Sensory Dysfunction, Microbial Infections, and Host Responses in Alzheimer's Disease.

Sensory functions of organs of the head and neck allow humans to interact with the environment and establish social bonds. With aging, smell, taste, vision, and hearing decline. Evidence suggests that accelerated impairment in sensory abilities can reflect a shift from healthy to pathological aging, including the development of Alzheimer's disease (AD) and other neurological disorders. While the drivers of early sensory alteration in AD are not elucidated, insults such as trauma and infections can affect sensory function. Herein, we review the involvement of the major head and neck sensory systems in AD, with emphasis on microbes exploiting sensory pathways to enter the brain (the "gateway" hypothesis) and the potential feedback loop by which sensory function may be impacted by central nervous system infection. We emphasize detection of sensory changes as first-line surveillance in senior adults to identify and remove potential insults, like microbial infections, that could precipitate brain pathology.

Current State of Open Source Force Fields in Protein-Ligand Binding Affinity Predictions.

In drug discovery, the in silico prediction of binding affinity is one of the major means to prioritize compounds for synthesis. Alchemical relative binding free energy (RBFE) calculations based on molecular dynamics (MD) simulations are nowadays a popular approach for the accurate affinity ranking of compounds. MD simulations rely on empirical force field parameters, which strongly influence the accuracy of the predicted affinities. Here, we evaluate the ability of six different small-molecule force fields to predict experimental protein-ligand binding affinities in RBFE calculations on a set of 598 ligands and 22 protein targets. The public force fields OpenFF Parsley and Sage, GAFF, and CGenFF show comparable accuracy, while OPLS3e is significantly more accurate. However, a consensus approach using Sage, GAFF, and CGenFF leads to accuracy comparable to OPLS3e. While Parsley and Sage are performing comparably based on aggregated statistics across the whole dataset, there are differences in terms of outliers. Analysis of the force field reveals that improved parameters lead to significant improvement in the accuracy of affinity predictions on subsets of the dataset involving those parameters. Lower accuracy can not only be attributed to the force field parameters but is also dependent on input preparation and sampling convergence of the calculations. Especially large perturbations and nonconverged simulations lead to less accurate predictions. The input structures, Gromacs force field files, as well as the analysis Python notebooks are available on GitHub.

To Design Scalable Free Energy Perturbation Networks, Optimal Is Not Enough.

Drug discovery is accelerated with computational methods such as alchemical simulations to estimate ligand affinities. In particular, relative binding free energy (RBFE) simulations are beneficial for lead optimization. To use RBFE simulations to compare prospective ligands in silico, researchers first plan the simulation experiment, using graphs where nodes represent ligands and graph edges represent alchemical transformations between ligands. Recent work demonstrated that optimizing the statistical architecture of these perturbation graphs improves the accuracy of the predicted changes in the free energy of ligand binding. Therefore, to improve the success rate of computational drug discovery, we present the open-source software package High Information Mapper (HiMap)─a new take on its predecessor, Lead Optimization Mapper (LOMAP). HiMap removes heuristics decisions from design selection and instead finds statistically optimal graphs over ligands clustered with machine learning. Beyond optimal design generation, we present theoretical insights for designing alchemical perturbation maps. Some of these results include that for n number of nodes, the precision of perturbation maps is stable at n·ln(n) edges. This result indicates that even an "optimal" graph can result in unexpectedly high errors if a plan includes too few alchemical transformations for the given number of ligands and edges. And, as a study compares more ligands, the performance of even optimal graphs will deteriorate with linear scaling of the edge count. In this sense, ensuring an A- or D-optimal topology is not enough to produce robust errors. We additionally find that optimal designs will converge more rapidly than radial and LOMAP designs. Moreover, we derive bounds for how clustering reduces cost for designs with a constant expected relative error per cluster, invariant of the size of the design. These results inform how to best design perturbation maps for computational drug discovery and have broader implications for experimental design.

Pre-Exascale Computing of Protein-Ligand Binding Free Energies with Open Source Software for Drug Design.

Nowadays, drug design projects benefit from highly accurate protein-ligand binding free energy predictions based on molecular dynamics simulations. While such calculations have been computationally expensive in the past, we now demonstrate that workflows built on open source software packages can efficiently leverage pre-exascale computing resources to screen hundreds of compounds in a matter of days. We report our results of free energy calculations on a large set of pharmaceutically relevant targets assembled to reflect industrial drug discovery projects.

Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field.

Force fields form the basis for classical molecular simulations, and their accuracy is crucial for the quality of, for instance, protein-ligand binding simulations in drug discovery. The huge diversity of small-molecule chemistry makes it a challenge to build and parameterize a suitable force field. The Open Force Field Initiative is a combined industry and academic consortium developing a state-of-the-art small-molecule force field. In this report, industry members of the consortium worked together to objectively evaluate the performance of the force fields (referred to here as OpenFF) produced by the initiative on a combined public and proprietary dataset of 19,653 relevant molecules selected from their internal research and compound collections. This evaluation was important because it was completely blind; at most partners, none of the molecules or data were used in force field development or testing prior to this work. We compare the Open Force Field "Sage" version 2.0.0 and "Parsley" version 1.3.0 with GAFF-2.11-AM1BCC, OPLS4, and SMIRNOFF99Frosst. We analyzed force-field-optimized geometries and conformer energies compared to reference quantum mechanical data. We show that OPLS4 performs best, and the latest Open Force Field release shows a clear improvement compared to its predecessors. The performance of established force fields such as GAFF-2.11 was generally worse. While OpenFF researchers were involved in building the benchmarking infrastructure used in this work, benchmarking was done entirely in-house within industrial organizations and the resulting assessment is reported here. This work assesses the force field performance using separate benchmarking steps, external datasets, and involving external research groups. This effort may also be unique in terms of the number of different industrial partners involved, with 10 different companies participating in the benchmark efforts.

Does the asthma-chronic obstructive pulmonary disease overlap syndrome (ACOS) exist? A narrative review from epidemiology and practice.

Asthma and chronic obstructive pulmonary disease (COPD) have traditionally been approached as separate entities that must be researched and treated separately. There is growing recognition, however, that a substantial proportion of patients with obstructive lung disease have characteristics of both asthma and COPD (termed the asthma-COPD overlap syndrome (ACOS)). Lung disease experts have difficulty defining ACOS, and many still resist accepting the possibility that asthma and COPD may be linked. It is likely that practicing clinicians may be equally confused about how to identify and treat ACOS. This narrative review aims to clarify concepts of ACOS definition, argues that the best way to understand ACOS is to view the chronic lung disease process longitudinally rather than cross-sectionally, and presents evidence that ACOS can be the end result of the natural history of severe asthma. The review also points out the serious gaps in knowledge regarding therapy for ACOS and presents emerging data supporting the intracellular respiratory pathogen Chlamydia pneumoniae as a possible common etiologic agent in severe asthma and ACOS.

Results of Engineering, Primary Care, Oncology Collaborative Regarding a Survey of Primary Care on a Re-Engineered Survivorship Care Plan.

Survivorship care plans (SCPs) may facilitate cancer survivorship care shared between oncologists and primary care, particularly for patients more likely to receive care across healthcare systems such as rural patients. However, limited research has addressed primary care clinicians' information or workflow needs with regard to SCPs. This study's objective was to assess primary care clinicians' perceived usefulness with a re-engineered SCP previously developed by applying engineering approaches and informed by primary care preferences. An emailed survey of primary care clinicians assessed perceived usefulness with the re-engineered SCP. Clinicians were recruited across the USA from primary care practice-based research networks (PBRNs) with high concentrations of rural practices. Over 90% of respondents (n = 111) agreed that (1) the re-engineered SCP was useful (n = 95) and (2) they would want to receive a similar SCP (n = 93). The majority demonstrated high agreement regarding the SCP's relevance, understandability, content, and ability to help provide better survivorship care. Perceived usefulness was consistent between rural and non-rural clinicians. Suggested improvements involved decreased length, addition of a bulleted list, and electronic health record integration. Results indicate that the majority of primary care clinicians perceive the re-engineered SCP as useful. However, primary care clinicians indicated continued barriers despite end-user specific alterations. Future research should investigate additional strategies to support primary care survivorship-related workload, provide essential SCP content, and improve survivorship care delivery.

Re-engineering Survivorship Care Plans to Support Primary Care Needs and Workflow: Results From an Engineering, Primary Care and Oncology Collaborative for Survivorship Health (EPOCH).

Maintaining the health of survivors requires communication, collaboration and care coordination between oncology and primary care. Primary care clinicians have been acknowledged as important recipients of survivorship care plans (SCPs); however, current SCP templates have not been evaluated for usefulness in the primary care context. We surveyed and interviewed primary care clinicians from a rural research network regarding SCP content, format and layout (phase 1), and potential use and clinical workflows around SCPs (phase 2). Based on these data, an existing SCP template was iteratively redesigned to better support survivorship care in the primary care setting. A total of 13 clinicians (9 MDs, 4 APPs) participated. Interviewees advocated for maintaining a single SCP document shared by survivors and clinicians. Changes to the SCP template included prioritizing follow-up over summary of treatment and removing or down-playing screening recommendations not impacted by cancer or cancer treatment. The re-engineered SCP was regarded as highly relevant for survivors, but clinicians noted the significant effort to "disassemble" SCPs in order to enter the information into on the receiving health record. Primary care clinicians value the information in SCPs but had important recommendations regarding content, layout, and format. Additionally, a significant effort appears to be required by recipients in order to extract SCP information for future use.

A Benchmark of Electrostatic Method Performance in Relative Binding Free Energy Calculations.

Relative free energy calculations are fast becoming a critical part of early stage pharmaceutical design, making it important to know how to obtain the best performance with these calculations in applications that could span hundreds of calculations and molecules. In this work, we compared two different treatments of long-range electrostatics, Particle Mesh Ewald (PME) and Reaction Field (RF), in relative binding free energy calculations using a nonequilibrium switching protocol. We found simulations using RF achieve comparable results to those using PME but gain more efficiency when using CPU and similar performance using GPU. The results from this work encourage more use of RF in molecular simulations.

Ensembler: A Simple Package for Fast Prototyping and Teaching Molecular Simulations.

Ensembler is a Python package that enables method prototyping using 1D and 2D model systems and allows deepening of the understanding of different molecular dynamics (MD) methods, starting from basic techniques to enhanced sampling and free-energy approaches. The ease of installing and using the package increases shareability, comparability, and reproducibility of scientific code developments. Here, we describe the implementation and usage of the package and provide an application example for free-energy calculation. The code of Ensembler is freely available on GitHub at https://github.com/rinikerlab/Ensembler.

Open Tibial Fracture Complicated by Wound Botulism: A Case Study.

Botulism is a neuroparalytic disease most commonly caused by foodborne ingestion of neurotoxin types A, B, and E, and is often fatal if untreated. Clinicians should be able to recognize the classic symptoms of botulinum intoxication (12). Owing to its rarity, there are a limited number of studies evaluating the clinical care of patients with wound botulism (10). We present an infected tibial non-union with botulism who underwent a successful radical excision and bone transport. The patient tolerated the procedure well.

Increasing system-wide implementation of opioid prescribing guidelines in primary care: findings from a non-randomized stepped-wedge quality improvement project.

BACKGROUND: Clinician utilization of practice guidelines can reduce inappropriate opioid prescribing and harm in chronic non-cancer pain; yet, implementation of "opioid guidelines" is subpar. We hypothesized that a multi-component quality improvement (QI) augmentation of "routine" system-level implementation efforts would increase clinician adherence to the opioid guideline-driven policy recommendations. METHODS: Opioid policy was implemented system-wide in 26 primary care clinics. A convenience sample of 9 clinics received the QI augmentation (one-hour academic detailing; 2 online educational modules; 4-6 monthly one-hour practice facilitation sessions) in this non-randomized stepped-wedge QI project. The QI participants were volunteer clinic staff. The target patient population was adults with chronic non-cancer pain treated with long-term opioids. The outcomes included the clinic-level percentage of target patients with a current treatment agreement (primary outcome), rates of opioid-benzodiazepine co-prescribing, urine drug testing, depression and opioid misuse risk screening, and prescription drug monitoring database check; additional measures included daily morphine-equivalent dose (MED), and the percentages of all target patients and patients prescribed ≥90 mg/day MED. T-test, mixed-regression and stepped-wedge-based analyses evaluated the QI impact, with significance and effect size assessed with two-tailed p < 0.05, 95% confidence intervals and/or Cohen's d. RESULTS: Two-hundred-fifteen QI participants, a subset of clinical staff, received at least one QI component; 1255 patients in the QI and 1632 patients in the 17 comparison clinics were prescribed long-term opioids. At baseline, more QI than comparison clinic patients were screened for depression (8.1% vs 1.1%, p = 0.019) and prescribed ≥90 mg/day MED (23.0% vs 15.5%, p = 0.038). The stepped-wedge analysis did not show statistically significant changes in outcomes in the QI clinics, when accounting for the comparison clinics' trends. The Cohen's d values favored the QI clinics in all outcomes except opioid-benzodiazepine co-prescribing. Subgroup analysis showed that patients prescribed ≥90 mg/day MED in the QI compared to comparison clinics improved urine drug screening rates (38.8% vs 19.1%, p = 0.02), but not other outcomes (p ≥ 0.05). CONCLUSIONS: Augmenting routine policy implementation with targeted QI intervention, delivered to volunteer clinic staff, did not additionally improve clinic-level, opioid guideline-concordant care metrics. However, the observed effect sizes suggested this approach may be effective, especially in higher-risk patients, if broadly implemented. TRIAL REGISTRATION: Not applicable.

Enhancing system-wide implementation of opioid prescribing guidelines in primary care: protocol for a stepped-wedge quality improvement project.

BACKGROUND: Systematic implementation of guidelines for opioid therapy management in chronic non-cancer pain can reduce opioid-related harms. However, implementation of guideline-recommended practices in routine care is subpar. The goal of this quality improvement (QI) project is to assess whether a clinic-tailored QI intervention improves the implementation of a health system-wide, guideline-driven policy on opioid prescribing in primary care. This manuscript describes the protocol for this QI project. METHODS: A health system with 28 primary care clinics caring for approximately 294,000 primary care patients developed and implemented a guideline-driven policy on long-term opioid therapy in adults with opioid-treated chronic non-cancer pain (estimated N = 3980). The policy provided multiple recommendations, including the universal use of treatment agreements, urine drug testing, depression and opioid misuse risk screening, and standardized documentation of the chronic pain diagnosis and treatment plan. The project team drew upon existing guidelines, feedback from end-users, experts and health system leadership to develop a robust QI intervention, targeting clinic-level implementation of policy-directed practices. The resulting multi-pronged QI intervention included clinic-wide and individual clinician-level educational interventions. The QI intervention will augment the health system's "routine rollout" method, consisting of a single educational presentation to clinicians in group settings and a separate presentation for staff. A stepped-wedge design will enable 9 primary care clinics to receive the intervention and assessment of within-clinic and between-clinic changes in adherence to the policy items measured by clinic-level electronic health record-based measures and process measures of the experience with the intervention. DISCUSSION: Developing methods for a health system-tailored QI intervention required a multi-step process to incorporate end-user feedback and account for the needs of targeted clinic team members. Delivery of such tailored QI interventions has the potential to enhance uptake of opioid therapy management policies in primary care. Results from this study are anticipated to elucidate the relative value of such QI activities.

Developmental Changes in Hepatic Organic Cation Transporter OCT1 Protein Expression from Neonates to Children.

Organic cation transporter 1 (OCT1) plays an important role in the disposition of clinically important drugs, and the capacity of OCT1 activity is presumed to be proportional to the protein expression level in organ tissues. Knowledge of OCT1 protein expression in children, especially neonates and small infants, is currently very limited. Here, we report on the characterization of OCT1 protein expression in neonatal, infant, and pediatric liver samples performed using immunoblot analysis. OCT1 protein expression was detected in liver samples from neonates as early as postnatal days 1 and 2. This youngest group showed significantly lower OCT1 expression normalized by glyceraldehyde-6-phosphate dehydrogenase (values given as means ± S.D. in arbitrary units; 0.03 ± 0.02, n = 7) compared with samples from patients aged 3 to 4 weeks (0.08 ± 0.03, n = 5, P < 0.01), 3 to 6 months (0.23 ± 0.15, n = 7, P < 0.01), 11 months to 1 year (0.42 ± 0.32, n = 6, P < 0.01), and 8 to 12 years (1.00 ± 0.44, n = 7, P < 0.01). These data demonstrate an age-dependent increase in OCT1 expression from birth up to 8 to 12 years of age, and the findings of this study contribute to the understanding of OCT1 functional capacity and its effect upon the disposition of OCT1 substrates in neonates and small infants.

Infection-mediated asthma: etiology, mechanisms and treatment options, with focus on Chlamydia pneumoniae and macrolides.

Asthma is a chronic respiratory disease characterized by reversible airway obstruction and airway hyperresponsiveness to non-specific bronchoconstriction agonists as the primary underlying pathophysiology. The worldwide incidence of asthma has increased dramatically in the last 40 years. According to World Health Organization (WHO) estimates, over 300 million children and adults worldwide currently suffer from this incurable disease and 255,000 die from the disease each year. It is now well accepted that asthma is a heterogeneous syndrome and many clinical subtypes have been described. Viral infections such as respiratory syncytial virus (RSV) and human rhinovirus (hRV) have been implicated in asthma exacerbation in children because of their ability to cause severe airway inflammation and wheezing. Infections with atypical bacteria also appear to play a role in the induction and exacerbation of asthma in both children and adults. Recent studies confirm the existence of an infectious asthma etiology mediated by Chlamydia pneumoniae (CP) and possibly by other viral, bacterial and fungal microbes. It is also likely that early-life infections with microbes such as CP could lead to alterations in the lung microbiome that significantly affect asthma risk and treatment outcomes. These infectious microbes may exacerbate the symptoms of established chronic asthma and may even contribute to the initial development of the clinical onset of the disease. It is now becoming more widely accepted that patterns of airway inflammation differ based on the trigger responsible for asthma initiation and exacerbation. Therefore, a better understanding of asthma subtypes is now being explored more aggressively, not only to decipher pathophysiologic mechanisms but also to select treatment and guide prognoses. This review will explore infection-mediated asthma with special emphasis on the protean manifestations of CP lung infection, clinical characteristics of infection-mediated asthma, mechanisms involved and antibiotic treatment outcomes.

Tokenism in patient engagement.

Background: Patient engagement throughout research is a way to generate more relevant patient-important research questions, methods and results with the ultimate aim of facilitating translation of research into practice. Tokenism is defined as the practice of making perfunctory or symbolic efforts to engage communities or patients. Objective: We wanted to explore how tokenism might influence engaging patients in research to help researchers work towards more genuine engagement. Methods: The Community Clinician Advisory Group and Patient and Clinician Engagement program held a workshop at the 2015 North American Primary Care Research Group meeting titled 'How Do We Move beyond Tokenism in Patient Engagement?' Patients, clinicians and academic researchers contributed examples of genuine and token engagement characteristics based on personal experience and knowledge. Data were iteratively collated and categorized into domains and items. Results: Examples of genuine and token engagement were categorized into three domains: Methods/Structure of engagement, Intent and Relationship building. Members with experience in patient-engaged research projects felt that longitudinal engagement was a key element to effectively translating research into local community and practice. Conclusions: The group (i) highly valued genuine intent and relationship building as elements to combat tokenism; (ii) noted that early genuine attempts at engagement may superficially resemble tokenism as researchers build enduring and trusting relationships with patient/community partners and (iii) emphasized the importance of seeking and utilizing patient experiences throughout research. These observations may contribute to more formal methods to help researchers (and reviewers) evaluate where engagement processes sit along the 'genuine-token' continuum.

Traumatic Complex Hawkins Type IV Talar Fracture: A Case Report.

Fracture-dislocations of the talus are one of the most complex injuries involving the foot and ankle. These injuries are often accompanied by additional traumatic orthopedic injuries, avascular necrosis, and infection. When approaching limb reconstruction and salvage, the overall prognosis and functionality of the limb are key factors to consider. In the present report, we draw attention to the importance of a multidisciplinary team approach for formulating a treatment plan that incorporates the talar injury and associated injuries or pathologic features. We also reviewed the published data related to avascular necrosis of the talus, open talar fracture management, and treatment outcomes.

Catalytic Mechanism of Mammalian Adenylyl Cyclase: A Computational Investigation.

Adenylyl cyclase (AC) catalyzes the synthesis of cyclic AMP, an important intracellular regulatory molecule, from ATP. We propose a catalytic mechanism for class III mammalian AC based on density functional theory calculations. We employ a model of the AC active site derived from a crystal structure of mammalian AC activated by Gα·GTP and forskolin at separate allosteric sites. We compared the calculated activation free energies for 13 possible reaction sequences involving proton transfer, nucleophilic attack, and elimination of pyrophosphate. The proposed most probable mechanism is initiated by deprotonation of 3'OH and water-mediated transfer of the 3'H to the γ-phosphate. Proton transfer is followed by changes in coordination of the two magnesium ion cofactors and changes in the conformation of ATP to enhance the role of 3'O as a nucleophile and to bring 3'O close to Pα. The subsequent phosphoryl transfer step is concerted and rate-limiting. Comparison of the enzyme-catalyzed and nonenzymatic reactions reveals that the active site residues lower the free energy barrier for both phosphoryl transfer and proton transfer and significantly shift the proton transfer equilibrium. Calculations for mutants K1065A and R1029A demonstrate that K1065 plays a significant role in shifting the proton transfer equilibrium, whereas R1029 is important for making the transition state of concerted phosphoryl transfer tight rather than loose.

Reserve autophagic capacity in alveolar epithelia provides a replicative niche for influenza A virus.

Autophagy contributes to cellular homeostasis through metabolite recycling and degradation of cytotoxic protein aggregates and damaged organelles. Although recent studies have established that the requirement for basal autophagy is largely tissue specific, the importance of autophagy for alveolar epithelial cell homeostasis remains an important knowledge gap. In the present study we generated two mouse models, with > 90% or > 50% recombination at the Atg5 locus in the distal respiratory epithelium, to assess the effect of dose-dependent decreases in autophagy on alveolar homeostasis. A 90% decrease in autophagy was well tolerated in young adult mice but resulted in alveolar septal thickening and altered lung mechanics in aged animals, consistent with accumulation of damage over time. By comparison, a 50% decrease in autophagy had no effect on alveolar structure or function throughout the murine life span, indicating that basal autophagy in this compartment exceeds that required for homeostasis. A 50% decrease in autophagy in the bronchoalveolar epithelium significantly attenuated influenza A/H3N2 viral replication, leading to improved lung structure and function and reduced morbidity and mortality after infection. The reserve of autophagic capacity in the alveolar epithelium may provide a niche for replication of influenza A virus.