Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein Expression Profiles in Exosomes of Bovine Mammary Epithelial Cell Line MAC-T Infected with Staphylococcus aureus

Mastitis is a widespread infectious disease in dairy farms, resulting in reduced milk production and quality. Staphylococcus aureus is one of the main pathogenic bacteria causing subclinical mastitis. Exosomes contain proteins, lipids, and nucleic acids, which are involved in many physiological and pathological functions. ABSTRACT Mastitis is a common and widespread infectious disease in dairy farms around the world, resulting in reduced milk production and quality. Staphylococcus aureus is one of the main pathogenic bacteria causing subclinical mastitis in dairy cows. S. aureus can activate inflammatory signaling pathways in bovine mammary epithelial cells. Exosomes produced by cells can directly transfer pathogen-related molecules from cell to cell, thus affecting the process of infection. Protein is the material basis of the immune defense function in the body; therefore, a comprehensive comparison of proteins in exosomes derived from S. aureus-infected (SA group) and normal (control group [C group]) bovine mammary epithelial MAC-T cells was performed using shotgun proteomics by a DIA approach. A total of 7,070 proteins were identified and quantified. Compared with the C group, there were 802 differentially expressed proteins (DEPs) identified in the SA group (absolute log2 fold change [|log2FC|] of ≥0.58; false discovery rate [FDR] of <0.05), among which 325 proteins were upregulated and 477 were downregulated. The upregulated proteins, including complement 3 (C3), integrin alpha-6 (ITGA6), apolipoprotein A1 (APOA1), annexin A2 (ANXA2), tripeptidyl peptidase II (TPP2), keratin 8 (KRT8), and recombinant desmoyokin (AHNAK), are involved mostly in host defense against pathogens, inflammation, and cell structure maintenance. KEGG enrichment analysis indicated that DEPs in S. aureus infection were involved in the complement and coagulation cascade, phagosome, extracellular matrix (ECM)-receptor interaction, and focal adhesion pathways. The results of this study provide novel information about proteins in the exosomes of MAC-T cells infected with S. aureus and could contribute to an understanding of the infectious mechanism of bovine mastitis. IMPORTANCE Mastitis is a widespread infectious disease in dairy farms, resulting in reduced milk production and quality. Staphylococcus aureus is one of the main pathogenic bacteria causing subclinical mastitis. Exosomes contain proteins, lipids, and nucleic acids, which are involved in many physiological and pathological functions. The expression of proteins in exosomes derived from bovine mammary epithelial cells infected by S. aureus is still barely understood. These results provide novel information about MAC-T-derived exosomal proteins, reveal insights into their functions, and lay a foundation for further studying the biological function of exosomes during the inflammatory response.
Collection of triatomines from sylvatic habitats by a Trypanosoma cruzi-infected scent detection dog in Texas, USA

Background Triatomine insects, vectors of the etiologic agent of Chagas disease (Trypanosoma cruzi), are challenging to locate in sylvatic habitats. Collection techniques used in the United States often rely on methods to intercept seasonally dispersing adults or on community scientists’ encounters. Neither method is suited for detecting nest habitats likely to harbor triatomines, which is important for vector surveillance and control. Furthermore, manual inspection of suspected harborages is difficult and unlikely to reveal novel locations and host associations. Similar to a team that used a trained dog to detect sylvatic triatomines in Paraguay, we worked with a trained scent detection dog to detect triatomines in sylvatic locations across Texas. Principle methodology/Findings Ziza, a 3-year-old German Shorthaired Pointer previously naturally infected with T. cruzi, was trained to detect triatomines. Over the course of 6 weeks in the fall of 2017, the dog and her handler searched at 17 sites across Texas. The dog detected 60 triatomines at 6 sites; an additional 50 triatomines were contemporaneously collected at 1 of these sites and 2 additional sites without the assistance of the dog. Approximately 0.98 triatomines per hour were found when only humans were conducting searches; when working with the dog, approximately 1.71 triatomines per hour were found. In total, 3 adults and 107 nymphs of four species (Triatoma gerstaeckeri, Triatoma protracta, Triatoma sanguisuga, and Triatoma indictiva) were collected. PCR testing of a subset revealed T. cruzi infection, including DTUs TcI and TcIV, in 27% of nymphs (n = 103) and 66% of adults (n = 3). Bloodmeal analysis of a subset of triatomines (n = 5) revealed feeding on Virginia opossum (Didelphis virginiana), Southern plains woodrat (Neotoma micropus), and eastern cottontail (Sylvilagus floridanus). Conclusion/Significance A trained scent detection dog enhanced triatomine detections in sylvatic habitats. This approach is effective at detecting nidicolous triatomines. Control of sylvatic sources of triatomines is challenging, but this new knowledge of specific sylvatic habitats and key hosts may reveal opportunities for novel vector control methods to block the transmission of T. cruzi to humans and domestic animals.
NON-AXISYMMETRIC PERPENDICULAR DIFFUSION OF CHARGED PARTICLES AND THEIR TRANSPORT ACROSS TANGENTIAL MAGNETIC DISCONTINUITIES

We investigate the transport of charged particles across magnetic discontinuities, focusing specifically on stream interfaces associated with co-rotating interaction regions in the solar wind. We argue that the magnetic field fluctuations perpendicular to the magnetic discontinuity, and usually also perpendicular to the mean magnetic field, are strongly damped in the vicinity of such a magnetic structure, leading to anisotropic perpendicular diffusion. Assuming that perpendicular diffusion arises from drifts in a turbulent magnetic field, we adopt a simplified approach to derive the relevant perpendicular diffusion coefficient. This approach, which we believe gives the correct principal dependences as expected from more elaborate calculations, allows us to investigate transport in different turbulent geometries, such as longitudinal compressional turbulence that may be present near the heliopause. Although highly dependent on the (possibly anisotropic) perpendicular length scales and turbulence levels, we generally find perpendicular diffusion to be strongly damped at magnetic discontinuities, which may in turn provide an explanation for the large particle gradients associated with these structures.
Experiments and modelling of active control of MHD instabilities

The plasma in a controlled thermonuclear fusion experiment is a complex nonlinear system, whose dynamics can be largely due to the interplay of multiple MagnetoHydroDynamic MHD instabilities that coexist together. The main aim of this Thesis work is to develop the knowledge on the active control of these instabilities, an important aspect of present controlled fusion research. The possibility to safely operate a plasma near instability limits, or even beyond them in regimes that are unstable without control, has a twofold advantage: it allows not only to extend the operational boundaries of the possible plasma scenarios and their performance, for example towards high normalized pressure or high plasma current, but also to explore new physics, that otherwise would remain veiled. The main principles of thermonuclear fusion and a brief introduction to the physics of the MHD instabilities investigated in this Thesis, namely Tearing Modes TMs, Resistive Wall Modes RWMs and sawteeth, is provided in Chapter 1. A distinctive feature of this Thesis is its interdisciplinary approach to the active control of MHD instabilities, which has required investigations on both physics and engineering aspects. This approach is necessary for the advance of MHD control, since the scienti c progress keeps up with the technological one, and vice versa. This Thesis work has been carried out in three di erent fusion experiments, all equipped with advanced real-time systems for active MHD control, based both on non axi-symmetric coils and wave heating and current drive. The work has been focused initially on the RFX-mod device at Consorzio RFX, Padua, Italy, and then extended to larger Tokamaks, namely DIII-D at General Atomics, San Diego, USA, and ASDEX Upgrade at Max-Planck-Institute für Plasmaphysik in Garching, Germany. These experiments will be described in Chapter 2. RFX-mod stands out among other machines for its exibility: besides being born as a Reversed Field Pinch RFP, it can operate also as a circular and D-shaped Tokamak. The MHD stability in both magnetic con gurations is guaranteed by its sophisticated MHD control system, based on a large number of
Toward a statistical validation of brain signatures as robust measures of behavioral substrates

The “brain signature of cognition” concept has garnered interest as a data‐driven, exploratory approach to better understand key brain regions involved in specific cognitive functions, with the potential to maximally characterize brain substrates of behavioral outcomes. Previously we presented a method for computing signatures of episodic memory. However, to be a robust brain measure, the signature approach requires a rigorous validation of model performance across a variety of cohorts. Here we report validation results and provide an example of extending it to a second behavioral domain. In each of two discovery data cohorts, we derived regional brain gray matter thickness associations for two domains: neuropsychological and everyday cognition memory. We computed regional association to outcome in 40 randomly selected discovery subsets of size 400 in each cohort. We generated spatial overlap frequency maps and defined high‐frequency regions as “consensus” signature masks. Using separate validation datasets, we evaluated replicability of cohort‐based consensus model fits and explanatory power by comparing signature model fits with each other and with competing theory‐based models. Spatial replications produced convergent consensus signature regions. Consensus signature model fits were highly correlated in 50 random subsets of each validation cohort, indicating high replicability. In comparisons over each full cohort, signature models outperformed other models. In this validation study, we produced signature models that replicated model fits to outcome and outperformed other commonly used measures. Signatures in two memory domains suggested strongly shared brain substrates. Robust brain signatures may therefore be achievable, yielding reliable and useful measures for modeling substrates of behavioral domains.
Recombinant Fusion Protein Vaccine Containing Clostridioides difficile FliC and FliD Protects Mice against C. difficile Infection

Bacterial flagella are involved in infection through their roles in host cell adhesion, cell invasion, auto-agglutination, colonization, the formation of biofilms, and the regulation and secretion of nonflagellar bacterial proteins that are involved in the virulence process. In this study, we constructed a fusion protein vaccine (FliCD) containing the Clostridioides difficile flagellar proteins FliC and FliD. ABSTRACT Bacterial flagella are involved in infection through their roles in host cell adhesion, cell invasion, auto-agglutination, colonization, the formation of biofilms, and the regulation and secretion of nonflagellar bacterial proteins that are involved in the virulence process. In this study, we constructed a fusion protein vaccine (FliCD) containing the Clostridioides difficile flagellar proteins FliC and FliD. The immunization of mice with FliCD induced potent IgG and IgA antibody responses against FliCD, protected mice against C. difficile infection (CDI), and decreased the C. difficile spore and toxin levels in the feces after infection. Additionally, the anti-FliCD serum inhibited the binding of C. difficile vegetative cells to HCT8 cells. These results suggest that FliCD may represent an effective vaccine candidate against CDI.
Risk factors associated with 30-day hospital readmissions among persons living with HIV in Nantong, China

Objective To estimate 30-day hospital readmission rates among persons living with HIV (PLWH) at the Nantong Infectious Disease Hospital in China and analyse the related risk factors. Methods A single-centre retrospective cohort study was conducted. There were 894 PLWH records obtained from the electronic medical record (EMR) system at the Nantong Infectious Disease Hospital in China, from October 2013 to February 2018. The 30-day readmission rates were calculated, and the risk factors were analysed by generalised estimating equations (GEEs). Results A total of 1153 hospitalizations from 894 patients were recorded between October 2013 and February 2018. The median time of 30-day readmissions was 13 days (interquartile range (IQR), 6–23). The reasons for all causes, acquired immunodeficiency syndrome (AIDS)-defining illnesses (ADIs), and non-AIDS-defining infections (non-ADIs) were 9.08, 13.52, and 7.91%, respectively. The results from the GEE analysis demonstrated that the risk factors associated with 30-days readmissions were as follows: no antiretroviral therapy (ART) prior to hospitalisations (odds ratio (OR) = 1.90, 95% confidence interval (CI): 1.21–3.00), low CD4 counts (OR = 2.17, 95% CI: 1.33–3.54), and multiple comorbidities (OR = 6.45, 95% CI: 1.62–25.73). Conclusion Early detection of HIV infection and early initiation of ART treatment are the keys to controlling 30-day readmissions.
Associations between lower extremity muscle fat fraction and motor performance in myotonic dystrophy type 2: A pilot study

Although muscle structure measures from magnetic resonance imaging (MRI) have been used to assess disease severity in muscular dystrophies, little is known about how these measures are affected in myotonic dystrophy type 2 (DM2). We aim to characterize lower extremity muscle fat fraction (MFF) as a potential biomarker of disease severity, and evaluate its relationship with motor performance in DM2.
Models of surface convection and dust clouds in brown dwarfs

The influence of dust grains on the atmospheres of brown dwarfs is visible in observed spectra. To investigate what prevents the dust grains from falling down, or how fresh condensable material is mixed up in the atmosphere to allow new grains to form, we performed 2D radiation-hydrodynamics simulations with CO5BOLD of the upper part of the convection zone and the atmosphere containing the dust cloud layers. We find that unlike in models of Cepheids, the convective overshoot does not play a major role. Instead, the mixing in the dust clouds is controlled by gravity waves.
Youth Sport Coaches’ Perceptions of Sexually Inappropriate Behaviors and Intimate Coach-Athlete Relationships

ABSTRACT Although sexual harassment and abuse in youth sport have received increasing research attention worldwide, less is known about youth coaches’ perceptions of sexually inappropriate behaviors and intimate relationships with athletes. The purpose of this exploratory study was to examine youth sport coaches’ perceptions of behaviors that can lead to potential sexual harassment and abuse, as well as to understand how coaches perceive coach-athlete sexual relationships. A cross-sectional survey was completed by 200 male coaches from various U.S. youth sport programs. Overall, a majority of coaches indicated behaviors associated with sexist comments and verbal/physical advances as sexually inappropriate. There was, however, a lack of consensus regarding what constitutes sexually inappropriate behaviors when the behavior was instruction-related/contextually dependent. Results were mixed regarding the perceptions of coach-athlete sexual relationships, with a notable number of coaches agreeing that sexual intimacies with young athletes (17 years or younger) are not always harmful and should not be prohibited. Based on a regression analysis, white coaches were more likely to exhibit negative perceptions about coach-athlete sexual relationships compared to ethnically diverse coaches. Overall, these findings warrant the development or reevaluation of policies and interventions aimed at preventing sexual harassment and abuse in the youth sport environment. Continued research is needed to better understand youth sport coaches as the perpetrators of sexual harassment and abuse.
Sodium Fluoride Exposure Leads to ATP Depletion and Altered RNA Decay in Escherichia coli under Anaerobic Conditions

Gram-negative Escherichia coli is a rod-shaped facultative anaerobic bacterium commonly found in microaerobic/anaerobic environments, including the dental plaques of warm-blooded organisms. These latter can be treated efficiently with fluoride-rich compounds that act as anticaries agents to prevent tooth decay. ABSTRACT Although fluoride-containing compounds are widely used to inhibit bacterial growth, the reprogramming of gene expression underlying cellular responses to fluoride, especially under anaerobic conditions, is still poorly understood. Here, we compare the genome-wide transcriptomic profiles of E. coli grown in the absence (control) or presence (20 and 70 mM) of sodium fluoride (NaF) under anaerobic conditions and assess the impact of fluoride-dependent ATP depletion on RNA turnover. Tiling array analysis revealed transcripts displaying altered abundance in response to NaF treatments. Quantile-based K-means clustering uncovered a subset of genes that were highly upregulated and then downregulated in response to increased and subsequently decreased fluoride concentrations, many of which (~40%) contained repetitive extragenic palindromic (REP) sequences. Northern blot analysis of some of these highly upregulated REP-containing transcripts (i.e., osmC, proP, efeO and yghA) confirmed their considerably enhanced abundance in response to NaF treatment. An mRNA stability analysis of osmC and yghA transcripts demonstrated that fluoride treatment slows down RNA degradation, thereby enhancing RNA stability and steady-state mRNA levels. Moreover, we demonstrate that turnover of these transcripts depends on RNase E activity and RNA degradosome. Thus, we show that NaF exerts significant effects at the whole-transcriptome level under hypoxic growth (i.e., mimicking the host environment), and fluoride can impact gene expression posttranscriptionally by slowing down ATP-dependent degradation of structured RNAs. IMPORTANCE Gram-negative Escherichia coli is a rod-shaped facultative anaerobic bacterium commonly found in microaerobic/anaerobic environments, including the dental plaques of warm-blooded organisms. These latter can be treated efficiently with fluoride-rich compounds that act as anticaries agents to prevent tooth decay. Although fluoride inhibits microbial growth by affecting metabolic pathways, the molecular mechanisms underlying its activity under anaerobic conditions remain poorly defined. Here, using genome-wide transcriptomics, we explore the impact of fluoride treatments on E. coli gene expression under anaerobic conditions. We reveal key gene clusters associated with cellular responses to fluoride and define its ATP-dependent stabilizing effects on transcripts containing repetitive extragenic palindromic sequences. We demonstrate the mechanisms controlling the RNA stability of these REP-containing mRNAs. Thus, fluoride can affect gene expression posttranscriptionally by stabilizing structured RNAs.
Non-anti TNFα biologic agents for noninfectious uveitis associated with systemic inflammatory diseases: a systematic review

ABSTRACT Introduction Noninfectious uveitis related to systemic inflammatory diseases represents a leading cause of blindness. Anti-TNFα agents are the first-line biologic therapy after traditional immunosuppressants, for ocular and systemic involvement. However, some patients fails anti-TNFα agents, due to primary inefficacy, loss of efficacy or adverse events. Areas covered This systematic review summarizes evidence on the efficacy and safety of non-anti-TNFα biologics in adult patients with noninfectious uveitis associated with systemic inflammatory diseases. The systematic review of PubMed and Embase yielded 3663 records, from which 16 studies were included (13 non-controlled, 3 controlled trials). Most studies focused on Behçet’s syndrome (BS) and juvenile idiopathic arthritis (JIA) and assessed the efficacy of tocilizumab (n = 11), rituximab (n = 3), secukinumab (n = 1), or anakinra/canakinumab (n = 1). A body of evidence supports the use of tocilizumab BS and JIA-associated uveitis, for improving visual acuity, reducing central macular thickness, inducing ocular remission, and sparing corticosteroids. Preliminary data suggest that rituximab may represent a valid alternative, particularly in JIA, while anakinra/canakinumab might play a role in BS-associated uveitis. The role of secukinumab appears limited. Expert opinion Current evidence encourages investigations on the efficacy and safety of non-anti-TNFα agents in noninfectious non-idiopathic uveitis.
Fluid Overload Precedes and Masks Cryptic Kidney Injury in Pediatric Acute Respiratory Distress Syndrome

OBJECTIVES: Given the complex interrelatedness of fluid overload (FO), creatinine, acute kidney injury (AKI), and clinical outcomes, the association of AKI with poor outcomes in critically ill children may be underestimated due to definitions used. We aimed to disentangle these temporal relationships in a large cohort of children with acute respiratory distress syndrome (ARDS). DESIGN: Retrospective cohort study. SETTING: Quaternary care PICU. PATIENTS: Seven hundred twenty intubated children with ARDS between 2011 and 2019. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Daily fluid balance, urine output (UOP), and creatinine for days 1–7 of ARDS were retrospectively abstracted. A subset of patients had angiopoietin 2 (ANGPT2) quantified on days 1, 3, and 7. Patients were classified as AKI by Kidney Disease Improving Global Outcomes (KDIGO) stage 2/3 then grouped by timing of AKI onset (early if days 1–3 of ARDS, late if days 4–7 of ARDS, persistent if both) for comparison of PICU mortality and ventilator-free days (VFDs). A final category of “Cryptic AKI” was used to identify subjects who met KDIGO stage 2/3 criteria only when creatinine was adjusted for FO. Outcomes were compared between those who had Cryptic AKI identified by FO-adjusted creatinine versus those who had no AKI. Conventionally defined AKI occurred in 26% of patients (early 10%, late 3%, persistent 13%). AKI was associated with higher mortality and fewer VFDs, with no differences according to timing of onset. The Cryptic AKI group (6% of those labeled no AKI) had higher mortality and fewer VFDs than patients who did not meet AKI with FO-adjusted creatinine. FO, FO-adjusted creatinine, and ANGPT2 increased 1 day prior to meeting AKI criteria in the late AKI group. CONCLUSIONS: AKI was associated with higher mortality and fewer VFDs in pediatric ARDS, irrespective of timing. FO-adjusted creatinine captures a group of patients with Cryptic AKI with outcomes approaching those who meet AKI by traditional criteria. Increases in FO, FO-adjusted creatinine, and ANGPT2 occur prior to meeting conventional AKI criteria.