Development of a liver disease-specific large language model chat interface using retrieval-augmented generation

BACKGROUND AND AIMS

Large language models (LLMs) have significant capabilities in clinical information processing tasks. Commercially available LLMs, however, are not optimized for clinical uses and are prone to generating hallucinatory information. Retrieval-augmented generation (RAG) is an enterprise architecture that allows the embedding of customized data into LLMs. This approach "specializes" the LLMs and is thought to reduce hallucinations.

APPROACH AND RESULTS

We developed "LiVersa," a liver disease-specific LLM, by using our institution's protected health information-complaint text embedding and LLM platform, "Versa." We conducted RAG on 30 publicly available American Association for the Study of Liver Diseases guidance documents to be incorporated into LiVersa. We evaluated LiVersa's performance by conducting 2 rounds of testing. First, we compared LiVersa's outputs versus those of trainees from a previously published knowledge assessment. LiVersa answered all 10 questions correctly. Second, we asked 15 hepatologists to evaluate the outputs of 10 hepatology topic questions generated by LiVersa, OpenAI's ChatGPT 4, and Meta's Large Language Model Meta AI 2. LiVersa's outputs were more accurate but were rated less comprehensive and safe compared to those of ChatGPT 4.

RESULTS

We evaluated LiVersa's performance by conducting 2 rounds of testing. First, we compared LiVersa's outputs versus those of trainees from a previously published knowledge assessment. LiVersa answered all 10 questions correctly. Second, we asked 15 hepatologists to evaluate the outputs of 10 hepatology topic questions generated by LiVersa, OpenAI's ChatGPT 4, and Meta's Large Language Model Meta AI 2. LiVersa's outputs were more accurate but were rated less comprehensive and safe compared to those of ChatGPT 4.

CONCLUSIONS

In this demonstration, we built disease-specific and protected health information-compliant LLMs using RAG. While LiVersa demonstrated higher accuracy in answering questions related to hepatology, there were some deficiencies due to limitations set by the number of documents used for RAG. LiVersa will likely require further refinement before potential live deployment. The LiVersa prototype, however, is a proof of concept for utilizing RAG to customize LLMs for clinical use cases.

AAV9-based PMM2 gene replacement augments PMM2 expression and improves glycosylation in primary fibroblasts of patients with phosphomannomutase 2 deficiency (PMM2-CDG)

Inherited deficiency of phosphomannomutase 2 (PMM2) (aka PMM2-CDG) is the most common congenital disorders of glycosylation (CDG) and has no cure. With debilitating morbidity and significant mortality, it is imperative to explore novel, safe, and effective therapies for the disease. Our Proof-of-Concept study showed that AAV9-PMM2 infection of patient fibroblasts augmented PMM2 expression and improved glycosylation. Thus, AAV9-PMM2 gene replacement is a promising therapeutic strategy for PMM2-CDG patients.

Development of a Liver Disease-Specific Large Language Model Chat Interface using Retrieval Augmented Generation

Background

Large language models (LLMs) have significant capabilities in clinical information processing tasks. Commercially available LLMs, however, are not optimized for clinical uses and are prone to generating incorrect or hallucinatory information. Retrieval-augmented generation (RAG) is an enterprise architecture that allows embedding of customized data into LLMs. This approach "specializes" the LLMs and is thought to reduce hallucinations.

Methods

We developed "LiVersa," a liver disease-specific LLM, by using our institution's protected health information (PHI)-complaint text embedding and LLM platform, "Versa." We conducted RAG on 30 publicly available American Association for the Study of Liver Diseases (AASLD) guidelines and guidance documents to be incorporated into LiVersa. We evaluated LiVersa's performance by comparing its responses versus those of trainees from a previously published knowledge assessment study regarding hepatitis B (HBV) treatment and hepatocellular carcinoma (HCC) surveillance.

Results

LiVersa answered all 10 questions correctly when forced to provide a "yes" or "no" answer. Full detailed responses with justifications and rationales, however, were not completely correct for three of the questions.

Discussions

In this study, we demonstrated the ability to build disease-specific and PHI-compliant LLMs using RAG. While our LLM, LiVersa, demonstrated more specificity in answering questions related to clinical hepatology - there were some knowledge deficiencies due to limitations set by the number and types of documents used for RAG. The LiVersa prototype, however, is a proof of concept for utilizing RAG to customize LLMs for clinical uses and a potential strategy to realize personalized medicine in the future.

Implementation of a Systematic, Digital Oncology Workflow for Patient Distress Screening in a National, Multi-Site Radiotherapy Outpatient Setting

PURPOSE/OBJECTIVE(S)

Distress screening is recommended as standard of care in oncology to improve the quality of personalized care for patients, however previously reported barriers have led to poor uptake and reporting of clinician follow up and interventions. Our purpose was to improve the quality of personalized care for patients with high patient participation rate (>50%), clinical and nurse workflow compliance rate (>70%) and create structured data for practice improvement. To achieve this purpose, an in-house systematic digital screen and templated well-being plan (WBP) workflow was implemented across 33 outpatient Radiation Oncology sites in a multi-institutional center.

MATERIALS/METHODS

An in-house digital version of the NCCN Distress Thermometer and Problem Checklist (DT) was built in the integrated web-based portal for patients to complete at home or in a clinic setting. A digital workflow was co-designed with clinicians with automatic integration of the DT PDF document into the Electronic Medical Record (EMR), assigned for doctor review. Nurses subsequently recorded screening actions in the WBP. An extensive engagement, education and support program was completed nationally with phased implementation after an initial pilot at 3 sites. Staff and patient feedback were documented and presented with the collated data for review.

RESULTS

The program was successfully implemented at 33 centers across Australia in the multi-site organization between March and October 2022. A total of 7788 distress screening forms were submitted with an uptake rate of 78% at baseline and 53% at end of treatment (EOT). DT document approval rates by doctors varied (41%-98%), and WBP was completed for 48-100% of patients, with variations of rates and use noted between states and individuals for both. Referrals were recorded in the WBP for 3% of patients, however, as up to 52% of documentation was not in a WBP (for some states), true referral numbers require further manual analysis. Pairwise analysis of screening scores between time points saw 42% of scores reduced, 34% increased and 24% with no change. Analysis of a subset of patients with increased or no change in score showed 57% had some change in categories of distress, 22% had complete change and 10% had no change.

CONCLUSION

With an increasing global focus on improving patient centered care, implementation of a systematic digital workflow for distress screening and supportive care was achieved resulting in patient identified stressors being addressed as standard of care. Key barriers reported, include confidence discussing screening results with patients and manual workflows at EOT. The provision of a rich data set can also highlight opportunities for clinical practice improvement, cohort-based focus, clinical quality indicators, benchmarking and reporting.

Cocaine screening in patients undergoing nasal reconstructive surgery: a cross-sectional, survey-based study of UK rhinology consultants

OBJECTIVE

This study aimed to explore the current practices of the UK rhinology consultant body in regard to cocaine screening in nasal reconstructive surgery.

METHOD

A 12-question online survey was distributed to rhinology consultants (October 2021 to February 2022) currently practising in the UK.

RESULTS

A total of 55 consultants responded. Fifty-three per cent asked patients about cocaine use prior to consideration of surgery, and 45 per cent performed cocaine testing prior to consideration of surgery. Of these, the majority employed urine testing alone (60 per cent), with hair testing being less common as a single screening modality (4 per cent). Sixteen per cent opted for both urine and hair testing. The most common reasons for not performing cocaine testing included patient history or clinical examination that was not suggestive of cocaine use (44 per cent), lack of formal guidelines (33 per cent) and lack of testing availability (27 per cent). Sixty-four per cent were in favour of a national policy for cocaine screening.

CONCLUSION

There is marked variation in cocaine screening practices for nasal reconstructive surgery among UK rhinologists.

CREB3L2 Regulates Hemidesmosome Formation during Epithelial Sealing

The long-term success rate of dental implants can be improved by establishing a favorable biological sealing with a high-quality epithelial attachment. The application of mesenchymal stem cells (MSCs) holds promise for facilitating the soft tissue integration around implants, but the molecular mechanism is still unclear and the general application of MSC sheet for soft tissue integration is also relatively unexplored. We found that gingival tissue-derived MSC (GMSC) sheet treatment significantly promoted the expression of hemidesmosome (HD)-related genes and proteins in gingival epithelial cells (GECs). The formation of HDs played a key role in strengthening peri-implant epithelium (PIE) sealing. Further, high-throughput transcriptome sequencing showed that GMSC sheet significantly upregulated the PI3K/AKT pathway, confirming that cell adhesion and HD expression in GECs were regulated by GMSC sheet. We observed that the expression of transcription factor CREB3L2 in GECs was downregulated. After treatment with PI3K pathway inhibitor LY294002, CREB3L2 messenger RNA and protein expression levels were upregulated. Further experiments showed that overexpression or knockdown of CREB3L2 could significantly inhibit or promote HD-related genes and proteins, respectively. We confirmed that CREB3L2 was a transcription factor downstream of the PI3K/AKT pathway and participated in the formation of HDs regulated by GMSC sheet. Finally, through the establishment of early implant placement model in rats, we clarified the molecular function of CREB3L2 in PIE sealing as a mechanical transmission molecule in GECs. The application of GMSC sheet-implant complex could enhance the formation of HDs at the implant-PIE interface and decrease the penetration distance of horseradish peroxidase between the implant and PIE. Meanwhile, GMSC sheet reduced the length of CREB3L2 protein expression on PIE. These findings elucidate the potential function and molecular mechanism of MSC sheet regulating the epithelial sealing around implants, providing new insights and ideas for the application of stem cell therapy in regenerative medicine.

Assessing the Compliance and Accuracy of a National Australian Head and Neck Cancer (HNC) Database

PURPOSE/OBJECTIVE(S)

Accurate cancer databases enable auditing of patient management, and this knowledge facilitates optimizing care. A multi-institutional organization, the largest single provider of radiation oncology services in Australia, has developed its own national database (ND). All patients are entered on the ND as a prerequisite for generating a radiotherapy prescription. A significant component of the ND is automated, but manual input from the treating radiation oncologist (RO) is also required. The purpose of this study was to assess the compliance and accuracy of the data entered on this ND for head and neck cancer (HNC) patients.

MATERIALS/METHODS

We included all HNC patients with either oral cavity cancer or oropharynx cancer (ICD-10 coding) treated between September 2021 and September 2022 to assess compliance. We randomly selected 25% of these cases and assigned them to 3 HNC ROs to manually review the accuracy of all clinical data points.

RESULTS

There were 166 HNC patients, 139 oropharynx and 27 oral cavity. Compliance in the 166 patients was excellent (94% or higher) for the majority of data points - age, gender, diagnosis ICD code, diagnosis date, laterality, TNM classification, radiotherapy dose, fractionation and technique and start and completion dates. Compliance was good (85% or more) for smoking history, use of chemotherapy, and p16 status (oropharynx). Compliance was poor (43%) for specific chemotherapy regimens. Accuracy was high (92% or higher) for diagnosis ICD code, smoking history, use of chemotherapy; good (87% or higher) for p16 status (oropharynx), laterality and histopathology; and poor for date of diagnosis (75%), TNM classification (62%) and specific chemotherapy regimens (29%).

CONCLUSION

The ND is a powerful tool for assessing patient care. Overall, compliance was very good. Accuracy was very good for most items, and we have highlighted areas where improvements can be made. This study shows that a compliant and accurate ND is achievable and supports the next goal of additional items to be included in the ND, specifically patient outcome data.

Vitamin D and smell impairment: a systematic literature review

OBJECTIVE

Smell impairment affects 60-80 per cent of individuals aged over 80 years. This review aimed to identify any association between vitamin D deficiency and smell impairment, and determine the efficacy of vitamin D to treat smell impairment.

METHODS

A literature search was conducted across four databases between the years 2000 and 2022. The literature screen was performed by two independent reviewers.

RESULTS

Seven articles were included in this review. Four studies examined the association between vitamin D deficiency and smell impairment, with three studies identifying a significant relationship. Three studies investigated the use of vitamin D as treatment for smell impairment, which found complete resolution or significant symptom improvement after vitamin D deficiency was treated.

CONCLUSION

This review identified limited studies on this topic. As vitamin D supplementation is relatively cost-efficient, further large-scale studies should be carried out to investigate the efficacy of vitamin D for treating anosmia.

AAV-based gene therapy prevents and halts the progression of dilated cardiomyopathy in a mouse model of phosphoglucomutase 1 deficiency (PGM1-CDG)

Phosphoglucomutase 1 (PGM1) deficiency is recognized as the third most common N-linked congenital disorders of glycosylation (CDG) in humans. Affected individuals present with liver, musculoskeletal, endocrine, and coagulation symptoms; however, the most life-threatening complication is the early onset of dilated cardiomyopathy (DCM). Recently, we discovered that oral D-galactose supplementation improved liver disease, endocrine, and coagulation abnormalities, but does not alleviate the fatal cardiomyopathy and the associated myopathy. Here we report on left ventricular ejection fraction (LVEF) in 6 individuals with PGM1-CDG. LVEF was pathologically low in most of these individuals and varied between 10% and 65%. To study the pathobiology of the cardiac disease observed in PGM1-CDG, we constructed a novel cardiomyocyte-specific conditional Pgm2 gene (mouse ortholog of human PGM1) knockout (Pgm2 cKO) mouse model. Echocardiography studies corroborated a DCM phenotype with significantly reduced ejection fraction and left ventricular dilation similar to those seen in individuals with PGM1-CDG. Histological studies demonstrated excess glycogen accumulation and fibrosis, while ultrastructural analysis revealed Z-disk disarray and swollen/fragmented mitochondria, which was similar to the ultrastructural pathology in the cardiac explant of an individual with PGM1-CDG. In addition, we found decreased mitochondrial function in the heart of KO mice. Transcriptomic analysis of hearts from mutant mice demonstrated a gene signature of DCM. Although proteomics revealed only mild changes in global protein expression in left ventricular tissue of mutant mice, a glycoproteomic analysis unveiled broad glycosylation changes with significant alterations in sarcolemmal proteins including different subunits of laminin-211, which was confirmed by immunoblot analyses. Finally, augmentation of PGM1 in KO mice via AAV9-PGM1 gene replacement therapy prevented and halted the progression of the DCM phenotype.

Measuring clinical trial set-up complexity: development and content validation of a pharmacy scoring tool to support workload planning

Introduction

Clinical trials are essential for advancing medical knowledge and patient care. Pharmacy plays a vital role in research delivery, safeguarding participants, healthcare professionals and Trusts by ensuring Investigational Medicinal Products (IMPs) are procured, handled, stored, dispensed and used safely. Data have emerged indicating that clinical trial protocols are increasingly more complex for site personnel to execute. Whilst various tools have been developed to support workload planning and costing of clinical trials for clinicians and nursing personnel, the equivalent tool for pharmacy activities is not available.1,2

Aim

This study aims to locally develop and validate a pharmacy scoring tool to assess clinical trial complexity at the set-up stage. Objectives are to develop pharmacy-scoring tool to quantify clinical trials execution complexity with respect to pharmacy activities and determine Content Validity Index (CVI) and Inter-Rater Agreement (IRA) of the scoring tool through an internal vetting process.

Methods

A three-stage process was used to develop and validate the scoring tool. Two researchers contextualised the pharmacy–specific items, organised the content and constructed the tool based on suitable elements for inclusion through a targeted literature search and outputs from an expert panel meeting. Four experts independently rated each items on its relevance, clarity and alignment with clinical trial complexity considerations at the set-up stage using a 4-point Likert scale. Following data analysis, researchers made a judgement on whether to retain, modify, omit or add new items to the tool. Where the desired level of content validity had not been achieved for an item, revisions were made following a group discussion and the tool was re-distributed to the same expert panel for a second round of assessment. Item level-CVI (I-CVI) and tool level-CVI (average-CVI) was calculated for each round. Four experts then utilised the revised tool to retrospectively review 20 random studies to evaluate clinical trial complexity scores independently. IRA among assessors was measured for each individual pharmacy-specific item by dividing the responses into dichotomous ratings (one or two vs. three or four). The study was deemed a service evaluation and approved by the Trust Pharmacy Research and Audit Group therefore ethical submission was waived.

Results

Fourteen pharmacy-specific items were identified for inclusion in the tool with a possible score of 0-3 points per item. The highest possible complexity score when adding up all items is 42 points with a scale of low 0-14, moderate >14-28, and high >28-42. Following two rounds of content validity assessment where clarity revisions were made to four items, 14 out of 14 scored I-CVI of 1 with overall tool level average-CVI score of 1. The IRA shows 100% agreement by item and tool.

Discussion/Conclusion

This clinical trial’s complexity-scoring tool is the first of its kind tailored for pharmacy set-up in the UK. Overall, the results from this study support validity and reliability (content and construct) of this locally developed tool. The formal agreement on the use of this tool with the Trust Research Lead has better facilitated workload and capacity planning as well as ensuing costings for Pharmacy clinical trial activities.

References

1. Department of Health. Attributing the Cost of health and social care Research & Development (AcORD) Published 2012. Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/351182/AcoRD_Guidance_for_publication_May_2012.pdf

2. Marta Calvin-Lamas et al. A complexity scale for clinical trials from a pharmacy perspective. European Journal of Hospital Pharmacy 2018;25:251-256

Measuring drug name similarity to prioritise the application of tall-man lettering in a computerised pharmacy dispensing system

Introduction

Medicine name similarity is a contributory factor to medication errors.1 Published lists exists highlighting medicine pairs that are easily confused; locally a Look-Alike-Sound-Alike (LASA) list has expanded over time with no formal system of triage. A multipronged approach is required to address LASA risks. Tall-Man Lettering (TML) is one intervention that uses uppercase lettering for the dissimilarities in look-alike drug names to alert staff to the risk of error.1 For greatest impact, it should be reserved for pairs with the highest risk for patient safety.

Aim

This study aimed to use Levenshtein Distance (LD), Bigram (Bi) and Trigram (Tri) methods to prioritise medicine pairs for TML in the Pharmacy dispensing system. Objectives were to: Produce a comprehensive list of medicines pairs; Establish normalised thresholds from LD, Bi and Tri to prioritise medicine pairs for TML; and, measure drug name similarity using validated software2 applying LD, Bi and Tri to medication pairs as a method of triage for orthographic assessment.

Methods

Approval was obtained by the Trust Pharmacy Research Committee. The need for ethical submission was waived. A LASA list was developed combining medicine name pairs from National Pharmacy Association list3, historical local list and internal incidents where medicine name confusion was cited. Duplicated, branded and non-stock pairs were excluded. A literature search was undertaken to identify published thresholds for accuracy and sensitivity of the methods in the measure of medicine name similarity. LD measures the minimum number of edit operations needed to transform one string into another; Bi and Tri measures the frequency in which two/three similar sequential strings appear within a medicine name respectively. Two assessors independently entered medicine pairs through a validated computer program2 applying LD, Bi and Tri to measure orthographic similarity. Normalised computed similarity scores (between 0-1 where higher values represent increased drug similarity) were collated on Microsoft excel for comparison against thresholds.

Results

Two-hundred and twelve medicine pairs were identified for review. The literature defined Bi and Tri thresholds at ≥0.3 and ≥0.1 respectively; in absence of this for LD, in-house thresholds were assessed then defined at ≥0.6. LD identified 84 medicine pairs; Bi identified 144; and Tri identified 158; none were uniquely found by LD, four by Bi and 18 by Tri. A final look-alike list with 82 medicine pairs meeting all three thresholds was identified for TML.

Discussion/Conclusion

Screening using all three methods led to a 61% reduction in medicines pairs allowing prioritisation of TML as an effective intervention based on look-alike pairs with the highest risk of error. This study focused on identifying orthographic similarity in ‘look-alike’ medicine pairs only. With no single intervention available to prevent LASA errors, future work can explore other interventions. In the absence of literature around normalised LD, the definition of an in-house threshold posed to be another limitation and an area where further exploratory work should be considered. As new LASA incidents arise or the Trust catalogue increases, these methods should be applied to triage their look-alike potential, confirming if TML is an appropriate intervention.

References

1. World Health Organisation. Look-alike, sound-alike medication names. patient safety solutions. 2007 May, Volume 1: Solution 1.

2. Strcmp2. [Internet] Department of Computer Science, University of Toronto: Aditya Bhargava [Date of publication unknown]. Available from: https://www.cs.toronto.edu/~aditya/strcmp2/, Work based on: Grzegorz Kondrak. N-gram similarity and distance. Proceedings of the Twelfth International Conference on String Processing and Information Retrieval. 2005 Nov; pp. 115—126.

3. The National Pharmacy Association Pharmacy Team. Look-alike sound-alike (LASA) items [Internet]. The National Pharmacy Association; 2021. Available from: https://www.npa.co.uk/information-and-guidance/look-alike-sound-alike-lasa-items/

Initial observations on the impact of implementation of a seven-day clinical pharmacy service on dispensary activity and performance

Introduction

The need for seven-day clinical pharmacy services is widely acknowledged, although limited, in the acute sector of the National Health Service.1,2 Timely medicine supply is integral to provision of improved clinical pharmacy services to patients across seven-days, and is essential in effective discharge planning. There is a paucity of evidence for implementation of seven-day clinical pharmacy services, including the impact of service transformation on dispensary activity and performance. This limits planning and development of seven-day pharmacy services.

Aim

To assess the impact of a seven-day clinical pharmacy service on dispensary activity and performance, at the main site of a tertiary-referral teaching hospital.

Methods

A seven-day clinical pharmacy service was implemented in October 2021. Prior to this, pharmacy services were largely dispensary-based with clinical pharmacy services for acute and neurosciences admission and limited ward-based services in other specialities. At implementation, clinical pharmacy technicians and pharmacists (n=16) provided patient-facing pharmaceutical care for 7.5-hours/day across all specialities over the weekend; this included medicines reconciliation, preparation of discharge-medication lists, independent prescribing, counselling and clinical review of prioritised patients. The weekend dispensary staffing, skill-mix and shift patterns were redesigned to facilitate staff release from the dispensary rota. Dispensing activity data were obtained from Ascribe for six months pre- and post-implementation (April 2021-March 2022). Data were categorised as inpatient/discharge and the mean number of items dispensed per month analysed using Microsoft Excel. Discharge turnaround performance was calculated as percentage of discharge prescriptions dispensed within two-hours of dispensary receipt and obtained from the Prescription Tracking System. Verbal staff feedback was sought 4-months post-implementation. The study was deemed a service evaluation by the Pharmacy Research and Audit Group and so ethical approval was not required.

Results

Twelve dispensing staff and one pharmacist were rostered to one of three daily 3.75-hour dispensary shift patterns. Following implementation, mean total inpatient dispensing activity increased from 12799 to 13250 items/month (3.5% increase) and mean weekend activity from 2184 to 2677 items/month (22.6% increase). Mean weekday inpatient activity was stable at 10615 to 10573 items/month. The mean discharge dispensing activity increased from 9065 to 9837 items/month (8.5% increase): mean weekday discharge from 8498 to 8622 items/month (1.5% increase); mean weekend activity from 569 to 1215 items/month (114% increase). Discharge turnaround performance remained stable with 85% discharge prescriptions dispensed within 2-hours, versus 84% pre-implementation. Weekday performance also remained stable - from 84% to 83% and the weekend performance increased from 85% to 92%. Dispensary staff fed-back that weekend shift patterns were effective, activity was manageable and shifts usually ran smoothly and finished on time.

Discussion/Conclusion

Introduction of a seven-day clinical pharmacy service led to an increase in weekend dispensary activity, which was not offset by decrease in weekday activity. Importantly, the dispensary performance was not negatively impacted and weekend discharge performance improved. Increases could be because of weekend medicines reconciliation, pro-active medication ordering and pharmacist-led preparation of discharge-medicine lists. Dispensary activity in Winter 2020 was atypical because of COVID-19, thus it was not feasible to compare data. Further review, including 12 months data would reduce impact of seasonal variations in NHS activity. Limitations include that patient data including length of stay and time to discharge were not within scope.

References

1. Anon. Transformation of seven day clinical pharmacy services in acute hospitals. 2016. http://www.england.nhs.uk/wp-content/uploads/2016/09/7ds-clinical-pharmacy-acute-hosp.pdf. Accessed 29 July 2022.

2. Anon. RPS professional standards for hospital pharmacy services. 2017. http://www.rpharms.com/recognition/setting-professional-standards/hospital-pharmacy-professional-standards. Accessed 29 July 2022.

Prevalence and potential clinical significance of near miss dispensing errors at a large teaching hospital in the United Kingdom (UK)

Introduction

Dispensing is a complex multi-step process where mistakes can arise at any stage leading to a potential to cause patient harm. Published literature identifies near miss dispensing error rates up to 2.7% in UK hospitals.1 Near misses are ‘a dispensing error detected by the checker before it reaches the patient’. Near miss audits are routinely undertaken across two main dispensaries at this teaching hospital where one dispensary (site 1) is automated and the other (site 2) is not.

Aim

To determine the frequency of near miss dispensing errors, by site, and review the potential clinical significance of near misses observed.

Methods

Locally adapted data collection tool based on Royal Pharmaceutical Society near miss error codes2 was developed and piloted. Details on prescription type, drug, dose, strength, route, formulation and near misses were included. Details of all medication orders dispensed were also recorded. Prospective observational audit of near misses identified at the checking bench was undertaken, on three separate days, across three consecutive months. Dean and Barber method3 was used for assessing potential clinical significance of near misses. Four independent assessors: two pharmacists; one nurse and one doctor; reviewed near misses for the likelihood to cause harm. The mean severity score attained across assessors was calculated. Approval was obtained by the Trust Pharmacy Research and Audit Committee. The need for ethical submission was waived.

Results

Overall 3027 items were dispensed; 1539 and 1488 at sites 1 and 2 respectively. There were 177 (5.8%) erroneous dispensed items involving 193 near misses in total (15 items had two near misses and one item had three near misses). Ninety one (5.9%) erroneous dispensed items were captured at site 1 and 86 (5.8%) at site 2 (χ 2, p=0.94). Overall 161 near miss descriptions were assessed for clinical significance: 97 (60.2%) minor, 63 (39.1%) moderate and one (0.6%) severe. Statistically significant difference in severity rating of near misses between prescription type (χ 2(2) = 32.268, p <0.001); mean ranks 80, 57, 125 for discharge, inpatient and outpatient prescriptions respectively. No statistical difference in severity rating of near misses between error type (χ 2(2) = 2.402, p =0.3).

Discussion/Conclusion

Local prevalence of near misses is higher than in published literature.1 However, the majority of errors were considered to have minor clinical impact on patients. Difficult to make direct comparisons between studies due to differences in research methods, definitions, operating systems and hospital settings. There was no statistical difference noted in prevalence between sites despite presence of automation at one and manual dispensing at the other. Two factors may explain this: Firstly, part-pack robotic dispensing, where generation of medication barcodes is a manual process and one subject to human input error itself; although not explored explicitly as part of this study. Secondly, lack of knowledge and complex prescriptions are known to be key contributory factors associated with dispensing errors, but the categories of drugs dispensed at a specialist tertiary dispensary (site 1) were broader and more complex. Further study is needed on the impact of part-pack robotic dispensing on dispensing errors.

References

1. James KL et al. Incidence, type and causes of dispensing errors. A review of literature. Int J Pharm Pract 2009; 17:9-30.

2. Royal Pharmaceutical Society [Internet]. Near Miss Error Log. London: Royal Pharmaceutical Society; 2015. Available from: RPS-NearMissError-LOG.pdf (rpharms.com)

3. Dean BS, Barber ND. A validated, reliable method for scoring the severity of medication errors. Am J Health Syst Pharm. 1999;56:57-62.

Rolling Up the Sleeve: Equitable, Efficient, and Safe COVID-19 Mass Immunization for Academic Medical Center Employees

BACKGROUND

Novel coronavirus disease 2019 (COVID-19) vaccine administration has faced distribution barriers across the United States. We sought to delineate our vaccine delivery experience in the first week of vaccine availability, and our effort to prioritize employees based on risk with a goal of providing an efficient infrastructure to optimize speed and efficiency of vaccine delivery while minimizing risk of infection during the immunization process.

OBJECTIVE

This article aims to evaluate an employee prioritization/invitation/scheduling system, leveraging an integrated electronic health record patient portal framework for employee COVID-19 immunizations at an academic medical center.

METHODS

We conducted an observational cross-sectional study during January 2021 at a single urban academic center. All employees who met COVID-19 allocation vaccine criteria for phase 1a.1 to 1a.4 were included. We implemented a prioritization/invitation/scheduling framework and evaluated time from invitation to scheduling as a proxy for vaccine interest and arrival to vaccine administration to measure operational throughput.

RESULTS

We allotted vaccines for 13,753 employees but only 10,662 employees with an active patient portal account received an invitation. Of those with an active account, 6,483 (61%) scheduled an appointment and 6,251 (59%) were immunized in the first 7 days. About 66% of invited providers were vaccinated in the first 7 days. In contrast, only 41% of invited facility/food service employees received the first dose of the vaccine in the first 7 days (p < 0.001). At the vaccination site, employees waited 5.6 minutes (interquartile range [IQR]: 3.9-8.3) from arrival to vaccination.

CONCLUSION

We developed a system of early COVID-19 vaccine prioritization and administration in our health care system. We saw strong early acceptance in those with proximal exposure to COVID-19 but noticed significant difference in the willingness of different employee groups to receive the vaccine.

Flupentixol/melitracen for chronic refractory cough after treatment failure with other neuromodulators

BACKGROUND: Gabapentin and baclofen are recommended for the treatment of chronic refractory cough (CRC). We investigated the efficacy of flupentixol/melitracen in patients unresponsive to these neuromodulators.METHODS: A total of 101 patients with CRC who failed to respond to gabapentin and baclofen were recruited, and treated with flupentixol/melitracen. The prevalence of cough resolution and changes in the Cough Symptom Score (CSS), cough thresholds to capsaicin, Hull Airway Reflux Questionnaire (HARQ), Leicester Cough Questionnaire (LCQ), Generalized Anxiety Disorder-7, Hamilton Anxiety Rating Scale, Patient Health Questionnaire-9, and Hamilton Depression Rating Scale-24 were evaluated after treatment.RESULTS: Ninety-eight patients (97.0%) completed the study. The overall successful cough resolution rate was 62.4% (63/101). Cough resolution was accompanied by an obvious decrease in the CSS and HARQ score and a remarkable increase in cough thresholds to capsaicin challenge and LCQ score, whereas anxiety and depression scores did not change significantly. The prevalence of adverse effects (e.g., insomnia and dizziness) was 21.8%. The prevalence of cough recurrence within 2 weeks after treatment cessation was 17.8%.CONCLUSION: Flupentixol/melitracen may be an efficacious option for CRC unresponsive to other neuromodulators.

Mid-treatment Fluorodeoxyglucose Positron Emission Tomography in Human Papillomavirus-related Oropharyngeal Squamous Cell Carcinoma Treated with Primary Radiotherapy: Nodal Metabolic Response Rate can Predict Treatment Outcomes

AIMS

To evaluate whether biomarkers derived from fluorodeoxyglucose positron emission tomography-computed tomography (FDG PET-CT) performed prior to (prePET) and during the third week (interim PET; iPET) of radiotherapy can predict treatment outcomes in human papillomavirus (HPV)-positive oropharyngeal squamous cell carcinoma (OPC).

MATERIALS AND METHODS

This retrospective analysis included 46 patients with newly diagnosed OPC treated with definitive (chemo)radiation and all patients had confirmed positive HPV status (HPV+OPC) based on p16 immunohistochemistry. The maximum standardised uptake value (SUV_max), metabolic tumour volume (MTV) and total lesional glycolysis (TLG) of primary, index node (node with the highest TLG) and total lymph nodes and their median percentage (≥50%) reductions in iPET were analysed, and correlated with 5-year Kaplan-Meier and multivariable analyses (smoking, T4, N2b-3 and AJCC stage IV), including local failure-free survival, regional failure-free survival, locoregional failure-free survival (LRFFS), distant metastatic failure-free survival (DMFFS), disease-free survival (DFS) and overall survival.

RESULTS

There was no association of outcomes with prePET parameters observed on multivariate analysis. A complete metabolic response of primary tumour was seen in 13 patients; the negative predictive value for local failure was 100%. More than a 50% reduction in total nodal MTV provided the best predictor of outcomes, including LRFFS (88% versus 47.1%, P = 0.006, hazard ratio = 0.153) and DFS (78.2% versus 41.2%, P = 0.01, hazard ratio = 0.234). More than a 50% reduction in index node TLG was inversely related to DMFFS: a better nodal response was associated with a higher incidence of distant metastatic failure (66.7% versus 100%, P = 0.009, hazard ratio = 3.0).

CONCLUSION

The reduction (≥50%) of volumetric nodal metabolic burden can potentially identify a subgroup of HPV+OPC patients at low risk of locoregional failure but inversely at higher risk of distant metastatic failure and may have a role in individualised adaptive radiotherapy and systemic therapy.

miR-18a expression in basal cell carcinoma and regulatory mechanism on autophagy through mTOR pathway

BACKGROUND

Basal cell carcinoma (BCC) is the most common form of skin carcinoma.

AIM

To investigate the function of key micro(mi)RNAs and to explore the potential molecular mechanisms involved in BCC.

METHODS

The microarray dataset GSE34535, which comprises seven BCC samples and seven control samples, was downloaded from the Gene Expression Omnibus database. Differentially expressed miRNAs (DE-miRNAs) were identified. We collected tissue samples from 20 patients with BCC and 20 healthy controls (HCs), to compare the miR-18a expression in their tissue samples. Expression of miR-18a in A431 and HaCaT cells was also assayed. Following this, we upregulated and downregulated miR-18a expression in A431 cells to examine the effects on cell proliferation, migration and apoptosis. To further investigate the relative mechanism, the proteins LC3, Beclin 1, Akt and mammalian target of rapamycin (mTOR) were examined by quantitative real-time PCR and Western blotting. For further verification, we examined the expression of LC3 in the 20 BCC and 20 HC tissue samples.

RESULTS

In total, 19 DE-miRNAs (13 upregulated and 6 downregulated) that were common to the BCC and HC groups were identified. Levels of miR-18a were about three-fold higher in BCC tissues and A431 cells compared with their respective control groups. In vitro, downregulation of miR-18a was shown to inhibit cell proliferation and activate autophagy via the Akt/mTOR signalling pathway, while upregulation of miR-18a promoted proliferation of these cells. LC3 was decreased in BCC compared with HC tissue samples.

CONCLUSIONS

Our data support an oncogenic role of miR-18a through a novel Akt/mTOR/Beclin 1/LC3 axis, and suggest that the antitumour effects of miR-18a inhibitor may make it suitable for BCC therapy.

3045Role of osteogenic circulating endothelial progenitor cells in dissemination of large arterial calcification in rheumatoid arthritis

Background

Rheumatoid arthritis is associated with both abnormal bone metabolism and atherogenesis but mechanistic links were missing.

Aim

This study aimed to investigate the role of osteocalcin (OCN)-expressing circulating endothelial progenitor cells (EPC)s in the severity and dissemination of systemic arterial calcifications in rheumatoid arthritis.

Methods

We performed flow cytometry studies in 145 consecutive patients with rheumatoid arthritis to determine osteogenic circulating levels of OCN-positive (OCN+) CD34+KDR+ and OCN+CD34+, versus conventional early EPC CD34+CD133+KDR+. Total calcium load of the thoracic aorta (ascending plus descending) and the carotid arteries were assessed by non-contrast computed tomography (CT) and contrast CT angiography.

Results

Osteogenic EPCs OCN+CD34+KDR+ (P=0.002) and OCN+CD34+ were strikingly associated with the clustered presence of aortic and carotid calcification (P=0.002 and 0.001 respectively, Figure). Multivariable analyses revealed that circulating OCN+CD34+KDR+ (B=14.4 [95% CI 4.0 to 24.8], P=0.007) and OCN+CD34+ (B=9.6 [95% CI 4.9 to 14.3], P<0.001) remained independently associated with increased aortic calcium load. OCN+CD34+ EPC (B=0.8 [95% CI 0.1 to 1.5], P=0.023), but not OCN+CD34+KDR+ EPC (B=1.2 [95% CI −0.2 to 2.6], P=0.09) was further independently associated with carotid calcium load. In comparison, conventional early EPC CD34+CD133+KDR+ had no significant association with aortic or carotid calcium load (P=0.46 and 0.88, respectively).

Conclusions

Circulating level of osteogenic EPC is associated with promulgated aortic and carotid calcification in patients with rheumatoid arthritis, suggesting a potential mechanistic role of the bone-vascular axis in pro-atherogenicity of rheumatic diseases.

Acknowledgement/Funding

General Research Fund, Hong Kong Research Grants Council

A novel phosphoglucomutase-deficient mouse model reveals aberrant glycosylation and early embryonic lethality

Patients with phosphoglucomutase (PGM1) deficiency, a congenital disorder of glycosylation (CDG) suffer from multiple disease phenotypes. Midline cleft defects are present at birth. Overtime, additional clinical phenotypes, which include severe hypoglycemia, hepatopathy, growth retardation, hormonal deficiencies, hemostatic anomalies, frequently lethal, early-onset of dilated cardiomyopathy and myopathy emerge, reflecting the central roles of the enzyme in (glycogen) metabolism and glycosylation. To delineate the pathophysiology of the tissue-specific disease phenotypes, we constructed a constitutive Pgm2 (mouse ortholog of human PGM1)-knockout (KO) mouse model using CRISPR-Cas9 technology. After multiple crosses between heterozygous parents, we were unable to identify homozygous life births in 78 newborn pups (P = 1.59897E-06), suggesting an embryonic lethality phenotype in the homozygotes. Ultrasound studies of the course of pregnancy confirmed Pgm2-deficient pups succumb before E9.5. Oral galactose supplementation (9 mg/mL drinking water) did not rescue the lethality. Biochemical studies of tissues and skin fibroblasts harvested from heterozygous animals confirmed reduced Pgm2 enzyme activity and abundance, but no change in glycogen content. However, glycomics analyses in serum revealed an abnormal glycosylation pattern in the Pgm2^+/- animals, similar to that seen in PGM1-CDG.

Salubrinal enhances eIF2α phosphorylation and improves fertility in a mouse model of Classic Galactosemia

Loss of galactose-1 phosphate uridylyltransferase (GALT) activity in humans results in Classic Galactosemia, and the GalT-deficient (GalT^-/-) mouse mimics the patient condition. GalT^-/- ovaries display elevated endoplasmic reticulum (ER) stress marker, BiP, and downregulated canonical phosphatidylinositol 3-kinase (Pi3k)/protein kinase B (Akt) growth/pro-survival signaling. Numbers of primordial follicles are reduced in the mutants, recapitulating the accelerated ovarian aging seen in human patients. We previously found that oral administration of the compound Salubrinal (an eIF2α phosphatase inhibitor), resulted in reduction of ovarian BiP expression, rescued Pi3k/Akt signaling, and a doubling of primordial follicles in GalT^-/- adults. Here, we further characterized galactosemic stress in GalT^-/- mice versus wild-type (WT) controls, and examined whether Salubrinal treatment improved broader reproductive parameters. We assessed the expression levels of factors of the unfolded protein response (UPR), and found that BiP, phospho-Perk, and phospho-eIF2α were all elevated in GalT^-/- ovaries. However, neither IKK activation (NFκB pathway) nor alternative Xbp1 splicing downstream of ER membrane protein Ire1α activation was induced, suggesting an Xbp1-independent UPR in galactosemic stress. Moreover, Salubrinal treatment significantly increased the number of ovulated eggs in mutant animals after gonadotrophic superovulation. Salubrinal treatment also normalized estrus cycle stage lengths and resulted in significantly larger litter sizes than vehicle-treated mutants. Overall, we show that Salubrinal protects against galactosemia-induced primordial follicle loss in a fashion that includes suppressing the de-phosphorylation of eIF2α, and that intervention in this way significantly improves and extends ovarian function, fertility, and fecundity.

Natural and inducible regulatory B cells are widely distributed in ovine lymphoid tissues

Regulatory B cells that produce IL-10 are now recognized as an important component of the immune system. We previously confirmed that IL-10 secreting CD21⁺ regulatory B cells (B_reg cells) were present in ovine jejunal Peyer's patches (JPP) and this IL-10 production suppressed IL-12 and IFN-γ secretion. It is not known, however, whether ovine B_reg cells are restricted to JPP or are present in other lymphoid tissues. Therefore, CD21⁺ B cells were purified from sheep JPP and from a variety of mucosal and systemic lymphoid tissues using magnetic cell sorting. Purified CD21⁺ B cells were stimulated with a TLR9-agonist, CpG oligodeoxynucleotide (CpG ODN), and the frequency of spontaneous and inducible (i) IL-10-secreting B cells was evaluated by ELISPOT. Spontaneous IL-10 secreting CD21⁺ B cells were present in mucosal (jejunal PP, parabronchial lymph nodes (LN), mesesnteric LN, and palatine tonsils) and systemic (spleen and blood) lymphoid tissues. Mucosal lymphoid tissues (parabronchial and mesenteric LNs and JPP) had the highest frequency of cells spontaneously secreting IL-10 while tonsils had the lowest. The frequency of B cells spontaneously secreting IL-10 was lowest in blood and spleen. There was large inter-animal variation in the frequency of CD21⁺ B cells spontaneously secreting IL-10 and no significant difference was detected following CpG ODN stimulation. When comparing within individual animals there was, however, a consistent increase in the frequency of CD21⁺ cells secreting IL-10 following CpG ODN stimulation versus stimulation with GpC control ODN. The presence of inducible (i)B_reg cells in ovine mucosal tissues supports previous evidence from mice indicating that B cells have the capacity to modulate inflammatory responses. The presence of iB_reg cells in ruminants may also provide a novel therapeutic target for both immunomodulatory drugs and vaccines designed to control antigen-specific mucosal inflammation.

Allogeneic adipose-derived stem cells suppress mTORC1 pathway in a murine model of systemic lupus erythematosus

OBJECTIVE

The aim of our study was to investigate the efficacy of adipose-derived stem cells (ADSC) transplantation in systemic lupus erythematosus (SLE) and to determine the mechanism of ADSC transplantation.

METHODS

B6.MRL/lpr mice were administered ADSC intravenously every week from age 28 to 31 weeks, while the lupus control group and the normal control received phosphate buffered solution (PBS) on the same schedule.

RESULTS

Compared with the lupus control group, the ADSC treatment group had a significant improvement of histologic abnormalities, serologic abnormalities, and immunologic function. Anti-double-stranded DNA antibodies, spleen/weight ratio, deposits of C3/IgG in the kidney, and serum creatinine and blood urea nitrogen levels were significantly decreased with the transplantation of ADSC. A significant decrease of the Th17/CD4⁺ T cell ratio in the spleen, the serum IL-17 concentration, as well as renal IL-17 expression was observed in the ADSC treatment group. Western blot results also showed that ADSC treatment had a lower expression of protein kinase B (Akt), p-Akt, mTOR, p-mTOR, p70S6K, p-p70S6K, and HIF-1α.

CONCLUSION

ADSC treatment can prevent the development of lupus nephritis and significantly ameliorate already-established disease. ADSC treatment reduced Akt, mTOR, p70S6K, HIF-1α, and that this inhibition can avert IL-17-induced inflammation, suggesting that ADSC may be a promising treatment for SLE.

Reversal of aberrant PI3K/Akt signaling by Salubrinal in a GalT-deficient mouse model

Classic Galactosemia is an autosomal recessive disorder caused by deleterious mutations in the GALT gene, which encodes galactose-1 phosphate uridylyltransferase enzyme (GALT: EC 2.7.7.12). Recent studies of primary skin fibroblasts isolated from the GalT-deficient mice demonstrated a slower growth rate, a higher level of endoplasmic reticulum (ER) stress, and down-regulation of the Phosphoinositide 3 kinase/Protein kinase B (PI3K/Akt) signaling pathway. In this study, we compared the expression levels of the PI3K/Akt signaling pathway in normal and GalT-deficient mouse tissues. In mutant mouse ovaries, phospho-Akt [pAkt (Ser473)] and pGsk3β were reduced by 62.5% and 93.5%, respectively (p<0.05 versus normal controls). In mutant cerebella, pAkt (Ser473) and pGsk3β were reduced by 62%, 50%, respectively (p<0.05). To assess the role of ER stress in the down-regulation of PI3K/Akt signaling, we examined if administration of Salubrinal, a chemical compound that alleviates ER stress, to GalT-deficient fibroblasts and animals could normalize the pathway. Our results demonstrated that Salubrinal effectively reversed the down-regulated PI3K/Akt signaling pathway in the mutant cells and animals to levels close to those of their normal counterparts. Moreover, we revealed that Salubrinal can significantly slow down the loss of Purkinje cells in the cerebella, as well as the premature loss of primordial ovarian follicles in young mutant mice. These results open the door for a new therapeutic approach for the patients with Classic Galactosemia.

Rapid Development of Specialty Population Registries and Quality Measures from Electronic Health Record Data*. An Agile Framework

BACKGROUND

Creation of a new electronic health record (EHR)-based registry often can be a "one-off" complex endeavor: first developing new EHR data collection and clinical decision support tools, followed by developing registry-specific data extractions from the EHR for analysis. Each development phase typically has its own long development and testing time, leading to a prolonged overall cycle time for delivering one functioning registry with companion reporting into production. The next registry request then starts from scratch. Such an approach will not scale to meet the emerging demand for specialty registries to support population health and value-based care.

OBJECTIVE

To determine if the creation of EHR-based specialty registries could be markedly accelerated by employing (a) a finite core set of EHR data collection principles and methods, (b) concurrent engineering of data extraction and data warehouse design using a common dimensional data model for all registries, and (c) agile development methods commonly employed in new product development.

METHODS

We adopted as guiding principles to (a) capture data as a byproduct of care of the patient, (b) reinforce optimal EHR use by clinicians, (c) employ a finite but robust set of EHR data capture tool types, and (d) leverage our existing technology toolkit. Registries were defined by a shared condition (recorded on the Problem List) or a shared exposure to a procedure (recorded on the Surgical History) or to a medication (recorded on the Medication List). Any EHR fields needed - either to determine registry membership or to calculate a registry-associated clinical quality measure (CQM) - were included in the enterprise data warehouse (EDW) shared dimensional data model. Extract-transform-load (ETL) code was written to pull data at defined "grains" from the EHR into the EDW model. All calculated CQM values were stored in a single Fact table in the EDW crossing all registries. Registry-specific dashboards were created in the EHR to display both (a) real-time patient lists of registry patients and (b) EDW-generated CQM data. Agile project management methods were employed, including co-development, lightweight requirements documentation with User Stories and acceptance criteria, and time-boxed iterative development of EHR features in 2-week "sprints" for rapid-cycle feedback and refinement.

RESULTS

Using this approach, in calendar year 2015 we developed a total of 43 specialty chronic disease registries, with 111 new EHR data collection and clinical decision support tools, 163 new clinical quality measures, and 30 clinic-specific dashboards reporting on both real-time patient care gaps and summarized and vetted CQM measure performance trends.

CONCLUSIONS

This study suggests concurrent design of EHR data collection tools and reporting can quickly yield useful EHR structured data for chronic disease registries, and bodes well for efforts to migrate away from manual abstraction. This work also supports the view that in new EHR-based registry development, as in new product development, adopting agile principles and practices can help deliver valued, high-quality features early and often.

Systemic lupus erythematosus and risk of preterm birth: a systematic review and meta-analysis of observational studies

We performed a meta-analysis to identify the association between systemic lupus erythematosus (SLE) and preterm birth. In this study, we studied the effects of SLE, SLE disease activity, a history of nephritis and active nephritis on preterm birth. Searches were conducted before 20 May 2016 of PubMed, Embase, Medline and Cochrane Library of literature and article reference lists. Eleven observational case-control studies and thirteen cohort studies met the inclusion criteria. The pooled relative risk (RR) for the risk of preterm birth in SLE patients versus controls was 2.05 (95% confidence interval (CI): 1.72-3.32); for active SLE patients versus inactive was 2.98 (95% CI: 2.32-3.83); for SLE patients with a history of lupus nephritis versus those without nephritis it was 1.62 (95% CI: 1.35-1.95); and for SLE patients with active nephritis versus those with quiescent nephritis it was 1.78 (95% CI: 1.17-2.70). In summary, this study identified a significant association in the above results. This association was more significant in active SLE patients versus inactive. With respect to SLE itself, active inflammation (such as disease activity) may be more hazardous for the management of the pregnancy. This suggests that it is essential to control disease activity in order to achieve a better outcome of SLE pregnancy.

Response of immune response genes to adjuvants poly [di(sodium carboxylatoethylphenoxy)phosphazene] (PCEP), CpG oligodeoxynucleotide and emulsigen at intradermal injection site in pigs

Understanding the mechanisms by which adjuvants mediate their effects provide critical information on how innate immunity influences the development of adaptive immunity. Despite being a critical vaccine component, the mechanisms by which adjuvants mediate their effects are not fully understood and this is especially true when they are used in large animals. This lack of understanding limits our ability to design effective vaccines. In the present study, we administered polyphosphazene (PCEP), CpG oligodeoxynucleotides (CpG), emulsigen or saline via an intradermal injection into pigs and assessed the impact on the expression of reported 'adjuvant response genes' over time. CpG induced a strong upregulation of the chemokine CXL10 several 'Interferon Response Genes', as well as TNFα, and IL-10, and a down-regulation of IL-17 genes. Emulsigen upregulated expression of chemokines CCL2 and CCL5, proinflammatory cytokines IL-6 and TNFα, as well as TLR9, and several IFN response genes. PCEP induced the expression of chemokine CCL2 and proinflammatory cytokine IL-6. These results suggest that emulsigen and CpG may promote recruitment of innate immune cells and Th1 type cytokine production but that PCEP may promote a Th-2 type immune response through the induction of IL-6, an inducer of B cell activity and differentiation.

Standard Information Models for Representing Adverse Sensitivity Information in Clinical Documents

BACKGROUND

Adverse sensitivity (e.g., allergy and intolerance) information is a critical component of any electronic health record system. While several standards exist for structured entry of adverse sensitivity information, many clinicians record this data as free text.

OBJECTIVES

This study aimed to 1) identify and compare the existing common adverse sensitivity information models, and 2) to evaluate the coverage of the adverse sensitivity information models for representing allergy information on a subset of inpatient and outpatient adverse sensitivity clinical notes.

METHODS

We compared four common adverse sensitivity information models: Health Level 7 Allergy and Intolerance Domain Analysis Model, HL7-DAM; the Fast Healthcare Interoperability Resources, FHIR; the Consolidated Continuity of Care Document, C-CDA; and OpenEHR, and evaluated their coverage on a corpus of inpatient and outpatient notes (n = 120).

RESULTS

We found that allergy specialists' notes had the highest frequency of adverse sensitivity attributes per note, whereas emergency department notes had the fewest attributes. Overall, the models had many similarities in the central attributes which covered between 75% and 95% of adverse sensitivity information contained within the notes. However, representations of some attributes (especially the value-sets) were not well aligned between the models, which is likely to present an obstacle for achieving data interoperability. Also, adverse sensitivity exceptions were not well represented among the information models.

CONCLUSIONS

Although we found that common adverse sensitivity models cover a significant portion of relevant information in the clinical notes, our results highlight areas needed to be reconciled between the standards for data interoperability.

Flow cytometry as an improved method for the titration of Chlamydiaceae and other intracellular bacteria

Chlamydiaceae is a family of intracellular bacteria causing a range of diverse pathological outcomes. The most devastating human diseases are ocular infections with C. trachomatis leading to blindness and genital infections causing pelvic inflammatory disease with long-term sequelae including infertility and chronic pelvic pain. In order to enable the comparison of experiments between laboratories investigating host-chlamydia interactions, the infectious titer has to be determined. Titer determination of chlamydia is most commonly performed via microscopy of host cells infected with a serial dilution of chlamydia. However, other methods including fluorescent ELISpot (Fluorospot) and DNA Chip Scanning Technology have also been proposed to enumerate chlamydia-infected cells. For viruses, flow cytometry has been suggested as a superior alternative to standard titration methods. In this study we compared the use of flow cytometry with microscopy and Fluorospot for the titration of C. suis as a representative of other intracellular bacteria. Titer determination via Fluorospot was unreliable, while titration via microscopy led to a linear read-out range of 16 - 64 dilutions and moderate reproducibility with acceptable standard deviations within and between investigators. In contrast, flow cytometry had a vast linear read-out range of 1,024 dilutions and the lowest standard deviations given a basic training in these methods. In addition, flow cytometry was faster and material costs were lower compared to microscopy. Flow cytometry offers a fast, cheap, precise, and reproducible alternative for the titration of intracellular bacteria like C. suis. © 2016 International Society for Advancement of Cytometry.

Data management challenges in analysis and synthesis in the ecosystem sciences

Open-data has created an unprecedented opportunity with new challenges for ecosystem scientists. Skills in data management are essential to acquire, manage, publish, access and re-use data. These skills span many disciplines and require trans-disciplinary collaboration. Science synthesis centres support analysis and synthesis through collaborative 'Working Groups' where domain specialists work together to synthesise existing information to provide insight into critical problems. The Australian Centre for Ecological Analysis and Synthesis (ACEAS) served a wide range of stakeholders, from scientists to policy-makers to managers. This paper investigates the level of sophistication in data management in the ecosystem science community through the lens of the ACEAS experience, and identifies the important factors required to enable us to benefit from this new data-world and produce innovative science. ACEAS promoted the analysis and synthesis of data to solve transdisciplinary questions, and promoted the publication of the synthesised data. To do so, it provided support in many of the key skillsets required. Analysis and synthesis in multi-disciplinary and multi-organisational teams, and publishing data were new for most. Data were difficult to discover and access, and to make ready for analysis, largely due to lack of metadata. Data use and publication were hampered by concerns about data ownership and a desire for data citation. A web portal was created to visualise geospatial datasets to maximise data interpretation. By the end of the experience there was a significant increase in appreciation of the importance of a Data Management Plan. It is extremely doubtful that the work would have occurred or data delivered without the support of the Synthesis centre, as few of the participants had the necessary networks or skills. It is argued that participation in the Centre provided an important learning opportunity, and has resulted in improved knowledge and understanding of good data management practices.

Gene of the month: PIK3CA

PIK3CA encodes the p110α catalytic subunit of phosphatidylinositol 3-kinase (PI3K) which through its role in the PI3K/Akt pathway is important for the regulation of important cellular functions such as proliferation, metabolism and protein synthesis, angiogenesis and apoptosis. Mutations in PIK3CA are known to be involved in a wide range of human cancers and mutant PIK3CA is thought to act as an oncogene. The specific PIK3CA inhibitor, NVP-BYL719, has displayed promising results in cancer therapy and is currently under clinical trials. Furthermore, PI3K regulates autophagy, a cellular process that recycles proteins and organelles through lysosomal degradation and has recently been recognised as an attractive therapeutic target due to its pro- and anti-cancer properties. Several studies have attempted to investigate the effects of combining the inhibition of both PI3K and autophagy in cancer therapy, and an in vivo model has demonstrated that the combined use of a concomitant PI3K and autophagy inhibitor induced apoptosis in glioma cells.

Characterization and identification of ubiquitin conjugation sites with E3 ligase recognition specificities

Background

In eukaryotes, ubiquitin-conjugation is an important mechanism underlying proteasome-mediated degradation of proteins, and as such, plays an essential role in the regulation of many cellular processes. In the ubiquitin-proteasome pathway, E3 ligases play important roles by recognizing a specific protein substrate and catalyzing the attachment of ubiquitin to a lysine (K) residue. As more and more experimental data on ubiquitin conjugation sites become available, it becomes possible to develop prediction models that can be scaled to big data. However, no development that focuses on the investigation of ubiquitinated substrate specificities has existed. Herein, we present an approach that exploits an iteratively statistical method to identify ubiquitin conjugation sites with substrate site specificities.

Results

In this investigation, totally 6259 experimentally validated ubiquitinated proteins were obtained from dbPTM. After having filtered out homologous fragments with 40% sequence identity, the training data set contained 2658 ubiquitination sites (positive data) and 5532 non-ubiquitinated sites (negative data). Due to the difficulty in characterizing the substrate site specificities of E3 ligases by conventional sequence logo analysis, a recursively statistical method has been applied to obtain significant conserved motifs. The profile hidden Markov model (profile HMM) was adopted to construct the predictive models learned from the identified substrate motifs. A five-fold cross validation was then used to evaluate the predictive model, achieving sensitivity, specificity, and accuracy of 73.07%, 65.46%, and 67.93%, respectively. Additionally, an independent testing set, completely blind to the training data of the predictive model, was used to demonstrate that the proposed method could provide a promising accuracy (76.13%) and outperform other ubiquitination site prediction tool.

Conclusion

A case study demonstrated the effectiveness of the characterized substrate motifs for identifying ubiquitination sites. The proposed method presents a practical means of preliminary analysis and greatly diminishes the total number of potential targets required for further experimental confirmation. This method may help unravel their mechanisms and roles in E3 recognition and ubiquitin-mediated protein degradation.

Implementing a bar-code assisted medication administration system: effects on the dispensing process and user perceptions

PURPOSE

We assessed the effects of a bar-code assisted medication administration system used without the support of computerised prescribing (stand-alone BCMA), on the dispensing process and its users.

METHODS

The stand-alone BCMA system was implemented in one ward of a teaching hospital. The number of dispensing steps, dispensing time and potential dispensing errors (PDEs) were directly observed one month before and eight months after the intervention. Attitudes of pharmacy and nursing staff were assessed using a questionnaire (Likert scale) and interviews.

RESULTS

Among 1291 and 471 drug items observed before and after the introduction of the technology respectively, the number of dispensing steps increased from five to eight and time (standard deviation) to dispense one drug item by one staff personnel increased from 0.8 (0.09) to 1.5 (0.12) min. Among 2828 and 471 drug items observed before and after the intervention respectively, the number of PDEs increased significantly (P<0.001). 'Procedural errors' and 'missing drug items' were the frequently observed PDEs in the after study. 'Perceived usefulness' and 'job relevance' of the technology decreased significantly (P=0.003 and P=0.004 respectively) among users who participated in the before (N=16) and after (N=16) questionnaires surveys. Among the interviewees, pharmacy staff felt that the system offered less benefit to the dispensing process (9/16). Nursing staff perceived the system as useful in improving the accuracy of drug administration (7/10).

CONCLUSION

Implementing a stand-alone BCMA system may slow down and complicate the dispensing process. Nursing staff believe the stand-alone BCMA system could improve the drug administration process but pharmacy staff believes the technology would be more helpful if supported by computerised prescribing. However, periodical assessments are needed to identify weaknesses in the process after implementation, and all users should be educated on the benefits of using this technology.