Whole-genome sequencing and phylogenetic analysis capture the emergence of a multi-drug resistant Salmonella enterica serovar Infantis clone from diagnostic animal samples in the United States.

Introduction: Salmonella enterica is a major cause of foodborne illness in the United States. A multi-drug resistant (MDR) emergent Salmonella Infantis (ESI) with a megaplasmid (pESI) was first identified in Israel and Italy and subsequently reported worldwide. The ESI clone carrying an extended spectrum ß-lactamase blaCTX-M-65 on a pESI-like plasmid and a mutation in the gyrA gene has recently been found in the United States in poultry meat. Methods: We analyzed the phenotypic and genotypic antimicrobial resistance, genomics and phylogeny of 200 S. infantis isolates from animal diagnostic samples. Results: Of these, 33.5% were resistant to at least one antimicrobial and 19.5% were multi-drug resistant (MDR). Eleven isolates from different animal sources were phenotypically and genetically similar to the ESI clone. These isolates had a D87Y mutation in the gyrA gene conferring reduced susceptibility to ciprofloxacin and harbored a combination of 6-10 resistance genes: blaCTX-M-65, aac(3)-IVa, aadA1, aph(4)-Ia, aph(3')-Ia, floR, sul1, dfrA14, tetA, and fosA. These 11 isolates carried class I and class II integrons and three virulence genes: sinH, involved in adhesion and invasion, ybtQ and ybtP, associated with iron transport. These isolates were also closely related to each other (separated by 7 to 27 SNPs) and phylogenetically related to the ESI clone recently found in the U.S. Discussion: This dataset captured the emergence of the MDR ESI clone in multiple animal species and the first report of a pESI-like plasmid in isolates from horses in the U.S.

Pharmacist driven antibiotic redosing in the emergency department.

STUDY OBJECTIVE: Determine whether an expanded emergency medicine (EM) pharmacist scope of practice reduces the frequency of major delays in subsequent antibiotic administration in patients boarded in the emergency department (ED). METHODS: A pre-post, quasi-experimental study conducted from November 2019-March 2020 at a single-center tertiary academic medical center following the implementation of an expanded EM pharmacist scope of practice. Adult patients were included if they received an initial antibiotic dose in the ED and deemed to be high-risk. Subsequent antibiotic doses were reordered by EM pharmacists for up to 24-h after the initial order pending ED length of stay (LOS). The historical control group consisted of retrospective chart review of cases from the previous year. RESULTS: The study identified that of the 181 participants enrolled, major delays in subsequent antibiotic administration occurred in 13% of the intervention group and 48% of the control group (p < 0.01). When compared to the control group, the intervention group had a significant decrease in the number of delays among antibiotics dosed at 6-h (39% vs 13%) and 8-h (60% vs 8%) intervals. For antibiotics dosed at 12-h intervals, no statistically significant difference was observed between the control and intervention groups respectively (19% vs 5%). A statistically significant lower incidence of in-hospital mortality was observed in the intervention group (3% vs 11%, p = 0.02). In the intervention group, 97% of patients received subsequent antibiotic doses while boarded in the ED, compared to 65% in the control group (<0.01). CONCLUSION: Expanding EM pharmacist scope of practice was associated with a significant reduction in the frequency of major delays in subsequent antibiotic administration as well as a decreased incidence of hospital mortality.

In vivo MRI evaluation of anabolic steroid precursor growth effects in a guinea pig model.

Anabolic steroids are widely used to increase skeletal muscle (SM) mass and improve physical performance. Some dietary supplements also include potent steroid precursors or active steroid analogs such as nandrolone. Our previous study reported the anabolic steroid effects on SM in a castrated guinea pig model with SM measured using a highly quantitative magnetic resonance imaging (MRI) protocol. The aim of the current study was to apply this animal model and in vivo MRI protocol to evaluate the growth effects of four widely used over-the-counter testosterone and nandrolone precursors: 4-androstene-3 17-dione (androstenedione), 4-androstene-3beta 17beta-diol (4-androsdiol), 19-nor-4-androstene-3beta-17beta-diol (bolandiol) and 19-nor-4-androstene-3 17-dione (19-norandrostenedione). The results showed that providing precursor to castrated male guinea pigs led to plasma steroid levels sufficient to maintain normal SM growth. The anabolic growth effects of these specific precursors on individual and total muscle volumes, sexual organs, and total adipose tissue over a 10-week treatment period, in comparison with those in the respective positive control testosterone and nandrolone groups, were documented quantitatively by MRI.

A novel 3-dimensional micro-ultrasound approach to automated measurement of carotid arterial plaque volume as a biomarker for experimental atherosclerosis.

Improved methods for non-invasive in vivo assessment are needed to guide development of animal models of atherosclerosis and to evaluate target engagement and in vivo efficacy of new drugs. Using novel 3D-micro-ultrasound technology, we developed and validated a novel protocol for 3D acquisition and analysis of imaging to follow lesion progression in atherosclerotic mice. The carotid arteries of ApoE receptor knockout mice and normal control mice were imaged within the proximal 2mm from the aortic branch point. Plaque volume along that length was quantified using a semi-automated 3D segmentation algorithm. Volumes derived by this method were compared to those calculated using 3-D histology post-mortem. Bland-Altman comparison revealed close correlation between these two measures of plaque volume. Furthermore, using a segmentation technique that captures early positive and 33 week negative remodeling, we found evidence that plaque volume increases linearly over time. Each animal and each plaque served as its own control, allowing accurate comparison. The high fidelity anatomical registration of this protocol provides increased spatial resolution and therefore greater sensitivity for measurement of plaque wall size, an advance over 2-dimensional measures of intimal-medial-thickening. Further, 3-dimensional analysis ensures a point of registration that captures functional markers in addition to the standard structural markers that characterize experimental atherosclerosis. In conclusion, this novel imaging protocol provides a non-invasive, accurate surrogate marker for experimental atherosclerosis over the life of the entire lesion.

A quantitative volumetric micro-computed tomography method to analyze lung tumors in genetically engineered mouse models.

Two genetically engineered, conditional mouse models of lung tumor formation, K-ras(LSL-G12D) and K-ras(LSL-G12D)/p53(LSL-R270H), are commonly used to model human lung cancer. Developed by Tyler Jacks and colleagues, these models have been invaluable to study in vivo lung cancer initiation and progression in a genetically and physiologically relevant context. However, heterogeneity, multiplicity and complexity of tumor formation in these models make it challenging to monitor tumor growth in vivo and have limited the application of these models in oncology drug discovery. Here, we describe a novel analytical method to quantitatively measure total lung tumor burden in live animals using micro-computed tomography imaging. Applying this methodology, we studied the kinetics of tumor development and response to targeted therapy in vivo in K-ras and K-ras/p53 mice. Consistent with previous reports, lung tumors in both models developed in a time- and dose (Cre recombinase)-dependent manner. Furthermore, the compound K-ras(LSL-G12D)/p53(LSL-R270H) mice developed tumors faster and more robustly than mice harboring a single K-ras(LSL-G12D) oncogene, as expected. Erlotinib, a small molecule inhibitor of the epidermal growth factor receptor, significantly inhibited tumor growth in K-ras(LSL-G12D)/p53(LSL-R270H) mice. These results demonstrate that this novel imaging technique can be used to monitor both tumor progression and response to treatment and therefore supports a broader application of these genetically engineered mouse models in oncology drug discovery and development.

Atherosclerosis inflammation imaging with 18F-FDG PET: carotid, iliac, and femoral uptake reproducibility, quantification methods, and recommendations.

UNLABELLED: Atherosclerosis imaging with 18F-FDG PET is useful for tracking inflammation within plaque and monitoring the response to drug therapy. Short-term reproducibility of this technique in peripheral artery disease has not been assessed, and the optimal method of 18F-FDG quantification is still debated. We imaged 20 patients with vascular disease using 18F-FDG PET twice, 14 d apart, and used these data to assess reproducibility measures and compare 2 methods of 18F-FDG uptake measurement. We also reviewed the literature on quantification methods to determine the optimal measures of arterial 18F-FDG uptake for future studies. METHODS: Twenty patients with vascular disease underwent PET/CT of the iliac, femoral, and carotid arteries 90 min after 18F-FDG administration. In 19 patients, repeat testing was performed at 2 wk. Coregistration and attenuation correction were performed with CT. Vessel 18F-FDG uptake was measured as both the mean and maximum blood-normalized standardized uptake value (SUV), known as the target-to-background ratio (TBR). We assessed interscan, interobserver, and intraobserver agreement. RESULTS: Nineteen patients completed both imaging sessions. The carotid and peripheral arteries all have excellent short-term reproducibility of the 18F-FDG signal, with intraclass correlation coefficients all greater than 0.8 for all measures of reproducibility. Both mean and maximum TBR measurements for quantifying 18F-FDG uptake are equally reproducible. 18F-FDG uptake was significantly higher in the carotid arteries than in both iliac and femoral vessels (P < 0.001 for both). CONCLUSION: We found that both mean and maximum TBR in the carotid, iliac, and femoral arteries were highly reproducible. We suggest the mean TBR be used for tracking systemic arterial therapies, whereas the maximum TBR is optimal for detecting and monitoring local, plaque-based therapy.

In vivo MRI quantification of individual muscle and organ volumes for assessment of anabolic steroid growth effects.

This study aimed to develop a quantitative and in vivo magnetic resonance imaging (MRI) approach to investigate the muscle growth effects of anabolic steroids. A protocol of MRI acquisition on a standard clinical 1.5 T scanner and quantitative image analysis was established and employed to measure the individual muscle and organ volumes in the intact and castrated guinea pigs undergoing a 16-week treatment protocol by two well-documented anabolic steroids, testosterone and nandrolone, via implanted silastic capsules. High correlations between the in vivo MRI and postmortem dissection measurements were observed for shoulder muscle complex (R=0.86), masseter (R=0.79), temporalis (R=0.95), neck muscle complex (R=0.58), prostate gland and seminal vesicles (R=0.98), and testis (R=0.96). Furthermore, the longitudinal MRI measurements yielded adequate sensitivity to detect the restoration of growth to or towards normal in castrated guinea pigs by replacing circulating steroid levels to physiological or slightly higher levels, as expected. These results demonstrated that quantitative MRI using a standard clinical scanner provides accurate and sensitive measurement of individual muscles and organs, and this in vivo MRI protocol in conjunction with the castrated guinea pig model constitutes an effective platform to investigate the longitudinal and cross-sectional growth effects of other potential anabolic steroids. The quantitative MRI protocol developed can also be readily adapted for human studies on most clinical MRI scanner to investigate the anabolic steroid growth effects, or monitor the changes in individual muscle and organ volume and geometry following injury, strength training, neuromuscular disorders, and pharmacological or surgical interventions.

Carpal tunnel release with a limited palmar incision: clinical results and pillar pain at 18 months follow-up.

Limited open carpal tunnel release was performed in 58 hands (44 patients) using a single 1.5 cm palmar incision according to the technique described by Lee and Strickland. The patients were assessed at regular intervals after surgery for hand functions and subjective symptoms, in particular pillar pain. There was rapid wound recovery with minimal post-operative pain and scarring, and return to functional activities within four weeks. At an average follow-up of 18 months (range 14-24 months), 91% of patients had complete or significant resolution of hand paraesthesia. No patient required further surgery. However, pillar pain was found in 48% of hands at four weeks, 21% at 12 weeks, 12% at six months, 9% at 12 months and 7% at the last follow-up. The significance of the incidence of pillar pain is discussed.

Boosting: an ensemble learning tool for compound classification and QSAR modeling.

A classification and regression tool, J. H. Friedman's Stochastic Gradient Boosting (SGB), is applied to predicting a compound's quantitative or categorical biological activity based on a quantitative description of the compound's molecular structure. Stochastic Gradient Boosting is a procedure for building a sequence of models, for instance regression trees (as in this paper), whose outputs are combined to form a predicted quantity, either an estimate of the biological activity, or a class label to which a molecule belongs. In particular, the SGB procedure builds a model in a stage-wise manner by fitting each tree to the gradient of a loss function: e.g., squared error for regression and binomial log-likelihood for classification. The values of the gradient are computed for each sample in the training set, but only a random sample of these gradients is used at each stage. (Friedman showed that the well-known boosting algorithm, AdaBoost of Freund and Schapire, could be considered as a particular case of SGB.) The SGB method is used to analyze 10 cheminformatics data sets, most of which are publicly available. The results show that SGB's performance is comparable to that of Random Forest, another ensemble learning method, and are generally competitive with or superior to those of other QSAR methods. The use of SGB's variable importance with partial dependence plots for model interpretation is also illustrated.

Cruciate ligament avulsion fractures.

PURPOSE: The objective of this study was to assess the variability of cruciate avulsion fractures. TYPE OF STUDY: Retrospective observational study. METHODS: Standardized radiographs and computed tomography (CT) examinations were performed in 40 patients (31 male, 9 female; age range, 10 to 77 years) with cruciate avulsion fractures. RESULTS: The average age of patients with anterior cruciate ligament (ACL) avulsion fractures was 21.5 years and that of patients with posterior cruciate ligament (PCL) avulsion fractures was 42.9 years. Two basic patterns of avulsion fracture emerged. ACL fractures were either partial (62%) (with avulsion of anteromedial bundle) or extended (38%) and were comminuted in 25%. PCL fractures were either complete (47%) or extended (53%) and were comminuted in 50%. CT helped delineate fracture margins, comminution and extent. CONCLUSIONS: Although there is considerable variability in fracture type, 2 basic patterns of ACL and PCL avulsion fractures exist. CT helps delineate these features as a prelude to surgical fixation. LEVEL OF EVIDENCE: Level III.

Random forest: a classification and regression tool for compound classification and QSAR modeling.

A new classification and regression tool, Random Forest, is introduced and investigated for predicting a compound's quantitative or categorical biological activity based on a quantitative description of the compound's molecular structure. Random Forest is an ensemble of unpruned classification or regression trees created by using bootstrap samples of the training data and random feature selection in tree induction. Prediction is made by aggregating (majority vote or averaging) the predictions of the ensemble. We built predictive models for six cheminformatics data sets. Our analysis demonstrates that Random Forest is a powerful tool capable of delivering performance that is among the most accurate methods to date. We also present three additional features of Random Forest: built-in performance assessment, a measure of relative importance of descriptors, and a measure of compound similarity that is weighted by the relative importance of descriptors. It is the combination of relatively high prediction accuracy and its collection of desired features that makes Random Forest uniquely suited for modeling in cheminformatics.

Anterior shoulder dislocation: quantification of glenoid bone loss with CT.

OBJECTIVE: In recurrent anterior shoulder dislocation, glenoid bone loss may predispose the patient to further dislocation and failure of a Bankart repair. This study investigates the quantification of glenoid bone loss in anterior shoulder dislocation using CT. SUBJECTS AND METHODS: CT examinations were performed on 40 patients (average age, 31 years; range, 13-82 years), comprising 46 shoulders with anterior dislocation and 34 contralateral normal shoulders. Twenty shoulders in 10 healthy subjects were also examined. Both shoulders were examined simultaneously. Image reconstruction included oblique sagittal reformatted images en face to the glenoid fossa. Seven aspects of glenoid fossa shape and size were measured, including the cross-sectional area, maximum width, maximum height, and flattening of the anterior glenoid curvature. RESULTS: Variable flattening of the anterior glenoid curvature was a feature in 42 (91%) of 46 dislocated shoulders although it was seen in only two (4%) of 54 normal shoulders. Anterior glenoid flattening increased exponentially with an increasing number of dislocations. Anterior glenoid flattening, decreased maximum glenoid width, and decreased maximum width-to-length ratio were the most useful measures of bone loss. Maximum glenoid width was smaller than on the contralateral side in 79% of patients with unilateral dislocation by an average of 3.0 mm (range, 0.1-10 mm) or 10.8% (range, 0.4-32%). Glenoid cross-sectional area was a less useful measure of glenoid bone loss. CONCLUSION: Flattening of the anterior glenoid curvature is shown in most patients with anterior dislocation. In unilateral dislocation, a comparison of maximum glenoid width with that on the contralateral side was the best discriminator of moderate to severe glenoid bone loss.

Energy-conserving low-order models for three-dimensional Rayleigh-Bénard convection.

Constructing hydrodynamic low-order models in the form of coupled gyrostats eliminates the possibility of certain unphysical behaviors, such as solutions diverging to infinity, that often appear in models resulting from ad hoc truncations of Galerkin approximations. In this paper, a simple low-order model in a gyrostatic form that conserves energy in the dissipationless limit (Model I) is constructed for three-dimensional (3D) Rayleigh-Bénard convection. It can be considered an energy-conserving extension of the model by Das et al. [Phys. Rev. E 62, R3051 (2000)] (Model II) that does not conserve energy and possesses solutions diverging to infinity. Also studied here is a smaller but energy-conserving subsystem of Model I that has the form of two coupled gyrostats (Model III). This new system is the 3D analog of the celebrated Lorenz model [J. Atmos. Sci. 20, 130 (1963)]. Stability diagrams and heat transport behavior are calculated and compared for the three models. Model I has improved qualitative agreement with experimental observations compared to that of Model II and Model III.