bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shuffle & untangle: novel untangle methods for solving the tanglegram layout problem
Authors: Nguyen Nghia , Chawshin Kurdistan , Berg Carl Fredrik , Varagnolo Damiano 
Published: February 2022

Abstract

Motivation
A tanglegram is a plot of two-tree-like diagrams, one facing the other, and having their labels connected by inter-tree edges. These two trees, which could be both phylogenetic trees and dendrograms stemming from hierarchical clusterings, have thus identically labelled leaves but different topologies. As a result, the inter-tree edges of a tanglegram can be intricately tangled and difficult to be analysed and explained by human readers. To better visualize the tanglegram (and thus compare the two dendrograms) one may try to untangle it, i.e. search for that series of flippings of the various branches of the two trees that minimizes the number of crossings among the inter-tree edges. The untanglement problem has received significant interest in the past decade, and several techniques have been proposed to address it. These techniques are computationally efficient but tend to fail at finding the global optimum configuration generating the least tangly tanglegram.

Results
We leverage the existing results to propose untanglement methods that are characterized by an overall slower convergence method than the ones in the literature, but that produce tanglegrams with lower entanglements.

Availability and implementation
One of the algorithms is implemented in Python, and available from https://github.com/schlegelp/tanglegram.
HAMdetector: a Bayesian regression model that integrates information to detect HLA-associated mutations
Authors: Habermann Daniel , Kharimzadeh Hadi , Walker Andreas , Li Yang , Yang Rongge , Kaiser Rolf , Brumme Zabrina L , Timm Jörg , Roggendorf Michael , Hoffmann Daniel 
Published: February 2022

AbstractMotivationA key process in anti-viral adaptive immunity is that the human leukocyte antigen (HLA) system presents epitopes as major histocompatibility complex I (MHC I) protein–peptide complexes on cell surfaces and in this way alerts CD8+ cytotoxic T-lymphocytes (CTLs). This pathway exerts strong selection pressure on viruses, favoring viral mutants that escape recognition by the HLA/CTL system. Naturally, such immune escape mutations often emerge in highly variable viruses, e.g. HIV or HBV, as HLA-associated mutations (HAMs), specific to the hosts MHC I proteins. The reliable identification of HAMs is not only important for understanding viral genomes and their evolution, but it also impacts the development of broadly effective anti-viral treatments and vaccines against variable viruses. By their very nature, HAMs are amenable to detection by statistical methods in paired sequence/HLA data. However, HLA alleles are very polymorphic in the human host population which makes the available data relatively sparse and noisy. Under these circumstances, one way to optimize HAM detection is to integrate all relevant information in a coherent model. Bayesian inference offers a principled approach to achieve this.ResultsWe present a new Bayesian regression model for the detection of HAMs that integrates a sparsity-inducing prior, epitope predictions and phylogenetic bias assessment, and that yields easily interpretable quantitative information on HAM candidates. The model predicts experimentally confirmed HAMs as having high posterior probabilities, and it performs well in comparison to state-of-the-art models for several datasets from individuals infected with HBV, HDV and HIV.Availability and implementationThe source code of this software is available at https://github.com/HAMdetector/Escape.jl under a permissive MIT license. The data underlying this article were provided by permission. Data will be shared on request to the corresponding author with permission of the respective co-authors.Supplementary informationSupplementary data are available at Bioinformatics online.
2 A Systematic Review on Clinical Efficacy and Cost-Effectiveness of Reverse Total Shoulder Arthroplasty or Hemiarthroplasty on Proximal Humeral Fractures
Authors: Zallipalli S.N. , Harish Kumar P. , Bethi R.R. , Kaur V. , Shejale N. 
Published: February 2022

Abstract

Introduction
Proximal humeral fractures (PHF) are one of the most challenging injuries to treat and recover from. Humeral fracture stems have become popular among individuals undergoing arthroplasty because of their superior ability to reduce and repair tuberosities. This study aims to determine better clinical, functional, and radiology outcomes and cost-effectiveness surgical management of PHF and Comparison of these outcomes among the surgical option.

Method
This systematic review includes the literature from the multi-database electronic search, i.e., Medline, PubMed, Embase, and web of science based on PRISMA guideline 2009. The data from the eligible literature meeting the study criteria were extracted and analysed.

Results
Reverse total shoulder arthroplasty (RTSA) provides better patients satisfaction and more improved functional outcomes when compared with shoulder hemiarthroplasty. Taking into consideration of healthcare perspective and payer perspective, RTSA was most cost-effective when compared to a hemiarthroplasty. Our work delivers significant baseline statistics about characteristics related to cost and outcomes of surgical approach for the management of PHF. RTSA can be considered as beneficial management of fracture Of PHF following the encouraging outcome of RTSA.

Conclusions
This systematic review provides favourable short to long-term functional outcomes of RTSA.
4 Cardiovascular Disease in Women with and Without Rheumatoid Arthritis
Authors: Mousa H. 
Published: February 2022

Abstract
Compare the incidence of coronary artery disease (CAD) in women with rheumatoid arthritis (RA) with that in women without RA, adjusting for traditional CAD risk factors (age, smoking, race, diabetes mellitus, hypercholesterolemia, hypertension, physical inactivity, family history, and obesity). A logistic regression analysis is used to control for confounders and other variables. To compare the incidence of coronary artery disease (CAD) in women with rheumatoid arthritis (RA) with that in women without RA, adjusting for traditional CAD risk factors (age, smoking, race, diabetes mellitus, hypercholesterolemia, hypertension, physical inactivity, family history, and obesity). A logistic regression analysis will be used to control for confounders and other variables. Data analysis is limited to all women who participated in the 2010 survey and of the 7844 who completed the 2010 Women's Health Survey, 7338 (93.5%) participants did not have rheumatoid arthritis, 310 (3.9%) have rheumatoid arthritis, and 196 (2.4%) were missing. Incidence rate of CAD is measured in both groups. Data analysis will be limited to all women who participated in the 2010 survey and of the 7844 who completed the 2010 Women's Health Survey, 7338 (93.5%) participants did not have rheumatoid arthritis, 310 (3.9%) have rheumatoid arthritis, and 196 (2.4%) were missing
6 Evaluation of Surgical Transfers Within the Neonatal Intensive Care Unit
Authors: Lee L. 
Published: February 2022

Abstract

Aim
To assess the outcomes of neonates born between 1st March 2013–7th July 2021 transferred out of the NICU at the RUH Bath for surgical investigation. To also undertake a study of neonates transferred with suspected necrotising enterocolitis looking at types of treatment received and long-term health outcomes.

Method
A retrospective search was undertaken evaluating records on the BadgerNet UK neonatal database. Outcomes following surgical diagnosis were then evaluated using Millennium, looking at discharge summaries, clinic notes and subsequent hospital admissions.

Results
93 neonates were identified as being transferred out for surgical investigation. 58% of patients were male (n = 54) and 42% female (n = 39). 70 were found to have at least one surgical diagnosis, with 80 surgical diagnoses identified. 60% were diagnosed with a congenital condition (n = 42). Overall mortality rate was 7.45%. 29 neonates were transferred out with suspected necrotising enterocolitis, 62% male (n = 18) and 38% female (n = 11). Average age at time of surgical transfer was 22 days. 48.3% were confirmed to have NEC (n = 14), 24% given an alternative diagnosis (n = 7) and 27.6% found to have normal investigation findings (n = 8). Average gestation of neonates with confirmed NEC was 30+0 weeks, average birthweight 1368g (3lb).

Conclusions
There are a broad range of surgical conditions amongst infants during the neonatal period, many associated with high levels of morbidity and mortality if left untreated. It is important to identify suspected surgical conditions as soon as possible through thorough assessment and multi-disciplinary team management amongst neonatologists, paediatricians, surgeons, and transfer teams; this ensures good prognostic outcomes.
8 Improving Management for Acute Cholecystitis and Biliary Pancreatitis – the ‘Hot Gallbladder Pathway’
Authors: Abdelsaid K. , Kam C.T. , Jayasankar B. , Balasubramaniam D. , Abdulaal Y. 
Published: February 2022

Abstract

Aim
There is a wide variation between National Health Service (NHS) hospitals in the management of patients with acute cholecystitis and biliary pancreatitis. 20–33% of patients will make repeat visits to hospital with gallstone-related symptoms before any surgical intervention performed. We established a ‘Hot Gallbladder Pathway’ with the aim for improving outcome and decreasing complications of these patients. The aim of this quality improvement project was to assess if a district general hospital (DGH) could provide a safe and effective ‘hot gallbladder’ service with a clear pathway.

Method
Quality improvement methods were used to integrate the ‘hot gallbladder pathway’ to manage patients with acute calculous cholecystitis and biliary pancreatitis. A prospective observational study with strict inclusion/ exclusion criteria and secure online data was conducted during a 13-month period. The data were then compared against existing National Institute for Health and Clinical Excellence (NICE) guidelines and further changes were recommended.

Results
We achieved almost 70% of the patients undergoing emergency laparoscopic cholecystectomy in both group of patients who met the pathway criteria within the expected time frame, compared with the pre-implementation result of 23% and national average of only 16% in England. None of the patients suffered from intraoperative complications or 30-day mortality.

Conclusions
A clear ‘hot gall bladder pathway’ is effective at improving care for patients requiring emergency laparoscopic cholecystectomy and potentially useful for other acute Trusts which their standard is below the NICE guideline.
11 Robotic Left Lower Sleeve Lobectomy with Bronchoplasty for the Removal of a Carcinoid Tumour
Authors: Tan G. , Dunning J. 
Published: February 2022

Abstract
Lung carcinoid tumours constitute approximately 1–2% of all pulmonary tumours. They are derived from enterochromaffin cells, which are also known as ‘Kulchitsky cells' and generally have indolent growth and development patterns. Carcinoid tumours are categorized as typical or atypical, depending on the number of mitoses per high power field and the presence of necrosis. In terms of management, surgical resection has been recognized to be the standard treatment for pulmonary carcinoid tumours. To our knowledge, the da Vinci system and robotic surgery have not been applied in sleeve lobectomies and bronchoplasty for the removal of carcinoid tumours in the United Kingdom. Therefore, we present a case of a sleeve lobectomy with bronchoplasty procedure for the removal of a carcinoid tumour located in the left lower lobe of the patient. The bronchus was repaired using a V-lock suture & Prolene sutures with the surgery performed using the da Vinci robotic surgical system.
13 Risk Documentation in Consent Form of Open Inguinal Hernia Repair
Authors: Hassan M. 
Published: February 2022

Abstract

Introduction
Inguinal hernia repair is amongst the most commonly performed general surgical operations. The high case load of groin repair in our hospital has the potential to have high risk of medical legal complications. The importance of discussing these potential complications with patients, allowing them to make informed decisions about their care, and clearly documenting them during the consent process, is clear.

Aim
We aimed to assess the quality and consistency of consent forms for open inguinal hernia repairs with emphasis on the risks being documented.

Objectives
Measure the compliance of Trust consent forms with (RCS) and British Hernia Society (BHS) 2016 guidelines and European Hernia Society (EHS) International guidelines for Groin Hernia Management (2019).

Method
Retrospective consent form analysis was carried out for all (38) open inguinal hernia repairs done during July-September 2020. The documentation of 13 pre-determined risks, was analysed, some specific to open inguinal hernia repairs, others general surgical complications.

Results
A total of 38 Trust consent forms were audited. Infection (100%) and bleeding (95%) were the most commonly documented risks. The documentation of chronic infection/abscess formation (5%), numbness (60%), testicular atrophy (31%) and scarring (34%) all increased compared to the two previous audit phases, the latter two significantly so. Unfortunately, many of the risks audited (8/13) showed a decrease in compliance with documentation with only two of the examined risks meeting the standard or ‘partially’ meeting it. Notably, recurrence and damage to other structures documentation dropped by over 10% (17% drop and 31% drop, respectively).
14 NICE CG188; Hot Gall Bladder Pathway in Emergency General Surgery - Are We Following the Guidelines?
Authors: Abdelsaid K. 
Published: February 2022

Abstract

Aim
1 - To compare the current standard of practice to existing guidelines and to make appropriate changes. 2 - To set a clear pathway for referring patients to the ‘hot laparoscopic cholecystectomy’ pathway. 3 - Avoid inappropriate booking for laparoscopic Cholecystectomy for patients who are not fulfilling the criteria of Hot Gall Bladder Pathway. 4 - Avoid unnecessary delay in performing Laparoscopic Cholecystectomy in patient with Acute Cholecystitis and mild Biliary Pancreatitis.

Method
It was a retrospective audit of all the patients who underwent Laparoscopic Cholecystectomy through Hot Gall Bladder Pathway between 1st February 2019 to 1st March 2020.
We screened a total of 134 patients who had been included in this pathway, 36 patient excluded.
1- Acute cholecystitis with no associated organ dysfunction 63 patients
2- Mild Acute Biliary Pancreatitis 35 patients

Results
Mild Acute Biliary Pancreatitis who underwent Laparoscopic Cholecystectomy within index admission or within 2 weeks of diagnosis 69 % (25/35).
Acute cholecystitis with no associated organ dysfunction (mild or moderate; Tokyo guideline grade I or II) who underwent Laparoscopic Cholecystectomy within week of diagnosis 68.2 % (43/63).

Conclusions
20 Incidence of Acute Kidney Injury in Neck of Femur Fracture Patients During the COVID-19 Pandemic in Princess Royal Hospital, Telford
Authors: Alaguraja P. , Younas W. , Mabeza T. , Makam A. , Khaleeq T. , Reading J. 
Published: February 2022

Abstract

Aim
Patients undergoing surgical repair of neck-of-femur (NOF) fractures are at higher risk of acute kidney injury (AKI). NICE and BOAST have published guidelines to help prevent the occurrence of AKI, including adequate fluid resuscitation pre- and post-operatively. An audit was conducted during the COVID-19 pandemic to explore whether the department was adhering to NICE guidelines.

Method
AKI was defined, as per NICE Clinical Knowledge Summaries, as an increase in serum creatinine levels by 26 µmol/L or greater. Data was collected prospectively starting from December 2020 to February 2021 in the Princess Royal Hospital during the COVID-19 pandemic. All patients with NOFs were included and data on sex, age, comorbidities, and type of surgery were collected.

Results
In total, 32 patients were included in the audit with an average age of 82 years; of these, eleven patients had dynamic hip screws and eighteen patients had hemiarthroplasties. Five patients had chronic kidney disease, six patients had previous myocardial infarctions and thirteen patients had hypertension. Two patients (6.3%) were found to have an AKI post-surgery with increased creatinine levels of 27 and 28 µmol/L. Both had hypertension and underwent hemiarthroplasties.

Conclusions
Complications such as AKIs are reversible and preventable. Especially during the COVID-19 pandemic such complications can increase morbidity and mortality of patients suffering from NOF leading to longer hospital stays. The low rate of AKI following NOF repair in our Department of Trauma and Orthopaedic is attributable to adherence to NICE and BOAST fluid resuscitation guidelines.
22 Lessons Learned During COVID-19 Pandemic, a Worldwide Survey: Part 1 -Evolution of Global Neurosurgical Practice
Authors: Garg K. , Deora H. , Wellington J. , Tandon V. , Mishra S. 
Published: February 2022

Abstract

Aim
During the COVID-19 pandemic, many surveys have analysed the impact of the virus spreading on everyday medical practice, including neurosurgery. However, no one has examined the perceptions of neurosurgeons towards the pandemic, their life changes, and the strategies they implemented to deal with their patients in such a difficult time.

Method
From April 2021 to May 2021, a modified Delphi method was used to construct, pilot, and refine the questionnaire. The first part focused on the evolution of global neurosurgical practice during the pandemic. This survey was distributed worldwide among 1000 neurosurgeons. The responses were then collected and critically analysed.

Results
Outpatient department practices changed with a rapid rise in teleservices. 63.9% of respondents reported that they had changed their OT practices to emergency cases with occasional elective cases. 40.0% of respondents and 47.9% of their family members reported having suffered from COVID-19 at some time. 56.2% of the respondents reported having felt depressed in the last 1 year. 80.6% of the respondents found online webinars to be a good source of learning. 47.8% of respondents tried to improve their neurosurgical knowledge, while 31.6% spent extra time in research activities during the COVID-19 pandemic.

Conclusions
Progressive increase in operative waiting lists, preferential use of telemedicine, reduction in the tendency to complete stoppage of physical clinic services and reduction in the administration and application of PPE kits were evident across the world. Respondents’ age impacted how the clinical services and impacted mental health across the global neurosurgical fraternity.
24 Mediastinal Ectopic Parathyroid Adenoma Causing Malignant Hypercalcaemia in a Young Female - a Case Report and Review of Literature
Authors: Bell A. , Razzaq Z. , Mustafa H. , Redmond H.P. 
Published: February 2022

Abstract
Ectopic parathyroid tissue can pose difficulties in diagnosis and management of patients with hyperparathyroidism. Due to the embryological origins of the inferior parathyroid glands from the 3rd pharyngeal arch where they develop with the thymus; they can have variable anatomical locations, including the anterior mediastinum. While the incidence of ectopic parathyroid glands varies in the literature mediastinal parathyroid tissue is extremely rare. This anatomical variation has important diagnostic and surgical ramifications for patients and is an important topic for trainees in medical endocrinology, endocrine surgery, and cardiothoracic surgery to be aware of.
We present the case of a 22-year-old woman who presented as an emergency with severe hypercalcaemia. Who was subsequently found to have an ectopic mediastinal parathyroid adenoma. She underwent surgery within days of her initial presentation providing her with an immediate cure and restoring her calcium homeostasis. Despite diagnostic and operative challenges, combined care from our endocrine and cardio-thoracic surgical teams ensured an uneventful post-operative recovery for this patient.
33 ECGs in the Surgical Patient - a Review of Practice
Authors: Siva S. , Basu S. 
Published: February 2022

Abstract

Aim
To Identify if baseline admission ECGs are performed for all emergency surgical patients over the age of 50 being admitted directly to General Surgery from the community. Aim to have 100% of patients &gt;50 years to have admission ECGs.

Method
We undertook a retrospective audit analysing the following parameters:
** This Hospital offers an in-hours (0900-1630, weekdays) ECG service via the cardiac physiology department.
We Conducted 3 cycles of 1 month duration each to assess findings.
Interventions:

Results
Cycle 1–50% (8/16) patients had admission ECGs. 50% (8/16) within 2 hours.
Cycle 2–54% (12/21) patients had admission ECGs. 43% (9/21) within 2 hours.
Cycle 3–71% (17/24) patients had admission ECGs. 62% (15/24) within 2 hours.

Conclusions
We noted improvement in admission ECGs through our interventions. Reminder emails were deemed useful. Barriers identified in After-hours ECGs being done on time due to clinical priorities. We identified a potential role for ECG-trained health-care professionals. 0900–1630 ECG service deemed valuable to admitting doctors. ECG machines were reviewed and found satisfactory. Possible delays in treatment could not be analysed with data collected. Hence, there is further scope to look into outcomes of delayed/missed ECGs e.g., delayed surgery / missed or alternative diagnosis.
37 Risk Documentation in the Laparoscopic Cholecystectomy Consent Form
Authors: Hassan M. , Riad M. 
Published: February 2022

Abstract

Background
Laparoscopic cholecystectomy is one of the most common elective operations performed with a significant risk of complications. GMC guidance on consent clearly emphasises the process of informed consent and shared decision making. Failure to warn patients of a significant complication can lead to potential medico-legal implications. The effectiveness of the consent process is evidenced in fully completed consent form.

Aim
We aim to access the quality of the consent forms for Laparoscopic cholecystectomy at our institution with emphasis on the documented risks.

Objectives
Re-audit of quality of records of consent form documentation over one month period for laparoscopic cholecystectomy. To measure the compliance of Trust consent forms with GMC guidelines.

Method
Consent forms for all elective laparoscopic cholecystectomy procedures done between July and September 2020 were obtained and retrospectively analysed. The data was collected specifically from the consent forms. A total of 39 consent forms were audited.

Results
A total of 39 consent forms were audited. The majority of the consenting was done by registrars. As with the first phase, bleeding (100%), CBD injury (97.4%), bile leak (69.2%), infection (100%), damage to local structures (79.5%), VTE (94.9%) remained well documented in the written consent. Open conversion was present on 97.4% consent forms.
8 out of 16 risks audited showed a increase in compliance whereas 8 showed an decrease compared to the previous round of the audit phase. In particular, scarring, retained stones, pancreatitis, respiratory complications, diarrhoea, and cardiac complications showed a particularly low rate.

Conclusions
Risk documentation on the consent forms remains quite varied. Education combined with a standardised consent form and patient information leaflet will improve the overall quality of consent forms.