A Mathematical Study of the Influence of Hypoxia and Acidity on the Evolutionary Dynamics of Cancer

Hypoxia and acidity act as environmental stressors promoting selection for cancer cells with a more aggressive phenotype. As a result, a deeper theoretical understanding of the spatio-temporal processes that drive the adaptation of tumour cells to hypoxic and acidic microenvironments may open up new avenues of research in oncology and cancer treatment. We present a mathematical model to study the influence of hypoxia and acidity on the evolutionary dynamics of cancer cells in vascularised tumours. The model is formulated as a system of partial integro-differential equations that describe the phenotypic evolution of cancer cells in response to dynamic variations in the spatial distribution of three abiotic factors that are key players in tumour metabolism: oxygen, glucose and lactate. The results of numerical simulations of a calibrated version of the model based on real data recapitulate the eco-evolutionary spatial dynamics of tumour cells and their adaptation to hypoxic and acidic microenvironments. Moreover, such results demonstrate how nonlinear interactions between tumour cells and abiotic factors can lead to the formation of environmental gradients which select for cells with phenotypic characteristics that vary with distance from intra-tumour blood vessels, thus promoting the emergence of intra-tumour phenotypic heterogeneity. Finally, our theoretical findings reconcile the conclusions of earlier studies by showing that the order in which resistance to hypoxia and resistance to acidity arise in tumours depend on the ways in which oxygen and lactate act as environmental stressors in the evolutionary dynamics of cancer cells

An efficient 2D inversion scheme for airborne frequency domain data

In many cases, inversion in 2D gives a better description of the subsurface compared with 1D inversion, but, computationally, 2D inversion is expensive, and it can be hard to use for large-scale surveys. We have developed an efficient hybrid 2D airborne frequency-domain electromagnetic inversion algorithm. Our hybrid scheme combines 1D and 2D inversions in a three-stage process, in which each step is progressively more accurate and computationally more expensive than the previous one. This results in an approximately 2x - 6x speedup compared with full 2D inversions, and with only minor changes to the inversion results. Our inversion structure is based on a regular grid, in which each sounding is discretized individually. The 1D modeling code uses layered models with derivatives derived through the finite-difference method, whereas our 2D modeling code uses an adaptive finite-element mesh, and it uses the adjoint-state method to calculate the derivatives. By incorporating the inversion grid structure into the 2D finite-element mesh, interpolation between the different meshes becomes trivial. Large surveys are handled by using local meshing to split large surveys into small sections, which retains the 2D information. The algorithm is heavily optimized and parallelized over the frequencies and sections, with good scalability even on nonuniform memory architecture systems, on which it is generally hard to achieve a satisfactory scaling. The algorithm has been tested successfully with various synthetic studies as well as field examples, of which results from two synthetic studies and a field example are shown

Subsurface imaging of water electrical conductivity, hydraulic permeability and lithology at contaminated sites by induced polarization

At contaminated sites, knowledge about geology and hydraulic properties of the subsurface and extent of the contamination is needed for assessing the risk and for designing potential site remediation. In this study, we have developed a new approach for characterizing contaminated sites through time-domain spectral induced polarization. The new approach is based on: (1) spectral inversion of the induced polarization data through a reparametrization of the Cole-Cole model, which disentangles the electrolytic bulk conductivity from the surface conductivity for delineating the contamination plume; (2) estimation of hydraulic permeability directly from the inverted parameters using a laboratory-derived empirical equation without any calibration; (3) the use of the geophysical imaging results for supporting the geological modelling and planning of drilling campaigns. The new approach was tested on a data set from the Grindsted stream (Denmark), where contaminated groundwater from a factory site discharges to the stream. Two overlapping areas were covered with seven parallel 2-D profiles each, one large area of 410 m 790m(5melectrode spacing) and one detailed area of 126m 742m(2melectrode spacing). The geophysical results were complemented and validated by an extensive set of hydrologic and geologic information, including 94 estimates of hydraulic permeability obtained from slug tests and grain size analyses, 89 measurements of water electrical conductivity in groundwater, and four geological logs. On average the IP-derived and measured permeability values agreed within one order of magnitude, except for those close to boundaries between lithological layers (e.g. between sand and clay), where mismatches occurred due to the lack of vertical resolution in the geophysical imaging. An average formation factor was estimated from the correlation between the imaged bulk conductivity values and the water conductivity values measured in groundwater, in order to convert the imaging results from bulk conductivity to water conductivity. The geophysical models were actively used for supporting the geological modelling and the imaging of hydraulic permeability andwater conductivity allowed for a better discrimination of the clay/lignite lithology from the porewater conductivity. Furthermore, high water electrical conductivity values were found in a deep confined aquifer, which is separated by a low-permeability clay layer from a shallow aquifer. No contamination was expected in this part of the confined aquifer, and confirmation wells were drilled in the zone of increased water electrical conductivity derived from the geophysical results.Water samples from the new wells showed elevated concentrations of inorganic compounds responsible for the increased water electrical conductivity in the confined aquifer and high concentrations of xenobiotic organic contaminants such as chlorinated ethenes, sulfonamides and barbiturates

High accuracy genotyping directly from genomic DNA using a rolling circle amplification based assay

BACKGROUND: Rolling circle amplification of ligated probes is a simple and sensitive means for genotyping directly from genomic DNA. SNPs and mutations are interrogated with open circle probes (OCP) that can be circularized by DNA ligase when the probe matches the genotype. An amplified detection signal is generated by exponential rolling circle amplification (ERCA) of the circularized probe. The low cost and scalability of ligation/ERCA genotyping makes it ideally suited for automated, high throughput methods. RESULTS: A retrospective study using human genomic DNA samples of known genotype was performed for four different clinically relevant mutations: Factor V Leiden, Factor II prothrombin, and two hemochromatosis mutations, C282Y and H63D. Greater than 99% accuracy was obtained genotyping genomic DNA samples from hundreds of different individuals. The combined process of ligation/ERCA was performed in a single tube and produced fluorescent signal directly from genomic DNA in less than an hour. In each assay, the probes for both normal and mutant alleles were combined in a single reaction. Multiple ERCA primers combined with a quenched-peptide nucleic acid (Q-PNA) fluorescent detection system greatly accellerated the appearance of signal. Probes designed with hairpin structures reduced misamplification. Genotyping accuracy was identical from either purified genomic DNA or genomic DNA generated using whole genome amplification (WGA). Fluorescent signal output was measured in real time and as an end point. CONCLUSIONS: Combining the optimal elements for ligation/ERCA genotyping has resulted in a highly accurate single tube assay for genotyping directly from genomic DNA samples. Accuracy exceeded 99 % for four probe sets targeting clinically relevant mutations. No genotypes were called incorrectly using either genomic DNA or whole genome amplified sample

GDNF and Parkinson's Disease : Where Next? A Summary from a Recent Workshop

The concept of repairing the brain with growth factors has been pursued for many years in a variety of neurodegenerative diseases including primarily Parkinson's disease (PD) using glial cell line-derived neurotrophic factor (GDNF). This neurotrophic factor was discovered in 1993 and shown to have selective effects on promoting survival and regeneration of certain populations of neurons including the dopaminergic nigrostriatal pathway. These observations led to a series of clinical trials in PD patients including using infusions or gene delivery of GDNF or the related growth factor, neurturin (NRTN). Initial studies, some of which were open label, suggested that this approach could be of value in PD when the agent was injected into the putamen rather than the cerebral ventricles. In subsequent double-blind, placebo-controlled trials, the most recent reporting in 2019, treatment with GDNF did not achieve its primary end point. As a result, there has been uncertainty as to whether GDNF (and by extrapolation, related GDNF family neurotrophic factors) has merit in the future treatment of PD. To critically appraise the existing work and its future, a special workshop was held to discuss and debate this issue. This paper is a summary of that meeting with recommendations on whether there is a future for this therapeutic approach and also what any future PD trial involving GDNF and other GDNF family neurotrophic factors should consider in its design.Peer reviewe

A la recerca del temple d'August a Tarragona: una experiència entre arqueologia i geofísica

La catedral de Tarragona està enclavada en l'espai més elevat de la ciutat. Els romans ocuparen aquest indret a partir de final del segle III aC i el convertiren en el campament militar des d'on iniciaren, a la Península, les lluites contra els cartaginesos, comandats per Anníbal. Tarraco fou punt d'arribada de les tropes que iniciaren la conquesta d'Iberia. En temps de l'emperador August Tarraco fou elevada a la categoria de capital de la Provincia Hispania Citerior i s'hi inicià una sèrie de transformacions urbanístiques d'acord amb el nou rang. És així que l'historiador Tàcit esmenta que l'any 15 dC una representació de tarraconenses van demanar a Tiberi autorització per aixecar un temple de culte al seu antecessor August, que podia haver estat el primer que se li dedicà fora de Roma. Així ens ho indiquen les fonts clàssiques: in omnes provincias exemplum. Finalment, l'epigrafia ens parla de l'existència del Concilium Prouinciae Hispaniae Citerioris, el màxim òrgan provincial. La major part d'estudis arqueològics que s'han desenvolupat fins ara coincideixen a ubicar el temple augustal a l'acròpolis de la ciutat, l'espai actualment ocupat per la catedral medieval de Tarragona

What's in a Name? Shifting Identities of Traditional Organized Crime in Canada in the Transnational Fight against the Calabrian ‘Ndrangheta

The Italian antimafia authorities have warned Canadian law enforcement about the risks and the growing concerns for the infiltration of clans of the Calabrian mafia, known as ‘ndrangheta, in Eastern Canada. The alarm linked to the rise of the ‘ndrangheta challenges the paradigms of traditional organized crime in Canada, because the ‘ndrangheta is presented as traditional but also innovative and more pervasive than other mafia-type groups. Through access to confidential investigations and interviews to key specialist law enforcement teams in Toronto and Montreal, this article investigates today's institutional perception of mafia – the ‘ndrangheta in particular – in Canada when compared to Italian conceptualizations. I will argue that the changes in narratives in Canada can be read in relation to changes in the Italian identity in the country, moving towards regionalization and specialist knowledge of ethnic differences