Advances towards the use of radical radiotherapy in malignant pleural mesothelioma

Background: The complex shape of the pleural cavity and the close proximity of normal radiosensitive structures render the delivery of radical radiotherapy in malignant pleural mesothelioma (MPM) challenging. However, the advent of conformal, intensity modulated radiotherapy (IMRT), where dose is selectively delivered to the tumour whilst sparing normal tissues, can facilitate safe dose escalation. SYSTEMS-2 is the only randomised controlled trial of radiotherapy dose escalation to be attempted in MPM and is comparing the palliative efficacy of two hypofractionated radiotherapy regimes to sites of pain using conformal techniques. Although traditionally associated with unacceptable late normal tissue toxicity, the success of stereotactic radiotherapy (SABR) and the discovery that two common malignancies exhibit low α/β ratios, has enhanced the popularity of hypofractionated regimes. While the radiobiology of MPM is not well understood, its slow growth and apparent radioresistance suggests that it may exhibit a low α/β ratio and therefore that it may respond more favourably to dose hypofractionation. Aims of thesis: To investigate the possibility of further radiotherapy dose escalation in MPM, beyond that delivered in the SYSTEMS-2 study. Methods: I. Novel radiotherapy dose constraints were generated for use in the SYSTEMS-2 study and tested on five patients from the SYSTEMS study. II. Multi criteria optimisation (MCO) software was used to assess whether the original dose escalated radiotherapy plans for the Glasgow cohort of SYSTEMS-2 could be improved, without compromising target volume coverage. III. A clinically relevant 3D in vitro spheroid model was used to investigate the radiobiology of two independent MPM cell lines (H2052 and 211H). Spheroids were established and exposed to the same total dose of ionising radiation (IR) delivered in different doses per fraction. Data was used to investigate response to dose fractionation and to estimate the α/β ratio of this tumour. IV. The response of H2052 and 211H spheroids to two radiosensiting agents was investigated in combination with fractionated radiotherapy. Spheroids were incubated with increasing concentrations of either NU7441 (a DNA-PKcs inhibitor) or A1331852 (a BH3 mimetic) before being exposed to fractionated IR. The immunohistochemical (IHC) expression of DNA-PKcs and Bcl-xL was explored in diagnostic biopsies obtained from MPM patients to investigate clinical validity of the targets. V. IHC expression of nine proteins, selected for their potential to impact on radioresponse, was analysed in diagnostic tumour tissue collected from SYSTEMS and SYSTEMS-2 patients. Expression data was correlated with baseline clinical trial data in all patients, and with clinical trial outcome data from SYSTEMS patients. Results: I. Initial planning studies showed that none of the five SYSTEMS patients met all of the SYSTEMS-2 dose constraints, but the plans were deemed to be potentially clinically acceptable and the constraints were taken forward in the trial. The value of familiarity with a planning technique was evidenced by the fact that all constraints were achieved when the cases were re-planned by the same staff member in April 2019. II. MCO re-planning of dose escalated SYSTEMS-2 plans achieved clinically significant dose reductions to organs at risk (OAR) without compromising target volume coverage in 13/20 cases. Plans which did not meet OAR constraints or conform to the prescribed target volume coverage may still have been clinically acceptable. III. In vitro studies confirmed that growth of MPM spheroids can be delayed by IR. Spheroids demonstrated sensitivity to changes in dose per fraction, with the greatest volume reductions observed in hypofractionated radiotherapy regimes. This data implies that these MPM cell lines may exhibit a low α/β ratio, a suggestion which was further supported by in vitro multi-fraction IR studies. IV. Data suggest that NU7441 and A1331852 are potent radiosensitisers of MPM spheroids and that both are valid clinical targets in MPM. The supposition that a BH3 mimetic may offer tumour specific radiosensitisation, combined with the observation that A1331852 demonstrated greatest efficacy with hypofractionated IR, suggests that this agent may be clinically valuable in the radiosensitisation of MPM. V. No statistically significant correlations were found between baseline clinical characteristics and expression of the proteins of interest and no potential biomarkers of radiosensitisation were identified in the SYSTEMS cohort. Conclusions: Novel dose constraints are being used to facilitate the delivery of hypofractionated, dose escalated palliative radiotherapy in the SYSTEMS-2 study. Results from this trial may guide future dose escalation in this disease and data from MCO planning studies suggest that further dose escalation to the target volume may be feasible without breaching OAR limits. In vitro studies suggest that MPM is sensitive to IR, responds more effectively to dose hypofractionation and may have a low α/β ratio. This data may be helpful in determining dose and fractionation regimes in future MPM radiotherapy trials. Combination of BH3 mimetics with IR may provide MPM specific radiosensitisation, achieving greatest efficacy with dose hypofractionation. Ongoing IHC analysis of tumour samples from the SYSTEMS-2 study may identify a biomarker of radiotherapy response which would be helpful in guiding radiotherapy treatment decisions for future patients. In summary, this thesis has investigated ways in which radiotherapy could be delivered with radical intent in MPM. Practical aspects of radiotherapy planning and delivery have been considered and are presented in conjunction with laboratory data to demonstrate how technical advances can be combined with an appreciation of disease radiobiology to facilitate radical treatment

Social Networks and Transnational Social Fields: A Review of Quantitative and Mixed-Methods Approaches

Ashton Verdery acknowledges assistance provided by the Population Research Institute, which is supported by an infrastructure grant by the Eunice Kennedy Shriver National Institute of Child Health and Human Development (R24-HD041025), and the Institute for CyberScience at Penn State University.Scholars of transnationalism have argued that migrants create transnational social fields or spaces that connect their place of origin to destination areas. Despite the centrality that social networks have in the definition of these concepts, quantitative and mixed-methods social network research is rare in research on transnationalism. This situation, however, has changed over the last decade, and the transnational social networks of migrants have been studied with multiple methodologies. So far, this literature has not been systematically evaluated. With the aim of taking stock of this research, we classify the literature into four types of approaches (individual, household, dyad/small set, and community) and review their distinct contributions regarding the functioning of immigrants' transnational networks, as well as the relative strengths and limitations of each approach. On the basis of our analysis, we discuss pathways for future investigation

Alternative tissue fixation for combined histopathological and molecular analysis in a clinically representative setting

Formalin is the principal tissue fixative used worldwide for clinical and research purposes. Despite optimal preservation of morphology, its preservation of DNA and RNA is poor. As clinical diagnostics increasingly incorporates molecular-based analysis, the requirement for maintaining nucleic acid quality is of increasing importance. Here we assess an alternative non-formalin-based tissue fixation method, PAXgene Tissue system, with the aim of better preserving nucleic acids, while maintaining the quality of the tissue to be used for vital existing diagnostic techniques. In this study, these criteria are assessed in a clinically representative setting. In total, 203 paired PAXgene Tissue and formalin-fixed samples were obtained. Blind-scored haematoxylin and eosin (H&E) sections showed comparable and acceptable staining. Immunohistochemistry (IHC) staining was suboptimal using existing protocols but improved with minor method adjustment and optimisation. Quality of DNA and RNA was significantly improved by PAXgene tissue fixation [RIN 2.8 versus 3.8 (p < 0.01), DIN 5.68 versus 6.77 (p < 0.001)], which translated into improved performance on qPCR assay. These results demonstrate the potential of PAXgene Tissue to be used routinely in place of formalin, maintaining adequate histological staining and significantly improving the preservation of biological molecules in the genomic era

Mesothelioma cells depend on the anti-apoptotic protein Bcl-xL for survival and are sensitized to ionizing radiation by BH3-mimetics

The incidence of mesothelioma continues to rise and prognosis remains dismal due to resistance to conventional therapies and few novel treatment options. Failure to activate apoptotic cell death is a resistance mechanism that may be overcome by inhibition of anti-apoptotic Bcl-2 proteins using BH3-mimetic drugs. We investigated the role of anti-apoptotic proteins in the radioresistance of mesothelioma, identifying clinically-relevant targets for radiosensitization and evaluating the activity of BH3-mimetics alone and in combination with radiotherapy in pre-clinical models. Mesothelioma cell lines 211H, H2052 and H226 exposed to BH3-mimetics demonstrated Bcl-xL dependence that correlated with protein expression and was confirmed by genetic knockdown. The Bcl-xL inhibitor A1331852 exhibited cytotoxic (EC50 0.13-1.42 μmol/L) and radiosensitizing activities (sensitizer enhancement ratios 1.3-1.8). Cytotoxicity was associated with induction of mitochondrial outer membrane permeabilization and caspase-3/7 activation. Efficacy was maintained in a three-dimensional model in which combination therapy completely eradicated mesothelioma spheroids. Clinical applicability was confirmed by immunohistochemical analysis of Bcl-2 proteins in patient samples and radiosensitizing activity of A1331852 in primary patient-derived mesothelioma cells. Mesothelioma cells exhibit addiction to the anti-apoptotic protein Bcl-xL and their intrinsic radioresistance can be overcome by small molecule inhibition of this novel therapeutic target

MILEPOST GCC: machine learning based research compiler

International audienceTuning hardwired compiler optimizations for rapidly evolving hardware makes porting an optimizing compiler for each new platform extremely challenging. Our radical approach is to develop a modular, extensible, self-optimizing compiler that automatically learns the best optimization heuristics based on the behavior of the platform. In this paper we describe MILEPOST GCC, a machine-learning-based compiler that automatically adjusts its optimization heuristics to improve the execution time, code size, or compilation time of specific programs on different architectures. Our preliminary experimental results show that it is possible to considerably reduce execution time of the MiBench benchmark suite on a range of platforms entirely automatically

Consistent patterns of common species across tropical tree communities

Trees structure the Earth's most biodiverse ecosystem, tropical forests. The vast number of tree species presents a formidable challenge to understanding these forests, including their response to environmental change, as very little is known about most tropical tree species. A focus on the common species may circumvent this challenge. Here we investigate abundance patterns of common tree species using inventory data on 1,003,805 trees with trunk diameters of at least 10 cm across 1,568 locations$^{1-6}$ in closed-canopy, structurally intact old-growth tropical forests in Africa, Amazonia and Southeast Asia. We estimate that 2.2%, 2.2% and 2.3% of species comprise 50% of the tropical trees in these regions, respectively. Extrapolating across all closed-canopy tropical forests, we estimate that just 1,053 species comprise half of Earth's 800 billion tropical trees with trunk diameters of at least 10 cm. Despite differing biogeographic, climatic and anthropogenic histories$^{7}$, we find notably consistent patterns of common species and species abundance distributions across the continents. This suggests that fundamental mechanisms of tree community assembly may apply to all tropical forests. Resampling analyses show that the most common species are likely to belong to a manageable list of known species, enabling targeted efforts to understand their ecology. Although they do not detract from the importance of rare species, our results open new opportunities to understand the world's most diverse forests, including modelling their response to environmental change, by focusing on the common species that constitute the majority of their trees

Gardens as Science Learning Contexts Across Educational Stages: Learning Assessment Based on Students' Graphic Representations

The educational use of daily-life contexts is considered a valuable strategy to promote meaningful science learning, since it facilitates the establishment of connections between previous knowledge, personal interests, and new learning. The aim of this work is to provide evidence to support the presence of gardens at educational centers, by assessing key science topics whose learning is promoted at the pre-school, primary, secondary, and university stages. To this end, we analyzed the paired graphic representations of "a garden" that students drew both before and after their participation in a garden-based learning program. Firstly, we obtained the frequency of appearance of every represented element, and afterward characterized the level of change between paired graphic representations. Sample size was of 24-19-25-29 pairs per stage, respectively. Across all stages, an overall improvement in students' graphic expression was observed, which can be attributed to their experience in the space. At the pre-school stage, the garden favored the establishment of some simple cause-effect relationships which were consolidated at the primary stage, and provided a climate of motivation and affectivity that was evident in the final drawings, given the enormous quantity of details represented, the level of the finished product, and the careful combination and variety of colors. The presence of elements related to water notably increased in final graphic representations from pre-school, primary, and secondary education, thus evidencing that the use of gardens facilitates an approach to responsible water management. At the university stage, students initially demonstrated good knowledge of conventional agriculture, while the gardening experience -which was based on permaculture practices- helped evolve their ideas toward an alternative model of cultivation. The most prevalent science learning across all stages was related to plant knowledge, particularly to their anatomical traits and diversity. Finally, the role of educational gardens as models for students was evidenced, which suggests the importance of teachers and institutions carefully considering which model to offer. Overall, our results support the legitimacy of incorporating gardens to educational centers, particularly for promoting contact with live plants and plant knowledge, and potentially for promoting contact with garden fauna and activities oriented toward learning about it

Consistent patterns of common species across tropical tree communities

D.L.M.C. was supported by the London Natural Environmental Research Council Doctoral Training Partnership grant (grant no. NE/L002485/1). This paper developed from analysing data from the African Tropical Rainforest Observatory Network (AfriTRON), curated at ForestPlots.net. AfriTRON has been supported by numerous people and grants since its inception. We sincerely thank the people of the many villages and local communities who welcomed our field teams and without whose support this work would not have been possible. Grants that have funded the AfriTRON network, including data in this paper, are a European Research Council Advanced Grant (T-FORCES; 291585; Tropical Forests in the Changing Earth System), a NERC standard grant (NER/A/S/2000/01002), a Royal Society University Research Fellowship to S.L.L., a NERC New Investigators Grant to S.L.L., a Philip Leverhulme Award to S.L.L., a European Union FP7 grant (GEOCARBON; 283080), Leverhulme Program grant (Valuing the Arc); a NERC Consortium Grant (TROBIT; NE/D005590/), NERC Large Grant (CongoPeat; NE/R016860/1) the Gordon and Betty Moore Foundation the David and Lucile Packard Foundation, the Centre for International Forestry Research (CIFOR), and Gabon’s National Parks Agency (ANPN). This paper was supported by ForestPlots.net approved Research Project 81, ‘Comparative Ecology of African Tropical Forests’. The development of ForestPlots.net and data curation has been funded by several grants, including NE/B503384/1, NE/N012542/1, ERC Advanced Grant 291585—‘T-FORCES’, NE/F005806/1, NERC New Investigators Awards, the Gordon and Betty Moore Foundation, a Royal Society University Research Fellowship and a Leverhulme Trust Research Fellowship. Fieldwork in the Democratic Republic of the Congo (Yangambi and Yoko sites) was funded by the Belgian Science Policy Office BELSPO (SD/AR/01A/COBIMFO, BR/132/A1/AFRIFORD, BR/143/A3/HERBAXYLAREDD, FED-tWIN2019-prf-075/CongoFORCE, EF/211/TREE4FLUX); by the Flemish Interuniversity Council VLIR-UOS (CD2018TEA459A103, FORMONCO II); by L’Académie de recherche et d’enseignement supérieur ARES (AFORCO project) and by the European Union through the FORETS project (Formation, Recherche, Environnement dans la TShopo) supported by the XIth European Development Fund. EMV was supported by fellowship from the CNPq (Grant 308543/2021-1). RAPELD plots in Brazil were supported by the Program for Biodiversity Research (PPBio) and the National Institute for Amazonian Biodiversity (INCT-CENBAM). BGL post-doc grant no. 2019/03379-4, São Paulo Research Foundation (FAPESP). D.A.C. was supported by the CCI Collaborative fund. Plots in Mato Grosso, Brazil, were supported by the National Council for Scientific and Technological Development (CNPq), PELD-TRAN 441244/2016-5 and 441572/2020-0, and Mato Grosso State Research Support Foundation (FAPEMAT)—0346321/2021. We thank E. Chezeaux, R. Condit, W. J. Eggeling, R. M. Ewers, O. J. Hardy, P. Jeanmart, K. L. Khoon, J. L. Lloyd, A. Marjokorpi, W. Marthy, H. Ntahobavuka, D. Paget, J. T. A. Proctor, R. P. Salomão, P. Saner, S. Tan, C. O. Webb, H. Woell and N. Zweifel for contributing forest inventory data. We thank numerous field assistants for their invaluable contributions to the collection of forest inventory data, including A. Nkwasibwe, ITFC field assistant.Peer reviewe

Global fine-resolution data on springtail abundance and community structure

Springtails (Collembola) inhabit soils from the Arctic to the Antarctic and comprise an estimated ~32% of all terrestrial arthropods on Earth. Here, we present a global, spatially-explicit database on springtail communities that includes 249,912 occurrences from 44,999 samples and 2,990 sites. These data are mainly raw sample-level records at the species level collected predominantly from private archives of the authors that were quality-controlled and taxonomically-standardised. Despite covering all continents, most of the sample-level data come from the European continent (82.5% of all samples) and represent four habitats: woodlands (57.4%), grasslands (14.0%), agrosystems (13.7%) and scrublands (9.0%). We included sampling by soil layers, and across seasons and years, representing temporal and spatial within-site variation in springtail communities. We also provided data use and sharing guidelines and R code to facilitate the use of the database by other researchers. This data paper describes a static version of the database at the publication date, but the database will be further expanded to include underrepresented regions and linked with trait data.</p

Basic science232. Certolizumab pegol prevents pro-inflammatory alterations in endothelial cell function

Background: Cardiovascular disease is a major comorbidity of rheumatoid arthritis (RA) and a leading cause of death. Chronic systemic inflammation involving tumour necrosis factor alpha (TNF) could contribute to endothelial activation and atherogenesis. A number of anti-TNF therapies are in current use for the treatment of RA, including certolizumab pegol (CZP), (Cimzia ®; UCB, Belgium). Anti-TNF therapy has been associated with reduced clinical cardiovascular disease risk and ameliorated vascular function in RA patients. However, the specific effects of TNF inhibitors on endothelial cell function are largely unknown. Our aim was to investigate the mechanisms underpinning CZP effects on TNF-activated human endothelial cells. Methods: Human aortic endothelial cells (HAoECs) were cultured in vitro and exposed to a) TNF alone, b) TNF plus CZP, or c) neither agent. Microarray analysis was used to examine the transcriptional profile of cells treated for 6 hrs and quantitative polymerase chain reaction (qPCR) analysed gene expression at 1, 3, 6 and 24 hrs. NF-κB localization and IκB degradation were investigated using immunocytochemistry, high content analysis and western blotting. Flow cytometry was conducted to detect microparticle release from HAoECs. Results: Transcriptional profiling revealed that while TNF alone had strong effects on endothelial gene expression, TNF and CZP in combination produced a global gene expression pattern similar to untreated control. The two most highly up-regulated genes in response to TNF treatment were adhesion molecules E-selectin and VCAM-1 (q 0.2 compared to control; p > 0.05 compared to TNF alone). The NF-κB pathway was confirmed as a downstream target of TNF-induced HAoEC activation, via nuclear translocation of NF-κB and degradation of IκB, effects which were abolished by treatment with CZP. In addition, flow cytometry detected an increased production of endothelial microparticles in TNF-activated HAoECs, which was prevented by treatment with CZP. Conclusions: We have found at a cellular level that a clinically available TNF inhibitor, CZP reduces the expression of adhesion molecule expression, and prevents TNF-induced activation of the NF-κB pathway. Furthermore, CZP prevents the production of microparticles by activated endothelial cells. This could be central to the prevention of inflammatory environments underlying these conditions and measurement of microparticles has potential as a novel prognostic marker for future cardiovascular events in this patient group. Disclosure statement: Y.A. received a research grant from UCB. I.B. received a research grant from UCB. S.H. received a research grant from UCB. All other authors have declared no conflicts of interes