Primary closure versus Graham patch omentopexy in perforated peptic ulcer: A systematic review and meta-analysis.

BACKGROUND: There are different methods to repair a perforated peptic ulcer, the two most frequently used are the Graham patch omentopexy and the primary closure. Currently there is no high-level evidence to provide guidance of the optimal method of repair. The aim of this study is to compare the outcomes of the two methods so as to provide improved guidance for surgeons undertaking this repair. METHODS: A systematic review and meta-analysis was conducted including any study that compared Graham patch omentopexy with primary closure in adults. Embase, Medline, Cochrane and Google's search engine were searched. The primary outcome was breakdown of the repair resulting in bile leak and the secondary outcomes were mortality, operation time, wound infection and time to start oral intake. The meta-analysis was conducted using Review Manager Software version 5:4. Outcome data were reported as odd ratios and weighted mean differences with their 95% confidence intervals. RESULTS: Of the 229 studies identified, 6 were suitable for analysis, 4 were retrospective, one was a prospective cohort study and one was a randomized controlled trial. Meta-analysis showed no difference in occurrence of bile leak or mortality between primary closure and Graham patch omentopexy (OR 0.64; 95% (0.26-1.54) & 0.66; 95% (0.25-1.76) respectively). There was no difference in the rates of wound infection OR 0.65; 95% (0.4-1.05). The duration of the operation was shorter in the primary closure group by 5.6 min; 95% (-21 + 10.4). CONCLUSION: There was no difference in the clinical outcomes between the two modes of repair.

The Pathophysiology, Presentation and Management of Ischaemic Colitis: A Systematic Review.

There are currently no guidelines on the long-term management of patients after an episode of acute ischaemic colitis. Our aim was to review the literature on the pattern of presentation and the pathophysiology of this condition and to understand the current status of the acute and long-term management of ischaemic colitis. Furthermore, we aim to provide recommendations for the clinicians in regard to the acute and long-term management of ischaemic colitis. A review of the English literature over the last 15 years was performed using Embase and Medline. Search terms were ischaemic OR ischemic, colitis OR colon. Two reviewers screened the papers against pre-determined eligibility criteria. A senior consultant surgeon performed a final overview. Three hundred sixty-eight papers were identified on the initial search; 318 were irrelevant and 17 were conference abstracts; both were excluded. Thirty-three full articles were assessed for suitability; nine were further excluded. Twenty-four articles were included in the final analysis and cross-referenced against those listed in the systematic reviews. There is a large clinical heterogeneity in inclusion criteria (histological, radiological, endoscopic, surgical specimen). Twelve out of 24 articles included patients only based on histological diagnosis. The definition of right and left (or nonright) ischaemic colitis was variable based on whether hepatic or splenic flexure was used as the cut-off point. Five retrospective case series highlighted that patients with isolated right-sided ischaemic colitis had a worse prognosis than those with left-sided colitis (higher mortality, need for surgery, length of hospital stay). The overall recurrence was 9%. There is a need for a higher-level evidence to guide clinicians on the long-term management of patients following an episode of acute colonic ischaemia. Further evidence is required to determine whether right colonic ischaemia should be managed differently from left.

Prognostic Factors for Survival among Patients with Small Bowel Neuroendocrine Tumours Associated with Mesenteric Desmoplasia.

BACKGROUND: Small intestinal neuroendocrine tumours (SI NETs) represent 30-50% of small bowel neoplasms and are often associated with diverse fibrotic complications. Mesenteric fibrosis is a hallmark of SI NETs which may cause substantial morbidity and is considered an adverse feature. However, survival analyses in this group of patients are lacking. METHODS: The aim of this retrospective study was to determine the overall survival (OS) and factors affecting prognosis in a large cohort of 147 patients with SI NETs and radiological evidence of mesenteric desmoplasia from our centre. The severity of desmoplasia was graded radiologically and its effect on OS and long-term complications was assessed. The median follow-up period was 82 months. RESULTS: The median OS was 8.7 years (95% CI 6.8-9.9) with an overall 5-year survival of 71%. The univariate analysis demonstrated that an age >65 years, a liver tumour burden >50% of the hepatic parenchyma, carcinoid heart disease, chromogranin A levels >10 times the upper limit of normal, and urinary 5-hydroxyindoleacetic acid (5-HIAA) levels >5 times the upper limit of normal were poor prognosticators, while primary resection was associated with a longer OS. However, only an age >65 years and urinary 5-HIAA levels >10 times the upper limit of normal remained statistically significant after multivariate analysis. The severity of mesenteric desmoplasia did not seem to demonstrate a statistically significant relationship to OS or long-term outcomes. CONCLUSION: This study is the first comprehensive survival analysis of patients with SI NETs associated with mesenteric desmoplasia and has provided important and clinically relevant epidemiological data for this group of patients.

Laparoscopic mesh placement during inguinal hernia repair: a meta-analysis of two methods of repair.

BACKGROUND: There are several modifications in the technique for the placement of mesh during laparoscopic inguinal hernia repair. One of these is a slit on the mesh to surround the cord structures which proponents of it suggest that it decreases the recurrence rate due to better anchoring of the mesh and lower risk of displacement. There is only low-level evidence in current literature examining the two methods. The present study aimed to provide stronger evidence in establishing whether the slit mesh technique is superior to the non-slit mesh technique. METHODS: The reporting of this systematic review was guided by the standards of the preferred reporting items for systematic review and meta-analysis statement and registered with PROSPERO (ID: CRD42022300629). Eligible studies had to compare the two methods of mesh placement slit Vs nonslit in laparoscopic Inguinal hernia repair and also report on at least one outcome. The outcomes were expressed in odd ratios with their 95% confidence intervals. Where significant heterogeneity existed a random effects model was used otherwise a fixed effects model was used. RESULTS: Five studies met the criteria for inclusion in quantitative analysis. Overall, there were 10 (1.5%) recurrences in the slit group compared to 12 (2.5%) in the non-slit group OR 0.62, 95% CI (0.27-1.41). There was no difference in the incidence of post-operative bleeding (OR 1.21, 95%CI 0.4-3.66), seroma formation (OR1.5, 95% CI 0.81-2.76), or post-operative neuralgia (OR 0.98, 95%CI 0.11-8.92) between the two groups. CONCLUSION: There was no difference between the two methods.

The impact of the COVID-19 pandemic on elective laparoscopic cholecystectomy: A retrospective Cohort study.

The coronavirus disease 2019 (COVID-19) pandemic had a significant impact on elective surgery for benign disease. We examined the effects of COVID-19 related delays on the outcomes of patients undergoing elective laparoscopic cholecystectomy (LC) in an upper gastrointestinal surgery unit in the UK. We have analysed data retrospectively of patients undergoing elective LC between 01/03/2019 to 01/05/2019 and 01/04/2021 to 11/06/2021. Demographics, waiting time to surgery, intra-operative details and outcome data were compared between the two cohorts. Indications for surgery were grouped as inflammatory (acute cholecystitis, gallstone pancreatitis, CBD stone with cholangitis) or non-inflammatory (biliary colic, gallbladder polyps, CBD stone without cholangitis). A p value of <0.05 was used for statistical significance. Out of the 159 patients included, 106 were operated pre-pandemic and 53 during the pandemic recovery phase. Both groups had similar age, gender, ASA-grades and BMI. In the pre-pandemic group, 68 (64.2%) were operated for a non-inflammatory pathology compared to 19 (35.8%) from the recovery phase cohort (p < 0.001). The waiting time to surgery was significantly higher amongst patients operated during the recovery phase (p = 0000.1). Less patients had complete cholecystectomy during the pandemic recovery phase (p = 0.04). There were no differences in intraoperative times and patient outcomes. These results demonstrate the impact of COVID-19 related delays to our cohort, however due to the retrospective nature of this study, the current results need to be backed up by higher evidence in order for strong recommendations to be made.

Spontaneous bacterial peritonitis: a prospective Greek multicenter study of its epidemiology, microbiology, and outcomes.

BACKGROUND: Spontaneous bacterial peritonitis (SBP) is an ominous complication of decompensated cirrhosis. This study aimed to assess several epidemiological, clinical, microbiological and outcome characteristics in Greek patients with SBP, as no solid representative nationwide data of this type was available. METHODS: During a 3-year period, 77 consecutive patients with SBP (61 male; median age: 67 years; model for end-stage liver disease [MELD] score: 20), diagnosed and followed in 5 tertiary liver units, were prospectively recruited and studied. Various prognostic factors for disease outcome were studied. RESULTS: Thirty-eight patients had alcohol-related cirrhosis, 17 viral hepatitis, 6 non-alcoholic steatohepatitis, 6 autoimmune liver diseases, and 10 cryptogenic cirrhosis. Hepatocellular carcinoma (HCC) was present in 23 (29.9%), whereas 10 (13%) had portal vein thrombosis. The first SBP episode at baseline was community-acquired in 53 (68.8%), while in 24 (31.1%) was hospital-acquired, with predominant symptoms abdominal pain and encephalopathy. A positive ascitic culture was documented in 36% of patients in the initial episode, with almost equal gram (+) and gram (-) pathogens, including 3 multidrug-resistant pathogens. Significant factors for 6-month survival were: higher MELD score, previous b-blocker use, lower serum albumin, higher lactate on admission and need for vasopressors, while factors for 12-month survival were MELD score and lactate. For overall survival, higher MELD score and lactate along with HCC presence were negative predictive factors. CONCLUSIONS: MELD score, lactate, albumin, HCC and treatment with vasopressors were predictive of survival in SBP patients. In hospital-acquired SBP the prevalence of difficult-to-treat pathogens was higher.

Building a semantically annotated corpus of clinical texts.

In this paper, we describe the construction of a semantically annotated corpus of clinical texts for use in the development and evaluation of systems for automatically extracting clinically significant information from the textual component of patient records. The paper details the sampling of textual material from a collection of 20,000 cancer patient records, the development of a semantic annotation scheme, the annotation methodology, the distribution of annotations in the final corpus, and the use of the corpus for development of an adaptive information extraction system. The resulting corpus is the most richly semantically annotated resource for clinical text processing built to date, whose value has been demonstrated through its use in developing an effective information extraction system. The detailed presentation of our corpus construction and annotation methodology will be of value to others seeking to build high-quality semantically annotated corpora in biomedical domains.

Computed tomography colonography: a retrospective analysis of outcomes of 2 years experience in a district general hospital.

BACKGROUND: Colonoscopy is the gold-standard investigation for direct luminal visualization of the large bowel. Studies have shown the efficacy of computed tomography colonography (CTC) is equivalent to colonoscopy in both cancer and polyp detection. METHODS: A retrospective review of patients undergoing CTC from January 2013 to October 2014 was performed. Patient demographics, indication for investigation, computed tomography findings, optical colonoscopy findings and histology results were recorded. RESULTS: Seven hundred and fifty-eight CTC were performed. Three hundred and seventeen patients were male (42%) and 441 (58%) were female. Endoscopy was advised in 209 cases. One hundred and twenty (16%) were deemed suspicious for cancer of whom 96 (80%) had optical colonoscopy. A total of 12 colorectal cancers were detected. Potential polyps were noted in 58 cases (8%). Forty-four patients underwent endoscopy (75%) and 17 polyps confirmed (38%). Two patients had foci of invasive cancer histologically. Significant extracolonic findings were identified in 60%, including five cases of gastric carcinomas. The most common other findings were gallstones and hernias. CONCLUSION: The rate of colorectal cancer detection in this study was 2%. The rate of biopsy proven cancer was 10% following a suspicious colonogram. Endoscopic correlation was not obtained in 20% of cases of radiological suspicion. CTC is as efficacious as optical colonoscopy for colorectal cancer and polyp detection.

Exploring semantic deep learning for building reliable and reusable one health knowledge from PubMed systematic reviews and veterinary clinical notes.

BACKGROUND: Deep Learning opens up opportunities for routinely scanning large bodies of biomedical literature and clinical narratives to represent the meaning of biomedical and clinical terms. However, the validation and integration of this knowledge on a scale requires cross checking with ground truths (i.e. evidence-based resources) that are unavailable in an actionable or computable form. In this paper we explore how to turn information about diagnoses, prognoses, therapies and other clinical concepts into computable knowledge using free-text data about human and animal health. We used a Semantic Deep Learning approach that combines the Semantic Web technologies and Deep Learning to acquire and validate knowledge about 11 well-known medical conditions mined from two sets of unstructured free-text data: 300 K PubMed Systematic Review articles (the PMSB dataset) and 2.5 M veterinary clinical notes (the VetCN dataset). For each target condition we obtained 20 related clinical concepts using two deep learning methods applied separately on the two datasets, resulting in 880 term pairs (target term, candidate term). Each concept, represented by an n-gram, is mapped to UMLS using MetaMap; we also developed a bespoke method for mapping short forms (e.g. abbreviations and acronyms). Existing ontologies were used to formally represent associations. We also create ontological modules and illustrate how the extracted knowledge can be queried. The evaluation was performed using the content within BMJ Best Practice. RESULTS: MetaMap achieves an F measure of 88% (precision 85%, recall 91%) when applied directly to the total of 613 unique candidate terms for the 880 term pairs. When the processing of short forms is included, MetaMap achieves an F measure of 94% (precision 92%, recall 96%). Validation of the term pairs with BMJ Best Practice yields precision between 98 and 99%. CONCLUSIONS: The Semantic Deep Learning approach can transform neural embeddings built from unstructured free-text data into reliable and reusable One Health knowledge using ontologies and content from BMJ Best Practice.

Deep learning meets ontologies: experiments to anchor the cardiovascular disease ontology in the biomedical literature.

BACKGROUND: Automatic identification of term variants or acceptable alternative free-text terms for gene and protein names from the millions of biomedical publications is a challenging task. Ontologies, such as the Cardiovascular Disease Ontology (CVDO), capture domain knowledge in a computational form and can provide context for gene/protein names as written in the literature. This study investigates: 1) if word embeddings from Deep Learning algorithms can provide a list of term variants for a given gene/protein of interest; and 2) if biological knowledge from the CVDO can improve such a list without modifying the word embeddings created. METHODS: We have manually annotated 105 gene/protein names from 25 PubMed titles/abstracts and mapped them to 79 unique UniProtKB entries corresponding to gene and protein classes from the CVDO. Using more than 14 M PubMed articles (titles and available abstracts), word embeddings were generated with CBOW and Skip-gram. We setup two experiments for a synonym detection task, each with four raters, and 3672 pairs of terms (target term and candidate term) from the word embeddings created. For Experiment I, the target terms for 64 UniProtKB entries were those that appear in the titles/abstracts; Experiment II involves 63 UniProtKB entries and the target terms are a combination of terms from PubMed titles/abstracts with terms (i.e. increased context) from the CVDO protein class expressions and labels. RESULTS: In Experiment I, Skip-gram finds term variants (full and/or partial) for 89% of the 64 UniProtKB entries, while CBOW finds term variants for 67%. In Experiment II (with the aid of the CVDO), Skip-gram finds term variants for 95% of the 63 UniProtKB entries, while CBOW finds term variants for 78%. Combining the results of both experiments, Skip-gram finds term variants for 97% of the 79 UniProtKB entries, while CBOW finds term variants for 81%. CONCLUSIONS: This study shows performance improvements for both CBOW and Skip-gram on a gene/protein synonym detection task by adding knowledge formalised in the CVDO and without modifying the word embeddings created. Hence, the CVDO supplies context that is effective in inducing term variability for both CBOW and Skip-gram while reducing ambiguity. Skip-gram outperforms CBOW and finds more pertinent term variants for gene/protein names annotated from the scientific literature.

A Case Study on Sepsis Using PubMed and Deep Learning for Ontology Learning.

We investigate the application of distributional semantics models for facilitating unsupervised extraction of biomedical terms from unannotated corpora. Term extraction is used as the first step of an ontology learning process that aims to (semi-)automatic annotation of biomedical concepts and relations from more than 300K PubMed titles and abstracts. We experimented with both traditional distributional semantics methods such as Latent Semantic Analysis (LSA) and Latent Dirichlet Allocation (LDA) as well as the neural language models CBOW and Skip-gram from Deep Learning. The evaluation conducted concentrates on sepsis, a major life-threatening condition, and shows that Deep Learning models outperform LSA and LDA with much higher precision.

Seventy-six-year-old woman with an unusual anatomy of the left ureter.

We present a case of a 76-year-old woman, who attended with features suggestive of renal colic; however on imaging, she was found to have a right pelvic kidney and a left-sided uretero-sciatic hernia (USH), identified on CT urography (CT urogram). She was managed conservatively as she had a normal renal function and reported no symptoms in follow-up appointments. USH are rare hernias, where the ureter herniates through the sciatic foramen. Patients might present with sepsis in which case they require emergency stenting either anterograde or retrograde or with pain in which a less urgent approach can be followed and plan for surgery. Our literature review only identified a small number of similar cases, and the most successful treatment method for those symptomatic patients who required a procedure was the surgical repair.

The BioHub Knowledge Base: Ontology and Repository for Sustainable Biosourcing.

BACKGROUND: The motivation for the BioHub project is to create an Integrated Knowledge Management System (IKMS) that will enable chemists to source ingredients from bio-renewables, rather than from non-sustainable sources such as fossil oil and its derivatives. METHOD: The BioHubKB is the data repository of the IKMS; it employs Semantic Web technologies, especially OWL, to host data about chemical transformations, bio-renewable feedstocks, co-product streams and their chemical components. Access to this knowledge base is provided to other modules within the IKMS through a set of RESTful web services, driven by SPARQL queries to a Sesame back-end. The BioHubKB re-uses several bio-ontologies and bespoke extensions, primarily for chemical feedstocks and products, to form its knowledge organisation schema. RESULTS: Parts of plants form feedstocks, while various processes generate co-product streams that contain certain chemicals. Both chemicals and transformations are associated with certain qualities, which the BioHubKB also attempts to capture. Of immediate commercial and industrial importance is to estimate the cost of particular sets of chemical transformations (leading to candidate surfactants) performed in sequence, and these costs too are captured. Data are sourced from companies' internal knowledge and document stores, and from the publicly available literature. Both text analytics and manual curation play their part in populating the ontology. We describe the prototype IKMS, the BioHubKB and the services that it supports for the IKMS. AVAILABILITY: The BioHubKB can be found via http://biohub.cs.manchester.ac.uk/ontology/biohub-kb.owl .

Transient quadriceps paresis following cocaine use.

A 31-year-old man presented with bilateral thigh muscle paralysis several hours after intranasal cocaine use. His blood results showed a creatine kinase (CK) level of 3447 u/L and a normal renal function. He made a marked recovery in just 2 h following the intravenous normal saline 0.9%, and was able to walk. He was discharged home the next day.

Brainstem tuberculosis.

We present a case of a 38-year-old-man who presented with 1-week history of developing weakness of peripheral and cranial nerves. His MRI scan of the brain showed a large cavitating lesion at the brainstem and two further lesions of the right cerebral cortex and his CT chest showed features of old tuberculosis (TB). The identification of acid-fast bacilli was confirmed by analysis of bronchoalveolar lavage taken during bronchoscopy. He was started on anti-TB medications and repeat MRI 3 months later confirmed shrinkage of the cavitating lesion.

Biliary contents in the chest drain tube: a finding not to ignore.

A 45-year-old man presented with a left-sided pneumothorax following an episode of forceful vomiting. His chest drain revealed biliary contents and his CT chest with oral contrast confirmed the diagnosis of oesophageal rupture. He was transferred for surgical repair to a tertiary centre. Biliary contents within a chest tube are an important clinical finding and should raise suspicion of Boerhaave's syndrome. Any delays should be avoided due to the high mortality.

Improving outcome following life-threatening gastrointestinal bleeding not amenable to endoscopy in an ASA grade 5 patient: lessons learned.

We present a 74-year-old woman, who developed massive haematemesis and hypovolaemic shock. Her management was challenging, as the bleeding site could not be identified during oesophagogastroduodenoscopy, she was not fit for a general anaesthesia and not able to lie flat due to heart failure, caused by pericardial effusion. She underwent an emergency laparotomy and gastrotomy under a combined thoracic epidural and lumbar spinal regional anaesthesia in a sitting position, 45° to horizontal plane. The bleeding site was identified as a Dieulafoy lesion on the posterior wall of the stomach and was controlled by under running the lesion. She had an uneventful recovery and is symptom-free post-surgery for a year at present.

Concurrent caecal and transverse colonic tuberculosis masquerating synchronous colonic carcinoma.

We present a 46-year-old Somalian woman, who attended our hospital, with 1 week history of worsening epigastric pain and vomiting, worse after eating on a background of 3 months history of four stones loss of weight, malaise and decreased appetite. CT scan of the abdomen revealed an annular 10 cm long mass of the right transverse colon with a second mass of the caecum raising concerns of a synchronous colonic cancer. She underwent an extended right hemi-colectomy due to the development of obstruction from the transverse colon lesion. The histology revealed caseating, transmural granulomatous inflammation consistent with tuberculosis. She had an uneventful recovery and was discharged on the tenth postoperative day on antituberculosis (anti-TB) medications. She reports complete resolution of her symptoms 4 months after discharge.