Modification of an outcome measure to follow symptoms of children with acute otitis media.

BACKGROUND: To modify a parent-reported acute otitis media severity of symptoms scale (AOM-SOS) to ensure that it accurately reflects parental concerns. METHODS: Using qualitative interviews with parents of children with acute otitis media (AOM) (n = 24), we generated 39 candidate items for inclusion in the new version of the scale. We determined the importance of each item by enrolling 50 other parents of children with AOM. We selected 15 items with high importance and used them to create a new version of the scale. During successive rounds of cognitive interviews, 3 items were dropped. Two additional items were dropped because they were highly correlated. We evaluated the psychometric properties of the new, 10-item version (version 6.0) in 139 children with AOM. RESULTS: AOM-SOS scores correlated with functional status (r = -0.53), parent assessment of child's pain level (r = 0.69), and overall symptom severity (r = 0.41). The internal consistency of the scale, as measured by Cronbach's alpha, was 0.90. Responsiveness (standardized response mean = 1.82) and test-retest reliability (0.77) were excellent and good, respectively. CONCLUSION: Data presented here support the use of the new version of the scale as a longitudinal measure of symptom burden in clinical trials of children with AOM. IMPACT STATEMENT: The AOM-SOS scale, which now incorporates parental views, can be used to track symptom severity in future efficacy trials in young children with acute otitis media. Data is presented on the validity, reliability, and responsiveness of the AOM-SOS scale. Otitis media is the most frequent indication for antibiotic use in young children. The AOM-SOS is one of the few validated disease specific scales available for use in efficacy trials of children with acute otitis media.

Genomic classification and antimicrobial resistance profiling of Streptococcus pneumoniae and Haemophilus influenza isolates associated with paediatric otitis media and upper respiratory infection.

Acute otitis media (AOM) is the most common childhood bacterial infectious disease requiring antimicrobial therapy. Most cases of AOM are caused by translocation of Streptococcus pneumoniae or Haemophilus influenzae from the nasopharynx to the middle ear during an upper respiratory tract infection (URI). Ongoing genomic surveillance of these pathogens is important for vaccine design and tracking of emerging variants, as well as for monitoring patterns of antibiotic resistance to inform treatment strategies and stewardship.In this work, we examined the ability of a genomics-based workflow to determine microbiological and clinically relevant information from cultured bacterial isolates obtained from patients with AOM or an URI. We performed whole genome sequencing (WGS) and analysis of 148 bacterial isolates cultured from the nasopharynx (N = 124, 94 AOM and 30 URI) and ear (N = 24, all AOM) of 101 children aged 6-35 months presenting with AOM or an URI. We then performed WGS-based sequence typing and antimicrobial resistance profiling of each strain and compared results to those obtained from traditional microbiological phenotyping.WGS of clinical isolates resulted in 71 S. pneumoniae genomes and 76 H. influenzae genomes. Multilocus sequencing typing (MSLT) identified 33 sequence types for S. pneumoniae and 19 predicted serotypes including the most frequent serotypes 35B and 3. Genome analysis predicted 30% of S. pneumoniae isolates to have complete or intermediate penicillin resistance. AMR predictions for S. pneumoniae isolates had strong agreement with clinical susceptibility testing results for beta-lactam and non beta-lactam antibiotics, with a mean sensitivity of 93% (86-100%) and a mean specificity of 98% (94-100%). MLST identified 29 H. influenzae sequence types. Genome analysis identified beta-lactamase genes in 30% of H. influenzae strains, which was 100% in agreement with clinical beta-lactamase testing. We also identified a divergent highly antibiotic-resistant strain of S. pneumoniae, and found its closest sequenced strains, also isolated from nasopharyngeal samples from over 15 years ago.Ultimately, our work provides the groundwork for clinical WGS-based workflows to aid in detection and analysis of H. influenzae and S. pneumoniae isolates.

Identifying Children Likely to Benefit From Antibiotics for Acute Sinusitis: A Randomized Clinical Trial.

Importance: The large overlap between symptoms of acute sinusitis and viral upper respiratory tract infection suggests that certain subgroups of children being diagnosed with acute sinusitis, and subsequently treated with antibiotics, derive little benefit from antibiotic use. Objective: To assess if antibiotic therapy could be appropriately withheld in prespecified subgroups. Design, Setting, and Participants: Randomized clinical trial including 515 children aged 2 to 11 years diagnosed with acute sinusitis based on clinical criteria. The trial was conducted between February 2016 and April 2022 at primary care offices affiliated with 6 US institutions and was designed to evaluate whether symptom burden differed in subgroups defined by nasopharyngeal Streptococcus pneumoniae, Haemophilus influenzae, or Moraxella catarrhalis on bacterial culture and by the presence of colored nasal discharge. Interventions: Oral amoxicillin (90 mg/kg/d) and clavulanate (6.4 mg/kg/d) (n = 254) or placebo (n = 256) for 10 days. Main Outcomes and Measures: The primary outcome was symptom burden based on daily symptom scores on a validated scale (range, 0-40) during the 10 days after diagnosis. Secondary outcomes included treatment failure, adverse events including clinically significant diarrhea, and resource use by families. Results: Most of the 510 included children were aged 2 to 5 years (64%), male (54%), White (52%), and not Hispanic (89%). The mean symptom scores were significantly lower in children in the amoxicillin and clavulanate group (9.04 [95% CI, 8.71 to 9.37]) compared with those in the placebo group (10.60 [95% CI, 10.27 to 10.93]) (between-group difference, -1.69 [95% CI, -2.07 to -1.31]). The length of time to symptom resolution was significantly lower for children in the antibiotic group (7.0 days) than in the placebo group (9.0 days) (P = .003). Children without nasopharyngeal pathogens detected did not benefit from antibiotic treatment as much as those with pathogens detected; the between-group difference in mean symptom scores was -0.88 (95% CI, -1.63 to -0.12) in those without pathogens detected compared with -1.95 (95% CI, -2.40 to -1.51) in those with pathogens detected. Efficacy did not differ significantly according to whether colored nasal discharge was present (the between-group difference was -1.62 [95% CI, -2.09 to -1.16] for colored nasal discharge vs -1.70 [95% CI, -2.38 to -1.03] for clear nasal discharge; P = .52 for the interaction between treatment group and the presence of colored nasal discharge). Conclusions: In children with acute sinusitis, antibiotic treatment had minimal benefit for those without nasopharyngeal bacterial pathogens on presentation, and its effects did not depend on the color of nasal discharge. Testing for specific bacteria on presentation may represent a strategy to reduce antibiotic use in this condition. Trial Registration: ClinicalTrials.gov Identifier: NCT02554383.

Use of bisphosphonates and the risk of osteonecrosis among cancer patients: a systemic review and meta-analysis of the observational studies.

PURPOSE: This study aims to systematically review observational studies evaluating the use of bisphosphonates (BPs) and risk of osteonecrosis of the jaw (ONJ) among cancer patients. METHODS: PubMed, Embase, and Cochrane Library were screened from database inception to Aug 2012. Two reviewers independently identified cohort and case-control studies evaluating the use of oral or intravenous (IV) BPs and the risk of ONJ and extracted the characteristics of the studies and risk estimates. Pooled estimates of odds ratios and 95 % confidence intervals were derived by random effects meta-analysis. Subgroup analyses were carried out according to patients' characteristics and route of BP use. RESULTS: We identified eight studies, including 1,389 cases and 569,620 controls. Use of BPs was associated with a significantly increased risk of ONJ (odds ratio (OR) 4.25; 95 % confidence interval (CI) 3.67-5.36; I (2) = 0 %). The summary OR was 4.22 (95 % CI 3.21-5.54; I (2) = 0 %) for adjusted studies. IV BPs were associated with higher risk (OR 4.27; 95 % CI 3.38-5.40; I (2) = 0 %) than oral BPs (OR 1.18; 95 % CI 0.89-1.56; I (2) = 0 %). Hospital-based studies were associated with higher risk estimates than population-based studies. CONCLUSION: The available evidence suggests that use of BPs in cancer patients is associated with a substantial risk for ONJ. Patients receiving IV BP are at the highest risk. It is important to assess oral health before initiating therapy and to avoid dental procedures during the active phase of intravenous BP therapy.

Development and Validation of an Automated Classifier to Diagnose Acute Otitis Media in Children.

Importance: Acute otitis media (AOM) is a frequently diagnosed illness in children, yet the accuracy of diagnosis has been consistently low. Multiple neural networks have been developed to recognize the presence of AOM with limited clinical application. Objective: To develop and internally validate an artificial intelligence decision-support tool to interpret videos of the tympanic membrane and enhance accuracy in the diagnosis of AOM. Design, Setting, and Participants: This diagnostic study analyzed otoscopic videos of the tympanic membrane captured using a smartphone during outpatient clinic visits at 2 sites in Pennsylvania between 2018 and 2023. Eligible participants included children who presented for sick visits or wellness visits. Exposure: Otoscopic examination. Main Outcomes and Measures: Using the otoscopic videos that were annotated by validated otoscopists, a deep residual-recurrent neural network was trained to predict both features of the tympanic membrane and the diagnosis of AOM vs no AOM. The accuracy of this network was compared with a second network trained using a decision tree approach. A noise quality filter was also trained to prompt users that the video segment acquired may not be adequate for diagnostic purposes. Results: Using 1151 videos from 635 children (majority younger than 3 years of age), the deep residual-recurrent neural network had almost identical diagnostic accuracy as the decision tree network. The finalized deep residual-recurrent neural network algorithm classified tympanic membrane videos into AOM vs no AOM categories with a sensitivity of 93.8% (95% CI, 92.6%-95.0%) and specificity of 93.5% (95% CI, 92.8%-94.3%) and the decision tree model had a sensitivity of 93.7% (95% CI, 92.4%-94.9%) and specificity of 93.3% (92.5%-94.1%). Of the tympanic membrane features outputted, bulging of the TM most closely aligned with the predicted diagnosis; bulging was present in 230 of 230 cases (100%) in which the diagnosis was predicted to be AOM in the test set. Conclusions and Relevance: These findings suggest that given its high accuracy, the algorithm and medical-grade application that facilitates image acquisition and quality filtering could reasonably be used in primary care or acute care settings to aid with automated diagnosis of AOM and decisions regarding treatment.

Biomarkers for febrile urinary tract infection in children.

Background: The current reference standard for pediatric urinary tract infection (UTI) screening, the leukocyte esterase (LE) dipstick test, has suboptimal accuracy. The objective of this study was to compare the accuracy of novel urinary biomarkers to that of the LE test. Methods: We prospectively enrolled febrile children who were evaluated for UTI based on their presenting symptoms. We compared the accuracy of urinary biomarkers to that of the test. Results: We included 374 children (50 with UTI, 324 without UTI, ages 1-35 months) and examined 35 urinary biomarkers. The urinary biomarkers that best discriminated between febrile children with and without UTI were urinary neutrophil gelatinase-associated lipocalin (NGAL), IL-1ß, CXCL1, and IL-8. Of all examined urinary biomarkers, the urinary NGAL had the highest accuracy with a sensitivity of 90% (CI: 82-98) and a specificity of 96% (CI: 93-98). Conclusion: Because the sensitivity of the urinary NGAL test is slightly higher than that of the LE test, it can potentially reduce missed UTI cases. Limitations of using urinary NGAL over LE include increased cost and complexity. Further investigation is warranted to determine the cost-effectiveness of urinary NGAL as a screening test for UTI.

Parents' experiences caring for children with acute otitis media: a qualitative analysis.

BACKGROUND: Little is known regarding parents' experiences caring for children with acute otitis media (AOM). This study aimed to explore parents' experiences caring for their child with AOM, identifying symptoms they observed, their thoughts and feelings about those symptoms, how they managed the episode, and what factors caused them to seek medical evaluation. METHODS: From October 2019 to February 2020, we conducted 24 semi-structured cross-sectional interviews with parents of children 3 to 36 months of age with AOM diagnosed at primary care offices associated with the Children's Hospital of Pittsburgh regarding (1) symptoms and behaviors that led parents to believe their child might have AOM; (2) symptoms that were most bothersome to parent and child; (3) what parents did in response to these symptoms; (4) motivations for seeking clinical care; and (5) parents' expectations regarding AOM resolution. Data were analyzed using template analysis, resulting in a hybrid inductive/deductive analytic process. RESULTS: We interviewed 24 parents within 72 h of diagnosis of AOM. Parents frequently believed ear tugging was the symptom most indicative of AOM, despite its presence in only half of the children in this sample. Parents consistently sought medical care when their child had an elevated temperature or lack of sleep, or when symptoms worsened or were unresponsive to home remedies. Parents of children with history of recurrent AOM had less difficulty identifying symptoms of AOM than parents of children with their first ear infection. CONCLUSIONS: Our findings provide insight into symptoms of AOM that cause parents concern and motivate the use of healthcare services. Parents differed in their abilities to observe and report symptoms of AOM. Thus, when interviewing parents who are concerned their preverbal child has AOM, rather than focusing on ear tugging and fever alone, providers should ascertain all unusual behaviors observed by the parent.

Reassessment of the Role of Race in Calculating the Risk for Urinary Tract Infection: A Systematic Review and Meta-analysis.

Importance: A previously reported prediction model included a child's race to estimate risk of urinary tract infection (UTI), but race-conscious medicine encourages investigating how race is likely to be a proxy for other factors that should instead be used for risk prediction. Objectives: To systematically review the available literature to evaluate the robustness of the association between race and UTI and to assess whether other variables could replace race as a variable in a previously developed prediction tool without adversely affecting its accuracy. Data Source: MEDLINE was searched through May 28, 2021. Study Selection: English-language studies that reported data on the prevalence of UTI according to race for children younger than 18 years were included. Data Extraction and Synthesis: Two independent reviewers assessed studies for risk of bias and abstracted data. Random-effects models were used to pool odds ratios, and meta-regression was used to explore heterogeneity. Main Outcomes and Measures: Odds of UTI among non-Black children vs Black children. Results: Sixteen studies (17 845 children) were included. In the primary analysis, which included 11 studies, the pooled odds ratio of UTI among non-Black children was 2.44-fold higher (95% CI, 1.87-3.20) than among Black children. The corresponding odds ratio in studies with low or very low risk of bias was 4.84-fold higher (95% CI, 3.16-7.41; I2 = 0%) among non-Black children than among Black children. Replacing race with history of UTI and duration of fever resulted in a model with similar accuracy (training cohort: overall sensitivity, 96% [95% CI, 94%-98%]; overall specificity, 35% [95%, 32%-38%]; overall area under the receiver operating characteristic curve, 0.80 [95% CI, 0.77-0.82]; validation cohort: overall sensitivity, 97% [95% CI, 90%-100%]; overall specificity, 32% [95% CI, 26%-37%]; overall area under the receiver operating characteristic curve, 0.84 [95% CI, 0.77-0.92]). Conclusions and Relevance: Although previous studies suggested that an association between race and UTI exists, because of the issues associated with the inclusion of race in decision models, we replaced the variable of race with history of UTI and duration of fever in a previously developed risk prediction model and found similar accuracy.

Measurement of a posterior occipitocervical fusion angle.

STUDY DESIGN: A method for evaluating occipitocervical neutral position is described. OBJECTIVE: To describe and measure a posterior occipitocervical angle (POCA) in normal subjects that can be used to guide contouring of fusion implants to achieve occipitocervical neutral fusion and for use in standardized testing of occipitocervical constructs. SUMMARY OF BACKGROUND DATA: The goal of occipitocervical fusion is to fuse the head in an ideal functional position. Several methods of estimating occipitocervical neutral position have been described and tested, yet none has been proven superior. An ideal method would easily and reproducibly aid in evaluating occipitocervical position intraoperatively and potentially aid in the design and testing of implant constructs. METHODS: Fifteen adult lateral cervical spine radiographs taken in occipitocervical neutral position and interpreted as normal by an experienced radiologist were studied. Analysis consisted of measurement of the POCA. The POCA is defined as the angle formed by the intersection of a line drawn tangential to the posterior aspect of the occipital protuberance and a line determined by the posterior aspect of the facets of the third and fourth cervical vertebrae. RESULTS: The mean POCA was 109.7 degrees with a SD of 5.7 degrees. Compilation of the data revealed a normal distribution of measurements where 80% of the POCA values were between 101 and 119 degrees. CONCLUSIONS: POCA is a simple measurement that may be valuable as an intraoperative tool during occipitocervical fusion and may aid the design and testing of fusion implants and their application in the operating room.

Conformational changes in protein function.

Conformational changes are the hallmarks of protein dynamics and are often intimately related to protein functions. Molecular dynamics (MD) simulation is a powerful tool to study the time-resolved properties of protein structure in atomic details. In this chapter, we discuss the various applications of MD simulation to the study of protein conformational changes, and introduce several selected advanced techniques that may significantly increase the sampling efficiencies, including locally enhanced sampling (LES), and grow-to-fit molecular dynamics (G2FMD).

DeepCut: Object Segmentation From Bounding Box Annotations Using Convolutional Neural Networks.

In this paper, we propose DeepCut, a method to obtain pixelwise object segmentations given an image dataset labelled weak annotations, in our case bounding boxes. It extends the approach of the well-known GrabCut [1] method to include machine learning by training a neural network classifier from bounding box annotations. We formulate the problem as an energy minimisation problem over a densely-connected conditional random field and iteratively update the training targets to obtain pixelwise object segmentations. Additionally, we propose variants of the DeepCut method and compare those to a naïve approach to CNN training under weak supervision. We test its applicability to solve brain and lung segmentation problems on a challenging fetal magnetic resonance dataset and obtain encouraging results in terms of accuracy.

Loop conformation and dynamics of the Escherichia coli HPPK apo-enzyme and its binary complex with MgATP.

Comparison of the crystallographic and NMR structures of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) suggests that the enzyme may undergo significant conformational change upon binding to its first substrate, ATP. Two of the three surface loops (loop 2 and loop 3) accounting for most of the conformational differences appear to be confined by crystal contacts, raising questions about the putative large-scale induced-fit conformational change of HPPK and the functional roles of the conserved side-chain residues on the loops. To investigate the loop dynamics in crystal-free environment, we carried out molecular dynamics and locally enhanced sampling simulations of the apo-enzyme and the HPPK.MgATP complex. Our simulations showed that the crystallographic B-factors underestimated the loop dynamics considerably. We found that the open-conformation of loop 3 in the binary complex is accessible to the apo-enzyme and is the favored conformation in solution phase. These results revise our previous view of HPPK-substrate interactions and the associated functional mechanism of conformational change. The lessons learned here offer valuable structural insights into the workings of HPPK and should be useful for structure-based drug design.

Comparison between Generalized-Born and Poisson-Boltzmann methods in physics-based scoring functions for protein structure prediction.

Continuum solvent models such as Generalized-Born and Poisson-Boltzmann methods hold the promise to treat solvation effect efficiently and to enable rapid scoring of protein structures when they are combined with physics-based energy functions. Yet, direct comparison of these two approaches on large protein data set is lacking. Building on our previous work with a scoring function based on a Generalized-Born (GB) solvation model, and short molecular-dynamics simulations, we further extended the scoring function to compare with the MM-PBSA method to treat the solvent effect. We benchmarked this scoring function against seven publicly available decoy sets. We found that, somewhat surprisingly, the results of MM-PBSA approach are comparable to the previous GB-based scoring function. We also discussed the effect to the scoring function accuracy due to presence of large ligands and ions in some native structures of the decoy sets.

Large-scale conformational dynamics of the HIV-1 integrase core domain and its catalytic loop mutants.

HIV-1 integrase is one of the three essential enzymes required for viral replication and has great potential as a novel target for anti-HIV drugs. Although tremendous efforts have been devoted to understanding this protein, the conformation of the catalytic core domain around the active site, particularly the catalytic loop overhanging the active site, is still not well characterized by experimental methods due to its high degree of flexibility. Recent studies have suggested that this conformational dynamics is directly correlated with enzymatic activity, but the details of this dynamics is not known. In this study, we conducted a series of extended-time molecular dynamics simulations and locally enhanced sampling simulations of the wild-type and three loop hinge mutants to investigate the conformational dynamics of the core domain. A combined total of >480 ns of simulation data was collected which allowed us to study the conformational changes that were not possible to observe in the previously reported short-time molecular dynamics simulations. Among the main findings are a major conformational change (>20 A) in the catalytic loop, which revealed a gatinglike dynamics, and a transient intraloop structure, which provided a rationale for the mutational effects of several residues on the loop including Q(148), P(145), and Y(143). Further, clustering analyses have identified seven major conformational states of the wild-type catalytic loop. Their implications for catalytic function and ligand interaction are discussed. The findings reported here provide a detailed view of the active site conformational dynamics and should be useful for structure-based inhibitor design for integrase.

The role of several kinases in mice tolerant to delta 9-tetrahydrocannabinol.

It has been suggested that the cannabinoid receptor type 1 (CB1), a G protein-coupled receptor, is internalized after agonist binding and activation of the second messenger pathways. It is proposed that phosphorylation enhances the down-regulation of the CB1 receptor, thus contributing to tolerance. Alterations in phosphorylation of proteins in the signal transduction cascade after CB1receptor activation could also alter tolerance to cannabinoids. We addressed our hypothesis by evaluating the role of several kinases in antinociceptive tolerance to Delta(9)-tetrahydrocannabinol (THC). We evaluated cAMP-dependent protein kinase (PKA) using KT5720, a PKA inhibitor; protein kinase C (PKC) using bisindolylmaleimide I, HCl (bis), a PKC inhibitor; cGMP-dependent protein kinase (PKG) using KT5823, a PKG inhibitor; beta-adrenergic receptor kinase (beta-ARK) using low molecular weight heparin (LMWH), a beta-ARK inhibitor; and phosphatidylinositol-3 kinase (PI3-K) using 2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one (LY294002), a PI3-K inhibitor and PP1, a Src family tyrosine kinase inhibitor. The cAMP analog used was dibutyryl-cAMP and the cGMP analog used was dibutyryl-cGMP. Our data indicate that selective kinases may be involved in cannabinoid tolerance. Mice and rats were rendered tolerant to Delta(9)-THC. The PKG inhibitor KT5823, the beta-ARK inhibitor LMWH, the PI3-K inhibitor LY294002, and inhibition of PKC by bis had no effect on tolerance. At a higher dose, bis attenuated the antinociceptive effect of delta(9)-THC in nontolerant mice. PP1, the Src family tyrosine kinase inhibitor, and KT5720, the PKA inhibitor, reversed THC-induced tolerance. In addition, inhibition of PKA reversed a decrease in dynorphin release shown to accompany THC tolerance in rats. These data support a role for PKA and Src tyrosine kinase in phosphorylation events in delta(9)-THC-tolerant mice.