The diagnostic performance of routinely acquired and reported computed tomography imaging in patients presenting with suspected pleural malignancy

Objectives: Contrast-enhanced computed tomography (CT) provides essential cross-sectional imaging data in patients with suspected pleural malignancy (PM). The performance of CT in routine practice may be lower than in previously reported research. We assessed this relative to ‘real-life’ factors including use of early arterial-phase contrast enhancement (by CT pulmonary angiography (CTPA)) and non-specialist radiology reporting. Materials and methods: Routinely acquired and reported CT scans in patients recruited to the DIAPHRAGM study (a prospective, multi-centre observational study of mesothelioma biomarkers) between January 2014 and April 2016 were retrospectively reviewed. CT reports were classified as malignant if they included specific terms e.g. “suspicious of malignancy”, “stage M1a” and benign if others were used e.g. “indeterminate”, “no cause identified”. All patients followed a standard diagnostic algorithm. The diagnostic performance of CT (overall and based on the above factors) was assessed using 2 × 2 Contingency Tables. Results: 30/345 (9%) eligible patients were excluded (non-contrast (n = 13) or non-contiguous CT (n = 4), incomplete follow-up (n = 13)). 195/315 (62%) patients studied had PM; 90% were cyto-histologically confirmed. 172/315 (55%) presented as an acute admission, of whom 31/172 (18%) had CTPA. Overall, CT sensitivity was 58% (95% CI 51–65%); specificity was 80% (95% CI 72–87%). Sensitivity of CTPA (performed in 31/315 (10%)) was lower (27% (95% CI 9–53%)) than venous-phase CT (61% (95% CI 53–68%) p = 0.0056). Sensitivity of specialist thoracic radiologist reporting was higher (68% (95% CI 55–79%)) than non-specialist reporting (53% (95% CI 44–62%) p = 0.0488). Specificity was not significantly different. Conclusion: The diagnostic performance of CT in routine clinical practice is insufficient to exclude or confirm PM. A benign CT report should not dissuade pleural sampling where the presence of primary or secondary pleural malignancy would alter management. Sensitivity is lower with non-thoracic radiology reporting and particularly low using CTPA

Survival prediction in mesothelioma using a scalable lasso regression model: instructions for use and initial performance using clinical predictors

Introduction: Accurate prognostication is difficult in malignant pleural mesothelioma (MPM). We developed a set of robust computational models to quantify the prognostic value of routinely available clinical data, which form the basis of published MPM prognostic models. Methods: Data regarding 269 patients with MPM were allocated to balanced training (n=169) and validation sets (n=100). Prognostic signatures (minimal length best performing multivariate trained models) were generated by least absolute shrinkage and selection operator regression for overall survival (OS), OS <6 months and OS <12 months. OS prediction was quantified using Somers DXY statistic, which varies from 0 to 1, with increasing concordance between observed and predicted outcomes. 6-month survival and 12-month survival were described by area under the curve (AUC) scores. Results: Median OS was 270 (IQR 140–450) days. The primary OS model assigned high weights to four predictors: age, performance status, white cell count and serum albumin, and after cross-validation performed significantly better than would be expected by chance (mean DXY0.332 (±0.019)). However, validation set DXY was only 0.221 (0.0935–0.346), equating to a 22% improvement in survival prediction than would be expected by chance. The 6-month and 12-month OS signatures included the same four predictors, in addition to epithelioid histology plus platelets and epithelioid histology plus C-reactive protein (mean AUC 0.758 (±0.022) and 0.737 (±0.012), respectively). The <6-month OS model demonstrated 74% sensitivity and 68% specificity. The <12-month OS model demonstrated 63% sensitivity and 79% specificity. Model content and performance were generally comparable with previous studies. Conclusions: The prognostic value of the basic clinical information contained in these, and previously published models, is fundamentally of limited value in accurately predicting MPM prognosis. The methods described are suitable for expansion using emerging predictors, including tumour genomics and volumetric staging

Total Station Mapping: Practical Examples from Alta and Baja California

The use of electronic total data stations for mapping archaeological sites is examined through two California case studies. Mission Santa Catalina, located in the high desert of Baja California, and a cluster of three shell mounds, located in a forest in the San Francisco Bay area, represent two different examples of organizing and implementing a mapping program using a total station. In this article, we will discuss the basic use of total stations for mapping archaeological sites and provide an overview of the process of creating digital maps from data obtained using a total station. The two case studies will offer in-depth consideration of different data collection strategies and techniques used for the production of digital maps, and we stress the broad application of total stations for accurate and efficient mapping in a variety of study settings

Special Feature Introduction: Indigenous Persistence in Colonial California

There are more than one hundred federally recognized Native American tribes found within the present-day borders of California, a roughly equivalent number of indigenous Californian communities who are either unrecognized or currently petitioning for recognition by the United States government, and another eight indigenous reserves just across the international border in Baja California, Mexico. This impressive array of more than 200 Native American communities is not surprising, given what oral narratives, early ethnography, and precontact archaeology tell us about the densely populated sociopolitical landscape comprised of many hundreds of small-scale autonomous tribes that existed before colonization in the late-1700s. Separating these two eras of Native California, however, is the colonial period—a time when indigenous peoples faced directed culture change in the Spanish missions, joined multiethnic communities at mercantile outposts, and suffered greatly due to disease, violence, and the disastrous policies of elimination enacted during the early American period

The agrin gene codes for a family of basal lamina proteins that differ in function and distribution

We isolated two cDNAs that encode isoforms of agrin, the basal lamina protein that mediates the motor neuron-induced aggregation of acetylcholine receptors on muscle fibers at the neuromuscular junction. Both proteins are the result of alternative splicing of the product of the agrin gene, but, unlike agrin, they are inactive in standard acetylcholine receptor aggregation assays. They lack one (agrin-related protein 1) or two (agrin-related protein 2) regions in agrin that are required for its activity. Expression studies provide evidence that both proteins are present in the nervous system and muscle and that, in muscle, myofibers and Schwann cells synthesize the agrin-related proteins while the axon terminals of motor neurons are the sole source of agrin

Diagnostic and prognostic biomarkers of malignant pleural mesothelioma

Malignant Pleural Mesothelioma (MPM) is an aggressive intrathoracic malignancy with an overall poor prognosis. MPM is associated with asbestos exposure but has a long latency period between exposure and disease development. Incidence of MPM in the UK is therefore still rising, predicted to reach a peak in 2020. The majority of patients with MPM present with breathlessness, frequently due to a pleural effusion and/or chest pain. Diagnosis of MPM can be difficult. Radiological detection of early stage MPM in particular can be challenging, as pleural tumour, nodularity or significant pleural thickening may not be evident. Diagnosis is further complicated by the low yield of pleural fluid cytology examination in MPM and pleural biopsy is therefore usually required to allow definitive diagnosis. This can be achieved under image guidance, at surgical thoracoscopy or at local anaesthetic thoracoscopy (LAT). A significant number of patients are either elderly or have co-morbidity precluding general anaesthesia and surgical thoracoscopy. Image-guided pleural biopsy is not always feasible, particularly in the absence of significant pleural thickening. LAT remains a limited resource in the UK. A non-invasive biomarker of MPM, which could be performed early in the patient’s presentation, and that could be available to most hospitals, would therefore be a major clinical advance, allowing clinicians to direct appropriate patients to specialist centres with access to LAT and specialist MDT input where MPM appears likely. There have been several potential blood biomarkers identified in the mesothelioma literature, including the most widely studied, Mesothelin, and more recently Fibulin-3 and SOMAscan™. Unfortunately study results have been variably limited by retrospective study design, inconsistent sampling time points, inconsistent results and lack of external validation, therefore despite initial promising results, none of these biomarkers have entered routine clinical practice for diagnosis. Similarly, utility of imaging biomarkers such as perfusion Computed Tomography (CT), Positron Emission Tomography (PET) and Dynamic Contrast Enhanced Magnetic Resonance Imaging (DCE-MRI) has been limited by high radiation dose, limited availability, and requirement for bulky (and therefore late stage) disease for assessment respectively. In chapter 2, study design, recruitment and preliminary results of the DIAPHRAGM (Diagnostic and Prognostic Biomarkers in the Rational Assessment of Mesothelioma) study are reported. A prospective, multi-centre study was designed, recruiting patients with suspected pleural malignancy (SPM) at initial presentation to secondary care services, from a mixture of academic and more clinical units in the UK and Ireland, in addition to asbestos-exposed control subjects. In one of the largest biomarker studies in mesothelioma to date, 639 patients with SPM and 113 asbestos-exposed control subjects were recruited over three years. Data cleaning is being finalised by the Cancer Research UK Clinical Trials Unit Glasgow at the time of writing. Preliminary results reveal that 26% (n=154) patients recruited to the SPM cohort were diagnosed with MPM, 33% (n=209) had secondary pleural malignancy and 34% (n=218) were diagnosed with benign pleural disease. A final diagnosis is awaited in 7% (n=47) at the time of writing. SOMAscan™ and Fibulin-3 biomarker analyses are ongoing and DIAPHRAGM will definitively answer the question of diagnostic utility of these blood biomarkers in routine clinical practice, in a ‘real-life’ MPM population, relative to that of Mesothelin. In chapter 3, contrast-enhanced MRI was performed in patients with suspected MPM and a novel MRI biomarker of pleural malignancy defined (Early Contrast Enhancement – ECE). ECE was defined as a peak in pleural signal intensity at or before 4.5 minutes after intravenous Gadobutrol administration. ECE assessment was successfully performed in all patients who underwent contrast-enhanced MRI. This included patients with pleural thickening 0.533AU/s), indicative of high tumour vascularity, was associated with poor median overall survival (12 months vs. 20 months, p=0.047). Staging of MPM represents an additional challenge to clinicians. This is due to the complex morphology and often rind-like growth pattern of MPM. In addition, delineation of pleural disease from adjacent structures such as intercostal muscle and diaphragm can be difficult to assess, particularly at CT, which is the most commonly used imaging modality for diagnostic and staging assessment in MPM. Current clinical staging frequently underestimates extent of disease, with a significant proportion of patients being upstaged at time of surgery, and is limited by high inter-observer variability. Recent studies have reported the prognostic significance of CT-derived tumour volume; however, many of these studies have been limited by the laborious or complex nature of tumour segmentation, significant inter-observer variability or challenges encountered in separating pleural tumour from adjacent structures, which are often of similar density. MRI is superior to CT in the detection of invasion of the chest wall and diaphragm in MPM. In Chapter 4, MRI was used to quantitatively assess pleural tumour volume in 31 patients with MPM using novel semi-automated segmentation methodology. Four different segmentation methodologies, using Myrian® segmentation software were developed and examined. Optimum methodology was defined, based on the accuracy of volume estimates of an MRI phantom, visual-based analysis, intra-observer agreement and analysis time. Using the optimum methodology, there was acceptable error around the MRI phantom volume (3.6%), a reasonable analysis time (approximately 14 minutes), good intra-observer agreement (intra-class correlation coefficient (ICC) 0.875) and excellent inter-observer agreement (ICC 0.962). Patients with a high MRI-estimated tumour volume (≥300cm3) had a significantly poorer median overall survival (8.5 months vs. 20 months) and was a statistically significant prognostic variable on univariate (HR 2.273 (95% CI 1.162 – 4.446), p=0.016) and multi-variate Cox proportional hazards model (HR 2.114 (95% CI 1.046 – 4.270), p=0.037)

The Marine Radiocarbon Reservoir Effect in Tomales Bay, California

This paper examines the marine reservoir effect for Tomales Bay, a 25.5-km-long tidal estuary along the northern coast of California. We determined the regional ∆R through radiocarbon (14C) measurements of pre-1950 shells from a museum collection as well as archaeologically recovered shell samples from a historical railroad grade of known construction date. These results are compared against four sets of paired shell and bone samples from two local archaeological sites. Our results indicate little spatial variation along the inner bay, but the proposed ∆R value is lower than those previously reported for nearby areas along the Pacific Coast. We also note potential variability in regional ∆R of approximately 200 14C years for the late Holocene, and comparison with an older paired bone and shell sample points toward more significant temporal variation earlier in tim

Finding Mid-19th Century Native Settlements: Cartographic and Archaeological Evidence from Central California

Historical maps have the potential to aid archaeological investigations into the persistence of Native American settlements during the mid-19th century, a time when many Native communities disappear from archaeological view. Focusing on Tomales Bay in central California, we evaluate the usefulness of historical maps as a way to discover and interpret archaeological deposits dating to the period, with the aim of better understanding indigenous patterns of residence at the transition from missionary to settler colonialism. In particular, we focus on diseños and plats created to document Mexican-era land grants as well as early maps produced by the General Land Office and United States Coast Survey. Although we note inconsistencies regarding the inclusion of indigenous settlements on historical maps, our case study offers an example of how archaeologists can employ historical maps and targeted archaeological ground-truthing to discover sites that are poorly represented in the historical and archaeological records