bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quasi-prime peptides: identification of the shortest peptide sequences unique to a species
Authors: Mouratidis Ioannis , Chan Candace S Y , Chantzi Nikol , Tsiatsianis Georgios Christos , Hemberg Martin , Ahituv Nadav , Georgakopoulos-Soares Ilias 
Published: April 2023

Abstract
Determining the organisms present in a biosample has many important applications in agriculture, wildlife conservation, and healthcare. Here, we develop a universal fingerprint based on the identification of short peptides that are unique to a specific organism. We define quasi-prime peptides as sequences that are found in only one species, and we analyzed proteomes from 21 875 species, from viruses to humans, and annotated the smallest peptide kmer sequences that are unique to a species and absent from all other proteomes. We also perform simulations across all reference proteomes and observe a lower than expected number of peptide kmers across species and taxonomies, indicating an enrichment for nullpeptides, sequences absent from a proteome. For humans, we find that quasi-primes are found in genes enriched for specific gene ontology terms, including proteasome and ATP and GTP catalysis. We also provide a set of quasi-prime peptides for a number of human pathogens and model organisms and further showcase its utility via two case studies for Mycobacterium tuberculosis and Vibrio cholerae, where we identify quasi-prime peptides in two transmembrane and extracellular proteins with relevance for pathogen detection. Our catalog of quasi-prime peptides provides the smallest unit of information that is specific to a single organism at the protein level, providing a versatile tool for species identification.
Interim Federal Health Program: Survey of use of supplemental benefits by paediatric health care providers
Authors: Leps Caroline , Monteiro Jessica , Barozzino Tony , Bowry Ashna , Rashid Meb , Sgro Michael , Suleman Shazeen 
Published: April 2023

Abstract

Objectives
The Interim Federal Health Program (IFHP) provides temporary healthcare coverage to refugees and refugee claimants. Previous research demonstrates that paediatric healthcare providers poorly utilize the IFHP, with low registration rates and limited understanding of the program. The objective of this study was to examine paediatric provider use of IFHP-covered supplemental benefits, and their experience with trying to access these benefits.

Methods
A one-time survey was administered via the Canadian Paediatric Surveillance Program in February 2020. Of those who had provided care to IFHP-eligible patients, descriptive tables and statistics were created looking at provider demographics, and experience using the IFHP supplemental benefits. A multinomial logistic regression was built to look at provider characteristics associated with trying to access supplemental benefits.

Results
Of the 2,753 physicians surveyed, there were 1,006 respondents (general paediatricians and subspecialists). Of the respondents, 526 had recently provided care to IFHP-eligible patients. Just over 30% of those who had recently provided care did not access supplemental benefits as they did not know they were covered by the IFHP. Of those who had tried to access supplemental benefits, over 80% described their experience as difficult, or very difficult.

Conclusions
Paediatric providers have a poor understanding of IFHP-covered supplemental benefits, which is cited as a reason for not trying to access supplemental benefits. Of those who do try to access these benefits, they describe the process as difficult. Efforts should be made to improve provider knowledge and streamline the process to improve access to healthcare for refugee children and youth.
The development of large public infrastructure projects: integrating policy and project studies models
Authors: Hudon Pierre-André , Floricel Serghei 
Published: April 2023

AbstractProject management theory often reduces development to a simplistic and smooth process of consultation leading to a consensual set of requirements. However, in large public infrastructure projects, this is rarely the case as development is often subject to major power struggles. This article shows that public policy theory has an excellent potential to shed a fresh light on project development. An integrated model combining the theoretical insights from the Advocacy Coalition Framework and project development studies is presented and illustrated using the case of a major Canadian city streetcar network megaproject. The implications of the model for understanding “wicked problems” are discussed.
OA12 Comparing disease manifestations and outcomes in juvenile-onset SLE and adult-onset SLE patients: a nested case-control study within a Singapore cohort
Authors: Thong Bernard Y , Khong Yan-Yi , Lim Xin-Rong , Howe Hwee-Siew 
Published: April 2023

Abstract

Background/Aims
To compare disease manifestations and outcomes of juvenile-onset SLE (jSLE) and adult-onset SLE (aSLE) patients using a nested case-control study of patients in a Singapore cohort.

Methods
A prospective cohort of SLE patients was established at Tan Tock Seng Hospital from 1 January 2002 to 31 December 2017. Sociodemographic, clinical, laboratory and treatment data were collected according to a standardised protocol. jSLE patients (≤18 years old) were selected from this cohort and matched for gender and disease duration in a 1:1 ratio with aSLE patients. Data from the enrolment visit (V0) and last visit (VL) were analysed in this study.

Results
There were 148 jSLE patients with sufficient information for analysis who were matched with 148 aSLE patients. Fever and lymphadenopathy (p &lt; 0.001) and hypocomplementemia (p = 0.002 at V0) were significantly more common in jSLE, while cardiovascular manifestations were significantly more common in aSLE patients (p = 0.008 at VL). Disease activity measured by the SLE Disease Activity Index (SLEDAI) was higher in the jSLE group at V0 (median SLEDAI 4 vs 2, p=0.05) and at VL (median SLEDAI 2.5 vs 0, p = 0.007). A significantly higher proportion of jSLE patients received immunosuppressants (intravenous cyclophosphamide, mycophenolate mofetil, azathioprine and ciclosporin) (p = 0.003 at V0, p &lt; 0.001 at VL) and intravenous methylprednisolone (p &lt; 0.001 at V0 and VL) compared to aSLE patients.

Conclusion
A higher proportion of jSLE patients have fever, lymphadenopathy, hypocomplementemia, or more active disease requiring greater use of immunosuppressants compared to aSLE patients. Early diagnosis and treatment of jSLE may prevent development of major organ involvement, in particular renal and neuropsychiatric.
Disclosure
B.Y. Thong: None. Y. Khong: None. X. Lim: None. H. Howe: None.
OA16 Identification of surrogate serum proteomic biomarkers associated with ultrasound power Doppler in psoriatic arthritis
Authors: Hum Ryan M , Nair Nisha , Ling Stephanie F , Barton Anne , Ho Pauline , Plant Darren 
Published: April 2023

Abstract

Background/Aims
An area of key unmet need in psoriatic arthritis (PsA) is the identification of biomarker(s) which predict those likely to respond to a specific therapy; in order to achieve that, an objective measure of disease activity would be ideal. Ultrasound power Doppler (PD) is a semi-quantitative measure of inflammation. However, ultrasound is time-consuming and requires specific expertise, whereas a blood-based surrogate biomarker of PD would be easier to apply clinically, and could serve as an objective outcome measure of response. Our aim is to identify proteomic biomarkers associated with PD in PsA patients.

Methods
Twenty-six patients with PsA (fulfilling CASPAR criteria) were recruited prospectively. All underwent 66-joint ultrasound examination and presence of PD was recorded. There were 7 patients without PD(-) and 19 with PD(+) detectable in at least 1 joint. Proteomics data for 1,073 proteins were generated using sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH MS). Proteins with high levels of missing data were filtered (&gt;30%) followed by random forest analysis. Differentially expressed proteins (DEPs) based on PD status were identified. Protein-protein interaction network analysis was performed using the search tool for retrieval of interacting genes (STRING), Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO).

Results
Following pre-processing, 553 proteins were available for analysis. Seventeen DEPs were identified (p-values &lt;0.05) (Table 1). Among these, ERAP2, an enzyme involved in MHC-I ligand processing and a known risk factor for inflammatory diseases, had the largest fold change (-0.64 95%CI -1.20 to -0.07, p = 0.03). Network analysis revealed that the 17 DEPs were significantly enriched (p &lt; 0.001) in the PD+ group. KEGG pathway analysis identified the association of the DEPs in leukocyte transendothelial migration (strength 1.5 FDR=0.04). GO analysis of the DEPs revealed involvement in immunoglobulin receptor binding (strength 2.28 FDR=0.03).

Conclusion
We identified several potential serum proteomic biomarkers correlated with disease activity, as assessed by the presence of PD, in PsA; these provide insights into the biological mechanisms underlying synovitis in PsA. Validation in a larger cohort and functional studies are required to determine the role of these proteins in mediating inflammation in PsA.
Disclosure
R.M. Hum: None. N. Nair: None. S.F. Ling: None. A. Barton: None. P. Ho: None. D. Plant: None.
OA30 Systemic sclerosis and cancer in the UK: an epidemiological analysis using the Clinical Practice Research Datalink
Authors: Pauling John D , Snowball Julia , McHugh Neil , McGrogan Anita 
Published: April 2023

Abstract

Background/Aims
After cardiopulmonary disease, cancer accounts for the highest proportion of deaths in systemic sclerosis (SSc), exceeding deaths attributed to renal disease and/or infection. Few population-based studies have assessed the burden of cancer in SSc. The present study investigated the association between cancer and SSc using the Clinical Practice Research Datalink (CPRD).

Methods
A validated case ascertainment strategy using combinations of diagnostic Read codes was applied to identify SSc patients in the CPRD with &gt;12 months of data within the time period 01/01/1998 to 31/12/2017. A cohort study design examined cancer occurrence following a diagnosis of SSc. Patients with SSc were matched to six non-SSc comparators by age, sex and GP practice using incident density sampling. Prevalent and incident cases of SSc were analysed separately. Information on date and type of diagnosis of cancer was recorded. Descriptive statistics and Cox analyses determined hazard ratios for cancer occurrence.

Results
From 10.1 million individuals in the CPRD, 1,588 of cases of SSc were identified (85.3% female). We identified 206 cancers that occurred following a diagnosis of SSc (116 in prevalent cohort and 90 amongst incident cohort) (Table). The three commonest cancers were mucocutaneous (4.5%), lung (2.1%) and breast (1.9%). Lung cancer was significantly more common in SSc (Table). Incidence of cancer was higher in SSc (17 vs. 13.8 per 1000 person years) with adjusted hazard ratios of 1.41 (95% CI 1.14-1.75) for prevalent cases and 1.32 (95% CI 1.04-1.67) for incident SSc cases. We did not identify a strong relationship between cancer occurrence and SSc onset. Incidence of cancer increased with age at SSc diagnosis and was higher in males. Death from any cause at 6 months was higher in patients with SSc and cancer.

Conclusion
We have identified an increased risk of cancer occurrence (primarily mucocutaneous and lung) in patients with SSc from the UK, particularly amongst males and patients with higher age at SSc diagnosis. These findings could support screening recommendations for cancer in SSc.
Disclosure
J.D. Pauling: Consultancies; Astra Zenaca, Janssen, Permeatus Inc., Sojournix Pharma, Boehringer Ingelheim. Honoraria; Janssen. Member of speakers’ bureau; Janssen. J. Snowball: None. N. McHugh: None. A. McGrogan: None.
P015 Rheumatology advice lines: how to manage rising demand and limited capacity?
Authors: Hider Samantha , Brownfield Ann , Doe Rebecca , Dutta Shouma , Ryan Sarah 
Published: April 2023

Abstract

Background/Aims
Advice lines services (ALS) are a key aspect of providing coordinated patient care in rheumatology. Demand for rapid access to specialist advice increased during the pandemic due to the disruption of routine outpatient services but it is not clear whether this demand is sustained. We aimed to investigate the changes in demand for ALS, how this varied pre/during COVID-19 and audit the effect upon response times. We also aimed to assess the impact of introducing an email advice service on demand.

Methods
We audited the number of advice line contacts of a single rheumatology department, serving a population of 500,000 people. The telephone adviceline is provided as an answer machine with an email advice service set up in April 2020. The outcome of each contact is recorded as a) advice only b) action required (e.g., prescription, blood test, GP letter) or c) required appointment (monitor/nurse/medical). We audited response times using the RCN guidelines of a two-day response1 as the gold standard.

Results
Demand for advice had been increasing pre-COVID with an average of 368 calls/month (1/1/19-1/7/19) to 420/month (1/7/19-31/12/19). Sixty percent were advice only calls but 27% required additional action. Response times met the audit standard in 97% of cases pre-COVID. During the first two months of COVID demand for advice services doubled, however demand continued to rise although outcomes were similar (Table 1). As the number of contacts increased the proportion of telephone contacts responded to within the audit standard fell. Numbers of email contacts were variable, but response times exceeded the audit standard.

Conclusion
This audit demonstrates the demand of adviceline services has continued to increase throughout the pandemic and beyond, impacting the ability of services to respond within a timely manner. Ongoing QI work is assessing mechanisms to manage increased demand (using healthcare support workers to triage calls) and investigating reasons for accessing ALS to ensure appropriate advice is available.
Disclosure
S. Hider: None. A. Brownfield: None. R. Doe: None. S. Dutta: None. S. Ryan: None.
P022 Successfully using video for DMARD and Biologic patient education
Authors: Penford Rian , Gwynne Catherine , Reith Angela , Wren Elaine , Mackay Kirsten 
Published: April 2023

Abstract

Background/Aims
Patients starting new medications were seen in the Rheumatology department in a F2F group session. This involved 4 nurse led clinics a week, (20-30 patients). It was an efficient way of counselling multiple patients with waiting times approximately 3 weeks. In 2020 the pandemic meant this was no longer possible. The switch to individual telephone education was time consuming.The aim of the digital solution was to educate patients safely, in the most efficient way possible. Delays in starting medication can have an adverse effect on achieving remission of disease and extended use of steroids.

Methods
Members of the Rheumatology team including Secretaries, Clinicians and Pharmacists met to discuss how best to implement this change. Scripts were written for 10 medication videos to reflect the safety advice and administration of each medication. The scripts are a representation of the paper information sent to the patients prior to video education. Patients are sent an email within (24/48hrs of being referred) with a link to the relevant medication video. We asked the patient to email us to say Yes or No that they wanted to start the new medication. Safety screening was completed by the nursing staff and Out Patient Pharmacy delivers the prescription to the patient.

Results
Audit figures May 2020 - April 2022 1038 patients were sent the video medication information. 69 of these patients requested a follow up telephone appointment. Patients satisfaction is recorded with a questionnaire and excellent satisfaction is maintained. Medication education clinics have been reduced from 4 to 1 per week to facilitate the 7% of patients requesting a further appointment. Time has been created to increase capacity for rapid access and follow up appointments.

Conclusion
Videos can be watched by patients friends and family.
FAQ’s e.g “I am taking antibiotics shall I stop my medication?” can be re-watched enhancing future safety. Supporting patient self management and lessening calls to the Rheumatology department.Video Medication Education has revolutionised our practice. Saving time and money whilst maintaining patient safety and satisfaction.
Disclosure
R. Penford: None. C. Gwynne: None. A. Reith: None. E. Wren: None. K. Mackay: None.
P063 COVID shielding stories: co-produced research to understand the voice of people living with arthritis and auto-immune disease
Authors: Sharp Charlotte A , Laidlaw Lynn , Fox Joyce , Sanders Caroline , Morris Rebecca , Dixon William 
Published: April 2023

Abstract

Background/Aims
Up to one-third of people with rheumatological conditions were required to ‘shield’ from COVID-19. This co-produced, qualitative research aimed to understand experiences of the shielding process and the impact of shielding upon people’s lives.

Methods
Adults who shielded due to rheumatological disease participated in audio-recorded interviews and focus groups (FGs). Framework analysis combined inductive and deductive approaches. Creative materials were collected. Two patient contributors proposed the study, are co-investigators, and conducted the research alongside a clinical academic and four-member patient advisory group. COREQ and GRIPP2 guidelines were followed. Full ethical approval was granted by the University of Manchester Research Ethics Committee (2021-11544-20348).

Results
Data were generated from 28 interview and 12 FG participants between October 2021--January 2022. 15 people contributed creative materials. Characteristics included 44/48 (85%) female, ages 18--75 years, non-white 10/48 (21%), all UK regions (Table 1). Corbin & Strauss’s theory, 'Three lines of work: Managing chronic illness', frames the findings. Shielding increased and shifted the burden of ‘illness work’ onto patients, e.g., in gaining access to vaccines and navigating risks and uncertainties due to COVID-19. ‘Life work’ was increased as participants struggled to access food and medicines. Participants’ self-identity was re-appraised in the context of their illness. Many feared for their lives because of their diagnosis for the first time, increasing ‘biographical work’. Participants’ perceived value to society changed over time: feeling equal to the general population at the first UK national lockdown; abandoned by society due to ‘freedom day’ and formal shielding's end. ‘Emotional work’ was added to ‘Three lines of work’. Shielding notification induced fear, stress, devastation, shock and disbelief, balanced by a feeling of being protected. Emotions experienced include anxiety, guilt, anger and frustration. Mental health problems were experienced, often for the first time. Many continued to shield beyond formal shielding's end.

Conclusion
This co-produced, qualitative research highlights experiences and impact of shielding including increased illness, life, biographical and emotional work. Clearer, personalised information would help shielders to understand their risk and vaccine response, informing re-integration into society.

Disclosure
C.A. Sharp: None. L. Laidlaw: None. J. Fox: None. C. Sanders: None. R. Morris: None. W. Dixon: Consultancies; WGD has received consultancy fees from Abbvie and Google, unrelated to this work.
P078 Bone health in men with prostate cancer on androgen deprivation therapy: audit and service development
Authors: Sheng Ziyan , Srivastava Puneet , Shah Jyoti , Yaqub Shahid , Laxminarayan Ramasharan , Ugur Antonia , Williams Simon , Broadhurst Sarah , Tipper Judith , Haynes Charlotte , Hui Michelle 
Published: April 2023

Abstract

Background/Aims
Androgen deprivation therapy (ADT) is commonly used in the treatment of prostate cancer. A significant complication of ADT use is osteoporosis. National and international guidelines recommend a fracture risk assessment (FRA) based on clinical factors and bone mineral density (BMD) to guide bone agent (BA) use and bone protection advice. We audit our current performance, and subsequently offer a novel interdisciplinary service to optimise patients’ bone health.

Methods
Retrospective hospital analysis of patients with metastatic prostate cancer or pre-radiotherapy seen in 2 hospitals over a 6-month period. Patients intended for &gt;6 months treatment were assessed against guideline standards and a retrospective FRA was performed.

Results
82 patients were captured. Age range 62 to 92, median age 77.3. 4.9% patients were already known to the osteoporosis service, but none had been referred for a bone health assessment with the commencement of ADT. Table 1 illustrates our performance against guidelines and the likely need for a BA in a post-hoc analysis at one site. As a result of the collaborative audit undertaken between the urology and osteoporosis services that demonstrated poor recognition of bone health in patients on ADT, the teams worked collaboratively to design a guideline for assessing and managing these patients. This included reviewing the information given to patients about the risk of ADT to bone health, resources that the urology team can signpost patients to, and the initiation of appropriate BA to be undertaken by an appropriately trained person/team.

Conclusion
ADT use can accelerate bone loss, therefore users need FRA and BMD assessments to appropriately guide management. Self-management to optimise bone health by patients can be improved by providing appropriate bone protection advice (regular exercise and adequate vitamin D and calcium intake). Bone health assessments in patients on ADT is a major unmet need that requires attention to minimise clinical risk to patients. The new assessment tool and management pathway in our Trust estimates 114 new patients annually requiring FRA with a maximum number of 372 DXA scans per year accounting for those requiring 2-yearly scans to monitor BMD until the age of 80.
Disclosure
Z. Sheng: None. P. Srivastava: None. J. Shah: None. S. Yaqub: None. R. Laxminarayan: None. A. Ugur: None. S. Williams: None. S. Broadhurst: None. J. Tipper: None. C. Haynes: None. M. Hui: None.