioestimulantes (Fertiactyl GZ ® e Ruterr AA ® ) e quatro concentracoes (0; 0,25; 0,50 e 0,75%). A unidade experimental foi composta por uma bandeja de 28 celulas, sendo que no momento das avaliacoes, foram consideradas como area util as 50 celulas centrais da bandeja. As caracteristicas avaliadas foram: massa seca da parte aerea e do sistema radicular, e comprimento de raiz. O bioestimulante Fertiactyl GZ, na concentracao de 0,75%, favo-receu a producao de mudas de melhor qualidade. Palavras-chaves Adicionais: Lactuva sativa L. ; nutricao de plantas; crescimento.
Origin, form and function of extraembryonic structures in teleost fishes

Teleost eggs have evolved a highly derived early developmental pattern within vertebrates as a result of the meroblastic cleavage pattern, giving rise to a polar stratified architecture containing a large acellular yolk and a small cellular blastoderm on top. Besides the acellular yolk, the teleost-specific yolk syncytial layer (YSL) and the superficial epithelial enveloping layer are recognized as extraembryonic structures that play critical roles throughout embryonic development. They provide enriched microenvironments in which molecular feedback loops, cellular interactions and mechanical signals emerge to sculpt, among other things, embryonic patterning along the dorsoventral and left–right axes, mesendodermal specification and the execution of morphogenetic movements in the early embryo and during organogenesis. An emerging concept points to a critical role of extraembryonic structures in reinforcing early genetic and morphogenetic programmes in reciprocal coordination with the embryonic blastoderm, providing the necessary boundary conditions for development to proceed. In addition, the role of the enveloping cell layer in providing mechanical, osmotic and immunological protection during early stages of development, and the autonomous nutritional support provided by the yolk and YSL, have probably been key aspects that have enabled the massive radiation of teleosts to colonize every ecological niche on the Earth. This article is part of the theme issue ‘Extraembryonic tissues: exploring concepts, definitions and functions across the animal kingdom’.
Prevalence of anxiety and depression in people with different types of cancer or haematologic malignancies: a cross-sectional study

Abstract Aims Cancer patients often present with psychological symptoms that affect their quality of life, physical health outcomes and survival. Two of the most frequent psychiatric comorbidities are anxiety and depression. However, the prevalence of these disorders among cancer patients remains unclear, as studies frequently report varying rates. In the present study, we aimed to provide robust point estimates for the prevalence of anxiety and depression for both a mixed cancer sample and for 13 cancer types separately, considering confounding variables. Methods In a sample of 7509 cancer outpatients (51.4% female), we used the Hospital Anxiety and Depression Scale to assess rates of anxiety and depression. Applying ordinal logistic regression models, we compared the prevalence of anxiety and depression between different cancer types, controlling for age and gender. Results About one third of our sample showed symptoms of anxiety (35.2%) or depression (27.9%), and every sixth patient had a very likely psychiatric condition, with women being more frequently affected. Elderly patients more often showed signs of depression. The prevalence of anxiety and depression was significantly higher in lung and brain cancer patients, than in other cancer patients. Lowest depression rates were found in breast cancer patients. Conclusions The prevalence of anxiety and depression is high in cancer patients. Type of cancer is an important predictor for anxiety and depressive symptoms, with lung and brain cancer patients being highly burdened. Considering a personalised medicine approach, physicians should take into account the high prevalence of psychiatric comorbidities and include psychiatric consultations in the treatment plan.
CONSTRAINING UV CONTINUUM SLOPES OF ACTIVE GALACTIC NUCLEI WITH Cloudy MODELS OF BROAD-LINE REGION EXTREME-ULTRAVIOLET EMISSION LINES

Understanding the composition and structure of the broad-line region (BLR) of active galactic nuclei (AGNs) is important for answering many outstanding questions in supermassive black hole evolution, galaxy evolution, and ionization of the intergalactic medium. We used single-epoch UV spectra from the Cosmic Origins Spectrograph (COS) on the Hubble Space Telescope to measure EUV emission-line fluxes from four individual AGNs with 0.49 ⩽ z ⩽ 0.64, two AGNs with 0.32 ⩽ z ⩽ 0.40, and a composite of 159 AGNs. With the Cloudy photoionization code, we calculated emission-line fluxes from BLR clouds with a range of density, hydrogen ionizing flux, and incident continuum spectral indices. The photoionization grids were fit to the observations using single-component and locally optimally emitting cloud (LOC) models. The LOC models provide good fits to the measured fluxes, while the single-component models do not. The UV spectral indices preferred by our LOC models are consistent with those measured from COS spectra. EUV emission lines such as N iv λ765, O ii λ833, and O iii λ834 originate primarily from gas with electron temperatures between 37,000 K and 55,000 K. This gas is found in BLR clouds with high hydrogen densities (nH ⩾ 1012 cm−3) and hydrogen ionizing photon fluxes (ΦH ⩾ 1022 cm−2 s−1).
Search for pulsations in the LMXB EXO 0748–676

We present here results from our search for X-ray pulsations of the neutron star in the low mass X-ray binary EXO 0748–676 at a frequency near the burst-oscillation frequency of 44.7 Hz. Using the observations made with the Proportional Counter Array onboard the Rossi X-ray Timing Explorer, we did not find any pulsations in the frequency band of 44.4 Hz to 45.0 Hz and obtained a 3σ upper limit of 0.47% on the pulsed fraction for any possible underlying pulsation in this frequency band. We also discuss the importance of EXO 0748–676 as a promising source for the detection of Gravitational Waves.
IS THE DUST CLOUD AROUND LAMBDA ORIONIS A RING OR A SHELL, OR BOTH?

The dust cloud around λ Orionis is observed to be circularly symmetric with a large angular extent (≈8°). However, whether the three-dimensional (3D) structure of the cloud is shell- or ring-like has not yet been fully resolved. We study the 3D structure using a new approach that combines a 3D Monte Carlo radiative transfer model for ultraviolet (UV) scattered light and an inverse Abel transform, which gives a detailed 3D radial density profile from a two-dimensional column density map of a spherically symmetric cloud. By comparing the radiative transfer models for a spherical shell cloud and that for a ring cloud, we find that only the shell model can reproduce the radial profile of the scattered UV light, observed using the S2/68 UV observation, suggesting a dust shell structure. However, the inverse Abel transform applied to the column density data from the Pan-STARRS1 dust reddening map results in negative values at a certain radius range of the density profile, indicating the existence of additional, non-spherical clouds near the nebular boundary. The additional cloud component is assumed to be of toroidal ring shape; we subtracted from the column density to obtain a positive, radial density profile using the inverse Abel transform. The resulting density structure, composed of a toroidal ring and a spherical shell, is also found to give a good fit to the UV scattered light profile. We therefore conclude that the cloud around λ Ori is composed of both ring and shell structures.
Waves in pulsar winds

The radio, optical, x-ray and gamma-ray nebulae that surround many pulsars are thought to arise from synchrotron and inverse Compton emission. The energy powering this emission as well as the magnetic fields and relativistic particles are supplied by a ‘wind’ driven by the central object. The inner parts of the wind can be described using the equations of MHD, but these break down in the outer parts, when the density of charge carriers drops below a critical value. This paper reviews the wave properties of the inner part (striped wind), and uses a relativistic two-fluid model (cold electrons and positrons) to re-examine the nonlinear electromagnetic modes that propagate in the outer parts. It is shown that in a radial wind, two solutions exist for circularly polarized electromagnetic modes. At large distances one of them turns into a freely expanding flow containing a vacuum wave, whereas the other decelerates, corresponding to a confined flow.
Paperfolding and modular functions : Dedicated to Professor Takashi Aoki on the occasion of his 60th birthday (Exponential Analysis of Differential Equations and Related Topics)

The two lacunary series $\chi$+(z)=\displaystyle \sum_{n\geq 0}z^{2^{n}}, x-(z)=\displaystyle \sum_{n\geq 0}(-1)^{n}z^{2^{n}} and $\xi$(z)=\displaystyle \sum_{n\geq 1}s_{n}z^{n}, s_{2n}=s_{n},s_{2n+1}=(-1)^{n} are all connected to the paperfolding. We study their behaviours at z=1 and some of their relations to modular functions. We also investigate the zeros of their partial sums.
The chemistry of the most metal-rich damped Lyman α systems at z ∼ 2 – II. Context with the Local Group

Using our sample of the most metal-rich damped Lyman $\alpha$ systems (DLAs) at z$\sim2$, and two literature compilations of chemical abundances in 341 DLAs and 2818 stars, we present an analysis of the chemical composition of DLAs in the context of the Local Group. The metal-rich sample of DLAs at z$\sim2$ probes metallicities as high as the Galactic disc and the most metal-rich dwarf spheroidals (dSphs), permitting an analysis of many elements typically observed in DLAs (Fe, Zn, Cr, Mn, Si, and S) in comparison to stellar abundances observed in the Galaxy and its satellites (in particular dSphs). Our main conclusions are: (1) non-solar [Zn/Fe] abundances in metal-poor Galactic stars and in dSphs over the full metallicity range probed by DLAs, suggest that Zn is not a simple proxy for Fe in DLAs and therefore not a suitable indicator of dust depletion. After correcting for dust depletion, the majority of DLAs have subsolar [Zn/Fe] similar to dSphs; (2) at [Fe/H]$\sim-0.5$, a constant [Mn/Fe]$\sim-0.5$ and near-solar [$\alpha$/Fe] (requiring an assumption about dust depletion) are in better agreement with dwarf galaxies than Galactic disc stars; (3) [$\alpha$/Zn] is usually solar or subsolar in DLAs. However, although low ratios of [$\alpha$/Fe] are usually considered more `dwarf-like' than `Milky Way-like', subsolar [Zn/Fe] in Local Group dwarfs leads to supersolar [$\alpha$/Zn] in the dSphs, in contrast with the DLAs. Therefore, whilst DLAs exhibit some similarities with the Local Group dwarf population, there are also notable differences.
Symmetry and its discontents : essays on the history of inductive probability

Part I. Probability: 1. Symmetry and its discontents 2. The rule of succession 3. Buffon, Price, and Laplace: scientific attribution in the eighteenth century 4. W. E. Johnson's sufficientness postulate. Part II. Personalities: 5 Abraham De Moivre and the birth of the Central Limit Theorem 6 Ramsey, truth, and probability 7. R. A. Fisher on the history of inverse probability 8. R. A. Fisher and the fiducial argument 9. Alan Turing and the Central Limit Theorem Part III. Prediction: 10. Predicting the unpredictable 11. The continuum of inductive methods revised.