Evaluating Confounding Control in Estimations of Influenza Antiviral Effectiveness in Electronic Health Plan Data.

Observational studies of oseltamivir use and influenza complications could suffer from residual confounding. Using negative control risk periods and a negative control outcome, we examined confounding control in a health-insurance-claims-based study of oseltamivir and influenza complications (pneumonia, all-cause hospitalization, and dispensing of an antibiotic). Within the Food and Drug Administration's Sentinel System, we identified individuals aged ≥18 years who initiated oseltamivir use on the influenza diagnosis date versus those who did not, during 3 influenza seasons (2014-2017). We evaluated primary outcomes within the following 1-30 days (the primary risk period) and 61-90 days (the negative control period) and nonvertebral fractures (the negative control outcome) within days 1-30. We estimated propensity-score-matched risk ratios (RRs) per season. During the 2014-2015 influenza season, oseltamivir use was associated with a reduction in the risk of pneumonia (RR = 0.72, 95% confidence interval (CI): 0.70, 0.75) and all-cause hospitalization (RR = 0.54, 95% CI: 0.53, 0.55) in days 1-30. During days 61-90, estimates were near-null for pneumonia (RR = 1.04, 95% CI: 0.95, 1.15) and hospitalization (RR = 0.94, 95% CI: 0.91, 0.98) but slightly increased for antibiotic dispensing (RR = 1.14, 95% CI: 1.08, 1.21). The RR for fractures was near-null (RR = 1.09, 95% CI: 0.99, 1.20). Estimates for the 2016-2017 influenza season were comparable, while the 2015-2016 season had conflicting results. Our study suggests minimal residual confounding for specific outcomes, but results differed by season.

Rab-E and its interaction with myosin XI are essential for polarised cell growth.

The fundamental process of polarised exocytosis requires the interconnected activity of molecular motors trafficking vesicular cargo within a dynamic cytoskeletal network. In plants, few mechanistic details are known about how molecular motors, such as myosin XI, associate with their secretory cargo to support the ubiquitous processes of polarised growth and cell division. Live-cell imaging coupled with targeted gene knockouts and a high-throughput RNAi assay enabled the first characterisation of the loss of Rab-E function. Yeast two-hybrid and subsequent in silico structural prediction uncovered a specific interaction between Rab-E and myosin XI that is conserved between P. patens and A. thaliana. Rab-E co-localises with myosin XI at sites of active exocytosis, and at the growing tip both proteins are spatiotemporally coupled. Rab-E is required for normal plant growth in P. patens and the rab-E and myosin XI phenotypes are rescued by A. thaliana's Rab-E1c and myosin XI-K/E, respectively. Both PpMyoXI and AtMyoXI-K interact with PpRabE14, and the interaction is specifically mediated by PpMyoXI residue V1422. This interaction is required for polarised growth. Our results suggest that the interaction of Rab-E and myosin XI is a conserved feature of polarised growth in plants.

Robust Survival-Based RNA Interference of Gene Families Using in Tandem Silencing of Adenine Phosphoribosyltransferase.

RNA interference (RNAi) enables flexible and dynamic interrogation of entire gene families or essential genes without the need for exogenous proteins, unlike CRISPR-Cas technology. Unfortunately, isolation of plants undergoing potent gene silencing requires laborious design, visual screening, and physical separation for downstream characterization. Here, we developed an adenine phosphoribosyltransferase (APT)-based RNAi technology (APTi) in Physcomitrella patens that improves upon the multiple limitations of current RNAi techniques. APTi exploits the prosurvival output of transiently silencing APT in the presence of 2-fluoroadenine, thereby establishing survival itself as a reporter of RNAi. To maximize the silencing efficacy of gene targets, we created vectors that facilitate insertion of any gene target sequence in tandem with the APT silencing motif. We tested the efficacy of APTi with two gene families, the actin-dependent motor, myosin XI (a,b), and the putative chitin receptor Lyk5 (a,b,c). The APTi approach resulted in a homogenous population of transient P. patens mutants specific for our gene targets with zero surviving background plants within 8 d. The observed mutants directly corresponded to a maximal 93% reduction of myosin XI protein and complete loss of chitin-induced calcium spiking in the Lyk5-RNAi background. The positive selection nature of APTi represents a fundamental improvement in RNAi technology and will contribute to the growing demand for technologies amenable to high-throughput phenotyping.

A COVID-19-ready public health surveillance system: The Food and Drug Administration's Sentinel System.

The US Food and Drug Administration's Sentinel System was established in 2009 to use routinely collected electronic health data for improving the national capability to assess post-market medical product safety. Over more than a decade, Sentinel has become an integral part of FDA's surveillance capabilities and has been used to conduct analyses that have contributed to regulatory decisions. FDA's role in the COVID-19 pandemic response has necessitated an expansion and enhancement of Sentinel. Here we describe how the Sentinel System has supported FDA's response to the COVID-19 pandemic. We highlight new capabilities developed, key data generated to date, and lessons learned, particularly with respect to working with inpatient electronic health record data. Early in the pandemic, Sentinel developed a multi-pronged approach to support FDA's anticipated data and analytic needs. It incorporated new data sources, created a rapidly refreshed database, developed protocols to assess the natural history of COVID-19, validated a diagnosis-code based algorithm for identifying patients with COVID-19 in administrative claims data, and coordinated with other national and international initiatives. Sentinel is poised to answer important questions about the natural history of COVID-19 and is positioned to use this information to study the use, safety, and potentially the effectiveness of medical products used for COVID-19 prevention and treatment.

Conditional genetic screen in Physcomitrella patens reveals a novel microtubule depolymerizing-end-tracking protein.

Our ability to identify genes that participate in cell growth and division is limited because their loss often leads to lethality. A solution to this is to isolate conditional mutants where the phenotype is visible under restrictive conditions. Here, we capitalize on the haploid growth-phase of the moss Physcomitrella patens to identify conditional loss-of-growth (CLoG) mutants with impaired growth at high temperature. We used whole-genome sequencing of pooled segregants to pinpoint the lesion of one of these mutants (clog1) and validated the identified mutation by rescuing the conditional phenotype by homologous recombination. We found that CLoG1 is a novel and ancient gene conserved in plants. At the restrictive temperature, clog1 plants have smaller cells but can complete cell division, indicating an important role of CLoG1 in cell growth, but not an essential role in cell division. Fluorescent protein fusions of CLoG1 indicate it is localized to microtubules with a bias towards depolymerizing microtubule ends. Silencing CLoG1 decreases microtubule dynamics, suggesting that CLoG1 plays a critical role in regulating microtubule dynamics. By discovering a novel gene critical for plant growth, our work demonstrates that P. patens is an excellent genetic system to study genes with a fundamental role in plant cell growth.

Design, synthesis and biological evaluation of indane derived GPR40 agoPAMs.

GPR40 (FFAR1 or FFA1) is a G protein-coupled receptor, primarily expressed in pancreatic islet ß-cells and intestinal enteroendocrine cells. When activated by fatty acids, GPR40 elicits increased insulin secretion from islet ß-cells only in the presence of elevated glucose levels. Towards this end, studies were undertaken towards discovering a novel GPR40 Agonist whose mode of action is via Positive Allosteric Modulation of the GPR40 receptor (AgoPAM). Efforts were made to identify a suitable GPR40 AgoPAM tool molecule to investigate mechanism of action and de-risk liver toxicity of GPR40 AgoPAMs due to reactive acyl-glucuronide (AG) metabolites.

Development of a stereoselective and scalable process for the preparation of a methylcyclobutanol-pyridyl ether.

The evolution of a scalable process for the preparation of methylcyclobutanol-pyridyl ether 1 is described. Key aspects of this development including careful control of the stereochemistry, elimination of chromatography, and application to kilogram-scale synthesis are addressed.

Synthesis of the γ-Secretase Modulator MK-8428.

The synthesis of the γ-secretase modulator MK-8428 (1) is described. The synthesis is highlighted by an enzyme-catalyzed reaction to access 3,4,5-trifluoro-(S)-phenylglycine, a 1-pot activation/displacement/deprotection sequence to introduce the aminooxy functionality and a dehydrative intramolecular cyclization under mild conditions to form the oxadiazine heterocycle of 1. In situ reaction monitoring was employed to understand the deleterious role of water during the formation of a methanesulfonate ester in the 1-pot activation/displacement/deprotection sequence.

Discovery of phenyl acetamides as potent and selective GPR119 agonists.

The paper describes the SAR/SPR studies that led to the discovery of phenoxy cyclopropyl phenyl acetamide derivatives as potent and selective GPR119 agonists. Based on a cis cyclopropane scaffold discovered previously, phenyl acetamides such as compound 17 were found to have excellent GPR119 potency and improved physicochemical properties. Pharmacokinetic data of compound 17 in rat, dog and rhesus will be described. Compound 17 was suitable for QD dosing based on its predicted human half-life, and its projected human dose was much lower than that of the recently reported structurally-related benzyloxy compound 2. Compound 17 was selected as a tool compound candidate for NHP (Non-Human Primate) efficacy studies.

Enantioselective Synthesis of α-Methyl-ß-cyclopropyldihydrocinnamates.

α- and ß-substitution of dihydrocinnamates has been shown to increase the biological activity of various drug candidates. Recently, we identified enantio- and diastereopure α-methyl-ß-cyclopropyldihydrocinnamates to be important pharmacophores in one of our drug discovery programs and endeavored to devise an asymmetric hydrogenation strategy to improve access to this valuable framework. We used high throughput experimentation to define stereoconvergent Suzuki-Miyaura cross-coupling conditions affording (Z)-α-methyl-ß-cyclopropylcinnamates and subsequent ruthenium-catalyzed asymmetric hydrogenation conditions affording the desired products in excellent enantio- and diastereoselectivities. These conditions were executed on multigram to kilogram scale to provide three key enantiopure α-methyl-ß-cyclopropyldihydrocinnamates with high selectivity.

Development of a novel class of potent and selective FIXa inhibitors.

Using structure based drug design (SBDD), a novel class of potent coagulation Factor IXa (FIXa) inhibitors was designed and synthesized. High selectivity over FXa inhibition was achieved. Selected compounds demonstrated oral bioavailability in rat IV/PO pharmacokinetic (PK) studies. Finally, the pharmacodynamics (PD) of this class of molecules was evaluated in Thrombin Generation Assay (TGA) in Corn Trypsin Inhibitor (CTI) citrated human plasma and demonstrated characteristics of a FIXa inhibitor.

Development of a novel tricyclic class of potent and selective FIXa inhibitors.

Using structure based drug design, a novel class of potent coagulation factor IXa (FIXa) inhibitors was designed and synthesized. High selectivity over FXa inhibition was achieved. Selected compounds were evaluated in rat IV/PO pharmacokinetic (PK) studies and demonstrated desirable oral PK profiles. Finally, the pharmacodynamics (PD) of this class of molecules were evaluated in thrombin generation assay (TGA) in Corn Trypsin Inhibitor (CTI) citrated human plasma and demonstrated characteristics of a FIXa inhibitor.

The long and winding road part 2. The CLP patient's journey, 0-21 years.

UNLABELLED: Patients with a cleft lip and palate (CLP) deformity require the highest standard of care that the NHS can provide and this requires multidisciplinary care from teams located in regional cleft centres. Care of these cases is from birth to adulthood and requires several phases of intervention, corresponding to the stages of facial and dental development. Management ideally starts pre-natally, following the initial diagnosis, and occasionally pre-surgical appliances are prescribed. The lip is ideally repaired within three months, followed by palate closure between 12 and 18 months. Careful monitoring is required in the first few years and ENT referral, where necessary, will diagnose middle ear infection, which commonly affects CLP patients. Speech therapy is an integral part of the ongoing care. Excellent oral hygiene is essential and preventive dietary advice must be given and regularly reinforced. Orthodontic expansion is often needed at 9 years of age in preparation for a bone graft and, once the permanent dentition erupts, definitive orthodontic treatment will be required. Maxillary forward growth may have been constrained by scarring from previous surgery, so orthognathic correction may be required on growth completion. Final orthodontic alignment and high quality restorative care will allow the patients to have a pleasing aesthetic result. CLP patients and their families will need continuing support from medical and dental consultants, specialist nurses, health visitors, speech and language specialists and, perhaps, psychologists. The first article in this series of two outlined the principles of care for the CLP patient and this second part illustrates this with a case report, documenting one patient's journey from birth to 21 years of age. CLINICAL RELEVANCE: A successful outcome for CLP patients requires a sound dentition.The general dental practitioner role is vital to establish and maintain excellent oral hygiene, a healthy diet and good routine preventive and restorative care. Understanding the total needs of CLP patients can help the dentist to provide high quality care as part of the multidisciplinary management.

A Commentary on Co-Processed API as a Promising Approach to Improve Sustainability for the Pharmaceutical Industry.

Pharmaceutical products represent a meaningful target for sustainability improvement and emissions reduction. It is proposed here that rethinking the standard, and often linear, approach to the synthesis of Active Pharmaceutical Ingredients (API) and subsequent formulation and drug product processing will deliver transformational sustainability opportunities. The greatest potential arguably involves API that have challenging physico-chemical properties. These can require the addition of excipients that can significantly exceed the weight of the API in the final dosage unit, require multiple manufacturing steps to achieve materials amenable to delivering final dosage units, and need highly protective packaging for final product stability. Co-processed API are defined as materials generated via addition of non-covalently bonded, non-active components during drug substance manufacturing steps, differing from salts, solvates and co-crystals. They are an impactful example of provocative re-thinking of historical regulatory and quality precedents, blurring drug substance and drug product operations, with sustainability opportunities. Successful examples utilizing co-processed API can modify properties with use of less excipient, while simultaneously reducing processing requirements by delivering material amenable to continuous manufacturing. There are also opportunities for co-processed API to reduce the need for highly protective packaging. This commentary will detail the array of sustainability impacts that can be delivered, inclusive of business, regulatory, and quality considerations, with discussion on potential routes to more comprehensively commercialize co-processed API technologies.

Enrichment of SARS-CoV-2 sequence from nasopharyngeal swabs whilst identifying the nasal microbiome.

Simultaneously characterising the genomic information of coronaviruses and the underlying nasal microbiome from a single clinical sample would help characterise infection and disease. Metatranscriptomic approaches can be used to sequence SARS-CoV-2 (and other coronaviruses) and identify mRNAs associated with active transcription in the nasal microbiome. However, given the large sequence background, unenriched metatranscriptomic approaches often do not sequence SARS-CoV-2 to sufficient read and coverage depth to obtain a consensus genome, especially with moderate and low viral loads from clinical samples. In this study, various enrichment methods were assessed to detect SARS-CoV-2, identify lineages and define the nasal microbiome. The methods were underpinned by Oxford Nanopore long-read sequencing and variations of sequence independent single primer amplification (SISPA). The utility of the method(s) was also validated on samples from patients infected seasonal coronaviruses. The feasibility of profiling the nasal microbiome using these enrichment methods was explored. The findings shed light on the performance of different enrichment strategies and their applicability in characterising the composition of the nasal microbiome.

The long and winding road--the journey of a cleft lip and palate patient part 1.

UNLABELLED: Patients with a cleft lip and palate (CLP) deformity require the highest standard of care that can be provided and this requires multidisciplinary care from teams located in regional cleft centres. Care of these cases is from birth to adulthood and requires several phases of intervention, corresponding to the stages of facial and dental development. Management ideally starts pre-natally, following the initial diagnosis, and occasionally pre-surgical appliances are prescribed. The lip is ideally repaired within three months, followed by palate closure between 12 and 18 months. Careful monitoring is required in the first few years and ENT referral, where necessary, will diagnose middle ear infection, which commonly affects CLP patients. Speech therapy is an integral part of the ongoing care. Excellent oral hygiene is essential and preventive dietary advice must be given and regularly reinforced. Orthodontic expansion is often needed at 9 years of age in preparation for a bone graft and, once the permanent dentition erupts, definitive orthodontic treatment will be required. Maxillary forward growth may have been constrained by scarring from previous surgery, so orthognathic correction may be required on growth completion. Final orthodontic alignment and high quality restorative care will allow the patients to have a pleasing aesthetic result. CLP patients and their families will need continuing support from medical and dental consultants, specialist nurses, health visitors, speech and language specialists and, perhaps, psychologists. These two articles outline the principles of care for the CLP patient and, secondly, illustrate this with a case report, documenting one patient's journey from birth to 21 years of age. CLINICAL RELEVANCE: A successful outcome for CLP patients requires a sound dentition.The general dental practitioner role is vital to establish and maintain excellent oral hygiene, a healthy diet and good routine preventive and restorative care. Understanding the total needs of CLP patients can help the dentist to provide high quality care as part of the multidisciplinary management.

Full Mouth Dental Restoration on a Treacher-Collins Patient Without Intubation.

Patients with Treacher Collins syndrome have a known difficult airway particularly if intubation is required. In most institutions that perform full mouth dental restoration (FMDR) procedures the patient is nasally intubated to protect the airway from debris and irrigation fluid. For patients with Treacher Collins syndrome the actual intubation and securing the airway can be more difficult and traumatic than the actual dental restoration itself. However, there is an airway technique using nasopharyngeal airways combined with a dental technique called "dry prepping" that can provide those patients a safe way of receiving an FMDR without intubation. A recent case report of a 29-month-old child with Treacher Collins syndrome received an FMDR without intubation.

The Curious Case of Lip Tongue Fusion: A Consequence of Suboptimal Oral Care.

Oral care is an often difficult and an unappreciated part of hospital life. Patients who are unable to provide their own care rely on assistance from hospital personnel. Most sequelae from suboptimal oral care often present over months if not years, in the form of dental caries and periodontal disease. We present an exception, where a 66-year-old patient who experienced widespread ulceration and necrosis from Capnocytophaga-related sepsis received suboptimal oral care, resulting in their tongue being fused to their lip. This was later divided by the oral and maxillofacial team resulting in restoration of full function. Future cases can be avoided in patients with similar symptoms, such as Stevens-Johnson syndrome or erythema multiforme, if rigorous oral care can be provided.

Using inpatient electronic medical records to study influenza for pandemic preparedness.

BACKGROUND: We assessed the ability to identify key data relevant to influenza and other respiratory virus surveillance in a large-scale US-based hospital electronic medical record (EMR) dataset using seasonal influenza as a use case. We describe characteristics and outcomes of hospitalized influenza cases across three seasons. METHODS: We identified patients with an influenza diagnosis between March 2017 and March 2020 in 140 US hospitals as part of the US FDA's Sentinel System. We calculated descriptive statistics on the presence of high-risk conditions, influenza antiviral administrations, and severity endpoints. RESULTS: Among 5.1 million hospitalizations, we identified 29,520 hospitalizations with an influenza diagnosis; 64% were treated with an influenza antiviral within 2 days of admission, and 25% were treated >2 days after admission. Patients treated >2 days after admission had more comorbidities than patients treated within 2 days of admission. Patients never treated during hospitalization had more documentation of cardiovascular and other diseases than treated patients. We observed more severe endpoints in patients never treated (death = 3%, mechanical ventilation [MV] = 9%, intensive care unit [ICU] = 26%) or patients treated >2 days after admission (death = 2%, MV = 14%, ICU = 32%) than in patients treated earlier (treated on admission: death = 1%, MV = 5%, ICU = 23%, treated within 2 days of admission: death = 1%, MV = 7%, ICU = 27%). CONCLUSIONS: We identified important trends in influenza severity related to treatment timing in a large inpatient dataset, laying the groundwork for the use of this and other inpatient EMR data for influenza and other respiratory virus surveillance.

Who gets treated for influenza: A surveillance study from the US Food and Drug Administration's Sentinel System.

OBJECTIVE: We describe the baseline characteristics and complications of individuals with influenza in the US FDA's Sentinel System by antiviral treatment timing. DESIGN: Retrospective cohort design. PATIENTS: Individuals aged ≥6 months with outpatient diagnoses of influenza in June 2014-July 2017, 3 influenza seasons. METHODS: We identified the comorbidities, vaccination history, influenza testing, and outpatient antiviral dispensings of individuals with influenza using administrative claims data from 13 data partners including the Centers for Medicare and Medicaid Services, integrated delivery systems, and commercial health plans. We assessed complications within 30 days: hospitalization, oxygen use, mechanical ventilation, critical care, ECMO, and death. RESULTS: There were 1,090,333 influenza diagnoses in 2014-2015; 1,005,240 in 2016-2017; and 578,548 in 2017-2018. Between 49% and 55% of patients were dispensed outpatient treatment within 5 days. In all periods >80% of treated individuals received treatment on the day of diagnosis. Those treated on days 1-5 after diagnosis had higher prevalences of diabetes, chronic obstructive pulmonary disease, asthma, and obesity compared to those treated on the day of diagnosis or not treated at all. They also had higher rates of hospitalization, oxygen use, and critical care. In 2014-2015, among those aged ≥65 years, the rates of hospitalization were 45 per 1,000 diagnoses among those treated on day 0; 74 per 1,000 among those treated on days 1-5; and 50 per 1,000 among those who were untreated. CONCLUSIONS: In a large, national analysis, approximately half of people diagnosed with influenza in the outpatient setting were treated with antiviral medications. Delays in outpatient dispensed treatment were associated with higher prevalence of comorbidities and higher rates of complication.