1,720,961 research outputs found
Leveraging Whole-Exome Sequencing and Mutational Signatures to Detect Homologous Recombination Deficiency in Cancer
No full textHomologous recombination is a high-fidelity DNA repair mechanism essential for maintaining genome stability. Impairment of this pathway, often due to BRCA1 or BRCA2 inactivation, leads to homologous recombination deficiency (HRD), forcing cells to rely on error-prone mechanisms for repairing DNA double-strand breaks, such as nonhomologous or microhomology-mediated end joining. HRD is a clinically important biomarker, particularly in breast and ovarian cancers, as it predicts responsiveness to platinum-based chemotherapies and PARP inhibitors. However, current tests in the clinical setting, mostly based on targeted panel sequencing, lack specificity and lead to a substantial number of false positives. In contrast, whole-genome sequencing, despite its high accuracy, remains largely confined to research because of high costs and logistical constraints. In this issue of Cancer Research, Abbasi and colleagues present HRProfiler, a machine learning-based tool that accurately detects HRD using whole-exome sequencing (WES) data, which is increasingly accessible in clinical oncology. Notably, it demonstrates improved sensitivity in the WES setting compared with existing tools, such as HRDetect and SigMA. As WES continues to gain traction, HRProfiler offers a promising step toward democratizing HRD detection and enabling more precise, genomics-guided treatment strategies.
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
계산 비교 유전체학을 통한 동물 생식세포 돌연변이 과정 추적 연구
No full text학위논문(박사) - 한국과학기술원 : 의과학대학원, 2022.2,[v, 108 p. :]A recently emerging concept of mutational signature has expanded our understanding of mutational processes in human cells. It is now widely accepted that the DNA triplet pattern of nucleotide changes is uniquely shaped by endogenous processes, encompassing spontaneous mutations and DNA repairs, and exogenous mutagens such as UV light, tobacco smoking, reactive oxygen species, and many others. Mutational signature is a hallmark of each of these processes manifested as a spectrum of trinucleotide change and more existence of such signatures are appearing in recent years as more data is added. While mutational signatures have been extensively studied in cancers and recently in normal tissues, however, it has been largely limited to somatic cells. Mutations in germ cells are indeed trickier and laborious to study and practically only de novo germline mutations may be confidently studied at the cost of, for example, using family trio data in humans and multi-generation inbreeding in mice. In this thesis, we explore the possibility of studying germline mutations using only reference genomes. We will discuss germline mutational processes in the lens of mutational signature and in a broader context possible. Particularly, we aim to reveal traces of germline mutational signatures in various lineages of animal species. Studying germline mutational processes in this regard is challenging in many ways, for we are looking several million years into the past in evolutionary history where the identifiability of mutational signals is elusive. We developed a computational pipeline to overcome difficulties that arise upon accurately capturing germline mutations and mutational signatures. As such, several layers of uncertainties inherent in the problem are discussed and dealt with justifiable approximations and novel computational approaches. Recent advances in our understanding of somatic mutational signatures in human cancer and non-cancer cells take an integral part throughout. It is shown that our method can accurately capture presumably a true picture of mutational processes operative in a recent evolutionary time span and that mutational processes have been relatively regular throughout the history of genome evolution in animal lineages. The methodology and data produced in this research may be used as a valuable source and provide insight for mutation studies regarding ancient genomes and the nature of genome evolution.한국과학기술원 :의과학대학원
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
Modeling the Angular Light Scattering by Red Blood Cells
No full textThe primary role of the red blood cell is delivering oxygen throughout the body. If it is affected, consequences include amnesia and numerous diseases such as malaria and sickle cell anemia. As prompt and inexpensive tests for blood screening are in demand, we have developed a faster and reliable way to measure parameters associated with the structure of red blood cells and size distribution of the cells in whole blood smear. Using the Born approximation and simulating red blood cell shape, we were able to determine the diameter, thickness, and other parameters related to the cell morphology. Given a phase image of red blood cell smear measured in our laboratory, we can determine the average and standard deviation of the diameter of red blood cells simultaneously, without analyzing cell by cell individually. This approach may open the door for a new generation of label-free testing.not peer reviewedSubmitted by Janice Progen ([email protected]) on 2014-01-16T21:08:39Z
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Item is restricted indefinitely.Undergraduate senior thesis not recommended for open accessunpublishedU of I Onl
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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