Efficient overexpression and purification of severe acute respiratory syndrome coronavirus 2 nucleocapsid proteins in Escherichia coli.

The fundamental biology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid protein (Ncap), its use in diagnostic assays and its potential application as a vaccine component have received considerable attention since the outbreak of the Covid19 pandemic in late 2019. Here we report the scalable expression and purification of soluble, immunologically active, SARS-CoV-2 Ncap in Escherichia coli. Codon-optimised synthetic genes encoding the original Ncap sequence and four common variants with an N-terminal 6His affinity tag (sequence MHHHHHHG) were cloned into an inducible expression vector carrying a regulated bacteriophage T5 synthetic promoter controlled by lac operator binding sites. The constructs were used to express Ncap proteins and protocols developed which allow efficient production of purified Ncap with yields of over 200 mg per litre of culture media. These proteins were deployed in ELISA assays to allow comparison of their responses to human sera. Our results suggest that there was no detectable difference between the 6His-tagged and untagged original Ncap proteins but there may be a slight loss of sensitivity of sera to other Ncap isolates.

Delivering clinical studies of exercise in the COVID-19 pandemic: challenges and adaptations using a feasibility trial of isometric exercise to treat hypertension as an exemplar.

The COVID-19 pandemic has significantly impacted on the delivery of clinical trials in the UK, posing complicated organisational challenges and requiring adaptations, especially to exercise intervention studies based in the community. We aim to identify the challenges of public involvement, recruitment, consent, follow-up, intervention and the healthcare professional delivery aspects of a feasibility study of exercise in hypertensive primary care patients during the COVID-19 pandemic. While these challenges elicited many reactive changes which were specific to, and only relevant in the context of 'lockdown' requirements, some of the protocol developments that came about during this unprecedented period have great potential to inform more permanent practices for carrying out this type of research. To this end, we detail the necessary adaptations to many elements of the feasibility study and critically reflect on our approach to redesigning and amending this ongoing project in order to maintain its viability to date. Some of the more major protocol adaptations, such as moving the study to remote means wherever possible, had further unforeseen and undesirable outcomes (eg, additional appointments) with regards to extra resources required to deliver the study. However, other changes improved the efficiency of the study, such as the remote informed consent and the direct advertising with prescreening survey. The adaptations to the study have clear links to the UK Plan for the future of research delivery. It is intended that this specific documentation and critical evaluation will help those planning or delivering similar studies to do so in a more resource efficient and effective way. In conclusion, it is essential to reflect and respond with protocol changes in the current climate in order to deliver clinical research successfully, as in the case of this particular study.

Diagnosis of Bacterial Tracheostomy-Associated Respiratory Tract Infections in Pediatric Patients.

OBJECTIVES: To identify demographic and clinical characteristics of children with fever and/or respiratory illness associated with a diagnosis of bacterial tracheostomy-associated respiratory tract infections (bTARTI). Secondary objectives included comparison of diagnostic testing, length of stay (LOS), and readmission rates between children diagnosed with bTARTI and others. METHODS: We performed a retrospective chart review of encounters over 1 year for fever and/or respiratory illness at a single academic children's hospital for children with tracheostomy dependence. Patient characteristics, features of presenting illness, and laboratory and imaging results were collected. Generalized linear mixed models were employed to study associations between patient characteristics, diagnosis of bTARTI, and impact on LOS or readmission rates. RESULTS: Among 145 children with tracheostomies identified, 79 children contributed 208 encounters. bTARTI was diagnosed in 66 (31.7%) encounters. Significant associations with bTARTI diagnosis included chest radiograph consistent with bacterial pneumonia (odds ratio [OR], 1.77; 95% confidence interval [CI], 1.50-2.08), positive tracheal aspirate culture (OR, 1.3; 95% CI, 1.05-1.61), higher white blood cell count (16.4 vs 13.1 × 103/µ; P = .03), change in oxygen requirement (OR, 1.14; 95% CI, 1.00-1.31), telephone encounter (OR, 1.41; 95% CI, 1.09-1.81), and living at home with family (OR, 1.42; 95% CI, 1.06-1.92). LOS for admitted patients with bTARTI was 2.19 times longer (CI, 1.23-3.88). CONCLUSIONS: In our single-center study, we identified several clinical and nonclinical factors associated with a diagnosis of bTARTI. Despite widespread use, few laboratory tests were predictive of a diagnosis of bTARTI. There is need for standardization in diagnosis.

Association of Models of Care for Kawasaki Disease With Utilization and Cardiac Outcomes.

OBJECTIVES: Describe the prevalence of different care models for children with Kawasaki disease (KD) and evaluate utilization and cardiac outcomes by care model. METHODS: Multicenter, retrospective cohort study of children aged 0 to 18 hospitalized with KD in US children's hospitals from 2017 to 2018. We classified hospital model of care via survey: hospitalist primary service with as-needed consultation (Model 1), hospitalist primary service with automatic consultation (Model 2), or subspecialist primary service (Model 3). Additional data sources included administrative data from the Pediatric Health Information System database supplemented by a 6-site chart review. Utilization outcomes included laboratory, medication and imaging usage, length of stay, and readmission rates. We measured the frequency of coronary artery aneurysms (CAAs) in the full cohort and new CAAs within 12 weeks in the 6-site chart review subset. RESULTS: We included 2080 children from 44 children's hospitals; 21 hospitals (48%) identified as Model 1, 19 (43%) as Model 2, and 4 (9%) as Model 3. Model 1 institutions obtained more laboratory tests and had lower overall costs (P < .001), whereas echocardiogram (P < .001) and immune modulator use (P < .001) were more frequent in Model 3. Secondary outcomes, including length of stay, readmission rates, emergency department revisits, CAA frequency, receipt of anticoagulation, and postdischarge CAA development, did not differ among models. CONCLUSIONS: Modest cost and utilization differences exist among different models of care for KD without significant differences in outcomes. Further research is needed to investigate primary service and consultation practices for KD to optimize health care value and outcomes.

Peptide transport in Bacillus subtilis - structure and specificity in the extracellular solute binding proteins OppA and DppE.

Peptide transporters play important nutritional and cell signalling roles in Bacillus subtilis, which are pronounced during stationary phase adaptations and development. Three high-affinity ATP-binding cassette (ABC) family transporters are involved in peptide uptake - the oligopeptide permease (Opp), another peptide permease (App) and a less well-characterized dipeptide permease (Dpp). Here we report crystal structures of the extracellular substrate binding proteins, OppA and DppE, which serve the Opp and Dpp systems, respectively. The structure of OppA was determined in complex with endogenous peptides, modelled as Ser-Asn-Ser-Ser, and with the sporulation-promoting peptide Ser-Arg-Asn-Val-Thr, which bind with K d values of 0.4 and 2 µM, respectively, as measured by isothermal titration calorimetry. Differential scanning fluorescence experiments with a wider panel of ligands showed that OppA has highest affinity for tetra- and penta-peptides. The structure of DppE revealed the unexpected presence of a murein tripeptide (MTP) ligand, l-Ala-d-Glu-meso-DAP, in the peptide binding groove. The mode of MTP binding in DppE is different to that observed in the murein peptide binding protein, MppA, from Escherichia coli, suggesting independent evolution of these proteins from an OppA-like precursor. The presence of MTP in DppE points to a role for Dpp in the uptake and recycling of cell wall peptides, a conclusion that is supported by analysis of the genomic context of dpp, which revealed adjacent genes encoding enzymes involved in muropeptide catabolism in a gene organization that is widely conserved in Firmicutes.

Comparison of a Teaching and Nonteaching Service at a Children's Hospital in the Community.

OBJECTIVE: The impact of trainees on inpatient patient care is incompletely understood. This study sought to discern the impact of trainees on patient outcomes and costs at a children's hospital in the community. We hypothesized that there would be no differences in patient outcomes and costs on an inpatient teaching service compared to a nonteaching service. As a secondary goal, we analyzed trainee evaluations. METHODS: The authors conducted a cohort study of patients hospitalized from October 1, 2016 to September 30, 2017 on an acute care unit in a children's hospital in the community. Using t test or Fisher exact test, the authors compared patient outcomes between teaching and nonteaching services including, length of stay, discharge times, readmission rates, rapid response team (RRT) calls, pediatric intensive care unit (PICU) transfers, hospital transfers, and costs. RESULTS: During the study period, there were 1066 patients admitted and discharged from the teaching service and 1038 from the nonteaching service. There were no statistically significant differences in patient demographics or patient complexity. Similarly, there were no differences in length of stay, discharge times, readmission rates, RRT calls, PICU transfers, hospital transfers or patient costs between services. Trainee evaluations of the inpatient experience were overwhelmingly positive. CONCLUSIONS: In a children's hospital in the community, there were no significant differences in patient outcomes and costs on a teaching service compared to a nonteaching service. Furthermore, trainee evaluations suggested a favorable learning experience, illustrating the feasibility of incorporating trainees into inpatient care in a nontraditional learner setting.

Feasibility study to assess the delivery of a novel isometric exercise intervention for people with stage 1 hypertension in the NHS: protocol for the IsoFIT-BP study including amendments to mitigate the risk of COVID-19.

BACKGROUND: Hypertension  (HTN) affects approximately 25% of the UK population and is a leading cause of mortality. Associated annual health care costs run into billions. National treatment guidance includes initial lifestyle advice, followed by anti-hypertensive medication if blood pressure (BP) remains high. However, adoption and adherence to recommended exercise guidelines, dietary advice and anti-hypertensive medication is poor. Four short bouts of isometric exercise (IE) performed 3 days per week (d/wk) at home elicits clinically significant reductions in BP in those with normal to high-normal BP. This study will determine the feasibility of delivering personalised IE to patients with stage 1 hypertension for whom lifestyle changes would be recommended before medication within NHS primary care. METHODS: This is a randomised controlled feasibility study. Participants were 18+ years, with stage 1 hypertension, not on anti-hypertensive medication and without significant medical contraindications. Trial arms will be standard lifestyle advice (control) or isometric wall squat exercise and standard lifestyle advice. Primary outcomes include the feasibility of healthcare professionals to deliver isometric exercise prescriptions in a primary care NHS setting and estimation of the variance of change in systolic BP. Secondary outcomes include accuracy of protocol delivery, execution of and adherence to protocol, recruitment rate, attrition, perception of intervention viability, cost, participant experience and accuracy of home BP. The study will last 18 months. Sample size of 100 participants (50 per arm) allows for 20% attrition and 6.5% incomplete data, based upon 74 (37 each arm) participants (two-sided 95% confidence interval, width of 1.33 and standard deviation of 4) completing 4 weeks. Ethical approval IRAS ID is 274676. DISCUSSION: Before the efficacy of this novel intervention to treat stage 1 hypertension can be investigated in any large randomised controlled trial, it is necessary to ascertain if it can be delivered and carried out in a NHS primary care setting. Findings could support IE viability as a prophylactic/alternative treatment option. TRIAL REGISTRATION: ISRCTN13472393 , registered 18 August 2020.

Kawasaki Disease and Multisystem Inflammatory Syndrome in Children: An Overview and Comparison.

Kawasaki disease (KD) and multisystem inflammatory syndrome in children (MIS-C) are inflammatory conditions that present diagnostic and therapeutic challenges to the physician. Although many of their features overlap, they are two distinct conditions. KD is a febrile illness most commonly affecting children younger than five years. It manifests with prolonged fever and at least four of the following features: bilateral bulbar conjunctivitis, mucositis, diffuse maculopapular rash, extremity changes, and cervical lymphadenopathy of 1.5 cm or more in diameter. Patients with MIS-C may have many of the same manifestations but tend to have higher rates of gastrointestinal and neurocognitive symptoms and signs of shock on presentation. Both conditions are associated with cardiac sequelae, including coronary artery aneurysms, although children with MIS-C are at high risk of developing ventricular dysfunction and depressed cardiac output. Lymphocytopenia, thrombocytopenia, elevated troponin, and elevated B-type natriuretic peptide are key laboratory findings of MIS-C that can help distinguish it from KD. The use of intravenous immune globulin is well established in KD and also appears to have a role in the treatment of MIS-C. Aspirin has been used in KD for an anti-inflammatory effect, and low-dose aspirin is recommended for MIS-C to reduce the risk of thrombosis. In addition to supportive care, patients with MIS-C may benefit from immunomodulatory medications, although data on this topic are evolving.

Barriers to Tobacco Cessation for Caregivers of Hospitalized Children: Perspectives of Pediatric Hospitalists.

OBJECTIVES: Secondhand smoke exposure is associated with adverse health outcomes in children, yet tobacco cessation efforts for caregivers of hospitalized children are lacking. We sought to explore pediatric hospitalists' attitudes and barriers to providing tobacco cessation for caregivers of hospitalized children. METHODS: We conducted a cross-sectional survey of pediatric hospitalists and fellows at 7 hospitals from November 1, 2018, to November 30, 2019. A 70-question anonymous survey was used to assess participants' perceptions of current practices, attitudes, and barriers to providing tobacco cessation support for caregivers of hospitalized children. We used descriptive statistics to summarize the data. RESULTS: Of 207 eligible participants, 100 responded (48%). A majority (79%) agreed that offering tobacco cessation counseling for caregivers is an important part of their role in caring for hospitalized children, but 79% never received tobacco cessation training. Only half of the participants were comfortable providing brief advice and few were comfortable prescribing nicotine replacement therapy. Identified barriers included lack of time (74%), perceived lack of interest from patients' caregivers (71%), and other medical conditions of the patient taking priority (70%). The majority of participants were interested in further training in tobacco cessation support. CONCLUSIONS: In this survey of 100 pediatric hospitalists, we found overall agreement that tobacco cessation support for caregivers of hospitalized children is important. However, most participants did not feel comfortable with provision of evidence-based counseling or pharmacotherapy because of identified barriers. Future work should target actionable barriers to improve provision of tobacco cessation support in this clinical setting.

Fragment-derived modulators of an industrial ß-glucosidase.

A fragment screen of a library of 560 commercially available fragments using a kinetic assay identified a small molecule that increased the activity of the fungal glycoside hydrolase TrBgl2. An analogue by catalogue approach and detailed kinetic analysis identified improved compounds that behaved as nonessential activators with up to a 2-fold increase in maximum activation. The compounds did not activate the related bacterial glycoside hydrolase CcBglA demonstrating specificity. Interestingly, an analogue of the initial fragment inhibits both TrBgl2 and CcBglA, apparently through a mixed-model mechanism. Although it was not possible to determine crystal structures of activator binding to 55 kDa TrBgl2, solution NMR experiments demonstrated a specific binding site for the activator. A partial assignment of the NMR spectrum gave the identity of the amino acids at this site, allowing a model for TrBgl2 activation to be built. The activator binds at the entrance of the substrate-binding site, generating a productive conformation for the enzyme-substrate complex.

Solution structure of the Hop TPR2A domain and investigation of target druggability by NMR, biochemical and in silico approaches.

Heat shock protein 90 (Hsp90) is a molecular chaperone that plays an important role in tumour biology by promoting the stabilisation and activity of oncogenic 'client' proteins. Inhibition of Hsp90 by small-molecule drugs, acting via its ATP hydrolysis site, has shown promise as a molecularly targeted cancer therapy. Owing to the importance of Hop and other tetratricopeptide repeat (TPR)-containing cochaperones in regulating Hsp90 activity, the Hsp90-TPR domain interface is an alternative site for inhibitors, which could result in effects distinct from ATP site binders. The TPR binding site of Hsp90 cochaperones includes a shallow, positively charged groove that poses a significant challenge for druggability. Herein, we report the apo, solution-state structure of Hop TPR2A which enables this target for NMR-based screening approaches. We have designed prototype TPR ligands that mimic key native 'carboxylate clamp' interactions between Hsp90 and its TPR cochaperones and show that they block binding between Hop TPR2A and the Hsp90 C-terminal MEEVD peptide. We confirm direct TPR-binding of these ligands by mapping 1H-15N HSQC chemical shift perturbations to our new NMR structure. Our work provides a novel structure, a thorough assessment of druggability and robust screening approaches that may offer a potential route, albeit difficult, to address the chemically challenging nature of the Hop TPR2A target, with relevance to other TPR domain interactors.

Towards a Smart Smoking Cessation App: A 1D-CNN Model Predicting Smoking Events.

Nicotine consumption is considered a major health problem, where many of those who wish to quit smoking relapse. The problem is that overtime smoking as behaviour is changing into a habit, in which it is connected to internal (e.g., nicotine level, craving) and external (action, time, location) triggers. Smoking cessation apps have proved their efficiency to support smoking who wish to quit smoking. However, still, these applications suffer from several drawbacks, where they are highly relying on the user to initiate the intervention by submitting the factor the causes the urge to smoke. This research describes the creation of a combined Control Theory and deep learning model that can learn the smoker's daily routine and predict smoking events. The model's structure combines a Control Theory model of smoking with a 1D-CNN classifier to adapt to individual differences between smokers and predict smoking events based on motion and geolocation values collected using a mobile device. Data were collected from 5 participants in the UK, and analysed and tested on 3 different machine learning model (SVM, Decision tree, and 1D-CNN), 1D-CNN has proved it's efficiency over the three methods with average overall accuracy 86.6%. The average MSE of forecasting the nicotine level was (0.04) in the weekdays, and (0.03) in the weekends. The model has proved its ability to predict the smoking event accurately when the participant is well engaged with the app.

Water Networks Can Determine the Affinity of Ligand Binding to Proteins.

Solvent organization is a key but underexploited contributor to the thermodynamics of protein-ligand recognition, with implications for ligand discovery, drug resistance, and protein engineering. Here, we explore the contribution of solvent to ligand binding in the Haemophilus influenzae virulence protein SiaP. By introducing a single mutation without direct ligand contacts, we observed a >1000-fold change in sialic acid binding affinity. Crystallographic and calorimetric data of wild-type and mutant SiaP showed that this change results from an enthalpically unfavorable perturbation of the solvent network. This disruption is reflected by changes in the normalized atomic displacement parameters of crystallographic water molecules. In SiaP's enclosed cavity, relative differences in water-network dynamics serve as a simple predictor of changes in the free energy of binding upon changing protein, ligand, or both. This suggests that solvent structure is an evolutionary constraint on protein sequence that contributes to ligand affinity and selectivity.

Variability in Kawasaki Disease Practice Patterns: A Survey of Hospitalists at Pediatric Hospital Medicine 2017.

OBJECTIVE: To explore practice variations in the care of patients with Kawasaki disease (KD) among pediatric hospitalist physicians (PHPs). METHODS: A 13-item questionnaire was developed by a multi-institutional group of KD experts. The survey was administered via live-audience polling by using smartphone technology during a KD plenary session at the 2017 Pediatric Hospital Medicine National Meeting, and simple descriptive statistics were calculated. RESULTS: Of the 297 session attendees, 90% responded to at least 1 survey question. Approximately three-quarters of respondents identified as PHPs practicing in the United States. The reported length of inpatient monitoring after initial intravenous immunoglobulin (IVIG) therapy demonstrated a wide time distribution (30% 24 hours, 36% 36 hours, and 31% 48 hours). Similarly, PHP identification of the treatment failure interval, indicated by recrudescent fever after IVIG, demonstrated a broad distribution (56% 24 hours, 27% 36 hours, and 16% 48 hours). Furthermore, there was variation in routine consultation with non-PHP subspecialists. In contrast, PHPs reported little variation in their choice of initial and refractory treatment of patients with KD. CONCLUSIONS: In a convenience sample at a national hospitalist meeting, there was variation in reported KD practice patterns, including observation time after initial treatment, time when the recurrence of fever after initial therapy was indicative of nonresponse to IVIG, and routine consultation of non-PHP subspecialists. These results may guide future study of KD practice patterns and inform efforts to improve evidence-based practices in the care of patients with KD.

Identifying probable post-traumatic stress disorder: applying supervised machine learning to data from a UK military cohort.

BACKGROUND: Early identification of probable post-traumatic stress disorder (PTSD) can lead to early intervention and treatment. AIMS: This study aimed to evaluate supervised machine learning (ML) classifiers for the identification of probable PTSD in those who are serving, or have recently served in the United Kingdom (UK) Armed Forces. METHODS: Supervised ML classification techniques were applied to a military cohort of 13,690 serving and ex-serving UK Armed Forces personnel to identify probable PTSD based on self-reported service exposures and a range of validated self-report measures. Data were collected between 2004 and 2009. RESULTS: The predictive performance of supervised ML classifiers to detect cases of probable PTSD were encouraging when compared to a validated measure, demonstrating a capability of supervised ML to detect the cases of probable PTSD. It was possible to identify which variables contributed to the performance, including alcohol misuse, gender and deployment status. A satisfactory sensitivity was obtained across a range of supervised ML classifiers, but sensitivity was low, indicating a potential for false negative diagnoses. CONCLUSIONS: Detection of probable PTSD based on self-reported measurement data is feasible, may greatly reduce the burden on public health and improve operational efficiencies by enabling early intervention, before manifestation of symptoms.

Working towards an objective segmental assessment of trunk control in children with cerebral palsy.

BACKGROUND: Physical therapy evaluations of motor control are currently based on subjective clinical assessments. Despite validation, these can still be inconsistent between therapists and between clinics, compromising the process of validating a therapeutic intervention and the subsequent generation of evidence-based practice (EBP) guidelines. EBP benefits from well-defined objective measurements that complement existing subjective assessments. RESEARCH QUESTION: The aim of this study was to develop an objective measure of head/trunk control in children with Cerebral Palsy (CP) using previously developed video-based methods of head/trunk alignment and absence of external support and compare these with the existing subjective Segmental Assessment of Trunk Control (SATCo). METHODS: Twelve children with CP were recruited and an average of 3 (±1.1) SATCo tests performed per child. The full SATCo was concurrently video-recorded from a sagittal view; markers were placed on specific landmarks of the head, trunk and pelvis to track and estimate head/trunk segment position. A simplified objective rule was created for control and used on videos showing no external support. This replicated the clinical parameters and enabled identification of the segmental-loss-of-control. The subjectively and objectively identified segmental-loss-of-control were compared using a Pearson Correlation Coefficient. RESULTS: An angular-threshold of 17° from alignment showed the minimum bias between the subjectively and the objectively measured segmental-loss-of-control (mean error =-0.11 and RMSE = 1.5) and a significant correlation (r = 0.78, r2 = 0.61, p < .01). SIGNIFICANCE: This study showed that simple objective video-based measurements can be used to reconstruct the subjective assessment of segmental head/trunk control. This suggests that a clinically-friendly video-based objective measure has future potential to complement subjective assessments and to assist in the generation of EBP guidelines. Further development will increase the information that can be extracted from video images and enable generation of a fully automated objective measure.

Increase of enzyme activity through specific covalent modification with fragments.

Modulation of enzyme activity is a powerful means of probing cellular function and can be exploited for diverse applications. Here, we explore a method of enzyme activation where covalent tethering of a small molecule to an enzyme can increase catalytic activity (kcat/KM) up to 35-fold. Using a bacterial glycoside hydrolase, BtGH84, we demonstrate how small molecule "fragments", identified as activators in free solution, can be covalently tethered to the protein using Michael-addition chemistry. We show how tethering generates a constitutively-activated enzyme-fragment conjugate, which displays both improved catalytic efficiency and increased susceptibility to certain inhibitor classes. Structure guided modifications of the tethered fragment demonstrate how specific interactions between the fragment and the enzyme influence the extent of activation. This work suggests that a similar approach may be used to modulate the activity of enzymes such as to improve catalytic efficiency or increase inhibitor susceptibility.

A 3-Week-Old With an Isolated "Blueberry Muffin" Rash.

A 3-week-old boy, former 39-week term infant, presented to the emergency department with a rash. One week before presentation, he developed dark, purple papules on his forehead, which then spread to the abdomen and inguinal regions. Throughout this time, he was eating well, gaining weight, developing appropriately, and was afebrile without cough, congestion, or rhinorrhea. On presentation, the patient was well appearing with normal vital signs. His weight was 4.83 kg (86th percentile for age), his length was 56 cm (47th percentile for age), and his head circumference was 37 cm (62nd percentile for age). On skin examination, there were scattered purpuric papules and macules on the scalp, forehead, trunk, abdomen, and inguinal region. Initial laboratory studies were remarkable only for mild anemia. Our expert panel examines the case, offers a differential for a child with a "blueberry muffin" rash, and makes diagnostic considerations.