Precision Neoantigen Discovery Using Large-Scale Immunopeptidomes and Composite Modeling of MHC Peptide Presentation.

Major histocompatibility complex (MHC)-bound peptides that originate from tumor-specific genetic alterations, known as neoantigens, are an important class of anticancer therapeutic targets. Accurately predicting peptide presentation by MHC complexes is a key aspect of discovering therapeutically relevant neoantigens. Technological improvements in mass spectrometry-based immunopeptidomics and advanced modeling techniques have vastly improved MHC presentation prediction over the past 2 decades. However, improvement in the accuracy of prediction algorithms is needed for clinical applications like the development of personalized cancer vaccines, the discovery of biomarkers for response to immunotherapies, and the quantification of autoimmune risk in gene therapies. Toward this end, we generated allele-specific immunopeptidomics data using 25 monoallelic cell lines and created Systematic Human Leukocyte Antigen (HLA) Epitope Ranking Pan Algorithm (SHERPA), a pan-allelic MHC-peptide algorithm for predicting MHC-peptide binding and presentation. In contrast to previously published large-scale monoallelic data, we used an HLA-null K562 parental cell line and a stable transfection of HLA allele to better emulate native presentation. Our dataset includes five previously unprofiled alleles that expand MHC diversity in the training data and extend allelic coverage in underprofiled populations. To improve generalizability, SHERPA systematically integrates 128 monoallelic and 384 multiallelic samples with publicly available immunoproteomics data and binding assay data. Using this dataset, we developed two features that empirically estimate the propensities of genes and specific regions within gene bodies to engender immunopeptides to represent antigen processing. Using a composite model constructed with gradient boosting decision trees, multiallelic deconvolution, and 2.15 million peptides encompassing 167 alleles, we achieved a 1.44-fold improvement of positive predictive value compared with existing tools when evaluated on independent monoallelic datasets and a 1.17-fold improvement when evaluating on tumor samples. With a high degree of accuracy, SHERPA has the potential to enable precision neoantigen discovery for future clinical applications.

Long term results with medpor® reconstruction of the anterior skull base at a single institute.

OBJECTIVES: To evaluate a technique of multi-layered CSF repair following endonasal anterior skull base surgery using medpor graft. DESIGN: Retrospective review of consecutive case series from a single centre. SUBJECTS: 68 cases of repair of CSF leaks utilising medpor identified from a larger prospectively maintained database of endonasal endoscopic procedures at our centre. METHODS: Retrospective review of a database of consecutive anterior skull base cases from 2016-2022, and further data collection from electronic hospital records. RESULTS: During follow up there were 7 cases of post-op CSF leak (10.3%). There were no radiological complications, and no cases of medpor removal or extrusion. Rates of infection were low, there were 3 (4.4%) cases of confirmed bacterial meningitis within our cohort. The mean length of stay was 4.7 days (median 3 days), with 16 cases discharged on the first post-operative day. CONCLUSIONS: Our experience of using medpor in anterior skull base reconstruction demonstrates that medpor is a readily available, easily handled, and reliable graft option with relatively low rates of infection and post-op CSF leak. Its use reduces the use of autologous graft materials and the associated donor site morbidity. Our long term follow up data further demonstrates the safety and efficacy of this technique.

Precision Neoantigen Discovery Using Large-scale Immunopeptidomes and Composite Modeling of MHC Peptide Presentation.

Major histocompatibility complex (MHC)-bound peptides that originate from tumor-specific genetic alterations, known as neoantigens, are an important class of anticancer therapeutic targets. Accurately predicting peptide presentation by MHC complexes is a key aspect of discovering therapeutically relevant neoantigens. Technological improvements in mass-spectrometry-based immunopeptidomics and advanced modeling techniques have vastly improved MHC presentation prediction over the past two decades. However, improvement in the sensitivity and specificity of prediction algorithms is needed for clinical applications such as the development of personalized cancer vaccines, the discovery of biomarkers for response to checkpoint blockade, and the quantification of autoimmune risk in gene therapies. Toward this end, we generated allele-specific immunopeptidomics data using 25 monoallelic cell lines and created Systematic HLA Epitope Ranking Pan Algorithm (SHERPA), a pan-allelic MHC-peptide algorithm for predicting MHC-peptide binding and presentation. In contrast to previously published large-scale monoallelic data, we used an HLA-null K562 parental cell line and a stable transfection of HLA alleles to better emulate native presentation. Our dataset includes five previously unprofiled alleles that expand MHC-binding pocket diversity in the training data and extend allelic coverage in under profiled populations. To improve generalizability, SHERPA systematically integrates 128 monoallelic and 384 multiallelic samples with publicly available immunoproteomics data and binding assay data. Using this dataset, we developed two features that empirically estimate the propensities of genes and specific regions within gene bodies to engender immunopeptides to represent antigen processing. Using a composite model constructed with gradient boosting decision trees, multiallelic deconvolution, and 2.15 million peptides encompassing 167 alleles, we achieved a 1.44-fold improvement of positive predictive value compared with existing tools when evaluated on independent monoallelic datasets and a 1.15-fold improvement when evaluating on tumor samples. With a high degree of accuracy, SHERPA has the potential to enable precision neoantigen discovery for future clinical applications.

Benchmarking short-term postoperative mortality across neurosurgery units: is hospital administrative data good enough for risk-adjustment?

BACKGROUND: Surgical mortality indicators should be risk-adjusted when evaluating the performance of organisations. This study evaluated the performance of risk-adjustment models that used English hospital administrative data for 30-day mortality after neurosurgery. METHODS: This retrospective cohort study used Hospital Episode Statistics (HES) data from 1 April 2013 to 31 March 2018. Organisational-level 30-day mortality was calculated for selected subspecialties (neuro-oncology, neurovascular and trauma neurosurgery) and the overall cohort. Risk adjustment models were developed using multivariable logistic regression and incorporated various patient variables: age, sex, admission method, social deprivation, comorbidity and frailty indices. Performance was assessed in terms of discrimination and calibration. RESULTS: The cohort included 49,044 patients. Overall, 30-day mortality rate was 4.9%, with unadjusted organisational rates ranging from 3.2 to 9.3%. The variables in the best performing models varied for the subspecialties; for trauma neurosurgery, a model that included deprivation and frailty had the best calibration, while for neuro-oncology a model with these variables plus comorbidity performed best. For neurovascular surgery, a simple model of age, sex and admission method performed best. Levels of discrimination varied for the subspecialties (range: 0.583 for trauma and 0.740 for neurovascular). The models were generally well calibrated. Application of the models to the organisation figures produced an average (median) absolute change in mortality of 0.33% (interquartile range (IQR) 0.15-0.72) for the overall cohort model. Median changes for the subspecialty models were 0.29% (neuro-oncology, IQR 0.15-0.42), 0.40% (neurovascular, IQR 0.24-0.78) and 0.49% (trauma neurosurgery, IQR 0.23-1.68). CONCLUSIONS: Reasonable risk-adjustment models for 30-day mortality after neurosurgery procedures were possible using variables from HES, although the models for trauma neurosurgery performed less well. Including a measure of frailty often improved model performance.

Natural history of post-operative non-functioning pituitary adenomas - a single centre cohort analysis.

PURPOSE: To study behaviour of endonasally operated non-functioning pituitary adenomas (NFPA) and propose a cost-effective stratified follow-up regimen. METHODS: A single centre retrospective cohort analysis from June 2009 till December 2019. All endonasally operated pituitary adenomas were identified with sub-analysis of the NFPA's. Patients of all age groups with radiological follow-up more than 30 months were included. Patients with any kind of cranial intervention performed < within 30 months of surgery were excluded. The post-operative MRI for this cohort was evaluated until either any intervention was performed or until the last follow-up. The maximal tumour diameter in any plane (mm) was measured from the MRI scans. The annual growth rate and the statistical relationship between age, sex, IHC, Ki-67, resection %, residual tumour was calculated. RESULTS: Out of 610 pituitary adenomas identified in the dataset, 116 patients met the inclusion criteria. Follow-up period ranged from 30 to 142 months (mean 78.5 months). A strong relationship existed between predicting tumour progression with first post-operative residue size (p = .001). A statistically significant relationship was found to be present between tumour growth and a residue of less than 10 mm diameter and 11-20 mm in diameter (Log rank p value .0216). On average, each patient with a residue < 5mm had MRI scans costing 976 £. CONCLUSION: Based on statistical analysis and internal validation of the growth rate of the residue, we have proposed MRI follow-up scans. These recommendations have the potential to save more than 300 £per patient towards MRI costs and can lay down a marker for defining time interval of serial scans for post-operative NFPA's.

The volume-outcome relationship for endoscopic transsphenoidal pituitary surgery for benign neoplasm: analysis of an administrative dataset for England.

BACKGROUND: Setting minimum annual volume thresholds for pituitary surgery in England is seen as one way of improving outcomes for patients and service efficiency. However, there are few recent studies from the UK on whether a volume-outcome effect exists, particularly in the era of endoscopic surgery. Such data are needed to allow evidence-based decision making. The aim of this study was to use administrative data to investigate volume-outcome effects for endoscopic transsphenoidal pituitary surgery in England. METHODS: Data from the Hospital Episodes Statistics database for adult endoscopic transsphenoidal pituitary surgery for benign neoplasm conducted in England from April 2013 to March 2019 (inclusive) were extracted. Annual surgeon and trust volume was defined as the number of procedures conducted in the 12 months prior to the index procedure. Volume was categorised as < 10, 10-19, 20-29, 30-39 and ≥40 procedures for surgeon volume and < 20, 20-39, 40-59, 60-79 and ≥80 procedures for trust volume. The primary outcome was repeat ETSPS during the index procedure or during a hospital admission within one-year of discharge from the index procedure. RESULTS: Data were available for 4590 endoscopic transsphenoidal pituitary procedures. After adjustment for covariates, higher surgeon volume was significantly associated with reduced risk of repeat surgery within one year (odds ratio (OR) 0.991 (95% confidence interval (CI) 0.982-1.000)), post-procedural haemorrhage (OR 0.977 (95% CI 0.967-0.987)) and length of stay greater than the median (0.716 (0.597-0.859)). A higher trust volume was associated with reduced risk of post-procedural haemorrhage (OR 0.992 (95% CI 0.985-0.999)), but with none of the other patient outcomes studied. CONCLUSIONS: A surgeon volume-outcome relationship exists for endoscopic transsphenoidal pituitary surgery in England.

Assessing national patterns and outcomes of pituitary surgery: is hospital administrative data good enough?

PURPOSE: Patterns of surgical care, outcomes, and quality of care can be assessed using hospital administrative databases but this requires accurate and complete data. The aim of this study was to explore whether the quality of hospital administrative data was sufficient to assess pituitary surgery practice in England. METHODS: The study analysed Hospital Episode Statistics (HES) data from April 2013 to March 2018 on all adult patients undergoing pituitary surgery in England. A series of data quality indicators examined the attribution of cases to consultants, the coding of sellar and parasellar lesions, associated endocrine and visual disorders, and surgical procedures. Differences in data quality over time and between neurosurgical units were examined. RESULTS: A total of 5613 records describing pituitary procedures were identified. Overall, 97.3% had a diagnostic code for the tumour or lesion treated, with 29.7% (n = 1669) and 17.8% (n = 1000) describing endocrine and visual disorders, respectively. There was a significant reduction from the first to the fifth year in records that only contained a pituitary tumour code (63.7%-47.0%, p < .001). The use of procedure codes that attracted the highest tariff increased over time (66.4%-82.4%, p < .001). Patterns of coding varied widely between the 24 neurosurgical units. CONCLUSION: The quality of HES data on pituitary surgery has improved over time but there is wide variation in the quality of data between neurosurgical units. Research studies and quality improvement programmes using these data need to check it is of sufficient quality to not invalidate their results.

Quantitative and functional visual field outcomes after endoscopic trans-sphenoidal pituitary adenectomy.

OBJECTIVE: Quantitative data on visual outcomes after trans-sphenoidal surgery is lacking in the literature. This study aims to address this by quantitatively assessing visual field outcomes after endoscopic trans-sphenoidal pituitary adenectomy using the capabilities of modern semi-automated kinetic perimetry. METHODS: Visual field area (deg2) calculated on perimetry performed before and after surgery was statistically analysed. Functional improvement was assessed against UK driving standards. RESULTS: Sixty-four patients (128 eyes) were analysed (May 2016-Nov 2019). I4e and I3e isopter area significantly increased after surgery (p < 0.0001). Of eyes with pre-operative deficits: 80.7% improved and 7.9% worsened; the median amount of improvement was 60% (IQR 6-246%). Median increase in I4e isopter was 2213deg2 (IQR 595-4271deg2) and in I3e isopter 1034 deg2 (IQR 180-2001 deg2). Thirteen out of fifteen (87%) patients with III4e data regained driving eligibility after surgery. Age and extent of resection (EOR) did not correlate with visual improvement. Better pre-operative visual field area correlated with a better post-operative area (p < 0.0001). However, the rate of improvement in the visual field area increased with poorer pre-operative vision (p < 0.0001). CONCLUSIONS: A median visual field improvement of 60% may be expected in over 80% of patients. Functionally, a significant proportion of patients can expect to regain driving eligibility. EOR did not impact on visual recovery. When the primary goal of surgery is alleviating visual impairment, optic apparatus decompression without the aim for gross total resection appears a valid strategy. Patients with the worst pre-operative visual field often experience the greatest improvement, and therefore, poor pre-operative vision alone should not preclude surgical intervention.

The weekend effect in neurosurgery: the Leeds general infirmary experience.

OBJECTIVE: In this article, we have studied what the impact of the 2016 contract has been on the weekend mortality rate in a single UK Neurosurgery centre for emergency admissions. METHODS: All adult neurosurgery admissions and mortality data from Leeds General Infirmary in 2016 and 2018 was included. Weekday was defined as between 00:01 am Monday and 23:59 Friday. Weekend was defined as anything outside this timeframe. In the first part of the analysis, we excluded all public holiday admissions and compared mortality risks between weekday and weekend admissions. A Cox proportional hazard model was used to examine the time to in-hospital death or censorship. From the model, we compared the hazard ratio of weekend-vs.-weekday admissions for 7-day, 30-day and overall mortalities as well as compared the hazard of mortality on each day of the week to Wednesday admission. In the second part of the analysis, we compared mortality risks of weekday admissions versus public holiday admissions. Finally, to further evaluate whether there was any change in service standard from 2016 to 2018, we assessed the odds ratio of mortality between admission in 2018 and 2016 on weekends and weekdays excluding public holidays. RESULTS: At 95% confidence interval, no significant difference in hazard ratio was found between admissions on different days in the week when compared to Wednesday in 2016 and 2018. There is a higher weekday admission 7-day mortality hazard ratio in 2018 compared to 2016 but overall there is no statistically significant difference in mortality hazard ratio between the two years. There is, however, a statistically significant difference in hazard ratio when comparing public holiday mortality in 2018 to weekday mortality. CONCLUSIONS: There was no weekend effect in our unit in 2016 or in 2018, however there is a public holiday effect in 2018.

CSF rhinorrhoea after endonasal intervention to the anterior skull base (CRANIAL): proposal for a prospective multicentre observational cohort study.

BACKGROUND: The endonasal transsphenoidal approach (TSA) has emerged as the preferred approach in order to treat pituitary adenoma and related sellar pathologies. The recently adopted expanded endonasal approach (EEA) has improved access to the ventral skull base whilst retaining the principles of minimally invasive surgery. Despite the advantages these approaches offer, cerebrospinal fluid (CSF) rhinorrhoea remains a common complication. There is currently a lack of comparative evidence to guide the best choice of skull base reconstruction, resulting in considerable heterogeneity of current practice. This study aims to determine: (1) the scope of the methods of skull base repair; and (2) the corresponding rates of postoperative CSF rhinorrhoea in contemporary neurosurgical practice in the UK and Ireland. METHODS: We will adopt a multicentre, prospective, observational cohort design. All neurosurgical units in the UK and Ireland performing the relevant surgeries (TSA and EEA) will be eligible to participate. Eligible cases will be prospectively recruited over 6 months with 6 months of postoperative follow-up. Data points collected will include: demographics, tumour characteristics, operative data), and postoperative outcomes. Primary outcomes include skull base repair technique and CSF rhinorrhoea (biochemically confirmed and/or requiring intervention) rates. Pooled data will be analysed using descriptive statistics. All skull base repair methods used and CSF leak rates for TSA and EEA will be compared against rates listed in the literature. ETHICS AND DISSEMINATION: Formal institutional ethical board review was not required owing to the nature of the study - this was confirmed with the Health Research Authority, UK. CONCLUSIONS: The need for this multicentre, prospective, observational study is highlighted by the relative paucity of literature and the resultant lack of consensus on the topic. It is hoped that the results will give insight into contemporary practice in the UK and Ireland and will inform future studies.

Enhanced recovery and accelerated discharge after endoscopic transsphenoidal pituitary surgery: safety, patient feedback, and cost implications.

BACKGROUND: Enhanced recovery after surgery (ERAS) is a constant motivation. There is growing evidence that an endoscopic (rather than microscopic) transsphenoidal approach to pituitary tumours can play a role, facilitating faster recovery and a commensurate reduction in length of stay (LOS). Reducing LOS is beneficial to both patients and healthcare systems. We sought to assess the safety, patient feedback, and resource implications of adopting an enhanced recovery and accelerated discharge policy for elective pituitary surgery. METHODS: We retrospectively assessed two consecutive cohorts of patients undergoing elective surgery for pituitary adenoma in a single UK centre between July 2016 and November 2019. The pre-ERAS cohort included 52 sequential patients operated prior to protocol change. The ERAS cohort included 55 sequential patients operated after a protocol change. Patient demographic data, tumour characteristics, intra- and post-operative CSF leak, the rate and cause of readmission (within 30 days), and the mean and median LOS were recorded. Patient feedback was collected from a subset of patients (n = 23) in the ERAS group. RESULTS: The two cohorts were well-matched with respect to their demographic, pathological, and operative characteristics. The rates of readmission within 30 days of discharge were similar between the two groups (8% pre-ERAS cohort, 9% ERAS cohort, p = 0.75). In the pre-ERAS cohort, the mean LOS was 4.5 days and median LOS was 3 days. This compares with significant reduction in LOS for the ERAS group: mean of 1.7 days and median of 1 day (p < 0.05). Thirty-nine of 55 patients in the ERAS group were discharged on post-operative day 1. Patient feedback was very positive in the ERAS group (mean patient satisfaction score of 9.7/10 using a Likert scale). CONCLUSIONS: An enhanced recovery protocol after elective endoscopic pituitary surgery is safe, reduces length of stay, and is associated with high patient satisfaction.

Identifying stochastic oscillations in single-cell live imaging time series using Gaussian processes.

Multiple biological processes are driven by oscillatory gene expression at different time scales. Pulsatile dynamics are thought to be widespread, and single-cell live imaging of gene expression has lead to a surge of dynamic, possibly oscillatory, data for different gene networks. However, the regulation of gene expression at the level of an individual cell involves reactions between finite numbers of molecules, and this can result in inherent randomness in expression dynamics, which blurs the boundaries between aperiodic fluctuations and noisy oscillators. This underlies a new challenge to the experimentalist because neither intuition nor pre-existing methods work well for identifying oscillatory activity in noisy biological time series. Thus, there is an acute need for an objective statistical method for classifying whether an experimentally derived noisy time series is periodic. Here, we present a new data analysis method that combines mechanistic stochastic modelling with the powerful methods of non-parametric regression with Gaussian processes. Our method can distinguish oscillatory gene expression from random fluctuations of non-oscillatory expression in single-cell time series, despite peak-to-peak variability in period and amplitude of single-cell oscillations. We show that our method outperforms the Lomb-Scargle periodogram in successfully classifying cells as oscillatory or non-oscillatory in data simulated from a simple genetic oscillator model and in experimental data. Analysis of bioluminescent live-cell imaging shows a significantly greater number of oscillatory cells when luciferase is driven by a Hes1 promoter (10/19), which has previously been reported to oscillate, than the constitutive MoMuLV 5' LTR (MMLV) promoter (0/25). The method can be applied to data from any gene network to both quantify the proportion of oscillating cells within a population and to measure the period and quality of oscillations. It is publicly available as a MATLAB package.

The learning curve for endoscopic trans-sphenoidal resection of pituitary macroadenomas. A single institution experience, Leeds, UK.

BACKGROUND: The object of this study was to assess whether increasing operative experience results in greater endoscopic trans-sphenoidal resection of pituitary macroadenomas and lower complications. METHODS: A retrospective single institution cohort study was performed. Subjects underwent endoscopic trans-sphenoidal resection of pituitary macroadenoma between July 2009 and July 2016 by three neurosurgeons. Following data collection, statistical analysis compared percentage of tumor resection and length of hospital stay (LOS) with experience. Complications including CSF leak are reported. RESULTS: In total, 142 patients (87 male, 55 female) mean age 55.1 were included. Surgeon 1 performed 106 cases; surgeon 2 performed 23 cases; and surgeon 3 performed 13 cases. Mean pre-operative tumor volumes were 8.18 cm3, 6.52 cm3, and 3.47 cm3 and post-operative volumes were 2.21, 1.74, and 1.93 cm3 for surgeons 1, 2, and 3, respectively. Respective percentage resections were 74.3, 77.2, and 52.1%. Analysis demonstrated no difference in tumor resection with increasing experience for all three surgeons (p = 0.11, p = 0.17, and p = 0.26). Tumor consistency and cavernous sinus involvement did not appear to affect tumor resection. Mean LOS was 5 days, 4 days, and 3 days, respectively, with no significant correlation with experience for all three surgeons. Intraoperative CSF leak incidence was 19/106 (18%) for surgeon 1, 6/23(26%) for surgeon 2, and 2/13(15%) for surgeon 3. Primary closure rate was 96.3% and only three other complications occurred. CONCLUSIONS: This study demonstrates that in our institution there is no statistically significant learning curve for the endoscopic resection of pituitary macroadenoma. However, there is a trend of improvement in tumor resection with experience for one surgeon. These findings suggest that the surgeons in our institution were capable of performing this procedure effectively with a low complication rate since adoption of the endoscopic technique in 2009.

From above or from below? That is the question. Comparison of the supraorbital approach with the endonasal approach. A cadaveric study.

BACKGROUND: Nowadays the endoscopic endonasal approach is increasingly being used to remove craniopharyngiomas, tuberculum sellae meningiomas and other presellar and parasellar lesions and its value in anterior skull base surgery is undisputed. Herein, we assess the relative advantages, disadvantages and feasibility of the keyhole eyebrow approach and the endonasal endoscopic approach in four cadaveric heads for the removal of presellar and parasellar lesions. METHODS: We used four cadaveric heads for 12 surgical dissections. The specimens were embalmed with two different techniques. Two bilateral supraorbital endoscopic assisted approaches and one transnasal expanded endonasal approach were performed for each head. We evaluated the feasibility, maneuverability and safety of each approach. We measured the operating room obtained with each approach and the distance from the main structures we reached. RESULTS: The technical feasibility of the endoscopic endonasal transphenoidal approach and the supraorbital eyebrow approach was reproduced in all four cadaveric heads. The transnasal approach gave us a good operating field medial to the two optic nerves and the two carotid arteries anteriorly until the frontal sinus and, posteriorly, the basilar artery, the emergence of the superior cerebellar arteries and posterior cerebral arteries. After performing the supraorbital approach, we viewed a wider field of the anterior skull base and we were able to reach the ipsilateral carotid artery, the optico-carotid recess, the pituitary stalk, the lamina terminalis until the contra lateral optic nerve and carotid artery, keeping a wider angle of maneuverability. CONCLUSIONS: Although the endoscopic transnasal approach has developed in leaps and bounds in the last decade, other transcranial approaches maintain their value. The supraorbital endoscopic approach is a minimally invasive approach and seems to be optimal for those lesions wider than 2 cm in the lateral extension and for all the paramedian lesions.

Endoscopic repair of the anterior skull base -is there a learning curve?

INTRODUCTION: Endoscopic anterior skull base surgery is now established practice. For skull base teams to manage complex pathology a variety of good dural repair techniques are required. However repairing certain skull base defects can be challenging. We look to see if a learning curve is associated with different types of CSF leaks in the anterior skull base Methods: Analysis of a prospectively collected database, contain 383 cases, on all endoscopic anterior skull base operations at one UK institution looking at CSF repair. Chi squared statistical analysis was undertaken comparing results from 2009 to 2013 with the 2014 to 2017 results. CSF leaks were categorised as either low flow with defects less than 2cm in diameter or high flow with defects greater than 2cm in diameter associated with a CSF void. RESULTS: 137 cases requiring repair were identified. Overall 96% of cases underwent successful primary repair with low flow CSF defects. The primary repair rate was similar in the early and later years. Successful repair of large anterior skull base defects was statistically more likely in the 2014-2017 group 96% compare to the 2009-2013 group 65%. CONCLUSIONS: A learning curve for small defects was not seen. However a learning curve does exist in relation to large defects with high flow over the first 20 cases.

Versatile genetic assembly system (VEGAS) to assemble pathways for expression in S. cerevisiae.

We have developed a method for assembling genetic pathways for expression in Saccharomyces cerevisiae. Our pathway assembly method, called VEGAS (Versatile genetic assembly system), exploits the native capacity of S. cerevisiae to perform homologous recombination and efficiently join sequences with terminal homology. In the VEGAS workflow, terminal homology between adjacent pathway genes and the assembly vector is encoded by 'VEGAS adapter' (VA) sequences, which are orthogonal in sequence with respect to the yeast genome. Prior to pathway assembly by VEGAS in S. cerevisiae, each gene is assigned an appropriate pair of VAs and assembled using a previously described technique called yeast Golden Gate (yGG). Here we describe the application of yGG specifically to building transcription units for VEGAS assembly as well as the VEGAS methodology. We demonstrate the assembly of four-, five- and six-gene pathways by VEGAS to generate S. cerevisiae cells synthesizing ß-carotene and violacein. Moreover, we demonstrate the capacity of yGG coupled to VEGAS for combinatorial assembly.

Conducting Real-Time Videofluoroscopic Swallow Study via Telepractice: A Preliminary Feasibility and Reliability Study.

A small number of studies have examined the feasibility of conducting videofluoroscopic swallow studies (VFSS) via telepractice. While the results have confirmed this potential, the systems tested to date have either reported issues that impacted the ability to analyze/interpret the VFSS recordings in real time, or they were not designed to enable real-time interpretation. Further system design is needed to establish a telepractice model that enables the VFSS assessment to be both guided and interpreted live in real time. The aim of this study was to test the feasibility and reliability of using a telepractice system to enable live VFSS assessment. Twenty adult patients underwent a VFSS assessment directed by a telepractice SLP with competency in VFSS located in another room of the hospital. The telepractice clinician led the sessions using a C20 Cisco TelePresence System. This was linked in real time via a secure telehealth network (at 4 megabits per second (Mbit/s)) to a C60 Cisco TelePresence System located in a fluoroscopy suite, connected to the digital fluoroscopy system. Levels of agreement were calculated between the telepractice clinician and a face-to-face clinician who simultaneously rated the VFSS in real time. High levels of agreement for swallowing parameters (range = 75-100 %; k = -0.34 to 1.0) and management decisions (range = 70-100 %, k = 0.64-1.0) were found. A post-session questionnaire revealed clinicians agreed that the telepractice system enabled successful remote assessment of VFSS. The findings support the potential to conduct live VFSS assessment via a telepractice model.

Retrospective analysis of anterior skull base CSF leaks and endoscopic repairs at Leeds.

OBJECTIVES: Over the past 10 years, endoscopic endonasal anterior skull base surgery has become established practice. Surgeons carrying out this surgery need to be able to endoscopically repair primary and secondary CSF leaks. A growing number of techniques have been adopted to date. This article highlights one UK institution's experience in the management of anterior skull base leaks, and how surgeons there have identified leak defect types that are difficult to seal and how they have adopted a new way of repairing them, which uses a fat ring. METHODS: Seventy-six patients requiring CSF leak repairs were identified form a prospective data base of 240 endoscopic anterior skull base procedures at the General Infirmary at Leeds performed between July 2009 and October 2015. RESULTS: Fifty-one cases have undergone an endoscopic primary repair of a skull base defect following resection of a lesion and, of these, 10 (19%) cases required a secondary repair. This was particularly over the planum sphenoidale area. Twenty-five cases had undergone an endoscopic repair as the primary procedure. This was due to a spontaneous leak in 7 cases, trauma in 3 cases, following craniotomy in 3 cases and following pituitary surgery in 2 cases. The remaining 10 were the secondary repairs referred to above. CONCLUSIONS: A number of techniques are effective in CSF repair. Defects over the planum sphenoidale and clivus are associated with the highest recurrence, requiring specific repair techniques. Utilisation of a 5 "F" repair helps to prevent recurrence in high risk defect cases over the optic chiasm. The 5 "F" repair used takes the form of placing intradural Fat and Fascia; next a Fat sealing ring is used, followed by a nasoseptal Flap; finally a supporting fragmentable pack is applied.

Diagnosis, medication, and surgical management for patients with trigeminal neuralgia: a qualitative study.

BACKGROUND: Trigeminal neuralgia (TN) is a serious health problem, causing brief, recurrent episodes of stabbing or burning facial pain, which patients describe as feeling like an electric shock. The consequences of living with the condition are severe. There is currently no cure for TN and management of the condition can be complex, often delayed by misdiagnosis. Patients' qualitative experiential accounts of TN have not been reported in the literature. Capturing subjective experiences can be used to inform the impact of the condition on quality of life and may contribute to a better understanding of current clinical practice with the aim of improving patient care. METHODS: Participants with TN (n = 16; 11 female), including those who have and have not undergone surgical intervention(s), took part in one of four focus groups. We conducted a thematic analysis within an essentialist framework using transcripts. RESULTS: The impact of TN and treatment on the lives of participants emerged as four predominant themes: (1) diagnosis and support with TN, (2) living in fear of TN pain, (3) isolation and social withdrawal, and (4) medication burden and looking for a cure. Each theme is discussed and illustrated with extracts from the transcripts. CONCLUSIONS: Key issues to address in the management of patients with TN include continued delays in diagnosis, persistent side effects from medication, and a lack of psychological support. Developing strategies to enhance the management of patients with TN, informed by a biopsychosocial approach and multidisciplinary team working, is essential to enhancing the provision of current care.