Nutritional virulence of Legionella pneumophila.

Legionella pneumophila is an environment organism that parasitizes a wide range of protozoa. Growth within the environmental host primes L. pneumophila for infection of human alveolar macrophages when contaminated aerosols are inhaled. Intracellular replication within either host requires the establishment a replicative niche, known as the Legionella-containing vacuole (LCV). Biogenesis of the LCV depends on the type IVb translocation system, the Dot/Icm, to translocation \u3e320 effectors into the host cytosol. Effectors are responsible for preventing lysosome fusion to the LCV, recruitment of ER-derived vesicles to the LCV, and modulation of a plethora of host processes to promote the intracellular survival and replication of L. pneumophila. Nutrient requirements of the pathogen are reflective of its intracellular lifecycle, consuming host amino acids for carbon and energy. Amino acids, particularly serine and cysteine, are used to generate pyruvate to feed into the TCA cycle, which is the main metabolic pathway for generation of energy. Endogenous levels of host amino acids are insufficient to support robust intracellular replication. Excess host amino acids are generated by the AnkB effector through ubiquitination and proteasomal degradation of host proteins in the cytosol. Host amino acids must be transported across the LCV membrane to be utilized by L. pneumophila. Host solute carrier (SLC) transporters are the most likely candidate to import amino acids into the LCV lumen, as they have been detected in the LCV proteome of multiple mass-spectrometry studies. We sought to confirm the role of human SLCs in nutrient acquisition during intracellular growth of L. pneumophila. No amino acid-transporting SLCs were confirmed to colocalize to the LCV by confocal microscopy. However, a glucose transporter, SLC2a1/Glut1 was shown to be recruited the LCV in a Dot/Icm-dependent manner. The role of glucose in intracellular replication of L. pneumophila is poorly understood. Glucose minimally used through glycolysis, but metabolized through the Enter-Doudoroff pathway. Glucose does not support the replication of L. pneumophila during in vitro growth. We identified 10 SLC-like transporters in L. pneumophila based on their structural similarity to human SLCs. We characterized the role of two putative SLC-like glucose transporters, LstA and LstB of L. pneumophila, in import of glucose and in intracellular replication within human macrophages and amoebae. Single transporter mutants decrease L. pneumophila’s ability to import glucose but do not affect the ability to replicate within the host. Interestingly, the double mutant, lstA/lstB, is severely defective for import of glucose and for intracellular replication within human macrophages and Acanthamoeba polyphaga. These data show that glucose uptake by the redundant transporters, LstA and LstB, is required for in vivo growth. L. pneumophila encodes putative amylases effectors that may be degrading host glycogen as a means to generate glucose that is imported by LstA and LstB. We characterized the L. pneumophila amylase, LamB, because of its uniqueness amongst Legionella species. Here we describe LamB as a functional amylase that is required for intracellular replication of L. pneumophila in human macrophages and A. polyphaga. Additionally, the lamB mutant is completely attenuated in intra-pulmonary proliferation in the A/J mouse model. Taken together, these data further characterize nutritional virulence of L. pneumophila

Recurrent urinary tract infections and prophylactic antibiotic use in women: a cross-sectional study in primary care

Background Despite the considerable morbidity caused by recurrent urinary tract infections (rUTIs), and the wider personal and public health implications from frequent antibiotic use, few studies adequately describe the prevalence and characteristics of women with rUTIs or those who use prophylactic antibiotics.Aim To describe the prevalence, characteristics, and urine profiles of women with rUTIs with and without prophylactic antibiotic use in Welsh primary care.Design and setting This was a retrospective cross-sectional study in Welsh general practice using the Secure Anonymised Information Linkage (SAIL) Databank.Method The characteristics of women aged ≥18 years with rUTIs or using prophylactic antibiotics from 2010 to 2020, and associated urine culture results from 2015 to 2020, are described.Results In total, 6.0% (n = 92 213/N = 1 547 919) had rUTIs, and 1.7% (n = 26 862/N = 1 547 919) were prescribed prophylactic antibiotics with the rates increasing after 57 years of age. Only 49.0% (n =13 149/N = 26 862) of users of prophylactic antibiotics met the definition of rUTIs before initiation. The study found that 80.8% (n = 44 947/N = 55 652) of women with rUTIs had a urine culture result in the preceding 12 months with high rates of resistance to trimethoprim and amoxicillin. Of women taking prophylactic antibiotics, 64.2% (n = 9926/N = 15 455) had a urine culture result before initiation and 18.5% (n = 320/N = 1730) of women prescribed trimethoprim had resistance to it on the antecedent sample.Conclusion A substantial proportion of women had rUTIs or incident prophylactic antibiotic use. However, 64.2% (n = 9926/N = 15 455) of women had urine cultured before starting prophylaxis. There was a high proportion of cultured bacteria resistant to two antibiotics used for rUTI prevention and evidence of resistance to the prescribed antibiotic. More frequent urine cultures for rUTI diagnosis and before prophylactic antibiotic initiation could better inform antibiotic choices

Myocardial infarction and stroke subsequent to urinary tract infection (MISSOURI): protocol for a self-controlled case series using linked electronic health records

Introduction There is increasing interest in the relationship between acute infections and acute cardiovascular events. Most previous research has focused on understanding whether the risk of acute cardiovascular events increases following a respiratory tract infection. The relationship between urinary tract infections (UTIs) and acute cardiovascular events is less well studied. Therefore, the aim of this study is to determine whether there is a causal relationship between UTI and acute myocardial infarction (MI) or stroke.Methods and analysis We will undertake a self-controlled case series study using linked anonymised general practice, hospital admission and microbiology data held within the Secure Anonymised Information Linkage (SAIL) Databank. Self-controlled case series is a relatively novel study design where individuals act as their own controls, thereby inherently controlling for time-invariant confounders. Only individuals who experience an exposure and outcome of interest are included.We will identify individuals in the SAIL Databank who have a hospital admission record for acute MI or stroke during the study period of 2010–2020. Individuals will need to be aged 30–100 during the study period and be Welsh residents for inclusion. UTI will be identified using general practice, microbiology and hospital admissions data. We will calculate the incidence of MI and stroke in predefined risk periods following an UTI and in ‘baseline’ periods (without UTI exposure) and use conditional Poisson regression models to derive incidence rate ratios.Ethics and dissemination Data access, research permissions and approvals have been obtained from the SAIL independent Information Governance Review Panel, project number 0972. Findings will be disseminated through conferences, blogs, social media threads and peer-reviewed journals. Results will be of interest internationally to primary and secondary care clinicians who manage UTIs and may inform future clinical trials of preventative therapy

Psychometric properties of the Arabic version of the international consultation on incontinence questionnaire on long-term catheter quality of life

Aim To translate the International Consultation on Incontinence Questionnaire (ICIQ) Long-Term Catheter Quality of Life (LTCqol) questionnaire (ICIQ-LTCqol) questionnaire from English to Arabic and evaluate its psychometric properties. Background Currently, no tool for Arabic speaking patients is available to measure the quality of life in patients using long-term urinary catheters. Design Translation and psychometric assessment of questionnaire. Methods The internal consistency and construct validity of the translated Arabic version of the ICIQ-LTCqol were evaluated in a convenience sample of 141 participants recruited from a hospital in Egypt from April to September 2017. Test-retest reliability was assessed for a sample of 15 participants who completed this version at two-time points. Construct validity was assessed by factor analysis. Results The translated Arabic version of the ICIQ-LTCqol showed satisfactory test-retest reliability and internal consistency, with Cronbach’s α = 0·75. Confirmatory factor analysis confirmed the same two factors (‘catheter function’ and ‘lifestyle’) structure as found in the English version of the tool supporting the construct validity of the translated questionnaire. Conclusion This original and significant study allows, for the first time, researchers and clinicians working with Arabic speaking patients, the opportunity to evaluate the quality of life in long-term urinary catheter users

Purchasing of tobacco-related and e-cigarette-related products within prisons before and after implementation of smoke-free prison policy: analysis of prisoner spend data across Scotland, UK

Objectives To examine the effect of smoke-free prison policy implementation in November 2018 on purchasing patterns in the prison canteen (shop). Design Interrupted time series. Setting All 12 closed, publicly run prisons in Scotland, UK. Participants People in custody (PiC) between August 2018 and end of March 2019 (n=11 944). Interventions Implementation of smoke-free prisons policy. Outcome measures Total spent on all products, nicotine-related products, and food and beverage products per week. Methods Canteen data were provided for the period July 2018–September 2019 by the Scottish Prison Service. In a series of generalised linear mixed effects models, the amount spent before and after implementation of smoke-free prison policy was compared for all purchases in the time period, and for PiC identified as ‘smokers’ and ‘non-smokers’ from their pre-implementation tobacco purchasing patterns. Results The amount spent on nicotine-related products significantly decreased from pre-implementation to post implementation (incident rate ratio (IRR) 0.40; 99% CI 0.33 to 0.51,

Adaptive piecewise equivalent circuit model with SOC/SOH estimation based on extended Kalman filter

Battery modelling plays a critical role in battery management tasks. A model that provides accurate estimations of state of charge and state of heath in varying operating conditions could significantly improve the performance of battery management systems. Departing from existing literature, this paper presents a self-adaptive Piecewise Equivalent Circuit Model (PECM) based on Extended Kalman Filter (EKF). While traditional Equivalent Circuit Models (ECM) are typically parameterized and validated for a specific range of working conditions (temperature, current and etc.), PECM is able to adapt itself to any working condition in real time. Established in the form of a combination of linear and nonlinear piecewise functions, the model parameters are continuously adjusted based on the measurement of voltage, current, and temperature. Another advantage of PECM is it does not require any prior tests in the lab, for example the Open Circuit Voltage (OCV) test which is time consuming and needs to be calibrated when aged. PECM is accurate, flexible and efficient. It has been validated for different battery chemistries, duty cycles, and temperatures. Furthermore, PECM comes with the State of Charge (SOC) and State of Health (SOH) estimation, which is shown in the model validation process and the degradation study. The results demonstrate that the piecewise parameter adaptation proposed in this paper can be applied to a range of different battery chemistries and at different aged states

Large-eddy simulation of three-dimensional dunes in a steady, unidirectional flow. Part 1. Turbulence statistics

We performed large-eddy simulations of flow over a series of three-dimensional dunes at laboratory scale (Reynolds number based on the average channel depth and streamwise velocity was 18 900) using the Lagrangian dynamic eddy-viscosity subgrid-scale model. The bedform three-dimensionality was imposed by shifting a standard two-dimensional dune shape in the streamwise direction according to a sine wave. The statistics of the flow are discussed in 10 cases with in-phase and staggered crestlines, different deformation amplitudes and wavelengths. The results are validated qualitatively against experiments. The three-dimensional separation of flow at the crestline alters the distribution of wall pressure, which in turn may cause secondary flow across the stream, which directs low-momentum fluid, near the bed, toward the lobe (the most downstream point on the crestline) and high-momentum fluid, near the top surface, toward the saddle (the most upstream point on the crestline). The mean flow is characterized by a pair of counter-rotating streamwise vortices, with core radius of the order of the flow depth. However, for wavelengths smaller than the flow depth, the secondary flow exists only near the bed and the mean flow away from the bed resembles the two-dimensional case. Staggering the crestlines alters the secondary motion; the fastest flow occurs between the lobe and the saddle planes, and two pairs of streamwise vortices appear (a strong one, centred about the lobe, and a weaker one, coming from the previous dune, centred around the saddle). The distribution of the wall stress and the focal points of separation and attachment on the bed are discussed. The sensitivity of the average reattachment length, depends on the induced secondary flow, the streamwise and spanwise components of the channel resistance (the skin friction and the form drag), and the contribution of the form drag to the total resistance are also studied. Three-dimensionality of the bed increases the drag in the channel; the form drag contributes more than in the two-dimensional case to the resistance, except for the staggered-crest case. Turbulent-kinetic energy is increased in the separated shear layer by the introduction of three-dimensionality, but its value normalized by the plane-averaged wall stress is lower than in the corresponding two-dimensional dunes. The upward flow on the stoss side and higher deceleration of flow on the lee side over the lobe plane lift and broaden the separated shear layer, respectively, affecting the turbulent kinetic energy

Large-eddy simulation of three-dimensional dunes in a steady, unidirectional flow. Part 2. Flow structures

We performed large-eddy simulations of the flow over a series of three-dimensional (3D) dunes at laboratory scale. The bedform three-dimensionality was imposed by shifting a standard two-dimensional (2D) dune shape in the streamwise direction according to a sine wave. The turbulence statistics were discussed in Part 1 of this article (Omidyeganeh & Piomelli, J. Fluid Mech., vol. 721, 2013, pp. 454–483). Coherent flow structures and their statistics are discussed concentrating on two cases with the same crestline amplitudes and wavelengths but different crestline alignments: in-phase and staggered. The present paper shows that the induced large-scale mean streamwise vortices are the primary factor that alters the features of the instantaneous flow structures. Wall turbulence is insensitive to the crestline alignment; alternating high- and low-speed streaks appear in the internal boundary layer developing on the stoss side, whereas over the node plane (the plane normal to the spanwise direction at the node of the crestline), they are inclined towards the lobe plane (the plane normal to the spanwise direction at the most downstream point of the crestline) due to the mean spanwise pressure gradient. Spanwise vortices (rollers) generated by Kelvin–Helmholtz instability in the separated shear layer appear regularly over the lobe with much larger length scale than those over the saddle (the plane normal to the spanwise direction at the most upstream point of the crestline). Rollers over the lobe may extend to the saddle plane and affect the reattachment features; their shedding is more frequent than in 2D geometries. Vortices shed from the separated shear layer in the lobe plane undergo a three-dimensional instability while being advected downstream, and rise toward the free surface. They develop into a horseshoe shape (similar to the 2D case) and affect the whole channel depth, whereas those generated near the saddle are advected downstream and toward the bed. When the tip of such a horseshoe reaches the free surface, the ejection of flow at the surface causes ‘boils’ (upwelling events on the surface). Strong boil events are observed on the surface of the lobe planes of 3D dunes more frequently than in the saddle planes. They also appear more frequently than in the corresponding 2D geometry. The crestline alignment of the dune alters the dynamics of the flow structures, in that they appear in the lobe plane and are advected towards the saddle plane of the next dune, where they are dissipated. Boil events occur at a higher frequency in the staggered alignment, but with less intensity than in the in-phase alignment

Latent Stochastic Differential Equations for Modeling Quasar Variability and Inferring Black Hole Properties

Active galactic nuclei (AGN) are believed to be powered by the accretion of matter around supermassive black holes at the centers of galaxies. The variability of an AGN's brightness over time can reveal important information about the physical properties of the underlying black hole. The temporal variability is believed to follow a stochastic process, often represented as a damped random walk described by a stochastic differential equation (SDE). With upcoming wide-field surveys set to observe 100 million AGN in multiple bandpass filters, there is a need for efficient and automated modeling techniques that can handle the large volume of data. Latent SDEs are well-suited for modeling AGN time series data, as they can explicitly capture the underlying stochastic dynamics. In this work, we modify latent SDEs to jointly reconstruct the unobserved portions of multivariate AGN light curves and infer their physical properties such as the black hole mass. Our model is trained on a realistic physics-based simulation of ten-year AGN light curves, and we demonstrate its ability to fit AGN light curves even in the presence of long seasonal gaps and irregular sampling across different bands, outperforming a multi-output Gaussian process regression baseline.Comment: 10 pages, 5 figures, accepted at the ICLR 2023 Workshop on Physics for Machine Learnin

Generation of a three-dimensional collagen scaffold-based model of the human endometrium.

The endometrium is the secretory lining of the uterus that undergoes dynamic changes throughout the menstrual cycle in preparation for implantation and a pregnancy. Recently, endometrial organoids (EO) were established to study the glandular epithelium. We have built upon this advance and developed a multi-cellular model containing both endometrial stromal and epithelial cells. We use porous collagen scaffolds produced with controlled lyophilization to direct cellular organization, integrating organoids with primary isolates of stromal cells. The internal pore structure of the scaffold was optimized for stromal cell culture in a systematic study, finding an optimal average pore size of 101 µm. EO seeded organize to form a luminal-like epithelial layer, on the surface of the scaffold. The cells polarize with their apical surface carrying microvilli and cilia that face the pore cavities and their basal surface attaching to the scaffold with the formation of extracellular matrix proteins. Both cell types are hormone responsive on the scaffold, with hormone stimulation resulting in epithelial differentiation and stromal decidualization