Risk and Safety in Engineering Processes

This research project focused on the treatment of safety risks in railways. Existing methodologies for assessment and management of the safety risk on railways are mostly empirical and have been developed out of a need to satisfy the regulatory requirements and in response to a number of major accidents. Almost all of these processes and methodologies have been developed in support of approvals of specific products or very simple systems and do not add up to a holistic coherent methodology suited for analysis of modern, complex systems, involving many vastly different constituents (software, hardware, people, products developed in different parts of the world, etc.). The complexities of modern railway projects necessitate a new approach to risk analysis and management. At the outset, the focus of the research was on the organisation of the family of existing system analysis methodologies into a coherent, heterogeneous methodology. An extensive review of existing methodologies and processes was undertaken and is summarised in this thesis. Relationships between different methodologies and their properties were investigated seeking to define the rules for embedding these into a hierarchical nest and relating their emergent properties. Four projects were utilised as case studies for the evaluation of existing methodologies and processes and initial development. This thesis describes the methodology adopted in support of development of the System Safety Case and the structure of the document. Based on that experience and knowledge a set of high level requirements was identified for an integrated, holistic system safety analysis and management process. A framework consisting of existing and novel methodologies and processes was developed and trialled on a real life project. During the trial several gaps in the process were identified and adequate new methodologies or processes defined and implemented to complete the framework. The trial was very successful and the new framework, referred to as the Engineering Safety Case Management Process is implemented across the London Underground Upgrades Directory

Antioxidant and cytotoxic potential of selected plant species of the boraginaceae family

Antioxidant activity is one of the most important properties of plant extracts. Antioxidants from natural sources have been intensively studied in the last few decades. The antioxidant contents of medicinal plants may contribute to the protection of diseases. Bioactive components of plants have a potential role in chemoprevention and inhibition of different phases of the malignant transformation process. Therefore, plant extracts and essential oils are in the focus of research, and in recent decades have been tested on a large number of malignant cell lines. The aim of this study was to examine antioxidant and cytotoxic potential of selected plant species from the Boraginaceae family. Determination of antioxidant activity was performed by ammonium-thiocyanate method. Testing citotoxic activity was performed by MTT test on cancer cell lines: HEP 2c (human larynx carcinoma), RD (human cell line-rhabdomyosarcoma) and L2OB (mouse tumor fibroblast line). The best antioxidant activity showed ethanol, acetone and chloroform extracts of Anchusa officinalis, Echium vulgare and Echium italicum. The tested extracts showed an inhibitory effect on cancer cells, but chloroform and acetone extracts of all three plant had the most effective effect on L2OB cells. Isolation of individual active components from this plants and their testing for cancer cells would be of great importance for this field of research

Glycolysis downregulation is a hallmark of HIV-1 latency and sensitizes infected cells to oxidative stress

HIV-1 infects lymphoid and myeloid cells, which can harbor a latent proviral reservoir responsible for maintaining lifelong infection. Glycolytic metabolism has been identified as a determinant of susceptibility to HIV-1 infection, but its role in the development and maintenance of HIV-1 latency has not been elucidated. By combining transcriptomic, proteomic, and metabolomic analyses, we here show that transition to latent HIV-1 infection downregulates glycolysis, while viral reactivation by conventional stimuli reverts this effect. Decreased glycolytic output in latently infected cells is associated with downregulation of NAD+/NADH. Consequently, infected cells rely on the parallel pentose phosphate pathway and its main product, NADPH, fueling antioxidant pathways maintaining HIV-1 latency. Of note, blocking NADPH downstream effectors, thioredoxin and glutathione, favors HIV-1 reactivation from latency in lymphoid and myeloid cellular models. This provides a “shock and kill effect” decreasing proviral DNA in cells from people living with HIV/AIDS. Overall, our data show that downmodulation of glycolysis is a metabolic signature of HIV-1 latency that can be exploited to target latently infected cells with eradication strategies

TOMOBFLOW: feature-preserving noise filtering for electron tomography

<p>Abstract</p> <p>Background</p> <p>Noise filtering techniques are needed in electron tomography to allow proper interpretation of datasets. The standard linear filtering techniques are characterized by a tradeoff between the amount of reduced noise and the blurring of the features of interest. On the other hand, sophisticated anisotropic nonlinear filtering techniques allow noise reduction with good preservation of structures. However, these techniques are computationally intensive and are difficult to be tuned to the problem at hand.</p> <p>Results</p> <p>TOMOBFLOW is a program for noise filtering with capabilities of preservation of biologically relevant information. It is an efficient implementation of the Beltrami flow, a nonlinear filtering method that locally tunes the strength of the smoothing according to an edge indicator based on geometry properties. The fact that this method does not have free parameters hard to be tuned makes TOMOBFLOW a user-friendly filtering program equipped with the power of diffusion-based filtering methods. Furthermore, TOMOBFLOW is provided with abilities to deal with different types and formats of images in order to make it useful for electron tomography in particular and bioimaging in general.</p> <p>Conclusion</p> <p>TOMOBFLOW allows efficient noise filtering of bioimaging datasets with preservation of the features of interest, thereby yielding data better suited for post-processing, visualization and interpretation. It is available at the web site <url>http://www.ual.es/%7ejjfdez/SW/tomobflow.html</url>.</p

Marker-free image registration of electron tomography tilt-series

<p>Abstract</p> <p>Background</p> <p>Tilt series are commonly used in electron tomography as a means of collecting three-dimensional information from two-dimensional projections. A common problem encountered is the projection alignment prior to 3D reconstruction. Current alignment techniques usually employ gold particles or image derived markers to correctly align the images. When these markers are not present, correlation between adjacent views is used to align them. However, sequential pairwise correlation is prone to bias and the resulting alignment is not always optimal.</p> <p>Results</p> <p>In this paper we introduce an algorithm to find regions of the tilt series which can be tracked within a subseries of the tilt series. These regions act as landmarks allowing the determination of the alignment parameters. We show our results with synthetic data as well as experimental cryo electron tomography.</p> <p>Conclusion</p> <p>Our algorithm is able to correctly align a single-tilt tomographic series without the help of fiducial markers thanks to the detection of thousands of small image patches that can be tracked over a short number of images in the series.</p

Доклиническое исследование парамагнитного контрастного усиления комплексом Mn(II) c димеркаптоянтарной кислотой при магнитно-резонансной томографии первичной опухоли и метастатических поражений при раке молочной железы

Aim of the study. We have studied the possibility of imaging of breast cancer in dogs by MRI with paramagnetic contrast enhancement using newly proposed agent Mn-dimercaptosuccinate (Mn-DMSA2, TMSuccimang), in dogs. Material and methods. In seven animals (veterinary patients) with breast cancer the MRI study was carried out, when sleeping (infusion of propofol), with contrast enhancement using Mn-DMSA2, as 0,5M solution, 0,1 mM/Kg of BW. The T1-w MRI scans were acquired before, and in 12–17 min after injection of Mn-DMSA2, TR=450–600 ms, TE=12–15 ms, matrix 256×256, field of view 250 mm, slice 2,5 mm thick. All studies were carried out using Toshiba Titan Vantage (1,5 Т, five animals) and Siemens Magnetom Open (0,2 Т, in two). The uptake of Mn-DMSA2 to tumor was quantified using Index of Enhancement, as ratio of intensity per voxel of the post-contrast image to the intensity of the pre-contrast initial one. Results. In all cases the uptake of Mn-DMSA2 was seen in the areas of both primary tumor and of metastases to lymph nodes and to the brain. Index of enhancement was: over primary tumor (n=7) — 1,52±0,19 (1,35; 1,83), over metastases to lymph nodes (n=12) 1,37±0,14 (1,12; 1,64), over peripheral zone of brain metastases (n=11) — 1,48±0,15 (1,29; 2,37), and over central zone of brain metastases (n=11) — 2,76±0,12 (1,48; 3,21). No any case demonstrated any complication or concomitant effect. Conclusion. Mn-DMSA2 is an perspective non-gadolinium paramagnetic contrast agent useful for diagnosis of both primary tumor and of metastases in breast cancer.Цель исследования. Изучалась возможность визуализации рака молочной железы у собак с помощью МРТ с контрастным усилением вновь предложенным парамагнитным контрастным средством (ПМКС) — Mn-димеркаптосукционатом (Mn-ДМСА2, TMСукциманг). Материалы и методы. У семи животных с впервые выявленным раком молочной железы, в состоянии медикаментозного сна (инфузия пропофола), была выполнена МР-томография с Mn-ДМСА2 , вводимым внутривенно, в виде 0,5 М раствора, 0,1 ммоль/кг массы тела, в Т1-взвешенном режиме, до и спустя 12–17 мин после введения Mn-ДМСА2 . TR=450–600 мс, TE=12–15 мс, в матрицу 256×256 при размере поля сканирования до 250×380 мм, среза 2,5–4 мм, с использованием Toshiba Titan Vantage (Toshiba Medical, 1,5 Т, у пяти животных) и Magnetom Open (Siemens Medical, 0,2 Т, у двух животных). Накопление Mn-ДМСА2 оценивалось по индексу усиления, как отношение интенсивности на элемент изображения после введения Mn-ДМСА2 к исходному. Результаты. Во всех случаях зрительно отмечено накопление Mn-ДМСА2 в области первичных опухолей, и метастазов в лимфатических узлах и головном мозге. Индексы усиления изображения составили: для первичной опухоли (n=7) — 1,52±0,19 (1,35; 1,83), для метастазов в лимфатические узлы (n=12) — 1,37±0,14 (1,12; 1,64), для метастазов в головной мозг в периферической зоне метастаза (n=11) 1,48±0,15 (1,29; 2,37), и для центральной зоны метастаза (n=11) — 2,76±0,12 (1,48; 3,21). Не отмечалось никаких осложнений и побочных действий введения Mn-ДМСА2. Заключение. Mn-ДМСА2 представляет собой парамагнитный негадолиниевый контрастный препарат, пригодный для выявления как первичной опухоли, так и метастатических поражений при раке молочной железы

Ignicoccus hospitalis and Nanoarchaeum equitans: ultrastructure, cell–cell interaction, and 3D reconstruction from serial sections of freeze-substituted cells and by electron cryotomography

Ultrastructure and intercellular interaction of Ignicoccus hospitalis and Nanoarchaeum equitans were investigated using two different electron microscopy approaches, by three-dimensional reconstructions from serial sections, and by electron cryotomography. Serial sections were assembled into 3D reconstructions, for visualizing the unusual complexity of I. hospitalis, its huge periplasmic space, the vesiculating cytoplasmic membrane, and the outer membrane. The cytoplasm contains fibres which are reminiscent to a cytoskeleton. Cell division in I. hospitalis is complex, and different to that in Euryarchaeota or Bacteria. An irregular invagination of the cytoplasmic membrane is followed by separation of the two cytoplasms. Simultaneous constriction of cytoplasmic plus outer membrane is not observed. Cells of N. equitans show a classical mode of cell division, by constriction in the mid-plane. Their cytoplasm exhibits two types of fibres, elongated and ring-shaped. Electron micrographs of contact sites between I. hospitalis and N. equitans exhibit two modes of interaction. One is indirect and mediated by thin fibres; in other cells the two cell surfaces are in direct contact. The two membranes of I. hospitalis cells are frequently seen in direct contact, possibly a prerequisite for transporting metabolites or substrates from the cytoplasm of one cell to the other. Rarely, a transport based on cargo vesicles is observed between I. hospitalis and N. equitans