bluuebunny/crossref_metadata_2025_split huggingface dataset:
P311 Detection and characterisation of extra-intestinal manifestations of IBD in clinical office notes using natural language processing
Authors: Stidham R , Yu D , Lahiri S , Vydiswaran V 
Published: January 2020

Abstract

Background
Extra-Intestinal Manifestations (EIM) occur in nearly 40% of patients with IBD and impact both disease experience and therapeutic decision-making, but are not well captured by administrative codes. We aimed to pilot computational natural language processing (NLP) methods to characterise EIMs using consultant notes.

Methods
Subjects with a diagnosis of IBD were identified in a single-centre retrospective review of electronic health records (EHR) between 2014–2017. Gastroenterology (GI) notes were annotated by two reviewers for the presence and activity of EIMs. EIM concepts were identified using NLP methods leveraging UMLS libraries and hand-crafted features. EIM characterisation occurred within a ±25-word window around identified EIMs with classifications including inactive concepts (negated, historical, resolved) and active concepts (improved, worsened, active but unchanged). Decisions on EIM status when repeatedly referenced in a document used section-based weighting for status inference, with greatest to least weight ranking for assessment/plan, subjective, past history, exam, and other, respectively. EIM status was classified as ambiguous when multiple conflicting references were present within the same document of approximately equal weight. Model development and testing used an 80/20 dataset split.

Results
In 4108 unique IBD patients, 1640 (39.9%) had at least 1 EIM identified. The mean age was 41.9 years, 47.2% were male, and 27.0% had biologic exposure. A total of 1240 manually annotated documents (first GI notes) were comprised of 51.1% arthritis, 16.5% ocular, 16.2% psoriasis, with erythema nodosum (EN), pyoderma gangrenosum (PG), and hidradenitis suppurativa (HS) together comprising 16.2% of the cohort. NLP models performed well for correctly classifying both EIM presence and status in a testing set, with overall accuracy, sensitivity, and specificity of 91.2%, 92.9% and 81.8% across all EIMs in notes automatically classified as non-ambiguous (Table 1). NLP methods identified EIM status classification as ambiguous in 38.9% of cases.

Conclusion
NLP methods can detect and classify EIMs with reasonable performance and efficiency compared with traditional manual chart review. Though source document variation and ambiguity present challenges, NLP offers exciting possibilities for population-based research and decision support.
P312 Introduction of bowel ultrasonography for follow-up of paediatric inflammatory bowel disease: A single-centre experience
Authors: Lev Zion R , Focht G , Asayag N , Turner D 
Published: January 2020

Abstract

Background
Bowel ultrasonography (BUS) for imaging of inflammatory bowel disease (IBD) is increasingly recognised as a prominent non-invasive tool to supplement, and in some cases replace traditional endoscopic and imaging modalities, with high sensitivity and specificity. The increasing number of gastroenterologists trained to perform BUS has transformed BUS into a bedside tool to guide routine clinical decision making and accurately monitor response to treatment. However, this process is still in its infancy in paediatric IBD. We present here data on the first 2 years of implementation of BUS performed by a paediatric gastroenterologist (RLT) at the paediatric IBD centre at Shaare Zedek Medical Center in Jerusalem. We aim to describe trends, results and clinical implications of the US studies performed during this period.

Methods
The electronic medical record system was searched for all BUS studies performed on IBD patients by RLT as part of his weekly IBD clinic between 2017–2019. Studies performed on other caregivers’ patients were excluded to ensure uniform documentation and nomenclature. Findings were classified as normal (wall thickness &lt;3 mm), mild (wall thickening 3–4 mm and blood flow &lt; Limberg 3) or significant signs of inflammation (wall thickness ≥4 mm or 3–4 mm with Limberg ≥3). Charts were reviewed to assess the impact of BUS findings on clinical management.

Results
A total of 83 bedside BUS studies were performed on 55 IBD patients (42 with Crohn’s – CD) during the study period, with a mean age of 15.1 ± 3.7 years. Thirty-four had one study (23 with CD), 15 had two (13 with CD) and 6 had three or more (all with CD). Overall, 32 studies were normal, 20 showed mild findings and 30 showed significant inflammation. Four studies found stenosis and one showed an abscess. Follow-up studies of initially active disease showed 10/16 (63%) with improvement, including 9/16 (56%) with sonographic remission. 22/83 (27%) studies were felt upon review to have had a direct impact on clinical decision-making. These included decisions not to switch therapy due to normal BUS despite symptoms, admission due to discovery of an abscess, decision to escalate therapy due to lack of sonographic improvement, and decision to continue adalimumab in the presence of a stricture due to favourable prognostic characteristics as per the CREOLE study.

Conclusion
Bedside BUS is a practical and useful tool that can be integrated into a paediatric IBD clinic, with the ability to provide relevant information in real-time and thus impact on day-to-day patient management.
P318 Artificial intelligence of the neural network-assistant for differential diagnosis of IBD
Authors: Skalinskaya M , Bakulin I , Skazyvaeva E , Rasmagina I , Mashevskii G , Shelyakina N , Ivanova K , Berest D 
Published: January 2020

Abstract

Background
Due to the lack of a ‘gold standard’ in the diagnosis of IBD the differential diagnosis between ulcerative colitis and Crohn′s disease can be very difficult. Verification of diagnosis of IBD takes a long time in majority of cases.

Methods
We have created an artificial neural network (ANN) of the multilayer perceptron type using the Neural Network Toolbox application from the MATLAB application package. Three types of images were used to train the ANN: the norm of the endoscopic picture of the colon, the endoscopic pictures of UC and CD. The first stage is the training of an artificial neural network to distinguish the presence or absence of pathology (29 images of the ‘normal colon’, 14 images of the CD, and 15 - UC). The second stage was to train the ANN to recognise the various forms of IBD. The network was trained on an array of 124 images (62 images of each class of pathologies). Each image was previously converted to the grayscale mode and then into a matrix of pixels. A vector with the number of elements equal to the size of the image was fed to the input of the perceptron.

Results
To solve the task of identifying the pathology a perceptron was built with 32,2784 input neurons, 10 hidden neurons and 2 output neurons which represent the conclusion that the image belongs to one of the two classes: norm or pathology. To solve the problem of differentiating CD and UC a perceptron was created with 364500 input neurons (this value was determined by the image resolution) and 2 output neurons representing the conclusion that the image belongs to one of the two classes: UC or CD. The best result in differentiation of pathology was shown by the ANN of MP 364500 type: 364500-20-2: 2, which total accuracy of recognition was 96,8%. The average accuracy of the developed model was 92.6%. However, in the control sample, the accuracy was 84.2%. This fact indicates that the model should be taught on more images. In addition to the ‘accuracy’ criterion, the ‘completeness’ parameter was used to evaluate the system. ‘Completeness’ for recognition of the image of the norm was the highest and equal to 1, for UC the criterion of ‘completeness’ was 0.89. The lowest ‘completeness’ was obtained when recognising the image of the CD (0.67).

Conclusion
ANN type MP 364500: 364500-20-2: 2 has shown the best results in the set targets. Efficiency in pathology recognition was 96.8%. The efficiency of the created ANN in solving the problem of recognition of different forms of IBD (UC/CD) can be described by the following parameters: specificity (Sp) −78.2%, sensitivity (Se) - 93.1%, accuracy (Ac) - 85,7%. The obtained ANN can be used to solve the problems of classification of endoscopic images of the intestine for the presence of IBD and for differential diagnosis.
P321 Prognosis of intestinal Behcet’s disease according to the Korean consensus-based diagnostic algorithm
Authors: JOO Y Y , Lee B I , Kim S J , Lee H H , Kim J S , Park J M , Cho Y S , Lee K M , Kim S W , Choi H , Choi M G 
Published: January 2020

Abstract

Background
Since the consensus-based diagnostic algorithm for intestinal Behcet’s disease (iBD) was proposed by the IBD Study Group of the Korean Association for the Study of Intestinal Diseases, there were few studies regarding the prognosis of iBD according to the diagnostic algorithm.

Methods
We reviewed the medical records of patients who had ileocecal ulcers with clinical impression of iBD from March 1986 to August 2019 in Seoul St. Mary’s Hospital and evaluated factors at the time of diagnosis which were related with adverse events (AEs, major operation or admission from iBD) and disease-free survival (DFS).

Results
Among 204 eligible patients, a total of 163 were included in the study after exclusion of 41 patients with ileocecal ulcers from other disorders. The male-to-female ratio was 1:1 and the mean age at the time of diagnosis was 48.9 ± 15.9. The number of definite, probable, suspected, and non-diagnostic iBD was 18 (11.0%), 64 (39.3%), 37 (22.7%), and 44 (27.0%), respectively. Patients with definite, probable, and suspected iBD developed more AEs compared with patients with non-diagnostic iBD (p = 0.026). After exclusion of patients with non-diagnostic iBD, univariate analysis showed accompanying haematologic disorders, haemoglobin &lt;10 g/dl, fever, colonic involvement, and hypoalbuminemia (&lt;3.0 g/dl) were significantly related to the development of AEs (all p &lt; 0.05). Multivariate analysis revealed accompanying haematologic disorders, haemoglobin &lt;10 g/dl, fever, and colonic involvement were significantly associated with development of AE (all p &lt; 0.05). Poor DFS was significantly associated with accompanying with haematologic disorders, haemoglobin &lt;10 g/dl, and colonic involvement (p &lt; 0.001, p = 0.022, and p = 0.034) in univariate analysis. Only haemoglobin &lt;10 g/dl was significant in multivariate analysis.

Conclusion
Patients with definite, probable, and suspected iBD have a poor prognosis compared with patients with non-diagnostic iBD. Accompanying with haematologic disorders, anaemia, fever, and colonic involvement at the time of diagnosis are poor prognostic factors in patients with iBD.
P344 Effectiveness of ustekinumab in refractory Crohn’s disease: A real-life experience in a tertiary referral centre
Authors: Truyens M , Geldof J , Dewitte G , Glorieus E , Hindryckx P , Lobaton Ortega T 
Published: January 2020

Abstract

Background
Ustekinumab (UST) is increasingly used in Belgium for moderate to severe Crohn’s disease (CD). The aim of the current study was to describe the real-life experience with UST in our tertiary centre.

Methods
A retrospective study was performed in patients with CD who were started on UST between December 2017 and August 2019. All patients received an initial intravenous (IV) dose of 6 mg/kg body-weight, followed by 8-weekly 90 mg subcutaneous UST. The clinical and endoscopic response was assessed by the physician after induction and during the maintenance phase.

Results
In total, 67 patients were included, of which the majority was refractory to anti-TNF and/or vedolizumab (Table 1). The median duration of treatment was 15 months (IQR 7–25). The clinical and endoscopic response is shown in Table 2. UST was discontinued in 16 patients (23.9%) after a median of 27.5 weeks (IQR 12.3–52.8). Reasons for discontinuation were a loss of response (LOR), including 5 patients who were in need of surgery (n = 10), primary non response (n = 3), malignancy (n = 1), adverse event (n = 1) and patients’ wish (n = 1).
In 29 patients (43.3%) optimisation of UST was necessary due to partial response (n = 13) or due to LOR (n = 16). The optimisation consisted of an IV re-induction in 2 patients, shortening of the dosage interval in 16 patients and a combination of both in 11 patients. The effect of optimisation could be assessed in 22 patients: 10 patients regained a good clinical response and 5 patients attained clinical remission after optimisation. In 7 patients UST was stopped despite optimisation, most often due to persistent LOR.

Conclusion
In this tertiary population of refractory CD patients, treatment with UST resulted in a clinical response in more than 70% of patients. Of note, 43.3% needed optimisation, with a good clinical response in almost half of the cases. The endoscopic response in this preliminary analysis was modest.
P346 Single-centre experience of ustekinumab: Therapeutic drug monitoring in Crohn’s disease patients
Authors: Liefferinckx C , Fassin M , Thomas D , Minsart C , Cremer A , Amininejad L , Tafciu V , Wambacq V , Van Gossum A , Franchimont D 
Published: January 2020

Abstract

Background
Therapeutic drug monitoring (TDM) is a diagnostic tool in the monitoring of anti-TNF therapies. Yet, the benefit for TDM of new biologics such as ustekinumab (USK) is still controversial in real-world experiences.

Methods
This monocentric retrospective study aims to correlate USK trough levels (TLs) with clinical and endoscopic data. All patients have given written consent to the Biobank (B2011/005). Endoscopic disease was defined as quiescent in absence of endoscopic lesions, mild disease in presence of few superficial ulcerations, moderate in presence of several ulcers and severe in presence of numerous deep ulcers and/or inflammatory stenosis. 313 serum USK samples from 67 Crohn’s disease patients were used to measure USK TL (USK ELISA, apDia) while 88 samples (at week 16, and before and after optimisation) were used to measure anti-drug antibody (ADA), using a drug-tolerant affinity capture elution anti-ustekinumab assay

Results
Demographic and baseline data of our population are presented in Table 1.

The median follow-up was 73 weeks (IQR 39–92). An optimisation due to loss of response was required in 44.8% of patients (n = 30) after a median time of 38 weeks (IQR 24–55). To evaluate the drug efficacy, an endoscopy was performed in 61% of cases at a median time of 35 weeks (IQR 27–47). TLs were 5.2 µg/ml (IQR 2.1–8.8), 1.7 µg/ml (IQR 0.3–4.3) and 2.6 µg/ml (IQR 0.6–4.1) at week 8, 16 and 24, respectively. TLs at week 8 were correlated to the induction IV dose administrated (r = 0.3, p = 0.03). At week 16, low TLs were associated with higher endoscopic activity in the follow-up (p = 0.02), although this was not the case at week 8 (p = 0.5) (Figure 1).

Patients not requiring an optimisation had higher TLs in maintenance than patients requiring optimisation (2.45 µg/ml (IQR 1.3–4.4) vs. 1.15 µg/ml (IQR 0.1–2.24), p = 0.008). Obviously, optimisation significantly increased TLs (1.15 µg/ml (IQR 0.1–2.24) vs. 6.6 µg/ml (IQR 2.3–11.3), p &lt; 0.001). ADA were undetectable in all the measured samples in maintenance.

Conclusion
This real-world experience confirms a drug exposure-endoscopic response relationship. Week 16 seems to be an appropriate time point to monitor drug exposure. Earlier USK TLs, at week 8, appear less valuable to be monitored due to the influence of initial IV dose. The absence of immunogenicity suggests that it is not a key driver in the loss of response.
P348 Clinical outcomes and response predictors of vedolizumab treatment for anti-TNF-failed patients with IBD in Korea: A prospective multicenter cohort study
Authors: Kim J , Yoon H , Lee K M , Jung S A , Park D I , Choi C H , Kim E S , Jung Y , Eun C S , Kim T O , Kang S B , Kim Y S , Seo G S , Lee C K , Im J P , Park S J , Byeon J S , Myung S J , Yang S K , Ye B D 
Published: January 2020

Abstract

Background
Vedolizumab (VDZ) inhibits gut lymphocyte trafficking by binding to α4β7 integrin, which can be effective for patients with Crohn’s disease (CD) or ulcerative colitis (UC). We aimed to investigate the clinical outcomes and response predictors of VDZ treatment for Korean patients with CD or UC, who were previously failed to anti-tumour necrosis factor (TNF) therapy.

Methods
Between August 2017 and November 2019, a total of 159 patients with CD (n = 81) or UC (n = 78) received a VDZ induction therapy from 16 centres and were prospectively enrolled. Of those, patients who were evaluated at week 14 after three induction doses of VDZ (week 0, 2, and 6) were analysed. The co-primary endpoints were corticosteroid-free clinical remission and endoscopic remission/response (for UC) at week 14. We also analysed predictors of corticosteroid-free clinical remission, persistence of vedolizumab and safety.

Results
A total of 153 patients were analysed (CD, 77 [50.3%]; male, 94 [61.4%]; median age, 40 years [range, 17–80]; median disease duration, 8.0 years [range, 0.1–38.0]). All patients had previously experienced failures to at least one anti-TNF agent (one, 105 [68.6%]; two, 44 [28.8%]; three, 4 [2.6%]). Corticosteroid-free clinical remission/response rates in CD and UC patients were 44.6%/51.8% and 39.4%/62.0%, respectively. In patients with UC, endoscopic remission and response rates defined by Mayo endoscopic subscore/ulcerative colitis endoscopic index of severity were 33.8%/14.1% and 55.4%/39.1%, respectively. Multivariate analysis revealed that a clinical response at week 6 were associated with a corticosteroid-free clinical remission at week 14 in both CD (Odds ratio [OR] 33.84, 95% confidence interval [CI] 6.25–183.31, p &lt; 0.001) and UC (OR 12.22, 95% CI 1.30–115.28, p = 0.029). In addition, UC patients with higher baseline levels of C-reactive protein (CRP) and faecal calprotectin were less likely to be in corticosteroid-free clinical remission (CRP &gt; 0.31 mg/dl: OR 0.05, 95% CI 0.00–0.60, p = 0.019; faecal calprotectin &gt; 2,000 μg/g: OR 0.04, 95% CI 0.00–0.93, p = 0.045). The cumulative probabilities of continuing VDZ after one year were 48.7% for CD and 65.7% for UC, respectively. During median 10 months of follow-up periods (range, 3–26 months), disease exacerbation was the most common adverse event (n = 73, 47.7%), followed by nasopharyngitis (n = 23, 15.0%) and arthralgia (n = 19, 12.4%).

Conclusion
In anti-TNF-failed Korean patients with CD and UC, VDZ induction therapy was effective with an acceptable safety profile. Early clinical response and higher inflammatory burden at baseline were associated with corticosteroid-free clinical remission after VDZ induction therapy.
P354 Objectively measured time spent sitting, standing upright, and stepping is associated with disease severity and faecal calprotectin in patients with ulcerative colitis
Authors: Raman M , Vallance J , Lyden K , Alana S , Ohland C , McCoy K , Kaur S , Panaccione R , Reimer R , Taylor L 
Published: January 2020

Abstract

Background
Sitting, lying down, standing upright, and stepping is predominant behaviours occurring throughout the 24-day, yet have not been explored in ulcerative colitis (UC). The purpose of this study was to explore whether objectively measured time spent sitting, lying down, standing upright, and stepping was associated with endoscopic and biomarker-based disease severity in UC patients.

Methods
Patients were recruited from the Foothills Medical Center in Calgary, Alberta. Each patient wore an activPAL™ inclinometer (PAL Technologies Limited, Glasgow, UK) for 7 days (minimum 4 days, and on at least one weekend day). Disease severity was measured using Mayo endoscopic subscore and classified as either normal/mild or moderate/severe. Stool samples were collected and faecal calprotectin (FCP), a measure of gut inflammation, was measured. Serum C-reactive protein (CRP)], a marker of systemic inflammation, was collected. Univariate analysis of covariance (ANCOVA) was used to examine associations between activPALTM behavioural variables, Mayo endoscopic subscore, FCP (&lt; or &gt;250 mg/g) and CRP (&lt; or &gt;5 mg/l). All models were controlled for age, gender, body mass index, and antibiotic use.

Results
21 patients (9 female, 12 male) consented to participate. Patients on average were 36 years of age (SD=8.9) and had a body mass index of 25.7 (2.4). For Mayo endoscopic subscore, 10 patients were normal/mild while 11 patients were moderate/severe. Mean FCP was 2288.6 (5453.9) and mean CRP was 4.9 (10.5). Per day, patients averaged 8443 (2731) steps, 497.6 (149.9) min sitting, 233.4 (72.9) min standing upright, and 536.3 (110.9) min lying down. Mayo endoscopic subscore was negatively associated with total number of steps (D=−3,331 steps, 95% CI: 5,450 to −1,212, p &lt; .01), trended toward decreased upright standing time (D = −108 min/day, 95% CI: −208.2 to −7.7, p = 0.09), and positively with total sitting time (D = 121.2 min/day, 95% CI: −23.5 to 266, p = 0.09). FCP was negatively associated with standing time (D = −102.4 min/day, 95% CI: −206.3 to 1.6, p = .05), trended toward decreased total number of steps (D=−1,956 steps, 95% CI: −4,482 to 569, p = .12), and was not associated with total sitting time (D = 63.8 min/day, 95% CI: −87.8 to 215.4, p = .38). CRP was not associated with any of the activPALTM variables. Time spent lying down was not associated with any UC outcomes.

Conclusion
There was an association between objective measures of daily activity behaviours including total steps, standing time, sitting time and UC biomarkers of disease activity. Future studies should continue to examine daily activity behaviours and UC health outcomes in larger sample sizes.