Genomic glucocorticoid action in embryonic mouse neural stem cells.

Prenatal exposure to synthetic glucocorticoids (sGCs) reprograms brain development and predisposes the developing fetus towards potential adverse neurodevelopmental outcomes. Using a mouse model of sGC administration, previous studies show that these changes are accompanied by sexually dimorphic alterations in the transcriptome of neural stem and progenitor cells (NSPCs) derived from the embryonic telencephalon. Because cell type-specific gene expression profiles tightly regulate cell fate decisions and are controlled by a flexible landscape of chromatin domains upon which transcription factors and enhancer elements act, we multiplexed data from four genome-wide assays: RNA-seq, ATAC-seq (assay for transposase accessible chromatin followed by genome wide sequencing), dual cross-linking ChIP-seq (chromatin immunoprecipitation followed by genome wide sequencing), and microarray gene expression to identify novel relationships between gene regulation, chromatin structure, and genomic glucocorticoid receptor (GR) action in NSPCs. These data reveal that GR binds preferentially to predetermined regions of accessible chromatin to influence gene programming and cell fate decisions. In addition, we identify SOX2 as a transcription factor that impacts the genomic response of select GR target genes to sGCs (i.e., dexamethasone) in NSPCs.

Establishment of four head and neck squamous cell carcinoma cell lines: importance of reference DNA for accurate genomic characterisation.

OBJECTIVE: There is significant interest in developing early passage cell lines with matched normal reference DNA to facilitate a precision medicine approach in assessing drug response. This study aimed to establish early passage cell lines, and perform whole exome sequencing and short tandem repeat profiling on matched normal reference DNA, primary tumour and corresponding cell lines. METHODS: A cell culture based, in vitro study was conducted of patients with primary human papillomavirus positive and human papillomavirus negative tumours. RESULTS: Four early passage cell lines were established. Two cell lines were human papillomavirus positive, confirmed by sequencing and p16 immunoblotting. Short tandem repeat profiling confirmed that all cell lines were established from their index tumours. Whole exome sequencing revealed that the matched normal reference DNA was critical for accurate mutational analysis: a high rate of false positive mutation calls were excluded (87.6 per cent). CONCLUSION: Early passage cell lines were successfully established. Patient-matched reference DNA is important for accurate cell line mutational calls.

The prevalence of human papillomavirus in paediatric tonsils in Southwestern Ontario.

OBJECTIVE: To determine the prevalence of human papillomavirus in paediatric tonsils in Southwestern Ontario, Canada. MATERIALS AND METHODS: Patients aged 0-18 years undergoing tonsillectomy were recruited. Two specimens (left and right tonsils) were collected from each participant. Tonsillar DNA was analysed using quantitative polymerase chain reaction to determine the presence of human papillomavirus subtypes 6, 11, 16 or 18. RESULTS: A total of 102 patients, aged 1-18 years (mean age of 5.7 years), were recruited. Ninety-nine surveys were returned. There were 44 females (44.4 per cent) and 55 males (55.6 per cent). Forty patients (40.4 per cent) were firstborn children and 73 (73.7 per cent) were delivered vaginally. Six mothers (6.1 per cent) and one father (1.0 per cent) had prior known human papillomavirus infection, and one mother (1.0 per cent) had a history of cervical cancer. All tonsil specimens were negative for human papillomavirus subtypes 6, 11, 16 and 18. CONCLUSION: No human papillomavirus subtypes 6, 11, 16 or 18 were found in paediatric tonsil specimens from Southwestern Ontario.

Ciclesonide activates glucocorticoid signaling in neonatal rat lung but does not trigger adverse effects in the cortex and cerebellum.

Synthetic glucocorticoids (sGCs) such as dexamethasone (DEX), while used to mitigate inflammation and disease progression in premature infants with severe bronchopulmonary dysplasia (BPD), are also associated with significant adverse neurologic effects such as reductions in myelination and abnormalities in neuroanatomical development. Ciclesonide (CIC) is a sGC prodrug approved for asthma treatment that exhibits limited systemic side effects. Carboxylesterases enriched in the lower airways convert CIC to the glucocorticoid receptor (GR) agonist des-CIC. We therefore examined whether CIC would likewise activate GR in neonatal lung but have limited adverse extra-pulmonary effects, particularly in the developing brain. Neonatal rats were administered subcutaneous injections of CIC, DEX or vehicle from postnatal days 1-5 (PND1-PND5). Systemic effects linked to DEX exposure, including reduced body and brain weight, were not observed in CIC treated neonates. Furthermore, CIC did not trigger the long-lasting reduction in myelin basic protein expression in the cerebral cortex nor cerebellar size caused by neonatal DEX exposure. Conversely, DEX and CIC were both effective at inducing the expression of select GR target genes in neonatal lung, including those implicated in lung-protective and anti-inflammatory effects. Thus, CIC is a promising, novel candidate drug to treat or prevent BPD in neonates given its activation of GR in neonatal lung and limited adverse neurodevelopmental effects. Furthermore, since sGCs such as DEX administered to pregnant women in pre-term labor can adversely affect fetal brain development, the neurological-sparing properties of CIC, make it an attractive alternative for DEX to treat pregnant women severely ill with respiratory illness, such as with asthma exacerbations or COVID-19 infections.

Current issues in the prevalence, diagnosis and management of hepatocellular carcinoma in Australia.

Hepatocellular carcinoma (HCC) is the commonest primary liver cancer encountered in the community and a leading cause of cancer morbidity and mortality. In Australia, there are several current important issues that need to be addressed in HCC management. There is a dramatically rising incidence of HCC in Australia with comparatively poorer outcomes in remote regions and in socioeconomic disadvantaged groups. Aboriginal people have a greater incidence of HCC on a background of increased liver disease prevalence and face several barriers to delivery of better healthcare outcomes compared to other Australians. The previously adopted use of imaging alone to diagnose HCC is now being challenged with biopsy likely to become increasingly necessary with the increased uptake of personalised medicine management. Managing HCC is complex involving many disciplines with the multidisciplinary team approach being the current accepted standard of care for patients. New immunotherapy combinations promise to offer patients with advanced HCC promising novel management options. However, the Australian inequities in prevalence, diagnosis and service provision, especially in Aboriginal people, need to be redressed concurrently with the adoption of new HCC management options.

Delay in diagnosis of patients with head-and-neck cancer in Canada: impact of patient and provider delay.

Background: Head-and-neck cancers (hncs) often present at an advanced stage, leading to poor outcomes. Late presentation might be attributable to patient delays (reluctance to seek treatment, for instance) or provider delays (misdiagnosis, prolonged wait time for consultation, for example). The objective of the present study was to examine the length and cause of such delays in a Canadian universal health care setting. Methods: Patients presenting for the first time to the hnc multidisciplinary team (mdt) with a biopsy-proven hnc were recruited to this study. Patients completed a survey querying initial symptom presentation, their previous medical appointments, and length of time between appointments. Clinical and demographic data were collected for all patients. Results: The average time for patients to have their first appointment at the mdt clinic was 15.1 months, consisting of 3.9 months for patients to see a health care provider (hcp) for the first time since symptom onset and 10.7 months from first hcp appointment to the mdt clinic. Patients saw an average of 3 hcps before the mdt clinic visit (range: 1-7). No significant differences in time to presentation were found based on stage at presentation or anatomic site. Conclusions: At our tertiary care cancer centre, a patient's clinical pathway to being seen at the mdt clinic shows significant delays, particularly in the time from the first hcp visit to mdt referral. Possible methods to mitigate delay include education about hnc for patients and providers alike, and a more streamlined referral system.

Dermatology consultation service at a large metropolitan hospital system serving minority populations.

BACKGROUND: Dermatology consultations in the inpatient hospital setting can improve diagnostic accuracy and management. OBJECTIVE: Characterize dermatologic diagnostic and treatment trends in the hospital setting and identify variables that may affect patient care. METHODS: Retrospective chart review from 1 January 2012 to 31 December 2017 at Jackson Memorial Hospital (JMH) (Miami, Florida, USA), an academic non-profit tertiary care centre affiliated with University of Miami Miller School of Medicine, was performed. Patients who received dermatology consultations in the emergency department (ED) or inpatient settings were included. Patient demographics, admission information, provisional diagnosis and management plans by primary teams, final diagnosis, management plans and testing recommendations by the dermatology consults team, and follow-up information were collected. Analysis using Microsoft Excel of how time to consultation, admission length, inpatient versus ED setting and primary team affected diagnostic accuracy was also performed. RESULTS: The 1004 consultations for 812 patients (n = 812) were reviewed (359 women, 453 men). Most patients were Hispanic (n = 359; 44.2%) or African American (n = 273; 33.6%). Mean admission length was 20.6 days (range 0-439; median 6). The most common consulting service was internal medicine (n = 452). In 387 cases (47.6%), primary teams did not give a provisional diagnosis. The most common provisional diagnoses were bacterial infection (n = 93), viral infection (n = 49) and drug reaction (n = 44). The most common diagnoses by dermatology were viral infection (n = 93), bacterial infection (n = 90) and drug reaction (n = 80). Dermatology consultation changed the provisional diagnosis in 55.7% of cases, more often in cases where consultation took place ≥2 days after admission (P < 0.05). Primary teams followed dermatology treatment recommendations in 85.2% of cases. CONCLUSION: Dermatology consultation improves diagnostic accuracy in skin disorders in the hospital setting and serves as a valuable resource for inpatient care. A notable aspect of data from this study is the unique patient population, predominantly comprised of underrepresented racial and ethnic minorities including Hispanics and African Americans.

Restoration of exocrine pancreatic function in older children with cystic fibrosis on ivacaftor.

Prior to the use of cystic fibrosis (CF) modulator therapy, exocrine pancreatic insufficiency in CF was thought to be irreversible. Improvement in pancreatic function on ivacaftor has been reported in open label studies in 1-5 year olds. The mechanism by which ivacaftor might improve exocrine pancreatic function is unclear. Although the effect of ivacaftor on pancreatic function may be more significant in younger children, evidence is mounting that there may still be potential for improvement in older children on long term therapy.

Closure of tracheocutaneous fistula using prefabricated conchal bowl cartilage and a supraclavicular flap.

BACKGROUND: Tracheocutaneous fistula represents one of the most troublesome complications of prolonged tracheostomy. Simple closure of a fistula can be ineffective, particularly in the context of prior surgery and adjuvant radiation. As such, modes of repair have expanded to include locoregional flaps and even free tissue transfers. OBJECTIVE: This paper describes a case of persistent tracheocutaneous fistula in an irradiated patient who had undergone previous unsuccessful attempts at repair. METHOD AND RESULTS: The use of regional fasciocutaneous supraclavicular flap with prefabricated conchal bowl cartilage resulted in successful closure of the tracheocutaneous fistula. CONCLUSION: This represents a novel technique for closure of such fistulas in patients for whom previous attempts have failed. This mode of repair should be added to the surgeon's repertoire of reparative techniques.

Combining Pseudopotential and All Electron Density Functional Theory for the Efficient Calculation of Core Spectra Using a Multiresolution Approach.

Broadly speaking, the calculation of core spectra such as electron energy loss spectra (EELS) at the level of density functional theory (DFT) usually relies on one of two approaches: conceptually more complex but computationally efficient projector augmented wave based approaches or more straightforward but computationally more intensive all electron (AE) based approaches. In this work we present an alternative method, which aims to find a middle ground between the two. Specifically, we have implemented an approach in the multiwavelet madness molecular DFT code that permits a combination of atoms treated at the AE and pseudopotential (PSP) level. Atoms for which one wishes to calculate the core edges are thus treated at an AE level, while the remainder can be treated at the PSP level. This is made possible thanks to the multiresolution approach of madness, which permits accurate and efficient calculations at both the AE and PSP level. Through examples of a small molecule and a carbon nanotube, we demonstrate the potential applications of our approach.

Structure-Property of Lithium-Sulfur Nanoparticles via Molecular Dynamics Simulation.

Lithium-sulfur (Li-S) batteries offer higher energy densities than most reported lithium-ion batteries. However, our understanding of Li-S battery is still largely unknown at the level of the nanoscale. The structural properties of Li-S materials were investigated via molecular dynamics (MD) simulations using the ReaxFF force field. Several Li-S nanoparticles with different Li/S composition ratios (2:1 and 2:8) and various structures are studied. Our MD simulations show that among the four structures we constructed for Li2S8 nanoparticles, the core-shell structure is the most thermodynamically stable one during the charging (delithiation) process. In contrast to bulk crystal Li2S, we find the presence of mixed lithium sulfide and polysulfide species are common features for these Li-S (Li2S, Li2S8) nanoparticles. The complex distribution of these sulfide and polysulfide speciation are dictated by both stoichiometry and local atomic structures in the nanoparticle. These findings will provide insight into further development of functionalized lithium-sulfur cathodes.

Nitric oxide activation facilitated by cooperative multimetallic electron transfer within an iron-functionalized polyoxovanadate-alkoxide cluster.

A series of NO-bound, iron-functionalized polyoxovanadate-alkoxide (FePOV-alkoxide) clusters have been synthesized, providing insight into the role of multimetallic constructs in the coordination and activation of a substrate. Upon exposure of the heterometallic cluster to NO, the vanadium-oxide metalloligand is oxidized by a single electron, shuttling the reducing equivalent to the {FeNO} subunit to form a {FeNO}7 species. Four NO-bound clusters with electronic distributions ranging from [VV3VIV2]{FeNO}7 to [VIV5]{FeNO}7 have been synthesized, and characterized via 1H NMR, infrared, and electronic absorption spectroscopies. The ability of the FePOV-alkoxide cluster to store reducing equivalents in the metalloligand for substrate coordination and activation highlights the ultility of the metal-oxide scaffold as a redox reservoir.

The use of standardized order sets to improve adherence to evidence-based postoperative management in major head and neck surgery.

BACKGROUND: Standardized order sets (SOSs) are clinical tools derived from clinical care pathways that have shown improved patient-recovery and economic benefits. The primary objective was to examine the effect of SOSs on adherence to evidence-based postoperative guidelines for laryngectomy patients. METHODS: A retrospective chart review comparing handwritten and SOS-based postoperative physician orders was conducted for consecutive laryngectomies performed (n=70) within a 3-year time period. Orders were analyzed for errors and deviations from evidence-based guidelines. Secondary outcome included complications such as thromboembolic disease, return to operating room, fistula formation, salivary bypass tube, length of hospital stay and death. RESULTS: Approximately 81% of cases utilizing handwritten orders had at least one error (n=36) compared to 38% in the group that used an SOS (n=34) (P<0.0001). Subgroup analyses demonstrated that errors in mechanical deep vein thrombosis prophylaxis (P<0.0001) and antibiotic prophylaxis (P=0.0173) orders were significantly reduced in the SOS group compared to the handwritten group. No significant differences were observed between the two groups for measured postoperative complications (P>0.05) and length of hospital stay (18.6 days in both SOS and handwritten orders groups). CONCLUSIONS: SOSs are associated with reduced errors in postoperative orders. They are important tools to improve adherence to standardized guidelines for surgeries requiring complex postoperative management. Clinical care pathways and Enhanced Recovery After Surgery protocols can use SOSs to ensure appropriate orders are being made.

The impact of seasonal operating room closures on wait times for oral cancer surgery.

BACKGROUND: Operating room slowdowns occur at specific intervals in the year as a cost-saving measure. We aim to investigate the impact of these slowdowns on the care of oral cavity cancer patients at a Canadian tertiary care centre. METHODS: A total of 585 oral cavity cancer patients seen between 1999 and 2015 at the London Health Science Centre (lhsc) Head and Neck Multidisciplinary Clinic were included in this study. Operating room hours and patient load from 2006 to 2014 were calculated. Our primary endpoint was the wait time from consultation to definitive surgery. Exposure variables were defined according to wait time intervals occurring during time periods with reduced operating room hours. RESULTS: Overall case volume rose significantly from 2006 to 2014 (p < 0.001), while operating room hours remained stable (p = 0.555). Patient wait times for surgery increased from 16.3 days prior to 2003 to 25.5 days in 2015 (p = 0.008). Significant variability in operating room hours was observed by month, with lowest reported for July and August (p = 0.002). The greater the exposure to these months, the more likely patients were to wait longer than 28 days for surgery (odds ratio per day [or]: 1.07, 95% confidence interval [ci]: 1.05 to 1.10, p < 0.001). Individuals seen in consultation preceding a month with below average operating room hours had a higher risk of disease recurrence and/or death (hazard ratio [hr]: 1.59, 95% ci: 1.10 to 2.30, p = 0.014). CONCLUSIONS: Scheduled reductions in available operating room hours contribute to prolonged wait times and higher disease recurrence. Further work is needed to identify strategies maximizing efficient use of health care resources without negatively affecting patient outcomes.

QMCPACK: an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids.

QMCPACK is an open source quantum Monte Carlo package for ab initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wavefunctions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary-field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performance computing architectures, including multicore central processing unit and graphical processing unit systems. We detail the program's capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://qmcpack.org.

Survival of patients with subglottic squamous cell carcinoma.

Objective: Subglottic squamous cell carcinoma is a rare subsite of laryngeal cancer that behaves more aggressively and portends a worse prognosis. Using a population-based cancer registry, our objective was to report overall survival (os) and laryngectomy-free survival (lfs) in patients diagnosed with subglottic squamous cell carcinoma, and to determine whether primary laryngectomy results in improved survival. Methods: This retrospective population-based study considered patients with a new diagnosis of squamous cell carcinoma in the province of Ontario over a 15-year period (1995-2009). The Ontario Cancer Registry was examined for patients with the diagnosis of interest during the period of interest. Linked population-based databases were used to obtain patient demographics, comorbidity measures, staging, survival, and primary treatment with laryngectomy. Results: Of 4927 patients identified to have laryngeal carcinoma, 89 were defined as having primary subglottic carcinoma (1.8%). In the subglottic cohort, 68 patients were men (76.4%), and mean age at diagnosis was 68 years (interquartile range: 60-77 years). The 5-year os was 47.2%, and the 5-year lfs was 31.5%. In 13 patients (15%), the primary treatment was laryngectomy, which, compared with primary radiation, did not predict for improved os. No differences in os or lfs were observed during the 15-year study period (os p = 0.42, lfs p = 0.83). Conclusions: The survival of patients with subglottic carcinoma is poor and has remained stable over time (1995-2009). Compared with primary radiation, primary treatment with laryngectomy does not appear to improve os.

A comparison of the sexually dimorphic dexamethasone transcriptome in mouse cerebral cortical and hypothalamic embryonic neural stem cells.

Fetal exposure to synthetic glucocorticoids reprograms distinct neural circuits in the developing brain, often in a sex-specific manner, via mechanisms that remain poorly understood. To reveal whether such reprogramming is associated with select molecular signatures, we characterized the transcriptome of primary, embryonic mouse cerebral cortical and hypothalamic neural progenitor/stem cells derived from individual male and female embryos exposed to the synthetic glucocorticoid, dexamethasone. Gene expression profiling by RNA-Seq identified differential expression of common and unique genes based upon brain region, sex, and/or dexamethasone exposure. These gene expression datasets provide a unique resource that will inform future studies examining the molecular mechanisms responsible for region- and sex-specific reprogramming of the fetal brain brought about by in utero exposure to excess glucocorticoids.

A paired comparison analysis of third-party rater thyroidectomy scar preference.

OBJECTIVE: To determine the length and position of a thyroidectomy scar that is cosmetically most appealing to naïve raters. METHODS: Images of thyroidectomy scars were reproduced on male and female necks using digital imaging software. Surgical variables studied were scar position and length. Fifteen raters were presented with 56 scar pairings and asked to identify which was preferred cosmetically. Twenty duplicate pairings were included to assess rater reliability. Analysis of variance was used to determine preference. RESULTS: Raters preferred low, short scars, followed by high, short scars, with long scars in either position being less desirable (p < 0.05). Twelve of 15 raters had acceptable intra-rater and inter-rater reliability. CONCLUSION: Naïve raters preferred low, short scars over the alternatives. High, short scars were the next most favourably rated. If other factors influencing incision choice are considered equal, surgeons should consider these preferences in scar position and length when planning their thyroidectomy approach.