Pedestrian flow in two dimensions: Optimal psychological stress leads to less evacuation time and decongestion

Collective motion is an innate ability of all living systems, which depends on physiological and psychosocial factors in the case of humans. Such a collective organization is becoming of great interest in collective motion in human crowds. Using a cellular automaton (CA) simulation model, we demonstrate that emergency egress from a two-dimensional corridor with optimal stress leads to less evacuation time and efficient mass evacuations. We study how three types of stress (i.e., mild stress, optimal stress, and anxiety) described in the literature have a significant impact on the collective dynamics. We found that low-stress levels could decrease the evacuation time in an entire occupied room since agents choose alternative routes rather than the shortest path to the exit and display cooperative behavior. Therefore, the combination of mild and optimal stress can lead to efficient evacuations. Also CA simulations may be used to find safer and more efficient ways to conduct mass evacuation procedures.

Simulating the city traffic complexity induced by traffic light periods

We revisited the global traffic light optimization problem through a cellular automata model, which allows us to address the relationship between the traffic lights and car routing. We conclude that both aspects are not separable. Our results show that a good routing strategy weakens the importance of the traffic light period for mid-densities, thus limiting the parameter space where such optimization is relevant. This is confirmed by analyzing the travel time normalized by the shortest path between the origin and destination. As an unforeseen result, we report what seems to be a power-law distribution for such quantities, indicating that the travel time distribution slowly decreases for long travel times. The power-law exponent depends on the density, traffic light period, and routing strategy, which in this case is parametrized by the tendency of agents to abandon a route if it becomes stagnant. These results could have relevant consequences on how to improve the overall traffic efficiency in a particular city, thus providing insight into useful measurements, which are often counter-intuitive, which may be valuable to traffic controllers that operate through traffic light periods and phases.

The biomolecule corona of lipid nanoparticles contains circulating cell-free DNA

The spontaneous adsorption of biomolecules onto the surface of nanoparticles (NPs) in complex physiological biofluids has been widely investigated over the last decade. Characterisation of the protein composition of the 'biomolecule corona' has dominated research efforts, whereas other classes of biomolecules, such as nucleic acids, have received no interest. Scarce, speculative statements exist in the literature about the presence of nucleic acids in the biomolecule corona, with no previous studies attempting to describe the contribution of genomic content to the blood-derived NP corona. Herein, we provide the first experimental evidence of the interaction of circulating cell-free DNA (cfDNA) with lipid-based NPs upon their incubation with human plasma samples, obtained from healthy volunteers and ovarian carcinoma patients. Our results also demonstrate an increased amount of detectable cfDNA in patients with cancer. Proteomic analysis of the same biomolecule coronas revealed the presence of histone proteins, suggesting an indirect, nucleosome-mediated NP-cfDNA interaction. The finding of cfDNA as part of the NP corona, offers a previously unreported new scope regarding the chemical composition of the 'biomolecule corona' and opens up new possibilities for the potential exploitation of the biomolecule corona for the enrichment and analysis of blood-circulating nucleic acids.

Blood-based RAS mutation testing: concordance with tissue-based RAS testing and mutational changes on progression

Aim: To determine the concordance between plasma and tissue RAS mutation status in metastatic colorectal cancer patients to gauge whether blood-based testing is a viable alternative. We also evaluated the change in mutation status on progression. Materials/methods: RAS testing was performed on plasma from patients commencing first-line therapy (OncoBEAM™ RAS CEIVD kit). Results were then compared with formalin-fixed paraffin embedded tumor samples. Results: The overall percentage agreement (concordance) was 86.0% (86/100), which demonstrates that blood-based testing is an alternative to tissue-based testing. Reproducibility was 100% between three laboratories and 20% showed changes in their RAS mutational status on progression. Conclusion: These results show good concordance between tissue and plasma samples and suggest the need for longitudinal plasma testing during treatment to guide management decisions.

Abstract 3810: Persistence of smoking signature 4 in the non-small cell lung cancer genome

Introduction Lung cancer is the most common cause of cancer-related death. Carcinogenic and endogenous processes driving somatic mutation acquisition in cancer can be extracted and defined as mutational signatures using whole genome sequencing (WGS). Tobacco smoke is the main aetiological cause of lung cancer, with mutational signature 4 representing the characteristic C>A transversions produced by smoking. Whilst smoking cessation has been shown to reduce lung cancer risk in epidemiological studies, there has been little exploration into the persistence of smoking 4 in NSCLC genomes after a patient has quit smoking. We investigated the extent and persistence of signature 4 in NSCLC genomes of current, ex- and never-smokers, correlating in particular with clinical history of smoking cessation.

Methods 132 NSCLC samples were resected from 131 patients in Greater Manchester. These samples were submitted to the 100,000 Genomes Project (Genomics England). WGS was performed on tumour specimens and matched blood samples. Data generated was processed by a standard pipeline devised by Genomics England. Tumour mutational burden (TMB), mutational signatures and copy number variation (CNV) were obtained. Clinical data collected included: smoking status, date of diagnosis, TNM stage, date of relapse and date of death (where relevant). Fisher's exact tests and Kruskal-Wallis tests were used for statistical comparisons, with Kaplan-Meier plots for survival.

Results Signature 4 was associated with a smoking history in 102/119 (85.7%) NSCLCs with a detailed smoking history available. In 17/119 (14.3%) patients with a smoking history but no signature 4 NSCLC, 15/17 (88.2%) patients quit smoking a median of 22 years ago (range 0.006 - 45 years). 6/7 (85.7%) never-smoker NSCLCs were non-signature 4 NSCLCs. 60/75 (80%) ex-smokers had sufficient smoking data to assess signature 4 persistence. Signature 4 endured in the lung tissue prior to tumour diagnosis for a median of 180 months (15 years) (range 1 - 600 months). There was no association between the time of smoking cessation and the time to NSCLC diagnosis (R2=0.0009, p=0.82). Non-signature 4 NSCLCs had a more diverse signature profile (signature 4: mean 4.36, 95% CI 4.13-4.58; non-signature 4: mean 5.52, 95% CI 4.95-6.09; p=<0.0001) with a lower TMB (signature 4: median 9.76/Mb, 95% CI 9.8-12.7; non-signature 4: median 2.02/Mb, 95% CI 1.3-9.3; p=<0.0001). There was no difference in relapse-free survival between signature 4 and non-signature 4 patients with early stage disease (signature 4: median 456 days, HR 0.999, 95% CI 0.419-2.385; non-signature 4: median 319 days, HR 1.001, 95% CI 0.417-2.399).

Conclusion The genomic alterations introduced by smoking persist for many years after smoking cessation. NSCLCs arising from smoking carry a distinctive identity compared to those from never-smokers, with higher TMBs driven primarily by signature 4. Whilst survival analysis is limited in this cohort, the pervasive contributions from smoking suggest that lung cancer screening programmes should include all patients with a smoking history.

Citation Format: Pantelis A. Nicola, Shereen Rafee, George Burghel, Andrew Wallace, Helene Schlecht, Eleanor Baker, Katie Baker, Lynsey Priest, Mathew Carter, Sharzad Moghadam, Jane Rogan, Robert G. Bristow, William Newman, Fiona H. Blackhall, Colin Lindsay. Persistence of smoking signature 4 in the non-small cell lung cancer genome [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3810.

Does following optimized routes for single cars improve car routing?

We study the impact of deserting a pre-established path, determined by a navigation software, on the overall city traffic. To do so, we consider a cellular automaton model for vehicular traffic, where the cars travel between two randomly assigned points in the city following three different navigation strategies based on the minimization of the individual paths or travel times. We found, in general, that, above a critical car density, the transport improves in all strategies if we decrease the time that the vehicles persist in trying to follow a particular strategy when a route is blocked, namely, the mean flux increases, the individual travel times decrease, and the fluctuations of density in the streets decrease; consequently, deserting helps prevent traffic jams.

Abstract B49: “Triple wild-type” co-mutational profile in early-stage KRAS-mutant lung cancer

Introduction: Kirsten rat sarcoma viral oncogene (KRAS) is the most frequently mutated oncogene in non-small cell lung cancer (NSCLC), occurring in approximately 30% of cases. Recent work suggests KRAS -mutant (KRASm) NSCLC is a microcosm for diverse immune checkpoint inhibitor responses, partly dictated by its co-mutation with TP53 (“KP” group=~1/3 cases, “immune hot”), STK11 (“KL” group=~1/3 cases, “immune cold”) or CDKN2A (“KC” group=~1/3 cases). Here we identify and describe genomic and clinical associations of a further subset of KRASm NSCLC defined by “triple WT” status for common KRASm co-mutations.

Method: Sequencing results from 364 early-stage NSCLC cases from the Cancer Research UK TRACERx program (whole-exome sequencing) and the Genomics England 100,000 genome program (whole-genome sequencing) were analyzed for KRASm, associated co-mutations in TP53, STK11 and CDKN2A, copy number changes in the RAS-RAF-MEK-ERK axis, tumor mutational burden (TMB) and mutational signatures. Clinical demographics and factors including tumor size, nodal status and stage were ascertained and assessed for statistical associations with sequencing data using the Mann-Whitney and Fisher’s exact tests.

Results: Overall, 143/364 lung cancer cases (39%) were KRASm with 65/143 (45%) tumors identified as “KP,” 26/143 (18%) as “KL,” and 3/143 (2%) as “KC.” There were 49/143 KRASm cases (34%) with no co-mutation in TP53, STK11 or CDKN2A, defined as “triple wild-type” (triple WT). Relative to the KP, KL and KC genotypes, there was a positive association of the KRAS G12D mutation with triple WT status: 10/49 cases, 20%; KP/KL/KC: 6/94 cases, 6%; p=0.022). In the 100,000-genome cohort, TMB was similar for the triple WT and KL groups but significantly lower than that observed for KP (KP: median 10.55 mut/Mb, 95% CI 8.8-15.33; triple WT: median 6.96, 95% CI 4.87-12.53; p=0.036). Despite this lower median TMB, smoking-associated mutational signature 4 was common in triple WT tumors (triple WT: 13/14 pts, 93%; overall 76/114 pts, 67%). In the triple WT group overall, there was a reduction of >50% in cancers with copy number changes of NF1 and NRAS. There was an inverse association between pathologic stage III tumors and KRASm triple WT genotype (p=0.0014).

Conclusion: There are a significant proportion of KRASm NSCLC patients whose tumors are triple WT for TP53, STK11 and CDKN2A. Despite their high frequency of smoking-associated mutational signatures, these tumors are characterized by low TMB and are more common in early-stage disease. They also associate more commonly with KRAS G12D. Our observations suggest a discrete KRASm subset that may have implications for stratification in trials of immune checkpoint inhibitors and/or targeted therapeutics of KRASm tumors.

Citation Format: Colin R. Lindsay, Pantelis Nicola, Mariam Jamal-Hanjani, Andrew Wallace, Gareth Wilson, George Burghel, Helene Schlecht, Katie Baker, Eleanour Baker, Lynsey Priest, Jane Rogan, Sharzad Moghadam, Mathew Carter, Caroline Dive, Robert G. Bristow, Charles Swanton, William Newman, Fiona Blackhall. “Triple wild-type” co-mutational profile in early-stage KRAS-mutant lung cancer [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr B49.

Abstract 1763: Tumor mutational burden, mutational signatures and copy number variation in lung cancer driven by the Ras-Raf-MEK-ERK pathway

Introduction: Lung cancer is the most common cause of cancer-related death. Kirsten rat sarcoma viral oncogene (KRAS) is the most frequently mutated gene in non-small cell lung cancer (NSCLC), occurring in approximately 30% of cases. We characterised the genomic landscape of NSCLCs with an aberrant Ras-Raf-MEK-ERK pathway.

Methods: 121 Greater Manchester patients with resected NSCLC were recruited into the UK 100,000 Genomes Project (Genomics England). Whole genome sequencing (WGS) was performed on tumor specimens and matched blood samples. Data generated was processed by a standard pipeline devised by Genomics England, then mined for mutations in the Ras-Raf-MEK-ERK pathway. NF1 mutation was assessed as a positive control for RAS pathway activation. Tumor mutational burden (TMB), mutational signature profiles and copy number variation (CNV) were also obtained. Clinical characteristics including tumor size, nodal status and stage were documented. Mann-Whitney and Fisher’s exact tests were used for statistical comparisons.

Results: Cancers from 42/121 (34.7%) patients (pts) had a RAS variant, of which 40/42 (95.2%) were KRAS alterations. A single NRAS-mutant adenocarcinoma (Q61L) was identified, as was a HRAS variant, not previously observed in squamous lung cancer (Q61L). Codon 12 was the most frequently mutated KRAS site with four mutant alleles (G12C 17/40 pts, G12V 6/40, G12D 4/40, G12A 2/40). Median TMB was not significantly different between KRAS-mutant cases (8.06, range 1.84-55.2) and KRAS-wildtype samples (7.1, range 0.98-45.32) (p=0.3). Smoking-associated signature 4 was the most common mutational process (37/40 pts, median 50%, range 20-70%), appearing in a mutually exclusive fashion from the intrinsic signature 1 (3/40 pts, median 20% range 10-30%). 47/121 pts (38.8%) showed a KRAS CNV with 34/47 (72.3%) being gains. For NF1, 12/121 (9.9%) variants were identified. 6/12 (50%) were missense variants, each with a different codon affected (5/12 splice site variants, 1/12 frameshift). Median TMB was not significantly higher in NF1-mutants (NF1m: median 11.54, range 4.47-28.27; NF1 WT: median 7.1, 0.98-55.2; p=0.065) and mutational signature 4 was again the most common (11/12, median 40%, range 20-60%). 37/121(30.6%) samples showed NF1 CNV, the majority of which were surprisingly gains (25/37 pts, 67.6%). In terms of clinical outcome, neither KRAS-mutant or NF1-mutant tumors were more likely to occur in later stage III disease (KRASm: 9/30 pts, 30%, p=0.817; NF1m: 5/11 cases, 45.5%; p=0.326).

Conclusions: Approximately one half of this NSCLC cohort recruited from Greater Manchester carried a Ras-Raf-MEK-ERK pathway aberration. These KRAS-mutant tumors were often at an early stage and driven by tobacco as their main aetiological process. The mutual exclusivity of signature 4 and 1 suggests there are further complexities to be established in Ras-driven NSCLC.

Citation Format: Pantelis A. Nicola, George Burghel, Andrew Wallace, Helene Schlecht, Eleanor Baker, Katie Baker, Lynsey Priest, Mathew Carter, Sharzad Moghadam, Jane Rogan, Robert G. Bristow, William Newman, Fiona Blackhall, Colin R. Lindsay. Tumor mutational burden, mutational signatures and copy number variation in lung cancer driven by the Ras-Raf-MEK-ERK pathway [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1763.

The Human In Vivo Biomolecule Corona onto PEGylated Liposomes: A Proof-of-Concept Clinical Study

The self-assembled layered adsorption of proteins onto nanoparticle (NP) surfaces, once in contact with biological fluids, is termed the "protein corona" and it is gradually seen as a determinant factor for the overall biological behavior of NPs. Here, the previously unreported in vivo protein corona formed in human systemic circulation is described. The human-derived protein corona formed onto PEGylated doxorubicin-encapsulated liposomes (Caelyx) is thoroughly characterized following the recovery of liposomes from the blood circulation of ovarian carcinoma patients. In agreement with previous investigations in mice, the in vivo corona is found to be molecularly richer in comparison to its counterpart ex vivo corona. The intravenously infused liposomes are able to scavenge the blood pool and surface-capture low-molecular-weight, low-abundance plasma proteins that cannot be detected by conventional plasma proteomic analysis. This study describes the previously elusive or postulated formation of protein corona around nanoparticles in vivo in humans and illustrates that it can potentially be used as a novel tool to analyze the blood circulation proteome.

The HER3 pathway as a potential target for inhibition in patients with biliary tract cancers

INTRODUCTION

Expression of human epidermal growth factor receptor (HER)2 and HER3 have been investigated in small BTC studies using variable scoring systems.

METHODS

HER2 and HER3 overexpression/amplification were explored following internationally agreed guidelines using immunohistochemistry (IHC) and fluorescent in-situ hybridisation (FISH), respectively. Logistic regression and survival analysis (Kaplan Meier, Log rank test and Cox Regression) were used for statistical analysis.

RESULTS

Sixty-seven eligible patients with Stage I/II (31.3%) or III/IV (68.7%) disease at diagnosis were included. Membrane HER2 overexpression/amplification was identified in 1 patient (1%). HER3 overexpression was predominantly cytoplasmic; the rate of overexpression/amplification of HER3 in membrane and cytoplasm was 16% [ampullary cancer (AMP) (1/13; 8%), gallbladder cancer (GBC) (1/10; 10%), intra-hepatic cholangiocarcinoma (ICC) (6/26; 23%), extra-hepatic cholangiocarcinoma (ECC) (3/18; 17%)] and 24% [AMP (1/13; 8%), GBC (1/10; 10%), ICC (10/26; 38%), ECC (4/18; 22%)], respectively.

CONCLUSIONS

A significant subset of patients with BTC expressed HER3. Inhibition of HER3 warrants further investigation. A better understanding of the downstream effects of HER3 in BTC requires further mechanistic investigations to identify new biomarkers and improve patient selection for future clinical trials.

Growth of Ni nanoclusters on irradiated graphene: a molecular dynamics study

We studied the soft landing of Ni atoms on a previously damaged graphene sheet by means of molecular dynamics simulations. We found a monotonic decrease of the cluster frequency as a function of its size, but few big clusters comprise an appreciable fraction of the total number of Ni atoms. The aggregation of Ni atoms is also modeled by means of a simple phenomenological model. The results are in clear contrast with the case of hard or energetic landing of metal atoms, where there is a tendency to form mono-disperse metal clusters. This behavior is attributed to the high diffusion of unattached Ni atoms, together with vacancies acting as capture centers. The findings of this work show that a simple study of the energetics of the system is not enough in the soft landing regime, where it is unavoidable to also consider the growth process of metal clusters.

PD-L1 expression and presence of TILs in small intestinal neuroendocrine tumours

BACKGROUND

The extent of resistance to immune surveillance in patients with well-differentiated (Wd) (grade 1/2) small-intestinal neuroendocrine tumours (Si-NETs) is unknown.

METHODS

Patients diagnosed with Wd Si-NETs (excluding appendix, which are considered to have a different biology to other midgut NETs) were eligible. Tumoural programmed death (PD)-ligand(L) 1 (PD-L1)/PD-L2/PD-1 and tumour infiltrating lymphocytes (TILs) [presence and phenotype] were analysed in archival tissue by immunohistochemistry (IHC); reverse transcription quantitative polymerase chain reaction (RT-qPCR) was used for confirmation of IHC results.

RESULTS

Of 109 patients screened, 62 were eligible: 54.8% were male; median age was 63.7 years (95%-CI 59.7-67.2); disease stage II: 4.8%, III: 40.3% and IV: 54.8%; 41.9% were functional. Analysed samples (67.1% from primary tumours, 32.9% from metastases) were of grade 1 (67.1%) or 2 (32.86%) with a median Ki-67 of 2%. From the total of 62 eligible patients, 70 and 63 samples were suitable for IHC and RT-qPCR analysis, respectively. PD-L1 expression within tumour cells and TILs were identified in 12.8% and 24.3% of samples respectively; 30% of samples showed PD-L1 expression within tumour cells and/or TILs. PD-1 was present in TILs in 22.8% of samples. Majority of samples showed significant presence of CD4+ (focal 42.86%; moderate 2.86%) and CD8+ (focal 92.86%; moderate 4.29%) TILs. IHC findings were confirmed with RT-qPCR; which showed higher expression levels of PD-L1 (p-value 0.007) and PD-1 (p-value 0.001) in samples positive for IHC compared to negative-IHC.

CONCLUSIONS

Thirty-percent of patients express PD-L1 within tumour cells and/or TILs. Identification of presence of TILs was also significant and warrant the investigation of immunotherapy in this setting.

Abstract 470: Application of sequencing, liquid biopsies and patient derived xenografts for personalized medicine in melanoma

BRAF/MEK inhibitors and immunotherapies have revolutionized care for patients with advanced melanoma, improving expected median survival from 9 months to 25-30 months, but the majority of patients still die of their disease. Personalized medicine strives to individualize and improve patient care. To individualize treatment decisions in advanced melanoma we analyzed 364 samples from 214 patients. We performed whole exome sequencing (WES) and circulating tumor DNA (ctDNA) analysis, and we developed patient derived xenografts (PDX). WES and targeted sequencing of ctDNA allowed us to predict responses to therapy and to identify and monitor mechanisms of resistance. WES of tumors revealed new therapeutic strategies in BRAF V600 wild-type and BRAF inhibitor-resistant melanoma and we validated these in patient derived xenografts (PDX). Thus, we describe a powerful combination of techniques for personalized medicine to improve the management of melanoma patients.

Citation Format: Maria R. Girotti, Gabriela Gremel, Rebecca Lee, Elena Galvani, Dominic Rothwell, Amaya Viros, Amit Kumar Mandal, Kok Haw Jonathan Lim, Grazia Saturno, Simon J Furney, Franziska Baenke, Malin Pedersen, Jane Rogan, Jacqueline Swan, Matthew Smith, Alberto Fusi, Deemesh Oudit, Nathalie Dhomen, Ged Brady, Caroline Dive, Richard Marais. Application of sequencing, liquid biopsies and patient derived xenografts for personalized medicine in melanoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 470.

Application of Sequencing, Liquid Biopsies, and Patient-Derived Xenografts for Personalized Medicine in Melanoma

Targeted therapies and immunotherapies have transformed melanoma care, extending median survival from ∼9 to over 25 months, but nevertheless most patients still die of their disease. The aim of precision medicine is to tailor care for individual patients and improve outcomes. To this end, we developed protocols to facilitate individualized treatment decisions for patients with advanced melanoma, analyzing 364 samples from 214 patients. Whole exome sequencing (WES) and targeted sequencing of circulating tumor DNA (ctDNA) allowed us to monitor responses to therapy and to identify and then follow mechanisms of resistance. WES of tumors revealed potential hypothesis-driven therapeutic strategies for BRAF wild-type and inhibitor-resistant BRAF-mutant tumors, which were then validated in patient-derived xenografts (PDX). We also developed circulating tumor cell-derived xenografts (CDX) as an alternative to PDXs when tumors were inaccessible or difficult to biopsy. Thus, we describe a powerful technology platform for precision medicine in patients with melanoma.

SIGNIFICANCE

Although recent developments have revolutionized melanoma care, most patients still die of their disease. To improve melanoma outcomes further, we developed a powerful precision medicine platform to monitor patient responses and to identify and validate hypothesis-driven therapies for patients who do not respond, or who develop resistance to current treatments.

Increased peri-ductal collagen micro-organization may contribute to raised mammographic density

BACKGROUND

High mammographic density is a therapeutically modifiable risk factor for breast cancer. Although mammographic density is correlated with the relative abundance of collagen-rich fibroglandular tissue, the causative mechanisms, associated structural remodelling and mechanical consequences remain poorly defined. In this study we have developed a new collaborative bedside-to-bench workflow to determine the relationship between mammographic density, collagen abundance and alignment, tissue stiffness and the expression of extracellular matrix organising proteins.

METHODS

Mammographic density was assessed in 22 post-menopausal women (aged 54-66 y). A radiologist and a pathologist identified and excised regions of elevated non-cancerous X-ray density prior to laboratory characterization. Collagen abundance was determined by both Masson's trichrome and Picrosirius red staining (which enhances collagen birefringence when viewed under polarised light). The structural specificity of these collagen visualisation methods was determined by comparing the relative birefringence and ultrastructure (visualised by atomic force microscopy) of unaligned collagen I fibrils in reconstituted gels with the highly aligned collagen fibrils in rat tail tendon. Localised collagen fibril organisation and stiffness was also evaluated in tissue sections by atomic force microscopy/spectroscopy and the abundance of key extracellular proteins was assessed using mass spectrometry.

RESULTS

Mammographic density was positively correlated with the abundance of aligned periductal fibrils rather than with the abundance of amorphous collagen. Compared with matched tissue resected from the breasts of low mammographic density patients, the highly birefringent tissue in mammographically dense breasts was both significantly stiffer and characterised by large (>80 μm long) fibrillar collagen bundles. Subsequent proteomic analyses not only confirmed the absence of collagen fibrosis in high mammographic density tissue, but additionally identified the up-regulation of periostin and collagen XVI (regulators of collagen fibril structure and architecture) as potential mediators of localised mechanical stiffness.

CONCLUSIONS

These preliminary data suggest that remodelling, and hence stiffening, of the existing stromal collagen microarchitecture promotes high mammographic density within the breast. In turn, this aberrant mechanical environment may trigger neoplasia-associated mechanotransduction pathways within the epithelial cell population.

Abstract 2432: A technology platform for personalized medicine in melanoma

We developed patient derived xenografts (PDX), performed whole exome sequencing (WES) and analyzed circulating tumor DNA (ctDNA) to complement clinical management of four melanoma patients. Synchronous treatment of patients and mice showed that PDX responses mirrored those of the patients’ tumor to BRAF inhibitors. PDXs were used to test second-line treatments in relapsed patients and to validate WES-based therapies in tumors that did not have a BRAF mutation. Longitudinal analysis of ctDNA was predictive of responses to targeted and immunotherapies, and to determine mechanisms of resistance. Thus, we describe a powerful combination of techniques for personalized medicine in melanoma and discuss the challenges and limitations of implementing these novel technologies in patient management.

Citation Format: Maria R. Girotti, Dominic Rothwell, Amaya Viros, Amit Kumar Mandal, Kok Haw J. Lim, Gabriela Gremel, Simon Furney, Malin Pedersen, Jane Rogan, Jacqueline Swan, Alberto Fusi, Ged Brady, Paul Lorigan, Caroline Dive, Richard Marais. A technology platform for personalized medicine in melanoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2432. doi:10.1158/1538-7445.AM2015-2432

Optimizing sharing of hospital biobank samples

Implementing technical guidelines and standards as well as ways to boost cooperation should facilitate sharing of hospital biobank samples.

Emerging findings in the Cancer Research UK stratified medicine program

TPS10633^

Background: Molecular analysis of tumours may be used to identify those predicted to benefit from novel targeted therapies. The Cancer Research UK programme is piloting plans to apply such testing broadly across the UK healthcare system, linking molecular phenotype to clinical outcomes. Methods: The Stratified Medicine Programme (SMP) aims to develop a model for high quality, large-scale molecular characterization of cancer specimens through an initiative developed in partnership with AstraZeneca, Pfizer, the UK Department of Health and academic researchers. Phase One of the SMP is a two year feasibility study. It aims to demonstrate the submission of consented blood samples and sections of surplus diagnostic formalin-fixed paraffin-embedded tumour tissue from 9,000 patients at centres across the UK to one of three ‘technology hubs’ for mutation testing of genes of potential clinical interest (KRAS, BRAF, NRAS, PIK3CA, TP53, PTEN, TMPRSS2-ERG, EGFR, EML4-ALK and KIT) in six selected tumour types. The tests are technically validated and will be completed in clinically relevant timescales. Data including pathological and treatment information and clinical outcome is also collected for the recruited patients, linked to the genetic data and stored in a central data repository hosted within the National Cancer Registration Service. The study opened in September 2011 at 7 sites across the UK and by the end of 2011, 760 patientswith breast, lung, prostate, colorectal, ovarian cancer or metastatic malignant melanoma had consented to participate. 142 sets of molecular results had been returned to clinical teams. Updated figures will be presented at the meeting, by which time the programme is projected to have accrued 4000 subjects. By 2013, we hope to have developed a scalable model for routine, high quality, prospective molecular characterisation of tumours for NHS cancer patients, with consent for the collection, storage and research use of population-scale genetic and clinical outcome data. We will report the emerging results from the Stratified Medicines Programme and early insights into implications for wider implementation across the UK healthcare system.

Optimization of photoluminescence of Y(2)O(3):Eu and Gd(2)O(3):Eu phosphors synthesized by thermolysis of 2,4-pentanedione complexes

Spherical shaped nanoparticles of series Y(2 - x)Eu(x)O(3) (x = 0.06, 0.10, 0.20, and 2) and Gd(2 - x)Eu(x)O(3) (x = 0.06, 0.10) were prepared by thermolysis of 2,4-pentanedione complexes of Y, Gd, and Eu. The bixbyite phase of Gd(2 - x)Eu(x)O(3) samples was formed at 500 degrees C, whereas the thermal decomposition of Y and Eu complexes' mixtures occurred at higher temperatures. Linearity in the concentration dependence on lattice parameter confirmed the formation of solid solutions. The distribution of Eu(3+) in Gd(2 - x)Eu(x)O(3) was changed with thermal annealing: in the as-prepared sample (x = 0.10) the distribution was preferential at C(3i) sites while in the annealed samples, Eu(3+) were distributed at both C(2) and C(3i) sites. Rietveld refinement of site occupancies as well as emission spectra showed a random distribution of cations in Y(2 - x)Eu(x)O(3). The photoluminescence (PL) measurements of the sample showed red emission with the main peak at 614 nm ((5)D(0)-(7)F(2)). The PL intensity increased with increasing concentration of Eu(3+) in both series. Infrared excitation was required to obtain good Raman spectra. The linear dependence of the main Raman peak wavenumber offers a non-destructive method for monitoring the substitution level and its homogeneity at the micron scale.

Characterization of the nontrivial and chaotic behavior that occurs in a simple city traffic model

We explore in detail the nontrivial and chaotic behavior of the traffic model proposed by Toledo et al. [Phys. Rev. E 70, 016107 (2004)] due to the richness of behavior present in the model, in spite of the fact that it is a minimalistic representation of basic city traffic dynamics. The chaotic behavior, previously shown for a given lower bound in acceleration/brake ratio, is examined more carefully and the region in parameter space for which we observe this nontrivial behavior is found. This parameter region may be related to the high sensitivity of traffic flow that eventually leads to traffic jams. Approximate scaling laws are proposed.

Resonance, criticality, and emergence in city traffic investigated in cellular automaton models

The complex behavior that occurs when traffic lights are synchronized is studied for a row of interacting cars. The system is modeled through a cellular automaton. Two strategies are considered: all lights in phase and a "green wave" with a propagating green signal. It is found that the mean velocity near the resonant condition follows a critical scaling law. For the green wave, it is shown that the mean velocity scaling law holds even for random separation between traffic lights and is not dependent on the density. This independence on car density is broken when random perturbations are considered in the car velocity. Random velocity perturbations also have the effect of leading the system to an emergent state, where cars move in clusters, but with an average velocity which is independent of traffic light switching for large injection rates.

Optimal control in a noisy system

We describe a simple method to control a known unstable periodic orbit (UPO) in the presence of noise. The strategy is based on regarding the control method as an optimization problem, which allows us to calculate a control matrix A. We illustrate the idea with the Rossler system, the Lorenz system, and a hyperchaotic system that has two exponents with positive real parts. Initially, a UPO and the corresponding control matrix are found in the absence of noise in these systems. It is shown that the strategy is useful even if noise is added as control is applied. For low noise, it is enough to find a control matrix such that the maximum Lyapunov exponent lambda(max)<0, and with a single non-null entry. If noise is increased, however, this is not the case, and the full control matrix A may be required to keep the UPO under control. Besides the Lyapunov spectrum, a characterization of the control strategies is given in terms of the average distance to the UPO and the control effort required to keep the orbit under control. Finally, particular attention is given to the problem of handling noise, which can affect considerably the estimation of the UPO itself and its exponents, and a cleaning strategy based on singular value decomposition was developed. This strategy gives a consistent manner to approach noisy systems, and may be easily adapted as a parametric control strategy, and to experimental situations, where noise is unavoidable.

Effect of pre-stress on the yield and flow of En 25 steel

Combined tension-torsion tests have been performed at constant stress ratios on En 25 steel, previously annealed and then subjected to a pre-stress in either tension or torsion.

The post-yield behaviour showed marked room-temperature creep and, in general, both the axial- and the shear-strain components could be expressed by the logarithmic creep equation. The direction of the incremental strain-ratio vector was initially markedly different from that shown in the previous tests on annealed En 25 steel, but rotated towards that direction with increased stress. The yield locus subsequent to each pre-stress was established by fulfilling two requirements: that it must pass through the stress space normal to all the plastic-strain-increment vectors it encounters; that each yield stress should be an extrapolation from the curves of creep coefficient plotted against stress and stress plotted against ‘long time’ strain.

The results show that a pre-stress hardens the material over that half of biaxial stress space bisected by the pre-stress axis and hardens it less or even softens it in the reverse half of that space. The cross-effect of a tensile pre-stress is greater than that of a torsion pre-stress and increasing the degree of pre-stress has a gradually reducing cross-effect.

Yield and subsequent flow behaviour of some annealed steels under combined stress

Constant-stress-ratio tests under combined tension-torsion have been performed on annealed En 25 and En 24 steels. The sharp yield behaviour of these materials enabled the initial yield locus to be clearly defined and this was close to that predicted by the Tresca criterion. Post-yield behaviour showed marked room-temperature creep of the logarithmic form ∊ = a ln t+ c, by both the axial- and shear-strain components. The strain-rate ratios and the strain ratios were normal to the yield locus and remained so for increasing stress.

The equivalent-plastic-work hypothesis did not produce satisfactory correlation of the combined-stress results and empirical equivalence of the strains was established by introducing a factor to account for the influence of combined stresses upon the magnitude of the resulting strains. This empirical equivalence also provided good correlation of the creep-strain rates and these results finally led to the complete correlation of the stress-strain-time behaviour of these materials at room temperature.

Universal and nonuniversal features in a model of city traffic

The complex behavior that occurs when traffic lights are synchronized is studied. Two strategies are considered: all lights in phase, and a "green wave" with a propagating green signal. It is found that traffic variables such as traveling time, velocity, and fuel consumption, near resonance, follow critical scaling laws. For the green wave, it is shown that time and velocity scaling laws hold even for random separation between traffic lights. These results suggest the concept of transient resonances, which can be induced by adaptively changing the phase of traffic lights. This may be important to consider when designing strategies for traffic control in cities, where short trajectories, and thus transient solutions, are likely to be relevant.

Modeling traffic through a sequence of traffic lights

We introduce a microscopic traffic model, based on kinematic behavior, which consists of a single vehicle traveling through a sequence of traffic lights that turn on and off with a specific frequency. The reconstructed function that maps the state of the vehicle from light to light displays complex behavior for certain conditions. This chaotic behavior, which arises by the discontinuous nature of the map, displays an essential ingredient in traffic patterns and could be of relevance in studying traffic situations.

EVA: a new theoretically based molecular descriptor for use in QSAR/QSPR analysis

A new descriptor of molecular structure, EVA, for use in the derivation of robustly predictive QSAR relationships is described. It is based on theoretically derived normal coordinate frequencies, and has been used extensively and successfully in proprietary chemical discovery programmes within Shell Research. As a result of informal dissemination of the methodology, it is now being used successfully in related areas such as pharmaceutical drug discovery. Much of the experimental data used in development remain proprietary, and are not available for publication. This paper describes the method and illustrates its application to the calculation of nonproprietary data, log P(ow), in both explanatory and predictive modes. It will be followed by other publications illustrating its application to a range of data derived from biological systems.

Indobufen in secondary prevention of transient ischaemic attack. Multicentre Ischaemic Attack Study Group

The secondary prevention of transient ischaemic attacks was assessed in 270 patients treated orally with 100 mg indobufen given twice daily for 12 months. After 1 month's treatment, the average number and average incidence of transient ischaemic attacks were reduced significantly (P less than 0.001) and remained suppressed throughout the treatment period. Treatment was interrupted in 17 patients: in two because of side-effects (gastric disturbances); in 10 because of fatal events (six completed strokes, two myocardial infarcts and two unrelated deaths); and in five due to poor protocol compliance. Progression to reversible ischaemic neurological deficit occurred in five patients. Most side-effects were mild and transient, mainly occurring in the first month of treatment. Overall, indobufen was judged to have good efficacy and safety by both patients and physicians.