LiDAR mapping of tidal marshes for ecogeomorphological modelling in the TIDE project

The European research project TIDE (Tidal Inlets Dynamics and Environment) is developing and validating coupled models describing the morphological, biological and ecological evolution of tidal environments. The interactions between the physical and biological processes occurring in these regions requires that the system be studied as a whole rather than as separate parts. Extensive use of remote sensing including LiDAR is being made to provide validation data for the modelling. This paper describes the different uses of LiDAR within the project and their relevance to the TIDE science objectives. LiDAR data have been acquired from three different environments, the Venice Lagoon in Italy, Morecambe Bay in England, and the Eden estuary in Scotland. LiDAR accuracy at each site has been evaluated using ground reference data acquired with differential GPS. A semi-automatic technique has been developed to extract tidal channel networks from LiDAR data either used alone or fused with aerial photography. While the resulting networks may require some correction, the procedure does allow network extraction over large areas using objective criteria and reduces fieldwork requirements. The networks extracted may subsequently be used in geomorphological analyses, for example to describe the drainage patterns induced by networks and to examine the rate of change of networks. Estimation of the heights of the low and sparse vegetation on marshes is being investigated by analysis of the statistical distribution of the measured LiDAR heights. Species having different mean heights may be separated using the first-order moments of the height distribution

The predictive and prognostic potential of plasma telomerase reverse transcriptase (TERT) RNA in rectal cancer patients

Background: Preoperative chemoradiotherapy (CRT) followed by surgery is the standard care for locally advanced rectal cancer, but tumour response to CRT and disease outcome are variable. The current study aimed to investigate the effectiveness of plasma telomerase reverse transcriptase (TERT) levels in predicting tumour response and clinical outcome. Methods: 176 rectal cancer patients were included. Plasma samples were collected at baseline (before CRT\ubcT0), 2 weeks after CRT was initiated (T1), post-CRT and before surgery (T2), and 4\u20138 months after surgery (T3) time points. Plasma TERT mRNA levels and total cell-free RNA were determined using real-time PCR. Results: Plasma levels of TERT were significantly lower at T2 (Po0.0001) in responders than in non-responders. Post-CRT TERT levels and the differences between pre- and post-CRT TERT levels independently predicted tumour response, and the prediction model had an area under curve of 0.80 (95% confidence interval (CI) 0.73\u20130.87). Multiple analysis demonstrated that patients with detectable TERT levels at T2 and T3 time points had a risk of disease progression 2.13 (95% CI 1.10\u20134.11)-fold and 4.55 (95% CI 1.48\u201313.95)-fold higher, respectively, than those with undetectable plasma TERT levels. Conclusions: Plasma TERT levels are independent markers of tumour response and are prognostic of disease progression in rectal cancer patients who undergo neoadjuvant therapy

Overexpression of squamous cell carcinoma antigen variants in hepatocellular carcinoma

Pathogenetic mechanisms of hepatocellular carcinoma (HCC) are stil unclear and new tools for diagnostic and therapeutic purposes are ongoing. We have assessed whether squamous cell carcinoma antigen (SCCA), a serpin overexpressed in neoplastic cells of epithelial origin, is also expressed in liver cancer. Squamous cell carcinoma antigen was evaluated by immunohistochemistry in 65 HCCs of different aetiology and in 20 normal livers. Proliferative activity was assessed using MIB-1 antibody. In 18 surgical samples, tumour and nontumour liver tissue was available for SCCA cDNA amplification and sequencing. Squamous cell carcinoma antigen was detected in 55 out of 65 (85%) tumour specimens, but in none of the 20 controls. In the majority of the cases, the positive signal was found in the cytoplasm of more than 50% of the hepatocytes. Low or undetectable SCCA (score less than or equal to1) was associated to lower MIB-1 labelling index, compared to cases with SCCA score greater than or equal to2 (mean +/-s.d.: 2%+/-2.4 vs 7.5%+/-10.3, P<0.05). Squamous cell carcinoma antigen mRNA could be directly sequenced in 14 out of 18 liver tumours but in none of the corresponding nontumour samples. From sequence alignment, a novel SCCA1 variant (G(351) to A) was identified in five cases, while SCCA1 was revealed in six cases and SCCA2 in three cases. In conclusion, SCCA variants are overexpressed in HCC, independently of tumour aetiology. A novel SCCA1 variant has been identified in one third of liver tumours

Neoplastic diseases in the domestic ferret (Mustela putorius furo) in Italy : classification and tissue distribution of 856 cases (2000-2010)

Background: The aim of this study was to describe the prevalence and tissue distribution of neoplasms in Italian ferrets, compared to the epidemiological data previously reported in USA and Japan. Methods: Signalment and diagnoses of pathological submissions received between 2000 and 2010 were searched; cases with the diagnosis of neoplasm were selected and original sections reviewed to confirm the diagnosis. Results: Nine-hundred and ten samples were retrieved, 690 of which included at least one tumour for a total of 856 tumours. Ferrets with multiple neoplasms were 134 (19.4%). Median age was 5years, and F/M ratio was 0.99. Endocrine neoplasms were the most common. Other frequent tumours were cutaneous mast cell tumours, sebaceous tumours, and lymphomas. Cutaneous squamous cell carcinomas (SCC) were consistently associated with sebaceous tumours. Twenty-four abdominal spindle cell tumours with an undefined origin were observed. Lymphomas and islet cell tumours had a lower incidence compared with previous extra-European studies. Discussion: Epidemiological information on ferret tumours derives from extra-European countries, mostly USA and Japan. In these countries similar distributions with minor discrepancies have been reported. Compared to previous reports, adrenal tumours were more frequent than pancreatic islet cell neoplasms, and a higher number of mesenchymal neoplasms arising from the adrenal capsule was noted. An unusual association between SCC and sebaceous gland neoplasms and a high number of intrabdominal spindle cell neoplasms with unclear primary origin were noted and grants further investigation. Conclusions: The tissue distribution of tumours recorded in this study paralleled previous findings in ferrets from USA and Japan. Some differences have been noted in the frequency of lymphoma, adrenal mesenchymal tumours and cutaneous tumours. Some tumours that are among the most common in other species seem to be uncommon in ferrets and are characterized by distinctive predilection sites

Non-Neutral Vegetation Dynamics

The neutral theory of biodiversity constitutes a reference null hypothesis for the interpretation of ecosystem dynamics and produces relatively simple analytical descriptions of basic system properties, which can be easily compared to observations. On the contrary, investigations in non-neutral dynamics have in the past been limited by the complexity arising from heterogeneous demographic behaviours and by the relative paucity of detailed observations of the spatial distribution of species diversity (beta-diversity): These circumstances prevented the development and testing of explicit non-neutral mathematical descriptions linking competitive strategies and observable ecosystem properties. Here we introduce an exact non-neutral model of vegetation dynamics, based on cloning and seed dispersal, which yields closed-form characterizations of beta-diversity. The predictions of the non-neutral model are validated using new high-resolution remote-sensing observations of salt-marsh vegetation in the Venice Lagoon (Italy). Model expressions of beta-diversity show a remarkable agreement with observed distributions within the wide observational range of scales explored (5⋅10(−1) m÷10(3) m). We also consider a neutral version of the model and find its predictions to be in agreement with the more limited characterization of beta-diversity typical of the neutral theory (based on the likelihood that two sites be conspecific or heterospecific, irrespective of the species). However, such an agreement proves to be misleading as the recruitment rates by propagules and by seed dispersal assumed by the neutral model do not reflect known species characteristics and correspond to averages of those obtained under the more general non-neutral hypothesis. We conclude that non-neutral beta-diversity characterizations are required to describe ecosystem dynamics in the presence of species-dependent properties and to successfully relate the observed patterns to the underlying processes