Deep learning application to automated classification of recommendations made by hospital pharmacists during medication prescription review

PURPOSE

Recommendations to improve therapeutics are proposals made by pharmacists during the prescription review process to address suboptimal use of medicines. Recommendations are generated daily as text documents but are rarely reused beyond their primary use to alert prescribers and caregivers. If recommendation data were easier to summarize, they could be used retrospectively to improve safeguards for better prescribing. The objective of this work was to train a deep learning algorithm for automated recommendation classification to valorize the large amount of recommendation data.

METHODS

The study was conducted in a French university hospital, at which recommendation data were collected throughout 2017. Data from the first 6 months of 2017 were labeled by 2 pharmacists who assigned recommendations to 1 of the 29 possible classes of the French Society of Clinical Pharmacy classification. A deep neural network classifier was trained to predict the class of recommendations.

RESULTS

In total, 27,699 labeled recommendations from the first half of 2017 were used to train and evaluate a classifier. The prediction accuracy calculated on a validation dataset was 78.0%. We also predicted classes for unlabeled recommendations collected during the second half of 2017. Of the 4,460 predictions reviewed, 67 required correction. When these additional labeled data were concatenated with the original dataset and the neural network was retrained, accuracy reached 81.0%.

CONCLUSION

To facilitate analysis of recommendations, we have implemented an automated classification system using deep learning that achieves respectable performance. This tool can help to retrospectively highlight the clinical significance of daily medication reviews performed by hospital clinical pharmacists.

Outcomes of total elbow arthroplasty in the treatment of distal humeral fractures in the elderly: A retrospective cohort comparison between primary arthroplasty and arthroplasty secondary to failed internal fixation

BACKGROUND

The primary objective of this study was to compare the clinical outcomes of total elbow arthroplasty as the index procedure in the treatment of traumatic distal humerus fractures, with secondary total elbow arthroplasty following failed internal fixation. The secondary objectives were to compare the complication rates and the radiographic results in the two groups. Our hypothesis was that the clinical results of total elbow arthroplasty performed secondarily to failed internal fixation were comparable to primary total elbow arthroplasty in the treatment of distal humerus fractures in the elderly population.

METHODS

We conducted a retrospective cohort comparison study, including 60 patients with a median age of 80 years (71-85), who either underwent a primary total elbow arthroplasty (group 1; 45 patients), or secondary total elbow arthroplasty following failed internal fixation (group 2; 15 patients), in the treatment of a post-traumatic supra and intercondylar fracture of the distal humerus, between January 2004 and January 2021. The clinical examination, including MEPS score and triceps proficiency test, complication rates and the need for re-operation were noted. The average clinical and radiographic follow-up was 40.8 months (24-120).

RESULTS

The clinical results of the two groups were comparable when looking at the MEPS score (90.00 [85.00, 100.00] p= 0.486). With regards to complications, there were 2 surgical site infections in group 1 and 3 in group 2 (p=0.099), 1 case of mechanical loosening of the humeral component in group 1 and 1 in group 2 (p= 0.448), and 1 patient with triceps insufficiency in group 1.

CONCLUSION

Secondary total elbow arthroplasty following failed internal fixation has shown good functional results, and a complication rate comparable to that of index total elbow arthroplasty in the treatment of articular fractures of the distal humerus in the elderly.

Rhinoconjunctivitis severity induced by cat exposure influences early and late asthmatic responses: Evidence from an environmental exposure chamber

BACKGROUND

The impact of allergic rhinoconjunctivitis on the early (EAR) and late asthmatic response (LAR) has yet to be assessed during optimal allergen exposure conditions.

OBJECTIVE

We aimed to assess predictive factors of the EAR and LAR and to evaluate the relation between rhinitis, conjunctivitis and asthma induced by cat allergen exposure in an environmental exposure chamber (EEC).

METHODS

Data from two cohort studies involving asthmatic patients with cat allergy who performed a cat allergen exposure challenge in ALYATEC EEC were analysed. Spirometry, visual analogue scale (VAS) for asthma, VAS for rhinitis, Total Nasal Symptoms Score, Total Ocular Symptoms Score (TOSS), Rhinoconjunctivitis Total Symptoms Score and Abelson score were used to assess asthma, rhinitis and conjunctivitis during and after exposure.

RESULTS

An EAR occurred in 65.1% of patients, 32.1% of whom had a LAR. The diameter of the prick test to cat allergens and non-specific bronchial hypersensitivity level were independent risk factors for EAR (p < .05). No independent risk factors for LAR were identified. Rhinoconjunctivitis severity during exposure correlated with the asthma VAS during EAR and LAR (p < .05). Allergen exposure time needed to trigger an EAR correlated with the Abelson score during exposure (p < .05). The asthma VAS and TOSS during exposure correlated with faster LAR occurrence (p < .05).

CONCLUSION

Prick test size and non-specific bronchial hypersensitivity level were confirmed as independent predictive factors of EAR during allergen exposure in an EEC. This study demonstrated the relation between the severity of rhinitis, conjunctivitis and asthma induced by allergen exposure for both EAR and LAR.

Sputum Inflammatory Patterns Are Associated With Distinct Clinical Characteristics in Patients with Occupational Asthma Independently of the Causal Agent

BACKGROUND AND OBJECTIVES

Background: Clinical heterogeneity in sensitizer-induced occupational asthma (OA) and its relationship to airway inflammatory profiles remain poorly elucidated. Objectives: To further characterize interactions between induced sputum inflammatory patterns, asthma-related outcomes, and the high- or low-molecular-weight category of causal agents in a large cohort of patients with OA.

METHODS

We conducted a multicenter, retrospective, cross-sectional study of 296 patients with OA confirmed by a positive specific inhalation challenge who completed induced sputum assessment before and 24 hours after challenge exposure.

RESULTS

Multivariate logistic regression analysis revealed that sputum eosinophilia ≥3% was significantly associated with a high dose of inhaled corticosteroid (OR [95%CI], 1.31 [1.11 1.55] for each 250-μg increment in daily dose), short-acting ß2-agonist use less than once a day (3.54 [1.82-7.00]), and the level of baseline nonspecific bronchial hyperresponsiveness (mild, 2.48 [1.21-5.08]; moderate/severe, 3.40 [1.44-8.29]). Sputum neutrophilia ≥76% was associated with age (1.06 [1.01-1.11]), male sex (3.34 [1.29-9.99]), absence of corticosteroid use (5.47 [2.09-15.16]), use of short-acting ß2-agonists once or more a day (4.09 [1.71-10.01]), ≥2 severe exacerbations during the previous 12 months at work (4.22 [1.14-14.99]), and isolated early reactions during the specific inhalation challenge (4.45 [1.85-11.59]).

CONCLUSIONS

The findings indicate that sputum inflammatory patterns in patients with OA are associated with distinct phenotypic characteristics and further highlight the differential effects of neutrophils and eosinophils on asthma-related outcomes. These associations between inflammatory patterns and clinical characteristics share broad similarities with findings reported in nonoccupational asthma and are not related to the type of causal agent.

Spectral Phasor Applied to Spectrally-Resolved Single Molecule Localization Microscopy

Spectrally-resolved single-molecule localization microscopy (srSMLM) has emerged as a powerful tool for exploring the spectral properties of single emitters in localization microscopy. By simultaneously capturing the spatial positions and spectroscopic signatures of individual fluorescent molecules, srSMLM opens up the possibility of investigating an additional dimension in super-resolution imaging. However, appropriate and dedicated tools are required to fully capitalize on the spectral dimension. Here, we propose the application of the spectral phasor analysis as an effective method for summarizing and analyzing the spectral information obtained from srSMLM experiments. The spectral phasor condenses the complete spectrum of a single emitter into a two-dimensional space, preserving key spectral characteristics for single-molecule spectral exploration. We demonstrate the effectiveness of spectral phasor in efficiently classifying single Nile Red fluorescence emissions from largely overlapping cyanine fluorescence signals in dual-color PAINT experiments. Additionally, we employed spectral phasor with srSMLM to reveal subtle alterations occurring in the membrane of Gram-positive Enterococcus hirae in response to gramicidin exposure, a membrane-perturbing antibiotic treatment. Spectral phasor provides a robust, model-free analytic tool for the detailed analysis of the spectral component of srSMLM, enhancing the capabilities of multi-color spectrally-resolved single-molecule imaging.

Targeted Single Particle Tracking with Upconverting Nanoparticles

Single particle tracking (SPT) is a powerful technique for real-time microscopic visualization of the movement of individual biomolecules within or on the surface of living cells. However, SPT often suffers from the suboptimal performance of the photon-emitting labels used to tag the biomolecules of interest. For example, fluorescent dyes have poor photostability, while quantum dots suffer from blinking that hampers track acquisition and interpretation. Upconverting nanoparticles (UCNPs) have recently emerged as a promising anti-Stokes luminescent label for SPT. In this work, we demonstrated targeted SPT using UCNPs. For this, we synthesized 30 nm diameter doped UCNPs and coated them with amphiphilic polymers decorated with polyethylene glycol chains to make them water-dispersible and minimize their nonspecific interactions with cells. Coated UCNPs highly homogeneous in brightness (as confirmed by a single particle investigation) were functionalized by immunoglobulin E (IgE) using a biotin-streptavidin strategy. Using these IgE-UCNP SPT labels, we tracked high-affinity IgE receptors (FcεRI) on the membrane of living RBL-2H3 mast cells at 37 °C in the presence and absence of antigen and obtained good agreement with the literature. Moreover, we used the FcεRI-IgE receptor-antibody system to directly compare the performance of UCNP-based SPT labels to organic dyes (AlexaFluor647) and quantum dots (QD655). Due to their photostability as well as their backgroundless and continuous luminescence, SPT trajectories obtained with UCNP labels are no longer limited by the photophysics of the label but only by the dynamics of the system and, in particular, the movement of the label out of the field of view and/or focal plane.

Ultrahigh Strength and Plasticity Mechanisms of Si and SiC Nanoparticles Revealed by First-Principles Molecular Dynamics

It is now well established that materials are stronger when their dimensions are reduced to the submicron scale. However, what happens at dimensions such as a few tens of nanometers or lower remains largely unknown, with conflicting reports on strength or plasticity mechanisms. Here, we combined first-principles molecular dynamics and classical force fields to investigate the mechanical properties of 1-2 nm Si and SiC nanoparticles. These compression simulations unambiguously reveal that the strength continues to increase down to such sizes, and that in these systems the theoretical bulk strength can be reached or even exceeded in some cases. Most of the nanoparticles yield by amorphization at strains greater than 20%, with no evidence of the β-tin phase for Si. Original and unexpected mechanisms are also identified, such as the homogeneous formation of a dislocation loop embryo for the ⟨111⟩ compression of SiC nanoparticles, and an elastic softening for the ⟨001⟩ compression of Si nanoparticles.

MEESSI-AHF score to estimate short-term prognosis of acute heart failure patients in the Emergency Department: a prospective and multicenter study

BACKGROUND

The assessment of acute heart failure (AHF) prognosis is primordial in emergency setting. Although AHF management is exhaustively codified using mortality predictors, there is currently no recommended scoring system for assessing prognosis. The European Society of Cardiology (ESC) recommends a comprehensive assessment of global AHF prognosis, considering in-hospital mortality, early rehospitalization rates and the length of hospital stay.

OBJECTIVE

We aimed to prospectively evaluate the performance of the Multiple Estimation of risk based on the Emergency department Spanish Score In patients with AHF (MEESSI-AHF) score in estimating short prognosis according to the ESC guidelines.

DESIGN, SETTINGS AND PATIENTS

A multicenter study was conducted between November 2020, and June 2021. Adult patients who presented to eleven French hospitals for AHF were prospectively included.

OUTCOME MEASURES AND ANALYSIS

According to MEESSI-AHF score, patients were stratified in four categories corresponding to mortality risk: low-, intermediate-, high- and very high-risk groups. The primary outcome was the number of days alive and out of the hospital during the 30-day period following admission to the Emergency Department (ED).

RESULTS

In total, 390 patients were included. The number of days alive and out of the hospital decreased significatively with increasing MEESSI-AHF risk groups, ranging from 21.2 days (20.3-22.3 days) for the low-risk, 20 days (19.3-20.5 days) for intermediate risk,18.6 days (17.6-19.6 days) for the high-risk and 17.9 days (16.9-18.9 days) very high-risk category.

CONCLUSION

Among patients admitted to ED for an episode of AHF, the MEESSI-AHF score estimates with good performance the number of days alive and out of the hospital.

HIV-1 Gag targeting to the plasma membrane reorganizes sphingomyelin-rich and cholesterol-rich lipid domains

Although the human immunodeficiency virus type 1 lipid envelope has been reported to be enriched with host cell sphingomyelin and cholesterol, the molecular mechanism of the enrichment is not well understood. Viral Gag protein plays a central role in virus budding. Here, we report the interaction between Gag and host cell lipids using different quantitative and super-resolution microscopy techniques in combination with specific probes that bind endogenous sphingomyelin and cholesterol. Our results indicate that Gag in the inner leaflet of the plasma membrane colocalizes with the outer leaflet sphingomyelin-rich domains and cholesterol-rich domains, enlarges sphingomyelin-rich domains, and strongly restricts the mobility of sphingomyelin-rich domains. Moreover, Gag multimerization induces sphingomyelin-rich and cholesterol-rich lipid domains to be in close proximity in a curvature-dependent manner. Our study suggests that Gag binds, coalesces, and reorganizes pre-existing lipid domains during assembly.

Advancing Spectrally-Resolved Single Molecule Localization Microscopy with Deep Learning

Spectrally-resolved single molecule localization microscopy (srSMLM) is a recent technique enriching single molecule localization microscopy with the simultaneous recording of spectra of the single emitters. srSMLM resolution is limited by the number of photons collected per emitters. Sharing a photon budget to record the localization and the spectroscopic information results in a loss of spatial and spectral resolution-or forces the sacrifice of one at the expense of the other. Here, srUnet-a deep-learning Unet-based image processing routine trained to increase the spectral and spatial signals to compensate for the resolution loss inherent in additionally recording the spectral component is reported. Both localization and spectral precision are improved by srUnet-particularly for the low-emitting species. srUnet increases the fraction of localization whose signal can be both spatially and spectrally characterized. It preserves spectral shifts and the linearity of the dispersion of light. It strongly facilitates wavelength assignment in multicolor experiments. srUnet is a simple post-processing add-on boosting srSMLM performance close to conventional SMLM with the potential to turn srSMLM into the new standard for multicolor single molecule imaging.

Daily socket comfort in transtibial amputee with a vacuum-assisted suspension system: study protocol of a randomized, multicenter, double-blind multiple N-of-1 trial

BACKGROUND

The main aim of this paper is to present the feasibility of rigorously designed multiple N-of-1 design in prosthetics research. While research of adequate power and high quality is often lacking in rehabilitation, N-of-1 trials can offer a feasible alternative to randomized controlled group trials, both increasing design power at group level and allowing a rigorous, statistically confirmed evaluation of effectiveness at a single patient level. The paper presents a multiple N-of-1 trial protocol, which aim is to evaluate the effectiveness of Unity, a prosthetic add-on suspension system for amputees, on patient-reported comfort during daily activities (main outcome measure), prosthesis wearing time, perception of limb-prosthesis fitting and stump volume and functional walking parameters.

METHODS

Multicenter, randomized, prospective, double-blind multiple N-of-1 trial using an introduction/withdrawal design alternating Unity connected/disconnected phases of randomized length on twenty patients with unilateral transtibial amputation. The primary outcome measure is the Prosthetic Socket Comfort Score (SCS), a validated measure of comfort, administered daily by an phone app designed for the study. Secondary outcomes measures will be collected during the 50 days period of the N-of-1 trial: (1) by the same app, daily for patient-reported limb-prosthesis fitting, stump volume variation, and daily wearing time of the prosthesis; (2) by a pedometer for the number of steps per day; (3) by blind assessors in the rehabilitation center during adjustment visits for functional walking parameter (L-Test, 6-minute walk test), and by the patient for the QUEST, and ABC-S. Effectiveness of the Unity system regarding SCS and daily secondary outcome measures will be tested by randomization test. The secondary outcome measures assessed during visits in the rehabilitation center will be analyzed by Non Overlap of All pairs. An estimate of the effect on the amputee population will be generated by aggregating each individual clinical trial (N-of-1 trial) by Hierarchical Bayesian methods.

DISCUSSION

This study protocol was designed to answer the question "which device is best for THIS patient" and to conclude at a group level on the effectiveness of a new devic, using a Multiple N-of-1 trial, which is promising but underused in prosthetics research so far.

TRIAL REGISTRATION

N° ID-RCB 2020-A01309-30 Clintrial.gov : NCT04804150 - Retrospectively registered March 20th 2021.

Study of Modifications Induced by Continued Direct Oral Anticoagulant Therapy during Atrial Fibrillation Ablation Procedures on Standard Hemostasis Parameters

Background: Unfractionated heparin (UFH) is used as an anticoagulant during the atrial fibrillation (AF) ablation procedure to prevent the occurrence of thromboembolic events. Guidelines recommend an activated clotting time (ACT) greater than 300 s (s) based on studies of patients treated with vitamin K antagonist (VKA) for their AF. However, direct oral anticoagulants (DOACs) have supplanted VKAs in AF and are now used as first-line therapy. It is recommended not to interrupt them during the procedure, which could interfere with the ACT measures. Objective: To assess the real-life relationship between ACT, DOAC concentrations, and UFH anti-Xa activity in patients treated by uninterrupted DOAC therapy. Methods: We conducted a single-center retrospective study. We analyzed consecutive patients with AF who underwent catheter ablation under DOAC therapy. Results: In total, 40 patients were included, including 15 (37.5%), 20 (50.0%), and 5 (12.5%) on rivaroxaban, apixaban, and dabigatran, respectively. Baseline ACT was significantly lower in the apixaban group. ACT was linearly correlated with the residual concentration of apixaban and dabigatran but not with rivaroxaban. After UFH injection, ACT was linearly correlated with the anti-Xa activity, regardless of DOAC. Patients in the apixaban group received a higher total dose of UFH during the procedure to achieve a target ACT > 300 s, which resulted in significantly higher anti-Xa activity during the procedure. Conclusion: Our results raise the question of optimal management of intra-procedural heparin therapy and highlight the limitations of the ACT test, particularly in patients on apixaban.

Cerebral and cognitive modifications in retired professional soccer players: TC-FOOT protocol, a transverse analytical study

INTRODUCTION

Soccer is the most popular sport in the world. This contact sport carries the risk of exposure to repeated head impacts in the form of subconcussions, defined as minimal brain injuries following head impact, with no symptom of concussion. While it has been suggested that exposure to repetitive subconcussive events can result in long-term neurophysiological modifications, and the later development of chronic traumatic encephalopathy, the consequences of these repeated impacts remain controversial and largely unexplored in the context of soccer players.

METHODS AND ANALYSIS

This is a prospective, single-centre, exposure/non-exposure, transverse study assessing the MRI and neuropsychological abnormalities in professional retired soccer players exposed to subconcussive impacts, compared with high-level athletes not exposed to head impacts. The primary outcome corresponds to the results of MRI by advanced MRI techniques (diffusion tensor, cerebral perfusion, functional MRI, cerebral volumetry and cortical thickness, spectroscopy, susceptibility imaging). Secondary outcomes are the results of the neuropsychological tests: number of errors and time to complete tests. We hypothesise that repeated subconcussive impacts could lead to morphological lesions and impact on soccer players' cognitive skills in the long term.

ETHICS AND DISSEMINATION

Ethics approval has been obtained and the study was approved by the Comité de Protection des Personnes (CPP) No 2021-A01169-32. Study findings will be disseminated by publication in a high-impact international journal. Results will be presented at national and international imaging meetings.

TRIAL REGISTRATION NUMBER

NCT04903015.

MRI dedicated to the emergency department for diplopia or dizziness: a cost-effectiveness analysis

OBJECTIVES

The purpose of this study was to compare the costs and organizational benefits of diagnostic workup without and with MRI dedicated to the ED.

METHODS

We conducted a prospective observational uncontrolled before-after study in one ED of a university hospital in France from July 1, 2018, and January 3, 2020. We included all consecutive patients presenting with dizziness or diplopia. The main outcomes were the clinical decision time of ED physicians and the total costs for each strategy. Outcomes were compared using propensity score with inverse probability weighting in the 2 arms and an incremental cost-effectiveness ratio (ICER) was calculated.

RESULTS

Among the 199 patients during the "before" period (average age: 60.4 years ± 17.6): 112 men (57%), and 181 during the "after" period (average age, 54.8 years ± 18.5): 107 men (59%), the average costs were €2701 (95% CI 1918; 3704) and €2389 (95% CI: €1627; 3280) per patient, respectively. The average time to clinical decision was 9.8 h (95% CI: 8.9 10.7) in the group "before" and 7.7 h (95% CI: 7.1; 8.4) in the group "after" (ICER: €151 saved for a reduction of 1 h in clinical decision time). The probabilistic sensitivity analysis estimated a 71% chance that the MRI dedicated to ED was dominant (less costly and more effective).

CONCLUSION

Easy access to MRI in the ED for posterior circulation stroke-like symptoms must be considered a relevant approach to help physicians for an appropriate and rapid diagnostic with reduction of costs.

TRIAL REGISTRATION

NCT03660852 KEY POINTS: • A dedicated MRI in the ED for diplopia or dizziness may be considered an efficient strategy improving diagnostic performance, reducing physicians' decision time, and decreasing hospital costs. • This strategy supports clinical decision-making with early treatment and management of patients with posterior circulation-like symptoms in the ED. • There is 71% chance that the MRI dedicated to ED was dominant (less costly and more effective) compared with a strategy without dedicated MRI.

Prospective evaluation of the connected biofeedback EMY Kegel trainer in the management of stress urinary incontinence

INTRODUCTION

The aim of this study was to evaluate changes in the quality of life with the connected biofeedback EMY Kegel trainer in patients suffering from stress urinary incontinence. Materiel and methods: This was a prospective, single-center, non-comparative study, which took place between September 2019 and October 2020, in the University Hospitals of Strasbourg. Eligible patients were instructed to use the EMY probe for a minimum of 10 min per day for five days per week. To assess quality of life and urinary symptoms, the Contilife and ICIQ-SF scores were completed each month until the final visit (M3). The PGI-I was also completed at 3 months to assess the benefit of the EMY Kegel Trainer.

RESULTS

A total of 55 patients were included. At the inclusion visit (M0), the mean Contilife and ICIQ-SF scores were respectively at 6.6 ± 1.5 and 10.5 ± 3.0 points. At the final visit (M3), the mean Contilife score increased to 9.2 ± 1.0, indicating an improvement in quality of life. The mean ICIQ-SF score decreased to 4.2 ± 4.0, indicating an improvement in urinary symptoms. The PGI-I questionnaire identified a positive assessement of the EMY Kegel trainer. On the 55 patients included, 35 (64%) reported completing at least 36 sessions during the study, i.e. an average of 3 sessions per week.

CONCLUSIONS

This study suggests that perineal rehabilitation by biofeedback using the EMY Kegel trainer might be beneficial.

Predictive factors of amoxicillin immediate hypersensitivity and validation of PEN-FAST clinical decision rule

BACKGROUND

The challenge of delabeling amoxicillin allergy is an important issue for patients and clinicians, especially when anaphylaxis is reported. A recent study has proposed a clinical decision rule, PEN-FAST, to identify low-risk penicillin allergies.

OBJECTIVE

To validate the PEN-FAST clinical decision rule in a population with high risk of suspected immediate amoxicillin allergy and to identify clinical predictive factors of amoxicillin immediate hypersensitivity.

METHODS

We retrospectively analyzed medical records of patients with a suspected immediate amoxicillin allergy who carried out an allergologic evaluation by a specialist in the Allergy Unit of Strasbourg University Hospital from 2015 to 2020.

RESULTS

A total of 142 adult patients (88 women [62.0%]; median age, 52 [interquartile range, 40.3-62.0] years) were analyzed. Most of them reported anaphylaxis (68.8%). Internal validation of PEN-FAST score revealed a good discrimination with area under the curve of 0.86 (95% confidence interval, 0.79-0.92). A cutoff of less than 3 points for PEN-FAST was used to classify 29 from 142 patients at low risk of allergy, of whom only 2 (6.9%) received positive results of allergy testing. The negative predictive value for successful delabeling was 0.93 (95% confidence interval, 0.77-0.99). Predictive clinical features for immediate amoxicillin hypersensitivity were time since reaction (P < .001), time elapsed between drug intake and first symptom (P < .001), severity grade reaction (P < .001), and treatment or hospitalization required (P < .001).

CONCLUSION

PEN-FAST has been validated to identify low-risk penicillin allergies in our European cohort of patients mainly reporting anaphylaxis. This is the first reported external validation of a penicillin allergy clinical decision rule internationally.

Occupational Asthma Caused by Quaternary Ammonium Compounds: A Multicenter Cohort Study

BACKGROUND

Quaternary ammonium compounds (QACs) are used extensively for cleaning and disinfection and have been documented in scattered reports as a cause of occupational asthma (OA) through bronchoprovocation tests (BPTs).

OBJECTIVE

To examine the clinical, functional, and inflammatory profile of QAC-induced OA compared with OA caused by other low-molecular weight (LMW) agents.

METHODS

The study was conducted in a retrospective multicenter cohort of 871 subjects with OA ascertained by a positive BPT. Subjects with QAC-induced OA (n = 22) were identified based on a positive BPT to QACs after exclusion of those challenged with cleaning products or disinfectants that contained other potential respiratory sensitizers. They were compared with 289 subjects with OA caused by other LMW agents.

RESULTS

Most subjects with QAC-induced OA were working in the health care sector (n = 14). A twofold or greater increase in the postchallenge level of nonspecific bronchial hyperresponsiveness was recorded in eight of 11 subjects with QAC-induced OA (72.7%) and in 49.7% of those with OA caused by other LMW agents. Although sputum assessment was available in only eight subjects with QAC-induced OA, they showed a significantly greater median (interquartile) increase in sputum eosinophils (18.1% [range, 12.1% to 21.1%]) compared with those with OA caused by other LMW agents (2.0% [range, 0% to 5.2%]; P < .001).

CONCLUSIONS

This study indicates that QAC-induced OA is associated with a highly eosinophilic pattern of airway response and provides further evidence supporting the sensitizing potential of QACs. The findings highlight the heterogeneous nature of the pathobiologic pathways involved in OA caused by LMW agents.

Discordance between immunochemistry of mismatch repair proteins and molecular testing of microsatellite instability in colorectal cancer

Background

DNA mismatch repair system deficiency (dMMR) is found in 15% of colorectal cancers (CRCs). Two methods are used to determine dMMR, immunohistochemistry (IHC) of MMR proteins and molecular testing of microsatellite instability (MSI). Only studies with a low number of patients have reported rates of discordance between these two methods, ranging from 1% to 10%.

Materials and methods

Overall, 3228 consecutive patients with CRCs from two centers were included. Molecular testing was carried out using the Pentaplex panel and IHC evaluated four (MLH1, MSH2, MSH6, and PMS2; cohort 1; n = 1085) or two MMR proteins (MLH1 and MSH2; cohort 2; n = 2143). The primary endpoint was the rate of discordance between MSI and MMR IHC tests.

Results

Fifty-one discordant cases (1.6%) were initially observed. Twenty-nine out of 51 discordant cases were related to IHC misclassifications. In cohort 1, after re-reading IHC and/or carrying out new IHC, 16 discordant cases were reclassified as nondiscordant. In cohort 2, after the addition of MSH6/PMS2 IHC and re-examination, 13 were reclassified as nondiscordant. In addition, 10 misclassifications of molecular tests were identified. Finally, only 12 discordant cases (0.4%) remained: 5 were proficient MMR/MSI and 7 were dMMR/microsatellite stable.

Conclusions

Our study confirmed the high degree of concordance between MSI and MMR IHC tests. Discordant cases must be reviewed, and if needed, tests must be repeated and analyzed by an expert team.

•

Concordance between MMR IHC (four proteins) and MSI molecular testing (Pentaplex) is superior to 98% in CRC cases

•

Most discordant cases are related to misinterpretation of the tests, which may lead to clinical management errors.

•

Discordant cases must be reviewed and tests must be repeated because most cases will be reclassified as nondiscordant.

Characterization of Occupational Eosinophilic Bronchitis in a Multicenter Cohort of Subjects with Work-Related Asthma Symptoms

BACKGROUND

Occupational eosinophilic bronchitis (OEB) has been described only as anecdotal case reports.

OBJECTIVE

We investigated the clinical and inflammatory characteristics of subjects with OEB identified in a cohort of subjects who completed a specific inhalation challenge (SIC) with occupational agents.

METHODS

In this retrospective multicenter study, OEB was defined by (1) a fall in FEV1 less than 15% during the SIC and the absence of nonspecific bronchial hyperresponsiveness both before and after the SIC and (2) a postchallenge increase of 3% or more in sputum eosinophils. The subjects who fulfilled these criteria were compared with 226 subjects with a negative SIC and 30 subjects with a positive SIC who failed to show baseline nonspecific bronchial hyperresponsiveness.

RESULTS

An isolated increase in postchallenge sputum eosinophils was documented in 33 of 259 subjects (13%) with a negative SIC. These subjects reported significantly more often an isolated cough at work compared with the negative and positive SIC controls. When compared with positive SIC controls, the subjects with OEB experienced less frequently work-related wheezing and reported a shorter duration of symptoms at work. The sensitivity of the post-SIC increase in fractional exhaled nitric oxide in identifying OEB among subjects with a negative SIC was low, ranging from 43% to 24% using cutoff values of 8 ppb to 17.5 ppb, whereas the specificity was high (90%-97%).

CONCLUSIONS

This study highlights the relevance of induced sputum analysis in the investigation of work-related asthma symptoms to identify isolated increases in sputum eosinophils that are consistent with a diagnosis of OEB.

Impact of High-Dose Prophylactic Anticoagulation in Critically Ill Patients With COVID-19 Pneumonia

BACKGROUND

Because of the high risk of thrombotic complications (TCs) during SARS-CoV-2 infection, several scientific societies have proposed to increase the dose of preventive anticoagulation, although arguments in favor of this strategy are inconsistent.

RESEARCH QUESTION

What is the incidence of TC in critically ill patients with COVID-19 and what is the relationship between the dose of anticoagulant therapy and the incidence of TC?

STUDY DESIGN AND METHODS

All consecutive patients referred to eight French ICUs for COVID-19 were included in this observational study. Clinical and laboratory data were collected from ICU admission to day 14, including anticoagulation status and thrombotic and hemorrhagic events. The effect of high-dose prophylactic anticoagulation (either at intermediate or equivalent to therapeutic dose), defined using a standardized protocol of classification, was assessed using a time-varying exposure model using inverse probability of treatment weight.

RESULTS

Of 538 patients included, 104 patients experienced a total of 122 TCs with an incidence of 22.7% (95% CI, 19.2%-26.3%). Pulmonary embolism accounted for 52% of the recorded TCs. High-dose prophylactic anticoagulation was associated with a significant reduced risk of TC (hazard ratio, 0.81; 95% CI, 0.66-0.99) without increasing the risk of bleeding (HR, 1.11; 95% CI, 0.70-1.75).

INTERPRETATION

High-dose prophylactic anticoagulation is associated with a reduction in thrombotic complications in critically ill patients with COVID-19 without an increased risk of hemorrhage. Randomized controlled trials comparing prophylaxis with higher doses of anticoagulants are needed to confirm these results.

TRIAL REGISTRY

ClinicalTrials.gov; No.: NCT04405869; URL: www.clinicaltrials.gov.

SARS-CoV-2 Pneumonia in Hospitalized Asthmatic Patients Did Not Induce Severe Exacerbation

BACKGROUND

Viral infections are known to exacerbate asthma in adults. Previous studies have found few patients with asthma among severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia cases. However, the relationship between SARS-CoV-2 infection and severe asthma exacerbation is not known.

OBJECTIVE

To assess the frequency of asthma exacerbation in patients with asthma hospitalized for SARS-CoV-2 pneumonia and compare symptoms and laboratory and radiological findings in patients with and without asthma with SARS-CoV-2 pneumonia.

METHODS

We included 106 patients between March 4 and April 6, 2020, who were hospitalized in the Chest Diseases Department of Strasbourg University Hospital; 23 had asthma. To assess the patients' asthma status, 3 periods were defined: the last month before the onset of COVID-19 symptoms (p1), prehospitalization (p2), and during hospitalization (p3). Severe asthma exacerbations were defined according to Global INitiative for Asthma guidelines during p1 and p2. During p3, we defined severe asthma deterioration as the onset of breathlessness and wheezing requiring systemic corticosteroids and inhaled β2 agonist.

RESULTS

We found no significant difference between patients with and without asthma in terms of severity (length of stay, maximal oxygen flow needed, noninvasive ventilation requirement, and intensive care unit transfer); 52.2% of the patients with asthma had Global INitiative for Asthma step 1 asthma. One patient had a severe exacerbation during p1, 2 patients during p2, and 5 patients were treated with systemic corticosteroids and inhaled β2 agonist during p3.

CONCLUSIONS

Our results demonstrate that patients with asthma appeared not to be at risk for severe SARS-CoV-2 pneumonia. Moreover, SARS-CoV-2 pneumonia did not induce severe asthma exacerbation.

FLIM-FRET Measurements of Protein-Protein Interactions in Live Bacteria

Protein-protein interactions (PPIs) control various key processes in cells. Fluorescence lifetime imaging microscopy (FLIM) combined with Förster resonance energy transfer (FRET) provide accurate information about PPIs in live cells. FLIM-FRET relies on measuring the fluorescence lifetime decay of a FRET donor at each pixel of the FLIM image, providing quantitative and accurate information about PPIs and their spatial cellular organizations. We propose here a detailed protocol for FLIM-FRET measurements that we applied to monitor PPIs in live Pseudomonas aeruginosa in the particular case of two interacting proteins expressed with highly different copy numbers to demonstrate the quality and robustness of the technique at revealing critical features of PPIs. This protocol describes in detail all the necessary steps for PPI characterization - starting from bacterial mutant constructions up to the final analysis using recently developed tools providing advanced visualization possibilities for a straightforward interpretation of complex FLIM-FRET data.

[Medical biostatistics with GMRC Shiny Stats - learning by doing]

Biostatistics are omnipresent in the scientific and medical literature and are an essential skill for any health student. We have developed a practical training tool - GMRC Shiny stats - an interactive application specifically dedicated to medical data statistical analysis. The application has been designed to provide an analysis workflow corresponding to the usual progression of an experienced statistician during data analysis. The most common statistical analyses can be performed (descriptive statistics, inferences according to frequentist methods, survival analyses, correlation, agreement measurements, etc.). GMRC Shiny stats is intuitive and user-friendly and assists students in choosing the most appropriate statistical tests. With all these functionalities, students can learn statistical analysis by doing. Getting involved in the statistical analysis and processing of their own data is likely to improve their biostatistics skills.

Machine learning application for incident prostate adenocarcinomas automatic registration in a French regional cancer registry

Cancer registries are collections of curated data about malignant tumor diseases. The amount of data processed by cancer registries increases every year, making manual registration more and more tedious.

OBJECTIVE

We sought to develop an automatic analysis pipeline that would be able to identify and preprocess registry input for incident prostate adenocarcinomas in a French regional cancer registry.

METHODS

Notifications from different sources submitted to the Bas-Rhin cancer registry were used here: pathology data and, ICD 10 diagnosis codes from hospital discharge data and healthcare insurance data. We trained a Support Vector Machine model (machine learning) to predict whether patient's data must be considered or not as a prostate adenocarcinoma incident case that should therefore be registered. The final registration of all identified cases was manually confirmed by a specialized technician. Text mining tools (regular expressions) were used to extract clinical and biological data from non-structured pathology reports.

RESULTS

We performed two successive analyses. First, we used 982 cases manually labeled by registrars from the 2014 dataset to predict the registration of 785 cases submitted in 2015. Then, we repeated the procedure using the 2089 cases labeled by registrars from the 2014 and 2015 datasets to predict the registration of 926 cases submitted in the 2016 data. The algorithm identified 663 cases of prostate adenocarcinoma in 2015, and 610 in 2016. From these findings, 663 and 531 cases were respectively added to the registry; and 641 and 512 cases were confirmed by the specialized technician. This registration process has achieved a precision level above 96 %. The algorithm obtained an overall precision of 99 % (99.5 % in 2015 and 98.5 % in 2016) and a recall of 97 % (97.8 % in 2015 and 96.9 % in 2016). When the information was found in pathology report, text mining was more than 90 % accuracy for major indicators: PSA test, Gleason score, and incidence date). For both PSA and tumor side, information was not detected in the majority of cases."

CONCLUSION

Machine learning was able to identify new cases of prostate cancer, and text mining was able to prefill the data about incident cases. Machine-learning-based automation of the registration process could reduce delays in data production and allow investigators to devote more time to complex tasks and analysis.

An overview of siderophore biosynthesis among fluorescent Pseudomonads and new insights into their complex cellular organization

Siderophores are iron-chelating molecules produced by bacteria to access iron, a key nutrient. These compounds have highly diverse chemical structures, with various chelating groups. They are released by bacteria into their environment to scavenge iron and bring it back into the cells. The biosynthesis of siderophores requires complex enzymatic processes and expression of the enzymes involved is very finely regulated by iron availability and diverse transcriptional regulators. Recent data have also highlighted the organization of the enzymes involved in siderophore biosynthesis into siderosomes, multi-enzymatic complexes involved in siderophore synthesis. An understanding of siderophore biosynthesis is of great importance, as these compounds have many potential biotechnological applications because of their metal-chelating properties and their key role in bacterial growth and virulence. This review focuses on the biosynthesis of siderophores produced by fluorescent Pseudomonads, bacteria capable of colonizing a large variety of ecological niches. They are characterized by the production of chromopeptide siderophores, called pyoverdines, which give the typical green colour characteristic of fluorescent pseudomonad cultures. Secondary siderophores are also produced by these strains and can have highly diverse structures (such as pyochelins, pseudomonine, yersiniabactin, corrugatin, achromobactin and quinolobactin).

Exploring protein-protein interactions with large differences in protein expression levels using FLIM-FRET

Many molecular processes within a cell are carried out by molecular machines built from a large number of proteins organized by their protein-protein interactions (PPIs). Exploring PPIs in their cellular context is critical to better understand the proteins functions. Förster resonance energy transfer measured by fluorescence lifetime imaging (FLIM-FRET) enables to monitor PPIs and to map their spatial organization in a living cell with high spatial and temporal specificity. But both the accurate measurement and the interpretation of multi-exponential FLIM-FRET data associated to mixtures of interacting and non-interacting proteins are difficult. Here we show that a simple diagram plot can find interesting visualization properties by clustering pixels with similar decay signatures. FLIM diagram plot can be used to provide valuable information about stoichiometry and binding mode in PPIs, even in the presence of large differences in protein expression levels of the different interacting partners. The proposed FLIM diagram plot is a useful visual approach for a more straightforward interpretation of complex lifetime data. This approach was applied for revealing critical features of PPIs in live Pseudomonas aeruginosa.

Phenotyping Occupational Asthma Caused by Acrylates in a Multicenter Cohort Study

BACKGROUND

While acrylates are well-known skin sensitizers, they are not classified as respiratory sensitizers although several cases of acrylate-induced occupational asthma (OA) have been reported.

OBJECTIVE

To evaluate the characteristics of acrylate-induced OA in a large series of cases and compare those with OA induced by other low-molecular-weight (LMW) agents.

METHODS

Jobs and exposures, clinical and functional characteristics, and markers of airway inflammation were analyzed in an international, multicenter, retrospective cohort of subjects with OA ascertained by a positive inhalation challenge to acrylates (n = 55) or other LMW agents (n = 418) including isocyanates (n = 125).

RESULTS

Acrylate-containing glues were the most prevalent products, and industrial manufacturing, dental work, and beauty care were typical occupations causing OA. Work-related rhinitis was more common in acrylate-than in isocyanate-induced asthma (P < .001). The increase in postchallenge fractional exhaled nitric oxide was significantly greater in acrylate-induced OA (26.0; 8.2 to 38.0 parts per billion [ppb]) than in OA induced by other LMW agents (3.0; -1.0 to 10.0 ppb; P < .001) or isocyanates (5.0; 2.0 to 16.0 ppb; P = .010). Multivariable models confirmed that OA induced by acrylates was significantly and independently associated with a postchallenge increase in fractional exhaled nitric oxide (≥17.5 ppb).

CONCLUSIONS

Acrylate-induced OA shows specific characteristics, concomitant work-related rhinitis, and exposure-related increases in fractional exhaled nitric oxide, suggesting that acrylates may induce asthma through different immunologic mechanisms compared with mechanisms through which other LMW agents may induce asthma. Our findings reinforce the need for a reevaluation of the hazard classification of acrylates, and further investigation of the pathophysiological mechanisms underlying their respiratory sensitizing potential.

Cluster analysis of indoor environmental factors associated with symptoms of mite allergy

BACKGROUND

The clinical efficacy of controlling environmental allergens as a component of allergic asthma treatment remains controversial. Multifaceted allergen reductions appeared to be the most efficient methods. However, they require home visits with indoor technicians.

OBJECTIVE

To examine the characteristics of indoor environments that might be related to symptoms of children and adult patients with mite allergic rhinitis and/or asthma.

METHODS

We included 315 patients allergic to house dust mites with rhinitis and/or asthma who had been visited at home by 2 medical indoor environment counselors (MIECs) from the Strasbourg University Hospital between January 2007 and June 2015. In a cluster analysis, we analyzed 42 characteristics of respiratory symptoms, dwelling characteristics, and indoor pollutants in this population.

RESULTS

Three clusters were defined among the patients. Cluster 1 included 55 patients, all with rhinitis, 32% with asthma, and all living in an urban area. Clusters 2 and 3 included 86 and 174 patients, respectively. The important factors in these 2 clusters were asthma incidence and exposure to different indoor pollutants, such as indoor perfumes, cleaning products, and tobacco smoke.

CONCLUSION

Our results underlined the variability of indoor environments and the importance of MIEC home visits to investigate individual patient environments and propose an appropriate avoidance management plan. Our results showed that sensitization to mite and exposure to indoor chemical pollutants were associated with severe asthma.

Severe Occupational Asthma: Insights From a Multicenter European Cohort

BACKGROUND

Although sensitizer-induced occupational asthma (OA) accounts for an appreciable fraction of adult asthma, the severity of OA has received little attention.

OBJECTIVE

The aim of this study was to characterize the burden and determinants of severe OA in a large multicenter cohort of subjects with OA.

METHODS

This retrospective study included 997 subjects with OA ascertained by a positive specific inhalation challenge completed in 20 tertiary centers in 11 European countries during the period 2006 to 2015. Severe asthma was defined by a high level of treatment and any 1 of the following criteria: (1) daily need for a reliever medication, (2) 2 or more severe exacerbations in the previous year, or (3) airflow obstruction.

RESULTS

Overall, 162 (16.2%; 95% CI, 14.0%-18.7%) subjects were classified as having severe OA. Multivariable logistic regression analysis revealed that severe OA was associated with persistent (vs reduced) exposure to the causal agent at work (odds ratio [OR], 2.78; 95% CI, 1.50-5.60); a longer duration of the disease (OR, 1.04; 95% CI, 1.00-1.07); a low level of education (OR, 2.69; 95% CI, 1.73-4.18); childhood asthma (OR, 2.92; 95% CI, 1.13-7.36); and sputum production (OR, 2.86; 95% CI, 1.87-4.38). In subjects removed from exposure, severe OA was associated only with sputum production (OR, 3.68; 95% CI, 1.87-7.40); a low education level (OR, 3.41; 95% CI, 1.72-6.80); and obesity (OR, 1.98; 95% CI, 0.97-3.97).

CONCLUSIONS

This study indicates that a substantial proportion of subjects with OA experience severe asthma and identifies potentially modifiable risk factors for severe OA that should be targeted to reduce the adverse impacts of the disease.

Are high- and low-molecular-weight sensitizing agents associated with different clinical phenotypes of occupational asthma?

BACKGROUND

High-molecular-weight (HMW) proteins and low-molecular-weight (LMW) chemicals can cause occupational asthma (OA) although few studies have thoroughly compared the clinical, physiological, and inflammatory patterns associated with these different types of agents. The aim of this study was to determine whether OA induced by HMW and LMW agents shows distinct phenotypic profiles.

METHODS

Clinical and functional characteristics, and markers of airway inflammation were analyzed in an international, multicenter, retrospective cohort of subjects with OA ascertained by a positive inhalation challenge response to HMW (n = 544) and LMW (n = 635) agents.

RESULTS

Multivariate logistic regression analysis showed significant associations between OA caused by HMW agents and work-related rhinitis (OR [95% CI]: 4.79 [3.28-7.12]), conjunctivitis (2.13 [1.52-2.98]), atopy (1.49 [1.09-2.05]), and early asthmatic reactions (2.86 [1.98-4.16]). By contrast, OA due to LMW agents was associated with chest tightness at work (2.22 [1.59-3.03]), daily sputum (1.69 [1.19-2.38]), and late asthmatic reactions (1.52 [1.09-2.08]). Furthermore, OA caused by HMW agents showed a higher risk of airflow limitation (1.76 [1.07-2.91]), whereas OA due to LMW agents exhibited a higher risk of severe exacerbations (1.32 [1.01-1.69]). There were no differences between the two types of agents in the baseline sputum inflammatory profiles, but OA caused by HMW agents showed higher baseline blood eosinophilia and a greater postchallenge increase in fractional nitric oxide.

CONCLUSION

This large cohort study describes distinct phenotypic profiles in OA caused by HMW and LMW agents. There is a need to further explore differences in underlying pathophysiological pathways and outcome after environmental interventions.

Finding Adequate Information: A Major Challenge for Policy-Makers in the Field of Cancer

Background and context: A global cancer epidemic is developing (GLOBOCAN 2012). In the case of low- and-middle-income countries, difficulties are cumulative: inadequate health systems, lack of training for professionals. Drastic decisions have to be taken in a very complex field. Good decision needs good information. What about information dedicated to policy-makers: to decide a question, they need specific information, marked by these features: synthetic, clear, scientifically validated. Actually, this is not easy to find. Moreover policy-makers can't really benefit from: 1. Information for health professionals which is complex and overabundant (the request “cancer” on PubMed “out” nearly 1.5 millions references). 2. Documents or testimonials for patients. Written by scientific societies or patients' associations, they mostly focus on 2 topics “understand your disease” and “how to cope with”. 3. Information from the Web, not always reliable in terms of quality. Strategy/Tactics: While policy advisors and international organizations provide appropriate studies and reports, mostly focused on “what should be done”, we believe that knowledge of basic cancer data are necessary to understand the proposals. We talk about issues like “what is cancer”, “what exactly cover radiotherapy, oncological surgery…”. Regarding French speaking Africa, Alliance Ligues Africaines and Méditérranéennes (ALIAM) and The French League have produced targeted information for decision-makers. The document was presented in Brazzaville in June 2017. Access to this book is free: www.livre-cancer.aliam.org . The editorial method was discussed and we made the choice to write short sheets, to quickly understand the useful definitions and problems. Rather than comprehensiveness, a pedagogical will and a desire for clarity guided the writing. Diagrams and photos had to be abundant to facilitate understanding. Moreover, this format allows a permanent update of the subjects and the introduction of new topics as needed. What was learned: On the basis of this experience, ALIAM and the league are convinced that a pedagogic document with an international vocation would be useful for all policy makers. Proposal for action: UICC would be the perfect organizer of a working group to produce such a document. The goal would be to develop a consensus text which resume essential data on all common themes of cancer. About 25 themes could be identified, e.g., definition and mechanisms of development of cancers, risk factors, screening and early diagnosis, anatomic pathology and telepathology, molecular biology, imaging and interventional radiology, surgery, radiotherapy, chemotherapy and innovative therapies, palliative care etc. Moreover, focus on specific location of cancer (breast, cervix, lung…) and pediatric cancers should be developed. Then, it would be easier for any world regions to supplement this validated information with additional specific data describing the local situation. Hierarchizing action priorities would be facilitated.

A Key Role for the Periplasmic PfeE Esterase in Iron Acquisition via the Siderophore Enterobactin in Pseudomonas aeruginosa

Enterobactin (ENT) is a siderophore (iron-chelating compound) produced by Escherichia coli to gain access to iron, an indispensable nutrient for bacterial growth. ENT is used as an exosiderophore by Pseudomonas aeruginosa with transport of ferri-ENT across the outer membrane by the PfeA transporter. Next to the pfeA gene on the chromosome is localized a gene encoding for an esterase, PfeE, whose transcription is regulated, as for pfeA, by the presence of ENT in bacterial environment. Purified PfeE hydrolyzed ferri-ENT into three molecules of 2,3-DHBS (2,3-dihydroxybenzoylserine) still complexed with ferric iron, and complete dissociation of iron from ENT chelating groups was only possible in the presence of both PfeE and an iron reducer, such as DTT. The crystal structure of PfeE and an inactive PfeE mutant complexed with ferri-ENT or a nonhydrolyzable ferri-catechol complex allowed identification of the enzyme binding site and the catalytic triad. Finally, cell fractionation and fluorescence microscopy showed periplasmic localization of PfeE in P. aeruginosa cells. Thus, the molecular mechanism of iron dissociation from ENT in P. aeruginosa differs from that previously described in E. coli. In P. aeruginosa, siderophore hydrolysis occurs in the periplasm, with ENT never reaching the bacterial cytoplasm. In E. coli, ferri-ENT crosses the inner membrane via the ABC transporter FepBCD and ferri-ENT is hydrolyzed by the esterase Fes only once it is in the cytoplasm.

The RNA Complement of Outer Membrane Vesicles From Salmonella enterica Serovar Typhimurium Under Distinct Culture Conditions

Bacterial outer membrane vesicles (OMVs), as well as OMV-associated small RNAs, have been demonstrated to play a role in host-pathogen interactions. The presence of larger RNA transcripts in OMVs has been less studied and their potential role in host-pathogen interactions remains largely unknown. Here we analyze RNA from OMVs secreted by Salmonella enterica serovar Typhimurium (S. Typhimurium) cultured under different conditions, which mimic host-pathogen interactions. S. Typhimurium was grown to exponential and stationary growth phases in minimal growth control medium (phosphate-carbon-nitrogen, PCN), as well as in acidic and phosphate-depleted PCN, comparable to the macrophage environment and inducing therefore the expression of Salmonella pathogenicity island 2 (SPI-2) genes. Moreover, Salmonella pathogenicity island 1 (SPI-1), which is required for virulence during the intestinal phase of infection, was induced by culturing S. Typhimurium to the stationary phase in Lysogeny Broth (LB). For each condition, we identified OMV-associated RNAs that are enriched in the extracellular environment relative to the intracellular space. All RNA classes could be observed, but a vast majority of rRNA was exported in all conditions in variable proportions with a notable decrease in LB SPI-1 inducing media. Several mRNAs and ncRNAs were specifically enriched in/on OMVs dependent on the growth conditions. Important to note is that some RNAs showed identical read coverage profiles intracellularly and extracellularly, whereas distinct coverage patterns were observed for other transcripts, suggesting a specific processing or degradation. Moreover, PCR experiments confirmed that distinct RNAs were present in or on OMVs as full-length transcripts (IsrB-1/2; IsrA; ffs; SsrS; CsrC; pSLT035; 10Sa; rnpB; STM0277; sseB; STM0972; STM2606), whereas others seemed to be rather present in a processed or degraded form. Finally, we show by a digestion protection assay that OMVs are able to prevent enzymatic degradation of given full-length transcripts (SsrS, CsrC, 10Sa, and rnpB). In summary, we show that OMV-associated RNA is clearly different in distinct culture conditions and that at least a fraction of the extracellular RNA is associated as a full-length transcripts with OMVs, indicating that some RNAs are protected by OMVs and thereby leaving open the possibility that those might be functionally active.

Critical shoulder angle: Measurement reproducibility and correlation with rotator cuff tendon tears

BACKGROUND

Associations have been reported linking rotator cuff tears (RCTs) to both greater lateral extension of the acromion and greater inclination of the glenoid cavity. These two factors combined can be assessed using a recently introduced parameter, the critical shoulder angle (CSA). The primary objective of this study was to confirm the association linking a high CSA value to RCTs, and the secondary objective was to assess the reproducibility of CSA measurement using a goniometer.

HYPOTHESIS

The null hypothesis was that the CSA value in a group of patients with RCTs was not significantly different from that in patients with anterior shoulder instability and a Bankart lesion, taken as the general population for this study.

METHODS

After a power estimation, we retrospectively included 28 patients with a mean age of 55.5 years who had surgery for RCTs and 27 patients with a mean age of 27.2 years who underwent anterior labral repair. Two surgeons used a goniometer to measure the CSA in each patient. Reproducibility was assessed based on Bland-Altman plots and Pearson's correlation coefficient.

RESULTS

The mean CSA was significantly higher (P=0.02) in the RCT group (36.4°±4.4°; range: 30°-46°) than in the labral-repair group (33.3°±3.8°; range: 25°-41°). Intra-observer reproducibility was 96.7% and inter-observer reproducibility was 95.5%.

CONCLUSION

Our results support previously published evidence that the CSA is significantly greater in patients with RCTs. Thus, an anatomical difference seems to exist between patients with RCTs and the general population. The CSA measured on a standard radiograph using a goniometer provides a reproducible assessment of this anatomical difference.

LEVEL OF EVIDENCE

IV, case-control epidemiological study with a power estimation.

Can the presence of an infection be predicted before a revision total hip arthroplasty? Preliminary study to establish an infection score

INTRODUCTION

The diagnosis of periprosthetic joint infection can be challenging, in part because there is no universal diagnostic test. Current recommendations include several diagnostic criteria, and are mainly based on the results of deep microbiological samples; however, these only provide a diagnosis after surgery. A predictive infection score would improve the management of revision arthroplasty cases. The purpose of this study was to define a composite infection score using standard clinical, radiological and laboratory data that can be used to predict whether an infection is present before a total hip arthroplasty (THA) revision procedure.

HYPOTHESIS

The infection score will make it possible to differentiate correctly between infected and non-infected patients in 75% of cases.

MATERIAL AND METHODS

One hundred and four records from patients who underwent THA revision for any reason were analysed retrospectively: 43 with infection and 61 without infection. There were 54 men and 50 women with an average age of 70±12 years (range 30-90). A univariate analysis was performed to look for individual discriminating factors between the data in the medical records of infected and non-infected patients. A multivariate analysis subsequently integrated these factors together. A composite score was defined and its diagnostic effectiveness was evaluated as the percentage of correctly classified records, along with its sensitivity and specificity.

RESULTS

The score consisted of the following individually weighed factors: body mass index, presence of diabetes, mechanical complication, wound healing disturbance and fever. This composite infection score was able to distinguish correctly between the infected patients (positive score) and non-infected patients (negative score) in 78% of cases; the sensitivity was 57% and the specificity 93%.

DISCUSSION

Once this score is evaluated prospectively, it could be an important tool for defining the medical - surgical strategy during THA revision, no matter the reason for revision.

LEVEL OF EVIDENCE

Level IV - retrospective study.

Quantitative sampling of conformational heterogeneity of a DNA hairpin using molecular dynamics simulations and ultrafast fluorescence spectroscopy

Molecular dynamics (MD) simulations and time resolved fluorescence (TRF) spectroscopy were combined to quantitatively describe the conformational landscape of the DNA primary binding sequence (PBS) of the HIV-1 genome, a short hairpin targeted by retroviral nucleocapsid proteins implicated in the viral reverse transcription. Three 2-aminopurine (2AP) labeled PBS constructs were studied. For each variant, the complete distribution of fluorescence lifetimes covering 5 orders of magnitude in timescale was measured and the populations of conformers experimentally observed to undergo static quenching were quantified. A binary quantification permitted the comparison of populations from experimental lifetime amplitudes to populations of aromatically stacked 2AP conformers obtained from simulation. Both populations agreed well, supporting the general assumption that quenching of 2AP fluorescence results from pi-stacking interactions with neighboring nucleobases and demonstrating the success of the proposed methodology for the combined analysis of TRF and MD data. Cluster analysis of the latter further identified predominant conformations that were consistent with the fluorescence decay times and amplitudes, providing a structure-based rationalization for the wide range of fluorescence lifetimes. Finally, the simulations provided evidence of local structural perturbations induced by 2AP. The approach presented is a general tool to investigate fine structural heterogeneity in nucleic acid and nucleoprotein assemblies.

Structural Insights into the HIV-1 Minus-strand Strong-stop DNA

An essential step of human immunodeficiency virus type 1 (HIV-1) reverse transcription is the first strand transfer that requires base pairing of the R region at the 3'-end of the genomic RNA with the complementary r region at the 3'-end of minus-strand strong-stop DNA (ssDNA). HIV-1 nucleocapsid protein (NC) facilitates this annealing process. Determination of the ssDNA structure is needed to understand the molecular basis of NC-mediated genomic RNA-ssDNA annealing. For this purpose, we investigated ssDNA using structural probes (nucleases and potassium permanganate). This study is the first to determine the secondary structure of the full-length HIV-1 ssDNA in the absence or presence of NC. The probing data and phylogenetic analysis support the folding of ssDNA into three stem-loop structures and the presence of four high-affinity binding sites for NC. Our results support a model for the NC-mediated annealing process in which the preferential binding of NC to four sites triggers unfolding of the three-dimensional structure of ssDNA, thus facilitating interaction of the r sequence of ssDNA with the R sequence of the genomic RNA. In addition, using gel retardation assays and ssDNA mutants, we show that the NC-mediated annealing process does not rely on a single pathway (zipper intermediate or kissing complex).

FRET-based assay to screen inhibitors of HIV-1 reverse transcriptase and nucleocapsid protein

During HIV-1 reverse transcription, the single-stranded RNA genome is converted into proviral double stranded DNA by Reverse Transcriptase (RT) within a reverse transcription complex composed of the genomic RNA and a number of HIV-1 encoded proteins, including the nucleocapsid protein NCp7. Here, we developed a one-step and one-pot RT polymerization assay. In this in vitro assay, RT polymerization is monitored in real-time by Förster resonance energy transfer (FRET) using a commercially available doubly-labeled primer/template DNA. The assay can monitor and quantify RT polymerization activity as well as its promotion by NCp7. Z-factor values as high as 0.89 were obtained, indicating that the assay is suitable for high-throughput drug screening. Using Nevirapine and AZT as prototypical RT inhibitors, reliable IC50 values were obtained from the changes in the RT polymerization kinetics. Interestingly, the assay can also detect NCp7 inhibitors, making it suitable for high-throughput screening of drugs targeting RT, NCp7 or simultaneously, both proteins.

Development and multi-centre evaluation of a method for assessing the severity of potential harm of medication reconciliation errors at hospital admission in elderly

BACKGROUND

Medication reconciliation is a powerful process to correct medication errors (ME) resulting from miscommunicated information at transitions of care. This study aims to develop and evaluate a scoring method for assessing the severity of potential harm of ME intercepted by medication reconciliation at hospital admission in elderly.

METHODS

The development of the scoring method was based on a literature search and the creation of a list of high-risk drugs used in outpatient care. The evaluation of the method was carried out in 7 French hospitals and was based on two criteria: the inter-rater reliability and acceptability. The assessment of the inter-rater reliability was based on intra-class correlation coefficient (ICC) calculations. Each hospital prospectively enrolled the 10 first patients aged 65 or older presenting with at least one ME. Seven blocks of 10 patients were formed. After randomization, each block was rated by practitioners from 3 hospitals. The assessment of the acceptability was based on a satisfaction questionnaire.

RESULTS

A clinical algorithm was developed. The inter-rater reliability of the method was validated by the overall agreement of the 7 hospitals ratings. The agreement was at least substantial (ICC>0.60) and in most of cases almost perfect (ICC>0.80). The acceptability of the method was judged as satisfactory.

CONCLUSION

This multi-centre project has validated an instrument for assessing the severity of potential harm of ME intercepted by medication reconciliation. This will allow studies to be conducted with large cohorts of patients in order to develop epidemiological databases of ME of potential clinical significance.

A new, faster, and safe nasal provocation test method for diagnosing mite allergic rhinitis

BACKGROUND

Diagnosing house dust mite (HDM) allergic rhinitis is difficult. The nasal provocation test (NPT) has been shown to be the most pertinent, but several methods are available. According to guidelines, the NPT requires a skin end-point titration and an objective measurement of nasal patency. Hence, NPT is time consuming and its use is limited.

OBJECTIVE

To evaluate the sensitivity, specificity, and safety of a new, more rapid, and simple alternative NPT (NPT-R) to HDM.

METHODS

Eighty-eight patients with from rhinitis (49 allergic to HDM and 39 controls with and without atopy) were included. Allergic rhinitis to HDM was confirmed by a "classic" NPT based on the Lebel score and rhinomanometry. After a period of 4 weeks, NPT-R was performed and only the clinical score was measured.

RESULTS

The study population was young (mean ± SD, 27.7 ± 8.5 years old), composed mostly of women (61 vs 27 men), and 24% reported asthma. The sensitivity and specificity of NPT-R were 83.7% and 100%, respectively. The correlation between the NPTs was statistically significant (0.833, P < .0001, n = 88) and the 2 NPTs were completely safe. Performing NPT-R was more rapid (mean ± SD, 22 ± 8 minutes) than the classic NPT (97 ± 20 minutes).

CONCLUSION

The NPT-R is safe and easier and faster than the classic NPT. This new method appears to be a very useful tool in the diagnosis of HDM allergic rhinitis when the diagnosis is uncertain or before initiating immunotherapy.

TRIAL REGISTRATION

ClinicalTrials.gov, identifier NCT01485523.

Reverse Transcriptase in Action: FRET-Based Assay for Monitoring Flipping and Polymerase Activity in Real Time

Reverse transcriptase (RT) of human immunodeficiency virus-1 (HIV-1) is a multifunctional enzyme that catalyzes the conversion of the single stranded viral RNA genome into double-stranded DNA, competent for host-cell integration. RT is endowed with RNA- and DNA-dependent DNA polymerase activity and DNA-directed RNA hydrolysis (RNase H activity). As a key enzyme of reverse transcription, RT is a key target of currently used highly active antiretroviral therapy (HAART), though RT inhibitors offer generally a poor resistance profile, urging new RT inhibitors to be developed. Using single molecule fluorescence approaches, it has been recently shown that RT binding orientation and dynamics on its substrate play a critical role in its activity. Currently, most in vitro RT activity assays, inherently end-point measurements, are based on the detection of reaction products by using radio-labeled or chemically modified nucleotides. Here, we propose a simple and continuous real-time Förster resonance energy transfer (FRET) based-assay for the direct measurement of RT's binding orientation and polymerase activity, with the use of conventional steady-state fluorescence spectroscopy. Under our working conditions, the change in binding orientation and the primer elongation step can be visualized separately on the basis of their opposite fluorescence changes and their different kinetics. The assay presented can easily discriminate non-nucleoside RT inhibitors from nucleoside RT inhibitors and determine reliably their potency. This one-step and one-pot assay constitutes an improved alternative to the currently used screening assays to disclose new anti-RT drugs and identify at the same time the class to which they belong.

Posterior surgery in high-grade spondylolisthesis

INTRODUCTION

High-grade L5-S1 spondylolisthesis alters sagittal spinopelvic balance, which can cause low back pain and progressive neurologic disorder. The present study assessed spondylolisthesis reduction and maintenance over time with L4-S1 versus L5-S1 fusion using a lever-arm system and posterior fusion combined with lumbosacral graft.

MATERIALS AND METHODS

Forty patients were operated on for symptomatic high-grade spondylolisthesis, 34 of whom had full pre- and post-operative radiological analysis, with a mean follow-up of 5.4years. There were 9 L5-S1 and 25 L4-S1 instrumentations. Analysis of spinopelvic and slipping parameters and the evolution of segmental lordosis compared results between L5-S1 and L4-S1 instrumentation.

RESULTS

Mean Taillard spondylolisthesis index decreased from 64% to 37% (P=0.0001). Overall sagittal spinopelvic balance was not significantly changed. Overall L1-S1 and segmental L4-L5 lordosis were not affected by instrumentation. Mean L5-S1 segmental lordosis increased from 11° to 18°. There was loss of reduction from 19° to 14° with L5-S1 instrumentation, in contrast to maintained reduction with L4-S1 instrumentation (P=0.006).

CONCLUSION

The lever-arm system provided anterior-posterior reduction of spondylolisthesis and corrected slippage. Postoperative change in overall sagittal spinopelvic balance was slight and constant. Posterior L4-S1 fusion provided better long-term control of L5-S1 lordosis reduction than the shorter L5-S1 fusion. Retrospective study of level IV.

Dynamic interactions of the HIV-1 Tat with nucleic acids are critical for Tat activity in reverse transcription

The HIV-1 transactivator of transcription (Tat) protein is thought to stimulate reverse transcription (RTion). The Tat protein and, more specifically, its (44–61) domain were recently shown to promote the annealing of complementary DNA sequences representing the HIV-1 transactivation response element TAR, named dTAR and cTAR, that plays a key role in RTion. Moreover, the kinetic mechanism of the basic Tat(44–61) peptide in this annealing further revealed that this peptide constitutes a representative nucleic acid annealer. To further understand the structure–activity relationships of this highly conserved domain, we investigated by electrophoresis and fluorescence approaches the binding and annealing properties of various Tat(44–61) mutants. Our data showed that the Tyr47 and basic residues of the Tat(44–61) domain were instrumental for binding to cTAR through stacking and electrostatic interactions, respectively, and promoting its annealing with dTAR. Furthermore, the annealing efficiency of the mutants clearly correlates with their ability to rapidly associate and dissociate the complementary oligonucleotides and to promote RTion. Thus, transient and dynamic nucleic acid interactions likely constitute a key mechanistic component of annealers and the role of Tat in the late steps of RTion. Finally, our data suggest that Lys50 and Lys51 acetylation regulates Tat activity in RTion.