Mathematics and Morphogenesis of the City: A Geometrical Approach

Cities are living organisms. They are out of equilibrium, open systems that never stop developing and sometimes die. The local geography can be compared to a shell constraining its development. In brief, a city's current layout is a step in a running morphogenesis process. Thus cities display a huge diversity of shapes and none of traditional models from random graphs, complex networks theory or stochastic geometry takes into account geometrical, functional and dynamical aspects of a city in the same framework. We present here a global mathematical model dedicated to cities that permits describing, manipulating and explaining cities' overall shape and layout of their street systems. This street-based framework conciliates the topological and geometrical sides of the problem. From the static analysis of several French towns (topology of first and second order, anisotropy, streets scaling) we make the hypothesis that the development of a city follows a logic of division / extension of space. We propose a dynamical model that mimics this logic and which from simple general rules and a few parameters succeeds in generating a large diversity of cities and in reproducing the general features the static analysis has pointed out.Comment: 13 pages, 13 figure

Modified protocol of harvesting, extraction, and normalization approaches for gas chromatography mass spectrometry-based metabolomics analysis of adherent cells grown under high fetal calf serum conditions

A gas chromatography mass spectrometry (GC-MS) metabolomics protocol was modified for quenching, harvesting, and extraction of metabolites from adherent cells grown under high (20%) fetal calf serum conditions. The reproducibility of using either 50% or 80% methanol for quenching of cells was compared for sample harvest. To investigate the efficiency and reproducibility of intracellular metabolite extraction, different volumes and ratios of chloroform were tested. Additionally, we compared the use of total protein amount versus cell mass as normalization parameters. We demonstrate that the method involving 50% methanol as quenching buffer followed by an extraction step using an equal ratio of methanol:chloroform:water (1:1:1, v/v/v) followed by the collection of 6 mL polar phase for GC-MS measurement was superior to the other methods tested. Especially for large sample sets, its comparative ease of measurement leads us to recommend normalization to protein amount for the investigation of intracellular metabolites of adherent human cells grown under high (or standard) fetal calf serum conditions. To avoid bias, care should be taken beforehand to ensure that the ratio of total protein to cell number are consistent among the groups tested. For this reason, it may not be suitable where culture conditions or cell types have very different protein outputs (e.g., hypoxia vs. normoxia). The full modified protocol is available in the Supplementary Materials

Deep learning-assisted peak curation for large-scale LC-MS metabolomics

Available automated methods for peak detection in untargeted metabolomics suffer from poor precision. We present NeatMS, which uses machine learning based on a convoluted neural network to reduce the number and fraction of false peaks. NeatMS comes with a pre-trained model representing expert knowledge in the differentiation of true chemical signal from noise. Furthermore, it provides all necessary functions to easily train new models or improve existing ones by transfer learning. Thus, the tool improves peak curation and contributes to the robust and scalable analysis of large-scale experiments. We show how to integrate it into different liquid chromatography–mass spectrometry (LC-MS) analysis workflows, quantify its performance, and compare it to various other approaches. NeatMS software is available as open source on github under permissive MIT license and is also provided as easy-to-install PyPi and Bioconda packages

Deep learning assisted peak curation for large scale LC-MS Metabolomics

Available automated methods for peak detection in untargeted metabolomics suffer from poor precision. We present NeatMS which uses machine learning to replace peak curation by human experts. We show how to integrate our open source module into different LC-MS analysis workflows and quantify its performance. NeatMS is designed to be suitable for large scale studies and improves the robustness of the final peak list

Progression-dependent altered metabolism in osteosarcoma resulting in different nutrient source dependencies

Osteosarcoma (OS) is a primary malignant bone tumor and OS metastases are mostly found in the lung. The limited understanding of the biology of metastatic processes in OS limits the ability for effective treatment. Alterations to the metabolome and its transformation during metastasis aids the understanding of the mechanism and provides information on treatment and prognosis. The current study intended to identify metabolic alterations during OS progression by using a targeted gas chromatography mass spectrometry approach. Using a female OS cell line model, malignant and metastatic cells increased their energy metabolism compared to benign OS cells. The metastatic cell line showed a faster metabolic flux compared to the malignant cell line, leading to reduced metabolite pools. However, inhibiting both glycolysis and glutaminolysis resulted in a reduced proliferation. In contrast, malignant but non-metastatic OS cells showed a resistance to glycolytic inhibition but a strong dependency on glutamine as an energy source. Our in vivo metabolic approach hinted at a potential sex-dependent metabolic alteration in OS patients with lung metastases (LM), although this will require validation with larger sample sizes. In line with the in vitro results, we found that female LM patients showed a decreased central carbon metabolism compared to metastases from male patients

Palaeozoic oolitic ironstone of the French Armorican Massif: a chemical and structural trap for orogenic base metal-As-Sb-Au mineralization during Hercynian strike-slip deformation.

In the Saint-Aubin-des-Châteaux quarry (Armorican Hercynian belt, western France), an epigenetic hydrothermal alteration affects an oolitic ironstone layer intercalated within the Lower Ordovician Grès armoricain Formation. The hydrothermal overprint produced pervasive and massive sulphidation with stratoid pyritized lenticular bodies within the oolitic ironstone layer. These sulphide lenses are spatially associated with strike-slip faults and extend laterally from them. Following the massive sulphidation stage (Fe-As, stage 1), subsequent fracturing allowed the deposition of base metals (stage 2) and Pb-Sb-Au (stage 3) parageneses in veins. The dominant brittle structures are vertical extension veins, conjugate shear veins and strike-slip faults of various orders. All these structures are filled with the same paragenetic sequence. Deformation analysis allows the identification of structures that developed incrementally via right lateral simple shear compatible with bulk strain affecting the Central Armorican Domain. Each increment corresponds to a fracture set filled with specific parageneses. Successive hydrothermal pulses reflect clockwise rotation of the horizontal shortening direction. Geothermometry on chlorite and arsenopyrite shows an input of hot hydrothermal fluids (maximum of 390-350°C) during the main sulphide stage 1. The subsequent stages present a marked temperature drop (300-275°C). Lead isotopes suggest that the lead source is similar for all hydrothermal stages and corresponds to the underlying Neo-proterozoic basement. Lead isotope data, relative ages of deformation and comparison with neighbouring deposits suggest large-scale fluid pulses occurred during the whole Hercynian orogeny rather than pulses restricted to the late Hercynian period. The vicinity of the Hercynian internal domain appears as a key-control for deformation and fluid flow in the oolitic ironstones which acted as a chemical and structural trap for the hydrothermal fluids. The epigenetic mineralization of Saint-Aubin-des-Châteaux appears to be very similar to epigenetic sulphidation described in BIF-hosted gold deposits

Дискурсивна стратегія як когнітивно-комунікативний феномен

Статья из специализированного выпуска научного журнала "Культура народов Причерноморья", материалы которого объединены общей темой "Язык и Мир" и посвящены общим вопросам Языкознания и приурочены к 80-летию со дня рождения Николая Александровича Рудякова.Стаття із спеціалізованого випуску наукового журналу "Культура народов Причерноморья", матеріали якого поєднані загальною темою "Мова і Світ" і присвячені загальним питанням мовознавства і приурочені до 80-річчя з дня народження Миколи Олександровича Рудякова

Analysis of adherent cell culture lysates with low metabolite concentrations using the Biocrates AbsoluteIDQ p400 HR kit

The AbsoluteIDQ p400 HR kit is a commercial product for targeted metabolomics. While the kit has been validated for human plasma and serum, adherent cell lysates have not yet been evaluated. We have optimized the detection of polar and lipid metabolites in cell lysates using the kit to enable robust and repeatable analysis of the detected metabolites. Parameters optimized include total cell mass, loading volume and extraction solvent. We present a cell preparation and analytical method and report on the performance of the kit with regard to detectability of the targeted metabolites and their repeatability. The kit can be successfully used for a relative quantification analysis of cell lysates from adherent cells although validated only for human plasma and serum. Most metabolites are below the limit of the Biocrates' set quantification limits and we confirmed that this relative quantification can be used for further statistical analysis. Using this approach, up to 45% of the total metabolites in the kit can be detected with a reasonable analytical performance (lowest median RSD 9% and 13% for LC and FIA, respectively) dependent on the method used. We recommend using ethanol as the extraction solvent for cell lysates of osteosarcoma cell lines for the broadest metabolite coverage and 25 mg of cell mass with a loading volume of 20 µL per sample