bluuebunny/crossref_metadata_2025_split huggingface dataset:
TCRconv: predicting recognition between T cell receptors and epitopes using contextualized motifs
Authors: Jokinen Emmi , Dumitrescu Alexandru , Huuhtanen Jani , Gligorijević Vladimir , Mustjoki Satu , Bonneau Richard , Heinonen Markus , Lähdesmäki Harri 
Published: December 2022

Abstract

Motivation
T cells use T cell receptors (TCRs) to recognize small parts of antigens, called epitopes, presented by major histocompatibility complexes. Once an epitope is recognized, an immune response is initiated and T cell activation and proliferation by clonal expansion begin. Clonal populations of T cells with identical TCRs can remain in the body for years, thus forming immunological memory and potentially mappable immunological signatures, which could have implications in clinical applications including infectious diseases, autoimmunity and tumor immunology.

Results
We introduce TCRconv, a deep learning model for predicting recognition between TCRs and epitopes. TCRconv uses a deep protein language model and convolutions to extract contextualized motifs and provides state-of-the-art TCR-epitope prediction accuracy. Using TCR repertoires from COVID-19 patients, we demonstrate that TCRconv can provide insight into T cell dynamics and phenotypes during the disease.

Availability and implementation
TCRconv is available at https://github.com/emmijokinen/tcrconv.

Supplementary information
Supplementary data are available at Bioinformatics online.
Insights from incorporating quantum computing into drug design workflows
Authors: Lau Bayo , Emani Prashant S , Chapman Jackson , Yao Lijing , Lam Tarsus , Merrill Paul , Warrell Jonathan , Gerstein Mark B , Lam Hugo Y K 
Published: December 2022

AbstractMotivationWhile many quantum computing (QC) methods promise theoretical advantages over classical counterparts, quantum hardware remains limited. Exploiting near-term QC in computer-aided drug design (CADD) thus requires judicious partitioning between classical and quantum calculations.ResultsWe present HypaCADD, a hybrid classical-quantum workflow for finding ligands binding to proteins, while accounting for genetic mutations. We explicitly identify modules of our drug-design workflow currently amenable to replacement by QC: non-intuitively, we identify the mutation-impact predictor as the best candidate. HypaCADD thus combines classical docking and molecular dynamics with quantum machine learning (QML) to infer the impact of mutations. We present a case study with the coronavirus (SARS-CoV-2) protease and associated mutants. We map a classical machine-learning module onto QC, using a neural network constructed from qubit-rotation gates. We have implemented this in simulation and on two commercial quantum computers. We find that the QML models can perform on par with, if not better than, classical baselines. In summary, HypaCADD offers a successful strategy for leveraging QC for CADD.Availability and implementationJupyter Notebooks with Python code are freely available for academic use on GitHub: https://www.github.com/hypahub/hypacadd_notebook.Supplementary informationSupplementary data are available at Bioinformatics online.
BS O03 Nutritional Complications After LaparoscopicRoux-en-Y Gastric Bypass and One-AnastomosisGastric Bypass: A Comparative Systematic Review and Meta-Analysis
Authors: Salman Mohamed , Noureldin Khaled , Issa Mohamed , Khalid Sadaf , Tourkey Mohamed , Elsherbiney Mohammed , Gebril Mahmoud , Salman Ahmed , Shaaban Hossam , Barkat Tanzeela , Elhaj Mujahid , Elewa Ahmed 
Published: December 2022

Abstract

Background
This systematic review and meta-analysis were done to assess the incidence of nutritional complications at follow-up after one-anastomosis gastric bypass (OAGB) and Roux-en-Y gastric bypass (RYGB).

Methods
A systematic review and meta-analysis were carried out involving studies that compared the nutritional complications of Roux-en-Y gastric bypass (RYGB) and one-anastomosis gastric bypass (OAGB); these included the incidence of malnutrition as well as deficiencies of other nutritional elements, such as total protein, albumin, calcium, and iron. A comprehensive search strategy was implemented in PubMed, Embase, and the Cochrane Library. Effect sizes included the pooled odds ratios (ORs) and 95% confidence intervals
(95% CIs), as well as mean differences (MDs) and 95% CIs of the percentage total weight loss (%TWL) and excess weight loss percentage (%EWL).

Results
Thirteen studies were included (12,964 patients, 66.27% females, 53.82% underwent OAGB). At the longest follow-up period (≥3 years), OAGB was associated with significantly higher %TWL (MD=5.41%, 95%CI, 1.52 to 9.29) and %EWL (MD=13.81%, 95%CI, 9.60 to 18.02) compared to RYGB. However, OAGB procedures were associated with malnutrition (OR=3.00, 95%CI, 1.68 to 5.36, p&lt;0.0001), hypoalbuminemia (OR=2.38, 95%CI, 1.65 to 3.43, p&lt;0.0001), hypoproteinemia (OR=1.85, 95%CI, 1.09 to 3.14, p=0.022), anemia (OR=1.38, 95%CI, 1.08 to 1.77, p=0.011), and hypocalcemia (OR=1.78, 95%CI, 1.01 to 3.12, p=0.046). On subgroup analyses, the proportions of anemia and hypoalbuminemia remained significantly higher at longer follow-up periods and in studies published in Asia.

Conclusions
Despite the favorable weight loss profile, the unfavorable nutritional consequences of OAGB merit further investigations to explore the malabsorptive element, ethnic variation, and the role of the biliopancreatic limb length.
BS O08 How Safe is a One-Night Stay Protocol for Patients Undergoing Elective Bariatric Surgery?
Authors: Hill Sarah , Thomas Christophe , Mahawar Kamal , Courtney Michael 
Published: December 2022

Abstract

Background
The availability and popularity of bariatric and metabolic surgery (BMS) continues to increase worldwide and in turn so do the resources allocated to it. The last NBSR report (2020) demonstrated that 70% of patients were discharged on the second postoperative day and 80% left after the third day. An amended protocol was implemented within our Trust switching from a 2–3 night stay and reducing this to a planned one-night stay for a more efficient service. This review evaluates the safety and efficacy of a one-night stay protocol.

Methods
All patients undergoing BMS between two sets of dates were retrospectively identified from our local database, pre and post protocol change. Group A (old protocol, July-December ’19) and Group B (one-night stay protocol, July ’20-July ’21). Group B capture time was extended due to smaller numbers due to COVID. Data gathered included: Patient demographics (Age, Gender, ASA, Weight, BMI); operation; length of stay (LOS); 30-day complications, 30-day mortality, and 30-day readmission rates. Descriptive statistics and Chi-squared test were used to analyse results.

Results
Group A had 94 patient and Group B 149 patients. Patient demographics, weight and ASA were similar in both groups. There were significantly more RYGB in Group A whilst more OAGBs and sleeves in Group B: RYGB; (48[51%] vs. 30[20%]), OAGB; (32[34%] vs. 80[53%]), Sleeve; (13[14%] vs. 36[24%]). Median LOS reduced from 3 days to 1 day and mean LOS 3.2 days to 1.3 days.
In Group B, 115 patients (77%) were discharged on post-operative day 1 vs. 18 (19%) in Group A. In the 34 (23%) of patients that required stay beyond day 1 in Group B the most common reason was post-operative nausea and vomiting (n=8). Other frequent reasons were pain (n=5), low urine output/AKI (n=5) and not tolerating oral diet (n=4).
There were no statistically significant differences between groups for 30-day complication (6[6%] vs. 5[3%] p=0.4) or re-admission (4[4%] vs. 8[5%] p=0.9) rates. In sub-group analysis, there was no difference between operation type and LOS/complication rates. In a review of the readmissions, it was not felt any were avoidable and only 1/8 readmissions were within 48h of discharge - this patient already had an extended admission.

Conclusions
This study demonstrated that a planned one-night stay following BMS is both safe and effective; facilitating early patient discharges whilst having the necessary safety netting steps for those who require a require an extended period in hospital. The next step would be to explore the safety of day case surgery for selected patients undergoing sleeve gastrectomy.
OGBN O02 Animation supported consent before elective laparoscopic cholecystectomy
Authors: Doganay Emre , Wald David , Parker Sam , Hughes Frances 
Published: December 2022

Abstract

Background
Patient understanding of surgical procedures is often incomplete at the time they are performed, invalidating consent, and exposing healthcare providers to complaints and claims of failure to inform. Remote consultations, language barriers and patient factors can hinder an effective consent pathway. New approaches are needed to support communication and shared decision-making.

Methods
Multi-language digital animations explaining laparoscopic cholecystectomy were introduced at The Royal London Hospital for patients who attended for elective surgery (www.explainmyprocedure.com). Patients completed questionnaires on the day of their procedure both before and after introduction of the animations. We assessed patient-reported understanding of the procedure, its intended benefits, the possible risks, and alternatives to treatment in 72 consecutive patients, 37 before (no animation group) and after 35 after introducing the animations into the consent pathway (animation group). Patient understanding in the two groups was compared.

Results
The two groups were well matched in respect of age, sex and whether English was their first spoken language. The proportions of patients who reported they completely understood the procedure, its benefits, risks, and alternatives in the no animation group were 54%, 57%, 38% and 24% and in the animation group, 91%, 91%, 74% and 77% respectively; p&lt;0.01 for each comparison.

Conclusions
The integration of multi-language laparoscopic cholecystectomy video animations into the patient consent pathway was associated with substantial improvement in reported understanding of the procedure, benefits, risks, and alternatives to treatment. This approach can be applied across all surgical disciplines in a standardised manner in an era of accelerated elective work and remote consultations.
OGBN V08 Day case explantation of a magnetic lower oesophagal sphincter augmentation device due to dysphagia
Authors: Ghanem Ahmed , Ahmed Ahmed 
Published: December 2022

Abstract

Background
Although laparoscopic Nissen fundoplication remains the gold standard surgical treatment of gastroesophageal reflux disease (GERD), the magnetic Lower oesophageal sphincter augmentation device (LINX ®) has been suggested as a safe alternative for patients with uncomplicated and early-stage disease.
The LINX device is a small flexible band of interlinked titanium beads with magnetic cores designed to mimic the body's natural defence mechanism against reflux in patients with GERD.
Concerns about the LINX procedure comprise erosions and dysphagia.
The purpose of this video is to show a safe technique for the removal of the device and how to check the integrity of the oesophagus.

Methods
A video presentation explaining the needed investigations before LINX removal and showing a safe technique for removal of LINX device and how to check oesophageal integrity afterwards.

Results
The LINX device was explanted safely the patient went home afterwards.

Conclusions
Explantation of t the LINX device can be done safely as a day case with precautions. Take home message is to carefully dissect the capsule around each bead and to use OGD to exclude any oesophageal injury.
OGC O01 Delayed surgical Intervention after Chemoradiotherapy in Esophageal cancer (DICE) study
Authors: Chidambaram Swathikan , Sgromo Bruno , Maynard Nick , Markar Sheraz 
Published: December 2022

Abstract

Background
Chemoradiotherapy (CRT) is a core component of curative treatment for esophageal cancer for locally advanced esophageal cancer. Salvage esophagectomy is undertaken in patients who experience recurrent or residual cancer post-CRT. This study aims determine the impact of delayed surgical intervention following chemoradiotherapy on survival from oesophageal cancer.

Methods
This was an international, multi-center, retrospective cohort study involving seventeen tertiary international centers, including patients who received CRT followed by surgery between 2010–2020. In the main analysis patients were divided into four groups based upon the interval between chemoradiotherapy and surgery (0–50, 51–100, 101–200 and &gt;200 days) to assess the impact upon 90-day mortality and 5-year overall survival (OS). Multivariable logistic and Cox regression provided hazard rations (HRs) with 95% confidence intervals (95%CI) adjusted for relevant patient, oncological and pathological confounding factors.

Results
2,867 patients who underwent oesophagectomy after CRT were included. The mean age of the cohort was 63.2 (9.47) years. 79.7% were male; and 87.2% had an ASA grade ≥2. After adjustment for relevant confounders, prolonged interval following CRT was associated with an increased 90-day mortality; compared to 0–50 (reference), 51–100 days (HR=1.54, 95%CI 1.04–2.29), 101–200 days (HR=2.14, 95%CI 1.37–3.35) and &gt;200 days (HR=3.06, 95%CI 1.64–5.69). Similarly, a poorer 5-year survival was also observed with prolonged interval following CRT compared to 0–50 (reference), 101–200 days (HR=1.41, 95%CI 1.17–1.70) and &gt;200 days (HR=1.64, 95%CI 1.24–2.17).

Conclusions
Prolonged interval following CRT and esophagectomy is associated with increased 90-day mortality and poorer long-term survival. Patients must be carefully considered and counselled regarding surveillance and salvage esophagectomy following CRT.
OGC O09 The clinical utilisation of tissue imaging Mass Spectrometry as a diagnostic model for Oesophageal Adenocarcinoma
Authors: Patel Pranav , Kumar Sacheen , Doria Luisa , Soares Renata , Abbassi-Ghadi Nima , Takats Zoltan , Hanna George 
Published: December 2022

Abstract

Background
The prevalence of Oesophageal adenocarcinoma (OA) in the United Kingdom has steadily risen since the 1970's. The majority of patients present with advanced disease. Early diagnosis utilising point of care testing may enable an increase in the number of patients managed on a potentially curative pathway. Tissue Imaging Mass Spectrometry by Desorption Electrospray (DESI-MS) is one such tool to differentiate the abundance of lipids in OA. This work presents the novel use of Mass Spectrometry (MS) imaging to identify variations in lipid abundance between OA and normal oesophagus (NO).

Methods
Tissue was sampled from specimens dissected immediately post-resection from the tumour and at 5-centimetre intervals in the proximal NO. Forty-one unique patient OA and NO tissue samples were analysed in triplicate by DESI-MS tissue imaging to differentiate Glycerophospholipids. A total of 246 DESI-MS images were correlated with paired formalin fixed Haematoxylin and Eosin stained tissue slides, the current gold standard cancer diagnostic test. Principle component analysis utilising a supervised model classified tissue types with a significance of p=0.01. Receiver operator curves (ROC) were used to determine the diagnostic sensitivity and specificity of DESI-MS for the identification of adenocarcinoma.

Results
Tissue analysis confirmed unsaturated Phosphatidylglycerols and Phosphatidic acids were significantly more abundant in OA compared to NO (p&lt;0.001). Tissue analysis by a Partial Least Square (PLS) supervised linear regression model classified cancer and non-cancer tissue with a confusion matrix classification of 93.3% and 70.8% for OA and NO (Figure 1a-c). A diagnostic sensitivity of 85% and specificity of 88% was determined by ROC curve. The abundance of Phosphatidylglycerol and Phosphatidylserine decreased proportionally in analysed tissue sections at 5cm and 10cm from the primary tumour, as did the degree of lipid unsaturation.

Conclusions
This work presents a novel tissue imaging MS model to differentiate lipid abundance in OA. An abundance ratio of 1.17:1 (OA:NO) of unsaturated Phosphatidylglycerol was diagnostic of cancer by DESI-MS with a high sensitivity and specificity. This MS tissue analysis model has the potential to enable accurate point of care diagnostics for OA. In addition, we suggest oesophageal cancer induced perturbation of Glycerophospholipid metabolism may be a potential target for future chemotherapeutics.
BS P02 Sleeve gastrectomy and gastric bypass day surgery: outcomes and experience from a single centre
Authors: Katz-Summercorn Annalise , Shah Runil , Arhi Chanpreet , Musendeki Debbie , Fitt Irene , McGrandles Rosie , Zalin Anjali , Rashid Farhan , Adil Md Tanveer , Jain Vigyan , Mamidanna Ravikrishna , Jambulingam Periyathambi , Munasinghe Aruna , Whitelaw Douglas , Al-Taan Omer 
Published: December 2022

Abstract

Background
Internationally, day case Bariatric surgery has been shown to be safe, feasible and economically beneficial. However, it has not been widely adopted in the UK. It requires careful patient selection and a mature enhanced recovery programme. We report on the outcomes and lessons learned during our 2.5-year experience of day case laparoscopic sleeve gastrectomies (LSG) and Roux-en-y gastric bypass (RYGB) operations.

Methods
A retrospective analysis was performed of all patients who were selected as candidates for day case Bariatric surgery in a single-centre since October 2019. Patients were considered eligible if they had a BMI &lt;60, lived within 30 minutes of the hospital, were having primary surgery with no additional procedure and were not on CPAP. All patients received a nurse-led telephone assessment on day 1. Rates of successful discharge, patient demographics, readmission and outcomes were analysed.

Results
Thirty-nine patients were identified as suitable candidates for day case operations: 24 (62%) RYGB, 15 (38%) LSG. The mean BMI was 46.5; 85% female. The main reason for not being considered was the patient living &gt;30 minutes away. Overall, 18 (13 RYGB, 5 LSG; 46.2%) were successfully discharged on the day of surgery. Fifteen (38.5%) were discharged on the first post-operative day and 6 (15.4%) stayed two or more days. The commonest reasons for failed discharge were nausea/vomiting 6 (15.4%) and logistical issues e.g. operation in the afternoon 6 (15.4%). There was one readmission within 30 days (sealed leak from the gastro-jejunal anastomosis) but no returns to theatre.

Conclusions
We have successfully performed day case Bariatric surgery in our centre. However, it is a logistical challenge and to date has only been carried out successfully on a small number of patients. The main challenge being the vast catchment area for our tertiary centre. Further work is needed to better define the parameters for patient eligibility in order to safely offer this to more patients.
OGBN P05 Is there still a role for routine histology in cholecystectomies for benign disease?
Authors: Hamid Mohammed , Kershaw Marie , Bhakthavalsalan Resya , Shivamurthy Rishika , Davies Sian , Ahmed Zuhair 
Published: December 2022

Abstract

Background
A movement towards selective histology for benign gallbladder disease is evolving in the United Kingdom (UK). Studies propose the reliance on macroscopic features to identify incidental gallbladder cancer (IGBC). We aimed to investigate the rate of dysplastic gallbladder histology, the rate of subtotal cholecystectomy and identify any selection criteria for selective histology.

Methods
A retrospective observational study examining patients who underwent a cholecystectomy, amid the COVID-19 pandemic, between January 2020 and June 2021. This study was carried out in a large Trust in the West Midlands, UK. Multivariate logistical regression models were used to identify patient factors associated with IGBC and compare outcomes between total and subtotal cholecystectomy.

Results
There were 959 patients; 631 (65.8%) elective and 328 (34.2%) emergency cholecystectomies. Median age was 48 (35–59) years, and 724 (75.5%) patients were female. 27 (2.8%) patients had a subtotal cholecystectomy with worse post-operative complications (Clavien-Dindo grade 3+, OR 4.69, p=0.026), however no patient suffered a common bile duct injury. Eight (0.8%) patients had IGBC of which 6/8 were diagnosed as cholelithiasis on ultrasound. Five IGBCs had no macroscopic features. One patient needed further surgery and chemotherapy. Gallbladder polyps on ultrasound was the only patient factor associated with increased likelihood of IGBC (OR 14.49, p=0.014).

Conclusions
We support the current recommendation of the UK Royal College of Pathologists to routinely examine all cholecystectomies removed for benign disease, given that macroscopic features may be absent in IGBC and no clear patient factors to support a selective approach.
EGS P08 Endoscopic ultrasound-guided transmural gallbladder drainage – Who can benefit?
Authors: Boreham Zoe , Taylor Luke , Al-Khafaji Nadeem , Abbadi Reyad , Alexandridis Efstratios , Brown Oliver , Byrne Benjamin , Karteszi Hedvig , Skipworth James , van Laarhoven Stijn 
Published: December 2022

Abstract

Background
Endoscopic ultrasound-guided gallbladder drainage (EGBD, cholecysto-duodenostomy) is a safe alternative to percutaneous gallbladder drainage (PGBD) for treatment of acute cholecystitis, and avoids morbidity from external drains. However it may complicate attempts at future cholecystectomy. We aimed to identify a patient subgroup that would not be fit for surgery in the future and therefore should be considered for EGBD.

Methods
Patients with cholecystitis were identified retrospectively using hospital coding (2012–2022). Additional codes for cholecystectomy and percutaneous drainage were used to identify subgroups. Patient characteristics were also collected. Charleston comorbidity index (CCI) and APACHEII score were calculated where data were available. Statistical analyses were performed in R (Welch t-test). Data are displayed (mean LC vs mean NLC, p value).

Results
5653 patients with cholecystitis were identified (3765 LC, 66.6%). 53(0.94%) underwent PGBD. 23(43%) subsequently underwent LC. Patients in the LC group were younger (62.2vs74 p=0.002) and had a lower CCI (3.6vs5.9 p=0.001) compared to the non-operative (NLC) group. APACHE scores were calculated in 40/53 patients (16 LC, 24 NLC) and were similar between groups (8.5vs10.6 p=0.76). BMI was calculated in 41 patients (18 LC, 23 NLC) and was not significantly different (30.0vs30.6 p=0.19).

Conclusions
We have identified an older, more comorbid subgroup of patients with severe cholecystitis who are unlikely to be fit for surgery and could potentially benefit from definitive EGBD. There remains a place for PGBD in patients that will eventually become suitable for LC.