Variational Autoencoders for Feature Exploration and Malignancy Prediction of Lung Lesions

Lung cancer is responsible for 21% of cancer deaths in the UK and five-year survival rates are heavily influenced by the stage the cancer was identified at. Recent studies have demonstrated the capability of AI methods for accurate and early diagnosis of lung cancer from routine scans. However, this evidence has not translated into clinical practice with one barrier being a lack of interpretable models. This study investigates the application Variational Autoencoders (VAEs), a type of generative AI model, to lung cancer lesions. Proposed models were trained on lesions extracted from 3D CT scans in the LIDC-IDRI public dataset. Latent vector representations of 2D slices produced by the VAEs were explored through clustering to justify their quality and used in an MLP classifier model for lung cancer diagnosis, the best model achieved state-of-the-art metrics of AUC 0.98 and 93.1% accuracy. Cluster analysis shows the VAE latent space separates the dataset of malignant and benign lesions based on meaningful feature components including tumour size, shape, patient and malignancy class. We also include a comparative analysis of the standard Gaussian VAE (GVAE) and the more recent Dirichlet VAE (DirVAE), which replaces the prior with a Dirichlet distribution to encourage a more explainable latent space with disentangled feature representation. Finally, we demonstrate the potential for latent space traversals corresponding to clinically meaningful feature changes.Comment: 10 pages (main paper), 5 pages (references), 5 figures, 2 tables, work accepted for BMVC 202

Formation of nascent char structure during the fast pyrolysis of mallee wood and low-rank coals

The structural evolution of nascent chars during the fast pyrolysis of a wood and two low-rank coals was investigated in this study. Western Australian Collie sub-bituminous coal, Victorian Loy Yang brown coal and Western Australian mallee wood were pyrolysed in a wire-mesh reactor that is capable of providing rapid heating rates (up to 5000 K s−1) and accurate holding time (in increments of 10 ms) at peak temperature. FT-Raman spectroscopy was used to characterise the key structural features of raw fuels and nascent chars. The combined use of a wire-mesh reactor and a FT-Raman spectroscopy has given insights into the structural transformation from coal/biomass to nascent chars. There were insignificant changes in the aromatic ring systems of two coals during the initial fast heating from room temperature to 600 °C. During holding at 600 °C, the changes that occurred in ring systems for the three fuels were different. Mallee wood and Loy Yang coal underwent more changes than Collie coal. In addition, mallee wood had ring condensation during holding at 600 °C up to 30s. However, little growth in large aromatic rings of two coals was observed during holding at 600 °C up to 50 s

Training programme in gasless laparoscopy for rural surgeons of India (TARGET study) - Observational feasibility study

Background: Benefits of laparoscopic surgery are well recognised but uptake in rural settings of low- and middle-income countries is limited due to implementation barriers. Gasless laparoscopy has been proposed as an alternative but requires a trained rural surgical workforce to upscale. This study evaluates a feasibility of implementing a structured laparoscopic training programme for rural surgeons of North-East India. Methods: A 3-day training programme was held at Kolkata Medical College in March 2019. Laparoscopic knowledge and Fundamentals of Laparoscopic Skills (FLS) were assessed pre and post simulation training using multiple choice questions and the McGill Inanimate System for Training and Evaluation of Laparoscopic Skills (MISTELS), respectively. Competency with an abdominal lift device was assessed using the Objective Structured Assessment of Technical Skills (OSATS) and live operating performance via the Global Operative Assessment of Laparoscopic Skills (GOALS) scores during live surgery. Costs of the training programme and qualitative feedback were evaluated. Results: Seven rural surgeons participated. There was an improvement in knowledge acquisition (mean difference in MCQ score 5.57 (SD = 4.47)). The overall normalised mean MISTELS score for the FLS tasks improved from 386.02 (SD 110.52) pre-to 524.40 (SD 94.98) post-training (p = 0.09). Mean OSATS score was 22.4 out of 35 (SD 3.31) indicating competency with the abdominal lift device whilst a mean GOALS score of 16.42 out of 25 (SD 2.07) indicates proficiency in performing diagnostic laparoscopy using the gasless technique during live operating. Costs of the course were estimated at 354 USD for trainees and 461 USD for trainers. Conclusion: Structured training programme in gasless laparoscopy improves overall knowledge and skills acquisition in laparoscopic surgery for rural surgeons of North-East India. It is feasible to deliver a training programme in gasless laparoscopy for rural surgeons. Larger studies are needed to assess the benefits for wider adoption in a similar context

FOxTROT2: innovative trial design to evaluate the role of neoadjuvant chemotherapy for treating locally advanced colon cancer in older adults or those with frailty

Treating older adults with cancer is increasingly important in modern oncology practice. However, we currently lack the high-quality evidence needed to guide optimal management of this heterogeneous group. Principally, historic under-recruitment of older adults to clinical trials limits our understanding of how existing evidence can be applied to this group. Such uncertainty is particularly prevalent in the management of colon cancer (CC). With CC being most common in older adults, many patients also suffer from frailty, which is recognised as being strongly associated with poor clinical outcomes. Conducting clinical trials in older adults presents several major challenges, many of which impact the clinical relevance of results to a real-world population. When considering this heterogeneous group, it may be difficult to define the target population, recruit participants effectively, choose an appropriate trial design, and ensure participants remain engaged with the trial during follow-up. Furthermore, after overcoming these challenges, clinical trials tend to enrol highly selected patient cohorts that comprise only the fittest older patients, which are not representative of the wider population. FOxTROT1 was the first phase III randomised controlled trial to illustrate the benefit of neoadjuvant chemotherapy (NAC) in the treatment of CC. Patients receiving NAC had greater 2-year disease-free survival compared to those proceeding straight to surgery. Outcomes for older adults in FOxTROT1 were similarly impressive when compared to their younger counterparts. Yet, this group inevitably represents a fitter subgroup of the older patient population. FOxTROT2 has been designed to investigate NAC in a full range of older adults with CC, including those with frailty. In this review, we describe the key challenges to conducting a robust clinical trial in this heterogeneous patient group, highlight our strategies for overcoming these challenges in FOxTROT2, and explain how we hope to provide clarity on the optimal treatment of CC in older adults

ABL1 regulates spindle orientation in adherent cells and mammalian skin

Despite the growing evidence for the regulated spindle orientation in mammals, a systematic approach for identifying the responsible genes in mammalian cells has not been established. Here we perform a kinase-targeting RNAi screen in HeLa cells and identify ABL1 as a novel regulator of spindle orientation. Knockdown of ABL1 causes the cortical accumulation of Leu-Gly-Asn repeat-enriched-protein (LGN), an evolutionarily conserved regulator of spindle orientation. This results in the LGN-dependent spindle rotation and spindle misorientation. In vivo inactivation of ABL1 by a pharmacological inhibitor or by ablation of the abl1 gene causes spindle misorientation and LGN mislocalization in mouse epidermis. Furthermore, ABL1 directly phosphorylates NuMA, a binding partner of LGN, on tyrosine 1774. This phosphorylation maintains the cortical localization of NuMA during metaphase, and ensures the LGN/NuMA-dependent spindle orientation control. This study provides a novel approach to identify genes regulating spindle orientation in mammals and uncovers new signalling pathways for this mechanism

Intestinal epithelial stem cells do not protect their genome by asymmetric chromosome segregation

The idea that stem cells of adult tissues with high turnover are protected from DNA replication-induced mutations by maintaining the same 'immortal' template DNA strands together through successive divisions has been tested in several tissues. In the epithelium of the small intestine, the provided evidence was based on the assumption that stem cells are located above Paneth cells. The results of genetic lineage-tracing experiments point instead to crypt base columnar cells intercalated between Paneth cells as bona fide stem cells. Here we show that these cells segregate most, if not all, of their chromosomes randomly, both in the intact and in the regenerating epithelium. Therefore, the 'immortal' template DNA strand hypothesis does not apply to intestinal epithelial stem cells, which must rely on other strategies to avoid accumulating mutations

Changing outcomes following pelvic exenteration for locally advanced and recurrent rectal cancer

Background Pelvic exenteration for locally advanced rectal cancer (LARC) and locally recurrent rectal cancer (LRRC) is technically challenging but increasingly performed in specialist centres. The aim of this study was to compare outcomes of exenteration over time. Methods This was a multicentre retrospective study of patients who underwent exenteration for LARC and LRRC between 2004 and 2015. Surgical outcomes, including rate of bone resection, flap reconstruction, margin status and transfusion rates, were examined. Outcomes between higher- and lower-volume centres were also evaluated. Results Some 2472 patients underwent pelvic exenteration for LARC and LRRC across 26 institutions. For LARC, rates of bone resection or flap reconstruction increased from 2004 to 2015, from 3.5 to 12.8 per cent, and from 12.0 to 29.4 per cent respectively. Fewer units of intraoperative blood were transfused over this interval (median 4 to 2 units; P = 0.040). Subgroup analysis showed that bone resection and flap reconstruction rates increased in lower- and higher-volume centres. R0 resection rates significantly increased in low-volume centres but not in high-volume centres over time (low-volume: from 62.5 to 80.0 per cent, P = 0.001; high-volume: from 83.5 to 88.4 per cent, P = 0.660). For LRRC, no significant trends over time were observed for bone resection or flap reconstruction rates. The median number of units of intraoperative blood transfused decreased from 5 to 2.5 units (P < 0.001). R0 resection rates did not increase in either low-volume (from 51.7 to 60.4 per cent; P = 0.610) or higher-volume (from 48.6 to 65.5 per cent; P = 0.100) centres. No significant differences in length of hospital stay, 30-day complication, reintervention or mortality rates were observed over time. Conclusion Radical resection, bone resection and flap reconstruction rates were performed more frequently over time, while transfusion requirements decreased

Paneth Cells in Intestinal Homeostasis and Tissue Injury

Adult stem cell niches are often co-inhabited by cycling and quiescent stem cells. In the intestine, lineage tracing has identified Lgr5+ cells as frequently cycling stem cells, whereas Bmi1+, mTert+, Hopx+ and Lrig1+ cells appear to be more quiescent. Here, we have applied a non-mutagenic and cell cycle independent approach to isolate and characterize small intestinal label-retaining cells (LRCs) persisting in the lower third of the crypt of Lieberkühn for up to 100 days. LRCs do not express markers of proliferation and of enterocyte, goblet or enteroendocrine differentiation, but are positive for Paneth cell markers. While during homeostasis, LR/Paneth cells appear to play a supportive role for Lgr5+ stem cells as previously shown, upon tissue injury they switch to a proliferating state and in the process activate Bmi1 expression while silencing Paneth-specific genes. Hence, they are likely to contribute to the regenerative process following tissue insults such as chronic inflammation

Modelling the Spatio-Temporal Cell Dynamics Reveals Novel Insights on Cell Differentiation and Proliferation in the Small Intestinal Crypt

We developed a slow structural relaxation model to describe cellular dynamics in the crypt of the mouse small intestine. Cells are arranged in a three dimensional spiral the size of which dynamically changes according to cell production demands of adjacent villi. Cell differentiation and proliferation is regulated through Wnt and Notch signals, the strength of which depends on the local cell composition. The highest level of Wnt activity is associated with maintaining equipotent stem cells (SC), Paneth cells and common goblet-Paneth cell progenitors (CGPCPs) intermingling at the crypt bottom. Low levels of Wnt signalling area are associated with stem cells giving rise to secretory cells (CGPCPs, enteroendocrine or Tuft cells) and proliferative absorptive progenitors. Deciding between these two fates, secretory and stem/absorptive cells, depends on Notch signalling. Our model predicts that Notch signalling inhibits secretory fate if more than 50% of cells they are in contact with belong to the secretory lineage. CGPCPs under high Wnt signalling will differentiate into Paneth cells while those migrating out from the crypt bottom differentiate into goblet cells. We have assumed that mature Paneth cells migrating upwards undergo anoikis. Structural relaxation explains the localisation of Paneth cells to the crypt bottom in the absence of active forces. The predicted crypt generation time from one SC is 4–5 days with 10–12 days needed to reach a structural steady state. Our predictions are consistent with experimental observations made under altered Wnt and Notch signalling. Mutations affecting stem cells located at the crypt floor have a 50% chance of being propagated throughout the crypt while mutations in cells above are rarely propagated. The predicted recovery time of an injured crypt losing half of its cells is approximately 2 days

Contemporary Management of Locally Advanced and Recurrent Rectal Cancer: Views from the PelvEx Collaborative

Pelvic exenteration is a complex operation performed for locally advanced and recurrent pelvic cancers. The goal of surgery is to achieve clear margins, therefore identifying adjacent or involved organs, bone, muscle, nerves and/or vascular structures that may need resection. While these extensive resections are potentially curative, they can be associated with substantial morbidity. Recently, there has been a move to centralize care to specialized units, as this facilitates better multi-disciplinary care input. Advancements in pelvic oncology and surgical innovation have redefined the boundaries of pelvic exenterative surgery. Combined with improved neoadjuvant therapies, advances in diagnostics, and better reconstructive techniques have provided quicker recovery and better quality of life outcomes, with improved survival This article provides highlights of the current management of advanced pelvic cancers in terms of surgical strategy and potential future developments