Miracle-dz/UniFAR-FTUs huggingface dataset:
Mapping cluster mass distributions via gravitational lensing of background galaxies

We present a new method for measuring the projected mass distributions of galaxy clusters. The gravitational amplification is measured by comparing the joint distribution in redshift and magnitude of galaxies behind the cluster with that of field galaxies. We show that the total amplification is directly related to the surface mass density in the weak field limit, and so it is possible to map the mass distribution of the cluster. The method is shown to be limited by discreteness noise and galaxy clustering behind the lens. Galaxy clustering sets a lower limit to the error along the redshift direction, but a clustering independent lensing signature may be obtained from the magnitude distribution at fixed redshift. Statistical techniques are developed for estimating the surface mass density of the cluster. We extend these methods to account for any obscuration by cluster halo dust, which may be mapped independently of the dark matter. We apply the method to a series of numerical simulations and show the feasibility of the approach. We consider approximate redshift information, and show how the mass estimates are degraded.
Diagnostic and therapeutic potential of RNASET2 in Crohn’s disease: Disease-risk polymorphism modulates allelic-imbalance in expression and circulating protein levels and recombinant-RNASET2 attenuates pro-inflammatory cytokine secretion

Ribonuclease T2 gene (RNASET2) variants are associated in genome wide association studies (GWAS) with risk for several autoimmune diseases, including Crohn’s disease (CD). In T cells, a functional and biological relationship exists between TNFSF15-mediated enhancement of IFN−γ production, mucosal inflammation and RNASET2. Disease risk variants are associated with decreased mRNA expression and clinical characteristics of severe CD; however, functional classifications of variants and underlying molecular mechanisms contributing to pathogenesis remain largely unknown. In this study we demonstrate that allelic imbalance of RNASET2 disease risk variant rs2149092 is associated with transcriptional and post-transcriptional mechanisms regulating transcription factor binding, promoter-transactivation and allele-specific expression. RNASET2 mRNA expression decreases in response to multiple modes of T cell activation and recovers following elimination of activator. In CD patients with severe disease necessitating surgical intervention, preoperative circulating RNASET2 protein levels were decreased compared to non-IBD subjects and rebounded post-operatively following removal of the inflamed region, with levels associated with allelic carriage. Furthermore, overexpression or treatment with recombinant RNASET2 significantly reduced IFN-γ secretion. These findings reveal that RNASET2 cis- and trans-acting variation contributed regulatory complexity and determined expression and provide a basis for linking genetic variation with CD pathobiology. These data may ultimately identify RNASET2 as an effective therapeutic target in a subset of CD patients with severe disease.
Risk factors of lymph node metastasis or lymphovascular invasion for superficial esophageal squamous cell carcinoma: A practical and effective predictive nomogram based on a cancer hospital data

Background Lymphovascular invasion (LVI) is mostly used as a preoperative predictor to establish lymph node metastasis (LNM) prediction models for superficial esophageal squamous cell carcinoma (SESCC). However, LVI still needs to be confirmed by postoperative pathology. In this study, we combined LNM and LVI as a unified outcome and named it LNM/LVI, and aimed to develop an LNM/LVI prediction model in SESCC using preoperative factors. Methods A total of 512 patients who underwent radical resection of SESCC were retrospectively collected. Logistic regression and least absolute shrinkage and selection operator (LASSO) regression were adopted to identify the predictive factors of LNM/LVI. Integrated discrimination improvement (IDI) and net reclassification improvement (NRI) were calculated to select the potential predictive factors from the results of LASSO and logistic regression. A nomogram for predicting LNM/LVI was established by incorporating these factors. The efficacy, accuracy, and clinical utility of the nomogram were, respectively, assessed with the area under the curve (AUC), calibration curve, and decision curve analysis (DCA). Finally, the random forest (RF) algorithm was used to further evaluate the impact of these factors included in the nomogram on LNM/LVI. Results Tumor size, tumor location, tumor invasion depth, tumor differentiation, and macroscopic type were confirmed as independent risk factors for LNM/LVI according to the results of logistic regression, LASSO regression, IDI, and NRI analyses. A nomogram including these five variables showed a good performance in LNM/LVI prediction (AUC = 0.776). The calibration curve revealed that the predictive results of this nomogram were nearly consistent with actual observations. Significant clinical utility of our nomogram was demonstrated by DCA. The RF model with the same five variables also had similar predictive efficacy with the nomogram (AUC = 0.775). Conclusion The nomogram was adopted as a final tool for predicting LNM/LVI because its risk score system made it more user-friendly and clinically useful than the random forest model, which can help clinicians make optimal treatment decisions for patients with SESCC.
A Comparison of Two Banded, Heavy Snowstorms with Very Different Synoptic Settings

Abstract Two banded, heavy snowstorms that occurred over the northern mid-Atlantic region are compared and contrasted. On 6–7 January 2002, a narrow, intense band of heavy snow was observed, along with several other weaker bands, embedded within a large area of moderate snow. On 19–20 January 2002, a single, broader band of heavy snow was observed, embedded within a broken area of light snow. The synoptic-scale settings associated with these two storms were strikingly dissimilar. In the first case, strong quasigeostrophic (QG) forcing for ascent was present just to the south of the heavy snowfall area. A highly amplified longwave trough was located over the Mississippi River valley, while a compact shortwave trough moved northward, up the east side of the longwave trough. The result was robust cyclogenesis off of the mid-Atlantic coast. In the second case, the relatively weaker QG forcing for ascent was located much farther southwest of the snowband. The flow aloft was much less amplified, with weaker cyc.
Exploitation of tumor antigens and construction of immune subtype classifier for mRNA vaccine development in bladder cancer

Background Bladder cancer (BLCA) is one of the most prevalent urinary system malignancies, with high mortality and recurrence. The present study aimed to identify potential tumor antigens for mRNA vaccines in BLCA and patient subtypes suitable for different immunotherapy. Methods Gene expression profiles, mutation data, methylation data, and corresponding clinical information were obtained from the Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and ArrayExpress databases. Immunohistochemical staining of microarrays was performed to assess protein expression levels of IGF2BP2 and MMP9. Differential gene analysis, survival analysis, correlation analysis, consensus clustering analysis, and immune cell infiltration analysis were conducted using R software. Finally, the R package “immcluster” was used based on Combat and eXtreme Gradient Boosting algorithms to predict immune clusters of BLCA samples. Results Two mutated, amplified, and over-expressed tumor antigens, IGF2BP2 and MMP9, were found to be associated with clinical outcomes and the abundance of antigen-presenting cells (APCs). Subsequently, three immune subtypes (BIS1, BIS2, and BIS3) were defined in the BLCA cohort. BIS3 subtype exhibited an “active” immune phenotype, while BIS1 and BIS2 subtypes have a “suppressive” immune phenotype. Patients in BIS1 and BIS2 had a poor prognosis compared to BIS3. BIS3 had a higher score in checkpoints or immunomodulators (CP) and immunophenoscore (IPS), while BIS1 and BIS2 scored higher in major histocompatibility complex-related molecules (MHC molecules). Meanwhile, BIS2 and BIS3 had a significantly higher tumor mutational burden (TMB) compared to patients with BIS1. Finally, the “immcluster” package was applied to the dataset, which has been shown to accurately predict the immune subtypes of BLCA samples in many cohorts. Conclusions IGF2BP2 and MMP9 were potential antigens for developing mRNA vaccines against BLCA. The results in the present study suggested that immunotherapy targeting these two antigens would be suitable for patients falling under the BIS2 subtype. R package “immcluster” could assist in screening suitable BLCA patients for antitumor therapy.
Negative symptoms in alcohol use disorder: A pilot study applying the two-factor model of negative symptoms to patients with alcohol use disorder

Background and aims Alcohol Use Disorder (AUD) is characterized by a reduction in goal-directed behavior, with alcohol use taking precedence over other areas of life. These features in AUD resemble negative symptoms in schizophrenia, especially the reduction in motivation and pleasure (MAP). Given the clinical similarities of negative symptoms across diagnostic categories, it comes as a surprise that there are few investigations on negative symptoms in alcohol and other substance use disorders. To our knowledge, our study is the first to assess negative symptoms in AUD based on a two-factorial approach, and to investigate the interrelation of these dimensions with the severity of AUD, and alcohol craving. Materials and methods We examined a sample of 42 patients with AUD at the Psychiatric University Hospital in Zurich. Participants provided self-report and interview-based measures of the severity of AUD, negative symptoms, and alcohol craving. Finally, we used data from the electronic health records of the patients. Results Patients with AUD show negative symptoms to a similar extent as patients with schizophrenia or bipolar disorder. We found a positive correlation between the extent of impairment within the MAP factor and overall severity of AUD. Furthermore, MAP negative symptoms were correlated with alcohol craving. In a linear regression, negative symptoms predicted alcohol craving whereas depression did not. Summary Negative symptoms as conceptualized for schizophrenia are prevalent in patients with AUD and associated with the severity of AUD. More specifically, severity of AUD correlates with diminished motivation and pleasure, highlighting the importance of disturbances in motivational functions in AUD. This is further supported by the correlation between negative symptoms and craving, a hallmark of AUD. Taken together, our findings suggest that negative symptoms might be a highly relevant but hitherto often neglected therapeutic target in AUD.
Low-Angle Grain Boundaries in YBa2Cu3O7-δ with High Critical Current Densities

The grain boundary network in high-Tc coated conductors consists of a large number of low angle grain boundaries with many types of misorientation. Using the bicrystal technique we have measured the critical current densities of the relevant YBa2Cu3O7- grain boundary misorientations as a function of grain boundary angle. We find that in the low angle regime [010]-tilt boundaries and [100]-twist boundaries reduce the critical current density much less than [001]-tilt boundaries. Transmission electron microscopy reveals a low defect density in these boundaries and we find that CuO2 planes cross these boundaries without interruption.
Disruption of the HLA-E/NKG2X axis is associated with uncontrolled HIV infections

The contribution of the HLA-E/NKG2X axis in NK-mediated control of HIV infection remains unclear. We have studied the relationship between HLA-E expression and phenotypical as well as functional characteristics of NK cells, in the context of chronic HIV infection and in an in vitro model of acute infection. High viremia in HIV+ individuals was related to increased HLA-E expression, and changes in NK subpopulations, especially a reduction of the CD56bright as well as an increase in adaptive NK subpopulation. Uncontrolled HIV infection was also characterized by a reversion of the NKG2A/NKG2C expression ratio and a loss of positive and negative regulation of NK mediated by HLA-E. This was reflected in a lower cytotoxic, degranulation and cytokine production capacity, especially in CD56bright and adaptive NK. In line with these results, HLA-E expression showed a positive correlation with viral growth inhibition in an in vitro model of acute infection at day 7, which was lost after 14 days of culture. Using HLA-E expressing K562 cells, we determined that only one out of 11 described HIV-derived HLA-E epitopes increased HLA-E surface stability. In spite of that, eight of the 11 epitopes were capable of increasing degranulation and three drove differences in NK-cell mediated cell lysis or cytokine secretion. In conclusion, our results indicate that HLA-E molecules presenting HIV-derived epitopes may sensitize target cells for NK lysis in early HIV infection. However, prolonged exposure to elevated HLA-E expression levels in vivo may lead to NK cell dysfunction and reduced viral control In chronic infection.
Constant rate infusion of diazepam or propofol for the management of canine cluster seizures or status epilepticus

Introduction Cluster seizures (CS) and status epilepticus (SE) in dogs are severe neurological emergencies that require immediate treatment. Practical guidelines call for constant rate infusion (CRI) of benzodiazepines or propofol (PPF) in patients with seizures not responding to first-line treatment, but to date only few studies have investigated the use of CRI in dogs with epilepsy. Study design Retrospective clinical study. Methods Dogs that received CRI of diazepam (DZP) or PPF for antiepileptic treatment during hospitalization at the Veterinary Teaching Hospital of the University of Turin for CS or SE between September 2016 and December 2019 were eligible for inclusion. Favorable outcome was defined as cessation of clinically visible seizure activity within few minutes from the initiation of the CRI, no seizure recurrence within 24 h after discontinuation of CRI through to hospital discharge, and clinical recovery. Poor outcome was defined as recurrence of seizure activity despite treatment or death in hospital because of recurrent seizures, catastrophic consequences of prolonged seizures or no return to an acceptable neurological and clinical baseline, despite apparent control of seizure activity. Comparisons between the number of patients with favorable outcome and those with poor outcome in relation to type of CRI, seizure etiology, reason for presentation (CS or SE), sex, previous AED therapy and dose of PPF CRI were carried out. Results A total of 37 dogs, with 50 instances of hospitalization and CRI administered for CS or SE were included in the study. CRI of diazepam (DZP) or PPF was administered in 29/50 (58%) and in 21/50 (42%) instances of hospitalization, respectively. Idiopathic epilepsy was diagnosed in 21/37 (57%), (13/21 tier I and 8/21 tier II); structural epilepsy was diagnosed in 6/37 (16%) of which 4/6 confirmed and 2/6 suspected. A metabolic or toxic cause of seizure activity was recorded in 7/37 (19%). A total of 38/50 (76%) hospitalizations were noted for CS and 12/50 (24%) for SE. In 30/50 (60%) instances of hospitalization, the patient responded well to CRI with cessation of seizure activity, no recurrence in the 24 h after discontinuation of CRI through to hospital discharge, whereas a poor outcome was recorded for 20/50 (40%) cases (DZP CRI in 12/50 and PPF CRI in 8/50). Comparison between the number of patients with favorable outcome and those with poor outcome in relation to type of CRI, seizure etiology, reason for presentation (CS or SE), sex and previous AED therapy was carried out but no statistically significant differences were found. Conclusions The present study is the first to document administration of CRI of DZP or PPF in a large sample of dogs with epilepsy. The medications appeared to be tolerated without major side effects and helped control seizure activity in most patients regardless of seizure etiology. Further studies are needed to evaluate the effects of CRI duration on outcome and complications.
Effects of a nutritional intervention on impaired behavior and cognitive function in an emphysematous murine model of COPD with endotoxin-induced lung inflammation

One cluster of the extrapulmonary manifestations in chronic obstructive pulmonary disease (COPD) is related to the brain, which includes anxiety, depression and cognitive impairment. Brain-related comorbidities are related to worsening of symptoms and increased mortality in COPD patients. In this study, a murine model of COPD was used to examine the effects of emphysema and repetitive pulmonary inflammatory events on systemic inflammatory outcomes and brain function. In addition, the effect of a dietary intervention on brain-related parameters was assessed. Adult male C57Bl/6J mice were exposed to elastase or vehicle intratracheally (i.t.) once a week on three consecutive weeks. Two weeks after the final administration, mice were i.t. exposed to lipopolysaccharide (LPS) or vehicle for three times with a 10 day interval. A dietary intervention enriched with omega-3 PUFAs, prebiotic fibers, tryptophan and vitamin D was administered from the first LPS exposure onward. Behavior and cognitive function, the degree of emphysema and both pulmonary and systemic inflammation as well as blood-brain barrier (BBB) integrity and neuroinflammation in the brain were assessed. A lower score in the cognitive test was observed in elastase-exposed mice. Mice exposed to elastase plus LPS showed less locomotion in the behavior test. The enriched diet seemed to reduce anxiety-like behavior over time and cognitive impairments associated with the presented COPD model, without affecting locomotion. In addition, the enriched diet restored the disbalance in splenic T-helper 1 (Th1) and Th2 cells. There was a trend toward recovering elastase plus LPS-induced decreased expression of occludin in brain microvessels, a measure of BBB integrity, as well as improving expression levels of kynurenine pathway markers in the brain by the enriched diet. The findings of this study demonstrate brain-associated comorbidities – including cognitive and behavioral impairments – in this murine model for COPD. Although no changes in lung parameters were observed, exposure to the specific enriched diet in this model appeared to improve systemic immune disbalance, BBB integrity and derailed kynurenine pathway which may lead to reduction of anxiety-like behavior and improved cognition.
A genealogical approach to variable-population-size models in population genetics

A general exchangeable model is introduced to study gene survival in populations whose size changes without density dependence. Necessary and sufficient conditions for the occurrence of fixation (that is the proportion of one of the types tending to 1 with probability 1) are obtained. These are then applied to the Wright–Fisher model, the Moran model, and conditioned branching-process models. For the Wright–Fisher model it is shown that certain fixation is equivalent to certain extinction of one of the types, but that this is not the case for the Moran model.
Extracellular vesicles from Trypanosoma cruzi-dendritic cell interaction show modulatory properties and confer resistance to lethal infection as a cell-free based therapy strategy

Extracellular vesicles (EVs) include a heterogeneous group of particles. Microvesicles, apoptotic bodies and exosomes are the most characterized vesicles. They can be distinguished by their size, morphology, origin and molecular composition. To date, increasing studies demonstrate that EVs mediate intercellular communication. EVs reach considerable interest in the scientific community due to their role in diverse processes including antigen-presentation, stimulation of anti-tumoral immune responses, tolerogenic or inflammatory effects. In pathogens, EV shedding is well described in fungi, bacteria, protozoan and helminths parasites. For Trypanosoma cruzi EV liberation and protein composition was previously described. Dendritic cells (DCs), among other cells, are key players promoting the immune response against pathogens and also maintaining self-tolerance. In previous reports we have demonstrate that T. cruzi downregulates DCs immunogenicity in vitro and in vivo. Here we analyze EVs from the in vitro interaction between blood circulating trypomastigotes (Tp) and bone-marrow-derived DCs. We found that Tp incremented the number and the size of EVs in cultures with DCs. EVs displayed some exosome markers and intracellular RNA. Protein analysis demonstrated that the parasite changes the DC protein-EV profile. We observed that EVs from the interaction of Tp-DCs were easily captured by unstimulated-DCs in comparison with EVs from DCs cultured without the parasite, and also modified the activation status of LPS-stimulated DCs. Noteworthy, we found protection in animals treated with EVs-DCs+Tp and challenged with T. cruzi lethal infection. Our goal is to go deep into the molecular characterization of EVs from the DCs-Tp interaction, in order to identify mediators for therapeutic purposes.
Mean joint residence time of two brownian particles in a sphere

We calculate the mean joint residence time of two Brownian particles in a sphere, for very general initial conditions. In particular, we focus on the dependence of this residence time as a function of the diffusion coefficients of the two particles. Our results can be useful for describing kinetics of bimolecular diffusion controlled reactions activated by catalytic sites.
Mid-Infrared Imaging of Young Stellar Objects

We present arcsecond resolution mid-infrared (8{endash}13 {mu}m) images and photometry of four young stellar objects (YSOs){emdash}L1551-IRS 5, HL Tau, AS 205, and AS 209 (V1121 Oph){emdash}taken with the Berkeley Mid-Infrared Camera. For AS 205, a known T Tauri binary, we also present near-infrared {ital JHK} images and {ital HKL}{prime} speckle imaging data. All three single stars are unresolved in our mid-IR images, consistent with current models of the circumstellar material associated with these objects. Our data are the first to resolve in the mid-IR both components of the close binary AS 205 (projected separation {approximately}1{center_dot}{double_prime}3 [210 AU]). Both stars are classical T Tauri stars and possess the 9.7 {mu}m silicate feature in emission. AS 205 North is the IR brighter star in our data, while published observations find it to be the optically fainter star. Assuming that the IR excesses of both components arise from circumstellar disks, we find the emitting regions (the inner few AU) of the disks to be optically thick in the mid-IR. Pre-main-sequence evolutionary models suggest that the AS 205 system is non-coeval; we discuss possible explanations for this result and comment on the evolutionary status of this young binary. All our objects, except perhaps ASmore » 205 South, exhibit changes in their mid-IR flux in measurements separated by intervals of days up to many years; the variations range from 30{percent}{endash}300{percent}. For the classical T Tauri stars AS 205 North and AS 209, the magnitude of the changes seems to discount the possibility that the mid-IR variations have the same origin as the optical and near-IR variability of T Tauri stars, namely, accretion-related features on or near the stellar photosphere. We speculate that the cause of the variability lies in the accretion disks of these objects; the data suggest disk accretion rate fluctuations of nearly an order of magnitude. (Abstract Truncated)« less