Relevant bibliographies by topics / Localisation workflow

Academic literature on the topic 'Localisation workflow'

Author: Grafiati
Published: 10 December 2022
Last updated: 28 January 2023

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Journal articles on the topic "Localisation workflow"

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Breckels, Lisa M., Claire M. Mulvey, Kathryn S. Lilley, and Laurent Gatto. "A Bioconductor workflow for processing and analysing spatial proteomics data." F1000Research 5 (December 28, 2016): 2926. http://dx.doi.org/10.12688/f1000research.10411.1.

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Spatial proteomics is the systematic study of protein sub-cellular localisation. In this workflow, we describe the analysis of a typical quantitative mass spectrometry-based spatial proteomics experiment using the MSnbase and pRoloc Bioconductor package suite. To walk the user through the computational pipeline, we use a recently published experiment predicting protein sub-cellular localisation in pluripotent embryonic mouse stem cells. We describe the software infrastructure at hand, importing and processing data, quality control, sub-cellular marker definition, visualisation and interactive exploration. We then demonstrate the application and interpretation of statistical learning methods, including novelty detection using semi-supervised learning, classification, clustering and transfer learning and conclude the pipeline with data export. The workflow is aimed at beginners who are familiar with proteomics in general and spatial proteomics in particular.
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Breckels, Lisa M., Claire M. Mulvey, Kathryn S. Lilley, and Laurent Gatto. "A Bioconductor workflow for processing and analysing spatial proteomics data." F1000Research 5 (July 3, 2018): 2926. http://dx.doi.org/10.12688/f1000research.10411.2.

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Spatial proteomics is the systematic study of protein sub-cellular localisation. In this workflow, we describe the analysis of a typical quantitative mass spectrometry-based spatial proteomics experiment using the MSnbase and pRoloc Bioconductor package suite. To walk the user through the computational pipeline, we use a recently published experiment predicting protein sub-cellular localisation in pluripotent embryonic mouse stem cells. We describe the software infrastructure at hand, importing and processing data, quality control, sub-cellular marker definition, visualisation and interactive exploration. We then demonstrate the application and interpretation of statistical learning methods, including novelty detection using semi-supervised learning, classification, clustering and transfer learning and conclude the pipeline with data export. The workflow is aimed at beginners who are familiar with proteomics in general and spatial proteomics in particular.
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Muñoz Sánchez, Pablo. "Video Game Localisation for Fans by Fans." Journal of Internationalization and Localization 1 (January 1, 2009): 168–85. http://dx.doi.org/10.1075/jial.1.07mun.

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The aim of this paper is to show the particularities of the so-called “romhacking”, a methodology developed by amateurs to localise mainly classic video games. In the first section, the concept and origin of the term “romhacking” is presented. The second section offers an overview of the workflow followed by romhackers to localise video games. In the third section, an analysis of the differences between professional and amateur translations is given. The fourth section includes a discussion of the legal aspects of this practice. The paper concludes with a reflection on the impact of amateur translations on the video game localisation industry.
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Flanagan, Keith, Sirintra Nakjang, Jennifer Hallinan, Colin Harwood, Robert P. Hirt, Matthew R. Pocock, and Anil Wipat. "Microbase2.0: A Generic Framework for Computationally Intensive Bioinformatics Workflows in the Cloud." Journal of Integrative Bioinformatics 9, no. 2 (June 1, 2012): 101–12. http://dx.doi.org/10.1515/jib-2012-212.

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Summary As bioinformatics datasets grow ever larger, and analyses become increasingly complex, there is a need for data handling infrastructures to keep pace with developing technology. One solution is to apply Grid and Cloud technologies to address the computational requirements of analysing high throughput datasets. We present an approach for writing new, or wrapping existing applications, and a reference implementation of a framework, Microbase2.0, for executing those applications using Grid and Cloud technologies. We used Microbase2.0 to develop an automated Cloud-based bioinformatics workflow executing simultaneously on two different Amazon EC2 data centres and the Newcastle University Condor Grid. Several CPU years’ worth of computational work was performed by this system in less than two months. The workflow produced a detailed dataset characterising the cellular localisation of 3,021,490 proteins from 867 taxa, including bacteria, archaea and unicellular eukaryotes. Microbase2.0 is freely available from http://www.microbase.org.uk/.
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Kern, Fabian, Tobias Fehlmann, Jeffrey Solomon, Louisa Schwed, Nadja Grammes, Christina Backes, Kendall Van Keuren-Jensen, David Wesley Craig, Eckart Meese, and Andreas Keller. "miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems." Nucleic Acids Research 48, W1 (May 6, 2020): W521—W528. http://dx.doi.org/10.1093/nar/gkaa309.

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Abstract Gene set enrichment analysis has become one of the most frequently used applications in molecular biology research. Originally developed for gene sets, the same statistical principles are now available for all omics types. In 2016, we published the miRNA enrichment analysis and annotation tool (miEAA) for human precursor and mature miRNAs. Here, we present miEAA 2.0, supporting miRNA input from ten frequently investigated organisms. To facilitate inclusion of miEAA in workflow systems, we implemented an Application Programming Interface (API). Users can perform miRNA set enrichment analysis using either the web-interface, a dedicated Python package, or custom remote clients. Moreover, the number of category sets was raised by an order of magnitude. We implemented novel categories like annotation confidence level or localisation in biological compartments. In combination with the miRBase miRNA-version and miRNA-to-precursor converters, miEAA supports research settings where older releases of miRBase are in use. The web server also offers novel comprehensive visualizations such as heatmaps and running sum curves with background distributions. We demonstrate the new features with case studies for human kidney cancer, a biomarker study on Parkinson’s disease from the PPMI cohort, and a mouse model for breast cancer. The tool is freely accessible at: https://www.ccb.uni-saarland.de/mieaa2.
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Holewijn, Rozemarije A., Maarten Bot, Pepijn van den Munckhof, and P. Richard Schuurman. "Implementation of Intraoperative Cone-Beam Computed Tomography (O-arm) for Stereotactic Imaging During Deep Brain Stimulation Procedures." Operative Neurosurgery 19, no. 3 (May 11, 2020): E224—E229. http://dx.doi.org/10.1093/ons/opaa110.

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Abstract BACKGROUND Intraoperative cone-beam computed tomography (iCBCT) allows for rapid 3-dimensional imaging. However, it is currently unknown whether this imaging technique offers sufficient accuracy for stereotactic registration during deep brain stimulation (DBS) procedures. OBJECTIVE To determine the accuracy of iCBCT, with the O-arm O2 (Medtronic), for stereotactic registration by comparing this modality to stereotactic magnetic resonance imaging (MRI). METHODS All DBS patients underwent a preoperative non-stereotactic 3 Tesla MRI, stereotactic 1.5 Tesla MRI, stereotactic O-arm iCBCT, postimplantation O-arm iCBCT, and postoperative conventional multidetector computed tomography (CT) scan. We compared stereotactic (X, Y, and Z) coordinates of the anterior commissure (AC), the posterior commissure (PC), and midline reference (MR) between stereotactic MRI and iCBCT. For localisation comparison of electrode contacts, stereotactic coordinates of electrode tips were compared between the postoperative multidetector CT and iCBCT. RESULTS A total of 20 patients were evaluated. The average absolute difference in stereotactic coordinates of AC, PC, and MR was 0.4 ± 0.4 mm for X, 0.4 ± 0.4 mm for Y, and 0.7 ± 0.5 mm for Z. The average absolute difference in X-, Y-, and Z-coordinates for electrode localisation (N = 34) was 0.3 ± 0.3 mm, 0.6 ± 0.3 mm, and 0.6 ± 0.6 mm. These differences were small enough not to be considered clinically relevant. CONCLUSION Stereotactic MRI and O-arm iCBCT yield comparable coordinates in pre- and postoperative imaging. Differences found are below the threshold of clinical relevance. Intraoperative O-arm CBCT offers rapid stereotactic registration and evaluation of electrode placement. This increases patient comfort and neurosurgical workflow efficiency.
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Pang, Lokman, Matthias Ernst, and Jennifer Huynh. "Development of a Multiplex Immunohistochemistry Workflow to Investigate the Immune Microenvironment in Mouse Models of Inflammatory Bowel Disease and Colon Cancer." International Journal of Molecular Sciences 22, no. 20 (October 12, 2021): 11001. http://dx.doi.org/10.3390/ijms222011001.

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Multiplex immunohistochemistry (mIHC) enables simultaneous staining of multiple immune markers on a single tissue section. Mounting studies have demonstrated the versatility of mIHC in evaluating immune infiltrates in different diseases and the tumour microenvironment (TME). However, the majority of published studies are limited to the analysis of human patient samples. Performing mIHC on formalin-fixed paraffin-embedded (FFPE) mouse tissues, particularly with sensitive antigens, remain challenging. The aim of our study was to develop a robust and reproducible protocol to uncover the immune landscape in mouse FFPE tissues. Effective antibody stripping while maintaining sensitivity to antigens and tissue adhesion to the glass slide is critical in developing an mIHC panel to allow successive rounds of staining. Thus, we identified a highly efficient stripping method that preserves signal intensity and antigenicity to allow multiple rounds of staining. We subsequently optimised an mIHC workflow with antibodies specific against CD4, CD8α, FOXP3 and B220 to identify distinct T and B cell populations on mouse FFPE tissues. Lastly, the application of this mIHC panel was validated in a mouse model of inflammatory bowel cancer, two allograft mouse models of spontaneous colon adenocarcinoma and a sporadic mouse model of colon cancer. Together, these demonstrate the utility of the aforementioned protocol in establishing the quantity and spatial localisation of immune cells in different pathological tissues.
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Rozova, Vlada S., Ayad G. Anwer, Anna E. Guller, Hamidreza Aboulkheyr Es, Zahra Khabir, Anastasiya I. Sokolova, Maxim U. Gavrilov, et al. "Machine learning reveals mesenchymal breast carcinoma cell adaptation in response to matrix stiffness." PLOS Computational Biology 17, no. 7 (July 23, 2021): e1009193. http://dx.doi.org/10.1371/journal.pcbi.1009193.

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Epithelial-mesenchymal transition (EMT) and its reverse process, mesenchymal-epithelial transition (MET), are believed to play key roles in facilitating the metastatic cascade. Metastatic lesions often exhibit a similar epithelial-like state to that of the primary tumour, in particular, by forming carcinoma cell clusters via E-cadherin-mediated junctional complexes. However, the factors enabling mesenchymal-like micrometastatic cells to resume growth and reacquire an epithelial phenotype in the target organ microenvironment remain elusive. In this study, we developed a workflow using image-based cell profiling and machine learning to examine morphological, contextual and molecular states of individual breast carcinoma cells (MDA-MB-231). MDA-MB-231 heterogeneous response to the host organ microenvironment was modelled by substrates with controllable stiffness varying from 0.2kPa (soft tissues) to 64kPa (bone tissues). We identified 3 distinct morphological cell types (morphs) varying from compact round-shaped to flattened irregular-shaped cells with lamellipodia, predominantly populating 2-kPa and >16kPa substrates, respectively. These observations were accompanied by significant changes in E-cadherin and vimentin expression. Furthermore, we demonstrate that the bone-mimicking substrate (64kPa) induced multicellular cluster formation accompanied by E-cadherin cell surface localisation. MDA-MB-231 cells responded to different substrate stiffness by morphological adaptation, changes in proliferation rate and cytoskeleton markers, and cluster formation on bone-mimicking substrate. Our results suggest that the stiffest microenvironment can induce MET.
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Captur, Gabriella, Eloisa Arbustini, Petros Syrris, Dina Radenkovic, Ben O'Brien, William J. Mckenna, and James C. Moon. "Lamin mutation location predicts cardiac phenotype severity: combined analysis of the published literature." Open Heart 5, no. 2 (October 2018): e000915. http://dx.doi.org/10.1136/openhrt-2018-000915.

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ObjectiveTwo LMNA genotype–phenotype cardiac correlations are reported: first, that cardiac involvement in multisystem laminopathies prevails with mutations upstream of the nuclear localisation signal (NLS); second, that worse outcomes occur with non-missense (compared with missense) mutations. We tested whether LMNA mutation DNA location and mutation subtype can predict phenotype severity in patients with lamin heart disease.MethodsWe used a semantic workflow platform and manual electronic literature search to identify published LMNA mutations with cardiac-predominant phenotype. Hierarchical cluster analysis (HCA) assembled lamin heart disease into classes based on phenotype severity. 176 reported causative mutations were classified and any relationships to mutation location/subtype assessed by contingency analysis.ResultsMore adverse phenotype was associated with mutation location upstream of the NLS (p=0.014, OR 2.38, 95% CI 1.19 to 4.80) but not with non-missense mutations (p=0.337, OR 1.36, 95% CI 0.72 to 2.57), although an association with non-missense mutations was identified in a subcluster with malignant ventricular arrhythmia (p=0.005, OR 2.64, 95% CI 0.76 to 9.21). HCA limited to the 65 mutations described on ClinVar as pathogenic/likely pathogenic showed similar findings (upstream of NLS, p=0.030, OR 4.78, 95% CI 1.28 to 17.83; non-missense, p=0.121, OR 2.64, 95% CI 0.76 to 9.21) as did analysis limited to pathogenic/likely pathogenic variants according to the American College of Medical Genetics and Genomics standards.ConclusionCardiac patients with an LMNA mutation located upstream versus downstream of the NLS have a more adverse cardiac phenotype, and some missense mutations can be as harmful as non-missense ones.
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Bolaños García-Escribano, Alejandro, Jorge Díaz-Cintas, and Serenella Massidda. "Subtitlers on the Cloud: The Use of Professional Web-based Systems in Subtitling Practice and Training." Tradumàtica: tecnologies de la traducció, no. 19 (December 31, 2021): 1–21. http://dx.doi.org/10.5565/rev/tradumatica.276.

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The bourgeoning and rapid evolution of cloud-based applications has triggered profound transformations in the audiovisual translation (AVT) mediascape. By drawing attention to the major changes that web-based ecosystems have introduced in localisation workflows, we set out to outline ways in which these new technological advances can be embedded in the AVT classroom. Along these lines, the present study sets out to explore the potential benefits of cloud platforms in AVT training curricula by exploring ways in which this technology can be exploited in subtitling training. An analysis of current subtitling practices and tools, localisation workflows, and in-demand skills in the AVT industry will be followed by an experience-based account on the use of cloud-based platforms in subtitler training environments to simulate and carry out a wide range of tasks. Our study pivots around the idea that cloud subtitling might prove useful to bridge the technological gap between academic institutions and the profession as well as to enhance the distance-learning provision of practice-oriented training in subtitling.
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Book chapters on the topic "Localisation workflow"

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Morera, Aram, Lamine Aouad, and J. J. Collins. "Assessing Support for Community Workflows in Localisation." In Business Process Management Workshops, 195–206. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-28108-2_20.

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Conference papers on the topic "Localisation workflow"

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Aslanyan, Artur Mihailovich, Arkadii Yurievich Popov, Ivan Aleksandrovich Zhdanov, Eugeny Sergeevich Pakhomov, Nikolay Petrovich Ibryaev, Maksim Aleksandrovich Kuznetsov, Vladimir Markovich Krichevsky, Marat Yurievich Garnyshev, and Rodion Vladimirovich Guss. "Localisation and Recovery Planning of the Remaining Hydrocarbon Reserves." In SPE Russian Petroleum Technology Conference. SPE, 2021. http://dx.doi.org/10.2118/206494-ms.

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Abstract The paper presents the results of a study project of 60+ well block of the large (> 1,000 wells) mature (30 year old) oilfield in Western Siberia with objective to localise and characterize residual recoverable reserves and propose the optimal economic scenario for further depletion. Low permeability, heterogeneous reserve structure along the cross-section, numerous induced hydraulic fractures in producing wells and numerous spontaneous fractures in injecting wells with dynamic behavior, aggravated by numerous behind-the-casing crossflows in almost every well have resulted in a very complex conditions of remaining reserves. The conventional methods of production analysis and surveillance (well testing and production logging) do not provide a consistent picture of the current distribution and conditions of the remaining reserves and required a deeper and more complex analysis. Development Opportunities Management workflow was chosen for this particular holistic study, which includes a set of interconnected studies, field surveillance, geological and flow modelling and culminated in field development planning based on the digital asset twin. (Ganiev, B., 2021) Digital asset twin was constructed based on results of this workflow with a full-range economical model, flow simulation over the thoroughly calibrated fine-grid 3D dynamic model and production complication model (dynamic behavior of the fractures and behind-casing channeling). The 3D model has been calibrated on results of the cross-well pressure-pulse surveillance, reservoir-oriented production logging and was validated by the results of the drilling of the transition wells. The digital asset twin was used to find the optimal investment scenario based on multivariate calculations with the help of digital assistants. Due to simplicity of the user interface and client-server design, the digital twin was made available for various corporate engineers and managers without any modelling skills to play around with their own ideas on possible production/investment scenarios which gave another level of validation of the ultimate field development plan. All activities carried out within the digital twin automatically generate a complete package of investment metrics (NPV, PI, IRR, MIRR, Cash Flow and many correlation graphs) to assess the economic efficiency of each package and select the most appropriate solution for further ultimate choice. The approved scenario was based around drilling 6 producing side-tracks in specific locations/trajectories, performing workovers on specific offset injectors and re-scheduling of the production/injection rates in all block wells. The results of the field development's activities implementation will be the subject of a future publication.
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