Miracle-dz/UniFAR-FTUs huggingface dataset:
Pulmonary, Gastrointestinal and Urogenital Pharmacology Effects of umbelliferone in a murine model of allergic airway inflammation

article i nfo The therapeutic effects of umbelliferone (30, 60 and 90 mg/kg), a coumarin isolated from Typha domingensis (Typhaceae) were investigated in a mouse model of bronchial asthma. BALB/c mice were immunized and challenged by nasal administration of ovalbumin. Treatment with umbelliferone (60 and 90 mg/kg) caused a marked reduction of cellularity and eosinophil numbers in bronchoalveolar lavage fluids from asthmatic mice. In addition,a decrease in mucus production andlung inflammationwere observed in mice treated with umbelliferone. A reduction of IL-4, IL-5, and IL-13, but not of IFN-γ, was found in bronchoalveolar lavage fluids of mice treated with umbelliferone, similar to that observed with dexamethasone. The levels of ovalbumin-specifi cI gE were not significantly altered after treatment with umbelliferone. In conclusion, our results demonstrate that umbelliferone attenuates the alteration characteristics of allergic airway inflammation. The investigation of the mechanisms of action of this molecule may contribute for the development of new drugs for the treatment of asthma.
Factors associated with mortality among asphyxiated newborns in a low-resource setting

Abstract Objective Neonatal asphyxia accounts for a quarter of neonatal deaths. We aimed to assess factors associated with mortality among asphyxiated neonates in a low-resource setting. Methods A retrospective observational study evaluating all neonates who were admitted for asphyxia to the Neonatal Intensive Care Unit (NICU) at Tosamaganga Hospital (Tanzania) in 2017–2018. Inclusion criteria were: Apgar score <7 at 5 min and/or failure to initiate spontaneous breathing and/or presence of sentinel events and/or clinical signs suggesting encephalopathy not explained by other obvious factors or early convulsions. Newborns with congenital malformations, birth weight <2000 g or those who died in the delivery room were excluded. Results NICU admission for perinatal asphyxia was 17.5%. In 169 neonates, mortality rate was 23% and was associated with being outborn, low 5-minute Apgar score, depressed clinical status at NICU admission, occurrence of infection or seizures within 24 h from admission, and receiving aminophylline during the hospital stay. Conclusions Perinatal asphyxia was responsible for a relevant proportion of NICU admissions and neonatal deaths in a low-resource setting. Appropriate clinical examination remains the main asset in settings with limited availability of diagnostic tools. Improvements in antenatal and perinatal care are needed to reduce mortality in asphyxiated newborns. Future studies should assess long-term outcome in survivors.
Mitochondrial bioenergetics and redox dysfunction in nephrotoxicity induced by pyrethroid permethrin are ameliorated by �avonoid-rich fraction

Recent studies suggest that mitochondrial bioenergetics and oxidative status perturbations may be common mechanisms involved in the progression of renal damage. The present study aimed to evaluate in vitro the potential anti-in�ammatory using membrane stabilization and protein denaturation inhibition assays and in vivo protective effect of �avonoid- rich fraction from Fumaria o�cinalis (EAF) against permethrin (PER) induced nephrotoxicity in male rat. Animals were allocated into four groups: control; EAF (200 mg/Kg BW); PER (34.05 mg/Kg BW); and PER (34.05 mg/Kg BW) + EAF (200 mg/Kg BW) for 7 days. Our results suggest that EAF inhibited signi�cantly protein denaturation and restored membrane stabilization. In vivo , permethrin-treated rats caused a substantial reduction of body weight gain and plasma calcium (Ca), phosphorus (P) and vitamin C levels as well as an increase of absolute and relative kidney weights and plasma lactate dehydrogenase (LDH) activity and kidney and mitochondria thiobarbituric acid reactive substance (TBARS), advanced oxidation protein product (AOPP) and protein carbonyl (PCO) levels. PER also caused renal and mitochondrial enzymatic and non-enzymatic antioxidant perturbation as well as mitochondrial NADH-ubiquinone reductase (complex I), ubiquinol cytochrome c reductase (complex III) and cytochrome c oxidase (complex IV) activities reduction associated with renal histopathological alterations. However, co-administration of EAF to the PER group restored oxidative status and mitochondrial bioenergetics. We suggest that EAF may be considered as a future therapeutic anti-in�ammatory and may be used singly or as a co-therapeutic in the treatment of diseases associated with mitochondrial oxidative stress.
Coronary Artery anomalies in PatienTs Undergoing transcatheter aortic valve REplacement. The CAPTURE registry

Background: The incidence and possible implications of coronary artery anomalies (CAA) in patients undergoing transcatheter aortic valve replacement (TAVR) are uncertain. Aims: To evaluate the impact of CAA on TAVR outcomes, and to suggest possible strategies to prevent CAA related complications. Methods: Among 2,164 consecutive patients who underwent TAVR in our center, 15 (0.69%) were identified to have a CAA, based on pre-operative Computed Tomography (CT) scans. Results: CT-angiography revealed the following features of CAA: the majority of anomalous CAA concerned the right coronary artery (80%), followed by the left main (13.3%) and the left circumflex (6.7%). An intramural course was observed only in 26.7% patients, whereas an acute take-off was detected in more than half of the study cohort (53.3%). High-risk sudden cardiac death features were observed in 6 (40%) patients. Technical success was 86.7%, device success was 80%. One patient experienced a cardiac arrest 15 minutes after procedure, resulting from occlusion of the anomalous right coronary artery with the ostium located at the right-to-non coronary commissure. There were no cases of ? moderate paravalvular leak or stroke. One non-cardiac related death was recorded 4 months after the procedure. Conclusions: The interaction between transcatheter bioprosthesis and different CAA types could lead to ominous sequelae, if not promptly recognized and treated accordingly.
Method to Test Etiologic Heterogeneity Among Non-Competing Diagnoses that Accrue Over Time: Application to Discriminating the Impact of Perinatal Exposures on Autism and Attention Deficit Hyperactivity Disorder

Background: Testing etiologic heterogeneity, whether a disorder subtype is more or less impacted by a risk factor, is important toward understanding causal pathways and optimizing statistical power. The study of mental health disorders especially benefits from strategic sub-categorization because these disorders are heterogenous and frequently co-occur. Existing methods to quantify etiologic heterogeneity are not appropriate for non-competing events in an open cohort of variable-length follow-up. Thus, we developed a new method. Methods: We estimated risks from urban residence, maternal smoking during pregnancy, and parental psychiatric history, with subtypes defined by the presence or absence of a co-diagnosis: autism alone, attention deficit hyperactivity disorder (ADHD) alone, and joint diagnoses of autism+ADHD. To calculate the risk of a single diagnosis (e.g. autism alone), we subtracted the risk for autism+ADHD from the risk for autism overall. We tested the equivalency of average risk ratios over time, using a Wald-type test and bootstrapped standard errors. Results: Urban residence was most strongly linked with autism+ADHD and least with ADHD only; maternal smoking was associated with ADHD only but not autism only; and parental psychiatric history exhibited similar associations with all subgroups. Conclusions: Our method allowed the calculation of appropriate p values to test strength of association, showing etiologic heterogeneity wherein 2 of these 3 risk factors exhibited different impacts across diagnostic subtypes. The method used all available data, avoided neurodevelopmental outcome misclassification, exhibited robust statistical precision, and is applicable to similar heterogeneous complex conditions using common diagnostic data with variable follow-up.
Analyse comparative des différents produits satellitaires d'estimation des précipitations en Amazonie brésilienne

Les circulations atmospheriques synoptiques et locales expliquent les variabilites spatiotemporelles des precipitations en Amazonie bresilienne. Ce vaste espace geographique est caracterise par un reseau pluviometrique peu dense et heterogene qui limite un suivi exhaustif des pluies. La teledetection est alors l´outil preferentiel afin de pallier cette lacune spatiale. Toutefois, les estimations quantitatives des precipitations (QPE) derivees des domaines spectraux des infrarouges (IR) et Micro-ondes (MO), ou de techniques multi canaux souffrent d´erreurs. Les sources d´incertitudes et biais des QPE peuvent provenir de la calibration des capteurs, de l´algorithmie et de l´echantillonnage des champs de pluie. Dans cette these, l´evaluation des algorithmes TRMM3B42(v6), CMORPH et PERSIANN s´appuie sur une base de donnees pluviometriques dont la fiabilite est assuree par un controle de qualite rigoureux. Sur la periode 2003-2009, l’inter comparaison des produits satellitaires montre un faible accord (coefficient de determination < 0,30) avec la base de reference en Amazonie bresilienne Legale. TRMM3B42(v6) presente la meilleure performance avec un echantillonnage correct des champs de pluie. En outre, un cas d’etudes montre que les erreurs des QPE par satellite sont plus importantes en milieu forestier, notamment pour le produit MO MWCOMB. Enfin, la correction des grilles satellitaires par PDF Matching permet de realiser une analyse climatologique approfondie et amelioree par rapport a la base de reference
High-resolution structure of a retroviral protease folded as a monomer

The crystal structure of Mason–Pfizer monkey virus protease folded as a monomer has been solved by molecular replacement using a model generated by players of the online game Foldit. The structure shows at high resolution the details of a retroviral protease folded as a monomer which can guide rational design of protease dimerization inhibitors as retroviral drugs.
Estimated HIV Incidence in the United States, 2006–2009

Background The estimated number of new HIV infections in the United States reflects the leading edge of the epidemic. Previously, CDC estimated HIV incidence in the United States in 2006 as 56,300 (95% CI: 48,200–64,500). We updated the 2006 estimate and calculated incidence for 2007–2009 using improved methodology. Methodology We estimated incidence using incidence surveillance data from 16 states and 2 cities and a modification of our previously described stratified extrapolation method based on a sample survey approach with multiple imputation, stratification, and extrapolation to account for missing data and heterogeneity of HIV testing behavior among population groups. Principal Findings Estimated HIV incidence among persons aged 13 years and older was 48,600 (95% CI: 42,400–54,700) in 2006, 56,000 (95% CI: 49,100–62,900) in 2007, 47,800 (95% CI: 41,800–53,800) in 2008 and 48,100 (95% CI: 42,200–54,000) in 2009. From 2006 to 2009 incidence did not change significantly overall or among specific race/ethnicity or risk groups. However, there was a 21% (95% CI:1.9%–39.8%; p = 0.017) increase in incidence for people aged 13–29 years, driven by a 34% (95% CI: 8.4%–60.4%) increase in young men who have sex with men (MSM). There was a 48% increase among young black/African American MSM (12.3%–83.0%; p<0.001). Among people aged 13–29, only MSM experienced significant increases in incidence, and among 13–29 year-old MSM, incidence increased significantly among young, black/African American MSM. In 2009, MSM accounted for 61% of new infections, heterosexual contact 27%, injection drug use (IDU) 9%, and MSM/IDU 3%. Conclusions/Significance Overall, HIV incidence in the United States was relatively stable 2006–2009; however, among young MSM, particularly black/African American MSM, incidence increased. HIV continues to be a major public health burden, disproportionately affecting several populations in the United States, especially MSM and racial and ethnic minorities. Expanded, improved, and targeted prevention is necessary to reduce HIV incidence.
CSI-Inpainter: Enabling Visual Scene Recovery from CSI Time Sequences for Occlusion Removal

Introducing CSI-Inpainter, a pioneering approach for occlusion removal using Channel State Information (CSI) time sequences, this work propels the application of wireless signal processing into the realm of visual scene recovery. Departing from traditional occlusion removal, CSI-Inpainter leverages CSI data to construct and refine obscured visual elements in a scene, facilitating recovery independent of lighting conditions. Validated through comprehensive testing in both office and industrial environments, CSI-Inpainter demonstrates a robust capacity for discerning and reconstructing occluded segments, establishing a new frontier for obstacle removal. This first-of-its-kind framework offers a transformative perspective on how environmental visual information can be extracted from CSI, thereby broadening the scope for computer vision applications in everyday contexts.
SMILEtrack: SiMIlarity LEarning for Occlusion-Aware Multiple Object Tracking

Despite recent progress in Multiple Object Tracking (MOT), several obstacles such as occlusions, similar objects, and complex scenes remain an open challenge. Meanwhile, a systematic study of the cost-performance tradeoff for the popular tracking-by-detection paradigm is still lacking. This paper introduces SMILEtrack, an innovative object tracker that effectively addresses these challenges by integrating an efficient object detector with a Siamese network-based Similarity Learning Module (SLM). The technical contributions of SMILETrack are twofold. First, we propose an SLM that calculates the appearance similarity between two objects, overcoming the limitations of feature descriptors in Separate Detection and Embedding (SDE) models. The SLM incorporates a Patch Self-Attention (PSA) block inspired by the vision Transformer, which generates reliable features for accurate similarity matching. Second, we develop a Similarity Matching Cascade (SMC) module with a novel GATE function for robust object matching across consecutive video frames, further enhancing MOT performance. Together, these innovations help SMILETrack achieve an improved trade-off between the cost (e.g., running speed) and performance (e.g., tracking accuracy) over several existing state-of-the-art benchmarks, including the popular BYTETrack method. SMILETrack outperforms BYTETrack by 0.4-0.8 MOTA and 2.1-2.2 HOTA points on MOT17 and MOT20 datasets. Code is available at http://github.com/pingyang1117/SMILEtrack_official.
Topical: Learning Repository Embeddings from Source Code using Attention

This paper presents Topical, a novel deep neural network for repository level embeddings. Existing methods, reliant on natural language documentation or naive aggregation techniques, are outperformed by Topical's utilization of an attention mechanism. This mechanism generates repository-level representations from source code, full dependency graphs, and script level textual data. Trained on publicly accessible GitHub repositories, Topical surpasses multiple baselines in tasks such as repository auto-tagging, highlighting the attention mechanism's efficacy over traditional aggregation methods. Topical also demonstrates scalability and efficiency, making it a valuable contribution to repository-level representation computation. For further research, the accompanying tools, code, and training dataset are provided at: https://github.com/jpmorganchase/topical.
Treatment and survival analysis for 40-year SEER data on upper esophageal cancer

Background Upper esophageal cancer (UEC) is rare in both Eastern and Western countries. The epidemiological characteristics and long-term survival of UEC patients are less known. In addition, the choice of optimal treatment for UEC has been controversial. Methods Cases of UEC (C15.3 and C15.0) arising during the period from 1973 to 2013 were identified and selected using the SEER database. Student's t-test and Pearson's chi-square test were used to compare the differences in parameters among different groups. Esophageal cancer-specific survival (ECSS) and overall survival (OS) rates were calculated by using the Kaplan–Meier method. Cox proportional hazard regression was used to analyze predictive factors. Results In the past 40 years, the cases of UEC have gradually increased, and the proportion of adenocarcinoma (AD) has gradually increased (from 3.6% to 11.8%, p < 0.001). There has been a significant increase (1973–1982 vs. 2004–2013) in median OS (7 months vs. 10 months, p < 0.001) and median ECSS (7 months vs. 11 months, p < 0.001) among UEC patients from 1973 to 2013. For the impact of different treatments, the results showed that the ECSS and OS of surgery without radiation (SWR) and radiation plus surgery (R+S) were superior to those of radiation without surgery (RWS). Subgroup analysis showed that ECSS and OS were highest among patients treated with SWR compared with R+S and RWS for patients with localized disease. For regional disease, ECSS and OS were highest among patients with R+S compared with SWR or RWS. Among patients with regional-stage squamous cell carcinoma (SCC), OS was higher with neoadjuvant radiotherapy or adjuvant radiotherapy compared with SWR. Multivariate analysis showed that radiotherapy sequence was dependently associated with OS among patients with regional-stage SCC. Conclusion Although the long-term survival of UEC remains poor, it has gradually increased since 1973. This should be closely related to the improvement of medical care over the past 40 years. Different treatment methods have a great influence on the long-term survival of UEC. For localized diseases, surgery may be a better choice. For regional disease, surgery plus adjuvant or neoadjuvant radiotherapy may be more beneficial to improve the long-term prognosis of UEC patients.
Towards Certification of Machine Learning-Based Distributed Systems

—Machine Learning (ML) is increasingly used to drive the operation of complex distributed systems deployed on the cloud-edge continuum enabled by 5G. Correspondingly, distributed systems’ behavior is becoming more non-deterministic in nature. This evolution of distributed systems requires the definition of new assurance approaches for the verification of non-functional properties. Certification, the most popular assurance technique for system and software verification, is not immediately applicable to systems whose behavior is determined by Machine Learning-based inference. However, there is an increasing push from policy makers, regulators, and industrial stakeholders towards the definition of techniques for the certification of non-functional properties (e.g., fairness, robustness, privacy) of ML. This article analyzes the challenges and deficiencies of current certification schemes, discusses open research issues and proposes a first certification scheme for ML-based distributed systems.
Paisley: Preliminary validation of a novel app‐based e‐Screener for ASD in children 18–36 months

The purpose of this study was to assess the validity of an autism e‐screener, Paisley, when utilized in a clinical research setting via a tablet application. The Paisley application used a series of play‐based activities, all of which incorporated varying aspects of the ASD‐PEDS. Participants included children (18–36 months; n = 198) referred for evaluation of autism spectrum disorder (ASD) and community providers (n = 66) with differing levels of familiarity with ASD. Community providers administered the Paisley application to children who then completed a comprehensive psychological evaluation. Based on comprehensive evaluation, 75% of children met diagnostic criteria for ASD. Paisley scores were significantly higher for children diagnosed with ASD (15.06) versus those not diagnosed (9.34). The newly determined cutoff ASD‐PEDS cutoff score of 13 had significantly higher specificity and positive predictive value than the originally proposed cutoff of 11. Results support the use of Paisley by community providers to identify autism risk in toddlers. Limitations and strengths of the work, as well as opportunities for future clinical validation, are described.
Periplasmic stress contributes to a trade-off between protein secretion and cell growth in Escherichia coli Nissle 1917

Abstract Maximizing protein secretion is an important target in the design of engineered living systems. In this paper, we characterize a trade-off between cell growth and per-cell protein secretion in the curli biofilm secretion system of Escherichia coli Nissle 1917. Initial characterization using 24-h continuous growth and protein production monitoring confirms decreased growth rates at high induction, leading to a local maximum in total protein production at intermediate induction. Propidium iodide (PI) staining at the endpoint indicates that cellular death is a dominant cause of growth reduction. Assaying variants with combinatorial constructs of inner and outer membrane secretion tags, we find that diminished growth at high production is specific to secretory variants associated with periplasmic stress mediated by outer membrane secretion and periplasmic accumulation of protein containing the outer membrane transport tag. RNA sequencing experiments indicate upregulation of known periplasmic stress response genes in the highly secreting variant, further implicating periplasmic stress in the growth–secretion trade-off. Overall, these results motivate additional strategies for optimizing total protein production and longevity of secretory engineered living systems Graphical Abstract
NLR receptors in plant immunity: making sense of the alphabet soup

Plants coordinately use cell‐surface and intracellular immune receptors to perceive pathogens and mount an immune response. Intracellular events of pathogen recognition are largely mediated by immune receptors of the nucleotide binding and leucine rich‐repeat (NLR) classes. Upon pathogen perception, NLRs trigger a potent broad‐spectrum immune reaction, usually accompanied by a form of programmed cell death termed the hypersensitive response. Some plant NLRs act as multifunctional singleton receptors which combine pathogen detection and immune signaling. However, NLRs can also function in higher order pairs and networks of functionally specialized interconnected receptors. In this article, we cover the basic aspects of plant NLR biology with an emphasis on NLR networks. We highlight some of the recent advances in NLR structure, function, and activation and discuss emerging topics such as modulator NLRs, pathogen suppression of NLRs, and NLR bioengineering. Multi‐disciplinary approaches are required to disentangle how these NLR immune receptor pairs and networks function and evolve. Answering these questions holds the potential to deepen our understanding of the plant immune system and unlock a new era of disease resistance breeding.