22 research outputs found
Comprehensive analysis of pathways in Coronavirus 2019 (COVID-19) using an unsupervised machine learning method
No full textThe World Health Organization (WHO) introduced “Coronavirus disease 19” or “COVID-19” as a novel coronavirus in March 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires the fast discovery of effective treatments to fight this worldwide crisis. Artificial intelligence and bioinformatics analysis pipelines can assist with finding biomarkers, explanations, and cures. Artificial intelligence and machine learning methods provide powerful infrastructures for interpreting and understanding the available data. On the other hand, pathway enrichment analysis, as a dominant tool, could help researchers discover potential key targets present in biological pathways of host cells that are targeted by SARS-CoV-2. In this work, we propose a two-stage machine learning approach for pathway analysis. During the first stage, four informative gene sets that can represent important COVID-19 related pathways are selected. These “representative genes” are associated with the COVID-19 pathology. Then, two distinctive networks were constructed for COVID-19 related signaling and disease pathways. In the second stage, the pathways of each network are ranked with respect to some unsupervised scorning method based on our defined informative features. Finally, we present a comprehensive analysis of the top important pathways in both networks. Materials and implementations are available at: https://github.com/MahnazHabibi/Pathway
In Vitro Glioblastoma Model on a Plate for Localized Drug Release Study from a 3D-Printed Drug-Eluted Hydrogel Mesh
No full textGlioblastoma multiforme (GBM) is an aggressive type of brain tumor that has limited treatment options. Current standard therapies, including surgery followed by radiotherapy and chemotherapy, are not very effective due to the rapid progression and recurrence of the tumor. Therefore, there is an urgent need for more effective treatments, such as combination therapy and localized drug delivery systems that can reduce systemic side effects. Recently, a handheld printer was developed that can deliver drugs directly to the tumor site. In this study, the feasibility of using this technology for localized co-delivery of temozolomide (TMZ) and deferiprone (DFP) to treat glioblastoma is showcased. A flexible drug-loaded mesh (GlioMesh) loaded with poly (lactic-co-glycolic acid) (PLGA) microparticles is printed, which shows the sustained release of both drugs for up to a month. The effectiveness of the printed drug-eluting mesh in terms of tumor toxicity and invasion inhibition is evaluated using a 3D micro-physiological system on a plate and the formation of GBM tumoroids within the microenvironment. The proposed in vitro model can identify the effective combination doses of TMZ and DFP in a sustained drug delivery platform. Additionally, our approach shows promise in GB therapy by enabling localized delivery of multiple drugs, preventing off-target cytotoxic effects
Vision-based Cost Maps for Safe Autonomous Navigation : Design and Evaluation of Vision-based Control Barrier Functions
No full textDesigning safety-critical systems for unfamiliar environments is a substantial challenge in the field of robotics. Control Barrier Functions (CBF) serve as a common tool for addressing this challenge. However, the definition of CBF based on perceptual input remains a relatively unexplored and complex area of research.
This thesis extends prior work, where the authors, including the author of this thesis, introduced the innovative concept of Vision-based Control Barrier Functions (V-CBF). V-CBF defines Control Barrier Functions using perceptual input obtained from an RGBD camera, enabling the avoidance of obstacles with arbitrary shapes in unknown environments. A pivotal element of V-CBF is the 2D customized cost map, which transforms the segmented unsafe sets into an appropriate format that satisfies the requirements of CBF. The design and evaluation of these cost maps play a crucial role in the proper generation of V-CBFs. However, this aspect has not been thoroughly extensively in previous research.
The thesis embarks on a comprehensive investigation of diverse methodologies for generating these essential cost maps. The proposed methods are rigorously implemented and assessed within the CARLA simulator. To offer a thorough evaluation, both qualitative and quantitative comparisons are conducted, drawing from industry-standard ISO 22737 guidelines and custom-designed metrics within the CARLA simulator environment.
Furthermore, to substantiate the practical applicability of V-CBF, it is implemented on an industrial mobile robot. This real-world deployment serves as a tangible demonstration of the effectiveness of V-CBF in unknown environments, emphasizing its potential beyond simulated contexts. The transition from simulation to tangible real-world implementation underscores the portability and robustness of V-CBF, signifying its relevance and promise in real-world scenarios
Post-Colonial Reading of Isabel Allende’s The Japanese Lover
No full textThis research will explore the result of studying different aspects of identity seeking and establishing it as a liminal-prone one in a hybridized atmosphere among the colonized in terms of post-colonial discourse, based on Bhabha’s theories in his book, The Location of Culture, and on Isabel Allende’s novel, The Japanese Lover (2015). This study strives to expose the way through which the colonized characters’ identities in the novel undergo radical transformation through the third space which is heavily laced with qualities like ambivalence, stereotype, mimicry, and unhomeliness. Isabel Allende is an author whose novels mostly are an attempt to delineate the process of identity shaping particularly in the USA, since identity has always been an obsession for human which is defined based on different properties, one of which refers to the nation, culture and the territories based on Bhabha’s notion of hybridity which stems from confrontation of the cultures of the oppressor and the oppressed in the process of colonization. Generally, subject of identity in post-colonialism discourse is one in which people especially the colonized seeks for attachment. It will be divulged through this analysis that how liminal quality which is created as the consequence of colonial discourses will result in creating a space in which the oppressed one undergo radical changes in forming identity and how their identities are susceptible to alteration and likely to be unstable and fugitive
Applications of image processing and machine learning techniques in wildlife monitoring and cancer cell characterization
No full textThis dissertation presents the application of state-of-art image classification and object detection techniques to two projects in the areas of wildlife monitoring and cancer cell characterization. The following presents a summary of the problem statement, solution approach, and major contributions for each of the two projects.
In the wildlife monitoring project, an automated vision system is proposed for animal detection in trail-camera images taken from a field under the administration of the Texas Parks and Wildlife Department. As traditional wildlife counting techniques are intrusive and labor-intensive to conduct, trail-camera imaging is a comparatively non-intrusive method for capturing wildlife activity. However, given the large volume of images produced from trail cameras, manual analysis of the images remains time-consuming and inefficient. For this purpose, a two-stage deep convolutional neural network pipeline is implemented to find animal-containing images in the first stage and then process these images to detect birds in the second stage. The animal classification system classifies animal images with 93% sensitivity and 96% specificity. The bird detection system achieves better than 93% sensitivity, 92% specificity, and 68% average Intersection-over-Union rate. This dissertation also addresses post-deployment issues related to data drift for the animal classification system as image features vary with seasonal changes. This system utilizes an automatic retraining algorithm to detect data drift and to update the system when necessary. Moreover, two statistical experiments are presented to explain the prediction behavior of the animal classification system. These experiments investigate the cues that steer the system towards a particular decision. Statistical hypothesis testing demonstrates that the presence of an animal in the input image significantly contributes to the system’s decisions.
The cell characterization study investigates the automatic detection and enumeration of circulating tumor cells in patient blood samples. Circulating tumor cells (CTCs) are invaluable biomarkers used in the early diagnosis and treatment of cancer. Microscopy images of isolated CTCs from patient blood samples are routinely acquired and analyzed for CTC detection and enumeration purposes. Due to the scarcity of CTCs in the patient blood sample, their manual characterization is a challenging task that involves a series of tedious cell staining and labeling procedures and laborious manual identification of the cells. This study proposes an automated detection and enumeration system to alleviate the lag in the enumeration process. The core of this system is an efficient and accurate convolutional neural network (CNN)-based model that performs label-free detection of MCF-7 breast cancer cells, as a proxy to CTCs, in brightfield images. The MCF-7 detection model achieves above 99% sensitivity and specificity. In addition, the average Intersection-over-Union rate of the proposed detector is better than 80%. For the training set generation, a fully automated workflow is presented that facilitates the efficient and easy labeling of brightfield images. Additionally, multiple experiments are designed and implemented to explore the prominent features that the CNN extracts and uses for distinguishing MCF-7 cells from white blood cells. The results of the experiments indicate that the designed CNN uses the size of the cell as the prominent distinguishing feature. Furthermore, if the size feature is eliminated, the CNN is still capable of extracting other features to distinguish MCF-7 cells, but with a 3% accuracy reduction. Finally, the robustness of the proposed MCF-7 detection model in the presence of various image intensity transformations is investigated. The results indicate that the F1-score of the detection model deteriorates by less than 0.2% in the presence of image intensity and contrast transformations. Therefore, the MCF-7 cell detection model has sufficient robustness with respect to variations in the intensity and contrast of the brightfield images.Embargo status: Restricted until 06/2022. To request the author grant access, click on the PDF link to the left
Corrigendum to “Impact of chronic opioid on cognitive function and spermatogenesis in rat: An experimental study” [Int J Reprod BioMed 2024; 22: 579-592]
No full textThe publisher has been informed of an error that occurred on page 579 in which the last authors affiliation must be changed to Department of Biology, Faculty of Sciences, Malayer University, Malayer, Iran. On behalf of the author, the publisher wishes to apologize for this error. The online version of the article has been updated on October 31, 2024 and can be found at https://doi.org/10.18502/ijrm.v22i7.16971
DigiSpec: Scoping Future Born-Digital Data Services for the Arts and Humanities: Case Reports
No full textThe DigiSpec Project was funded by the UK Arts and Humanities Research Council in 2022 under its “Scoping Future Data Services for the Arts and Humanities” programme.
As part of the evidence base for its report, the project collected twenty short Case Reports from experts in the field of born-digital data services. Each of these describes the current and future activities and requirements of a significant UK project or service.
These Case Reports are published in this collection. The DigiSpec Project also commissioned three longer Case Studies, which are being published separately-
TABLE of CONTENTS
Author
Project
Pages
David Beavan, Timothy Hobson (Alan Turing Institute)
Living with Machines
1-4
Giles Bergel, Abhishek Dutta, Andrew Zisserman (University of Oxford)
National Library of Scotland Chapbooks
5-8
Aruna Bhaugeerutty (Oxford)
Oxford University Museums Digital Collections Service
9-12
Samantha Blickhan (Zooniverse & Adler Planetarium)
ALICE: The Aggregate Line Inspector & Collaborative Editor
13-14
Toby Burrows (University of Oxford)
Knowledge graphs – Mapping Manuscript Migrations
15-19
Alan Chamberlain (University of Nottingham)
Rider Spoke – Riders Have Spoken (Archive)
20-21
Arianna Ciula (King’s College London)
King’s Digital Lab Infrastructure at King’s College London
22-28
Ian Cooke (British Library)
The UK Web Archive
29-32
Ian Cooke & Stella Wisdom (British Library), Graeme Hawley (National Library of Scotland)
Emerging formats
33-37
Tim Crawford, Golnaz Badkobeh, & David Lewis (Goldsmiths University of London), Alastair Porter (Universitat Pompeu Fabra, Barcelona), Laurent Pugin & Rodolfo Zitellini (RISM Digital, Bern)
F-Tempo (Full-Text search of Early Music Prints Online)
38-41
Nicholas Cronk, Birgit Mikus (University of Oxford)
Challenges of Scholarly Editions: Digital Voltaire and Digital d’Holbach
42-44
Neil Jefferies (University of Oxford), Peter Cornwell (Data Futures)
Annotation: anəstor
45-47
Neil Jefferies (University of Oxford), Peter Cornwell (Data Futures)
Redelivery: freizo
48-50
Huw Jones (Cambridge University)
Cambridge Digital Library – TEI Metadata
51-54
Christopher Melen (Royal National College of Music)
PriSM Sample RNN
55-58
Kieron Niven (Archaeology Data Service)
High Speed 2 (HS2) Historic Environment Digital Archive
59-63
Rachel Proudfoot, Nicola Barnet, Masud Khokar, John Salter (University of Leeds)
White Rose Etheses Online: theses as complex digital objects
64-69
Gethin Rees (British Library)
Open Geospatial Data Application and Services viewer (OGDAS)
70-72
Pedro Maximo Rocha & Amy Sampson (The National Archives)
Environmental monitoring system and its integration with digital twins
73-75
Martin Wynne (University of Oxford)
Literary and Linguistic Data Service [formerly Oxford Text Archive]
76-78The "DigiSpec: Scoping future born-digital data services for the arts and humanities" project was funded by the UK Arts and Humanities Research Council (AHRC) under research grant number AH/W007592/1
Tarihî ve sosyo-kültürel yönleriyle bir ilhanlı başkenti: Meraga
No full textMeraga şehri tarih boyunca çok sayıda tarihî hadiselere sahne olmuş ve birçok devletin dikkatini çekmiştir. Biz bu çalışmamızda Meraga şehrinin tarihini, siyaseti ve kültürel durumunu eski zamanlarda özellikle İlhanı döneminde ve kısa bir şekilde de bugünkü durumunu araştıracağız.Çalışmamız dört bölümden oluşmuştır. Giriş kısmında İran Türklüğü hakkında kısa bilgi verildikten sonra birinci bölümde Meraga hakkında açıklama yapılmıştır. Birinci bölüm dört kısma ayrılmıştır. İlk önce Meraga’nın coğrafyası hakkında bilgi verilecek ardından da çeşitli kaynaklarda çeşitli isimlerle adlandırılan Meraga ismi için kısa bilgi verilmiştir. Üçüncü kısımda ise tarihsel süreç içerisinde Meraga’nı anlatmışız ve son kısımda da Meraga’nın bugünkü sosyo-kültürel durumu hakkında bilgi verilmiştir.Çalışmamızın ikinci bölümünde İlhanlı çağında Meraga şehrinin siyasi ve soysa-kültürel durumundan bahsedilmiştir. Ayrıca, bu bölüm tezimizin ana kısmını oluşturmuştır. İlhanlı dönemi kısa bir şekilde açıklandıktan sonra Meraga şehrinin istilası ve ardından da bölümün önemli kısmı yani “Hülâgü döneminde Meraga” ele alınmıştır. Son kısımda Hülâgü sonrası Meraga ve İlhanlıların Moğollar döneminde yerleşim yerleri ve Meraga’nın vergi durumu anlatılmıştır.Tezimizin üçüncü bölümünde İlhanlı devri müellifler ve seyyahların Meraga şehri için görüşleri açıklanmış ve Meraga şehrinin tarihi eserleri anlatılmıştır. Meraga şehrinin mimarisi ve burada yapılmış olan kale ve kümbetler için bilgi verilmiştir. Ardından da doğal ve yapay hadiselerden dolayı aradan giden tarihi eserlerden bahsedilmiştir. Sonra bölümün önemli kısmı Meraga Rasathanesi ayrıntılı bir şekilde açıklanmıştır. Rasathanede çalışanlar, rasathanenin durumu, aletleri, kütüphanesi ve rasathanenin kurucusu Nasirüddin Tusi hakkında bilgi verilmiştir.Çalışmamızın son bölümünde de Meraga şehrinde yetişen şair ve ediplerden bahsedilmiştir.Abstract The city of Meraga throughout history been the scene of historic events and has attracted the attention of many states. İn this study the history the city of Meraga, new politics and cultural status of the ancient times and particularly during Ilhan will investigate the current situation in a short way. Our study consisted of four sections. After giving brief information about Iran Turkishness it is explained in the preamble to Meraga about in the first chapter. The first section is divided into four parts. First a short description for the name Curiosity called by various names in various sources will then be given information about the geography Meraga are given. In the third part in the historical process and we're told the Meraga were informed about the current socio-cultural situation in the last part Meraga. The city of Meraga in Ilkhanid era in the second part of the study the case and peel the political and cultural been mentioned. In addition, this chapter is the main part of this thesis. Ilkhanid period after the invasion of the city of Meraga described in a short form and important part of the section that is then "Hulagu period of Meraga" is discussed. İn the last section, the Ilkhanate after Hulagu the Mongol era settlements and tax status Meraga explained. Ilkhanid era in the third chapter the author describes the vision for the city of wonder and curiosity of travelers and described historical monuments of the city. Information was given to the city of Meraga and castle architecture and tombs that are made here. Then the leading natural and historic monuments are mentioned together because of the artificial event. Then Observatory Meraga important part of the movement is described in detail. Employees at the observatory, the observatory's status, equipment, library and observatory founder Nasiruddin Tusi has been about. In the last part of the study and whether the poet was also mentioned that grows in the city of wonder
Therapeutic Effects of Topical Tranexamic Acid in Comparison with Hydroquinone in Treatment of Women with Melasma
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Author Correction: Integrated genomic sequencing in myeloid blast crisis chronic myeloid leukemia (MBC-CML), identified potentially important findings in the context of leukemogenesis model
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