1,721,021 research outputs found
Spike-in enhanced phosphoproteomics uncovers synergistic signaling responses to MEK inhibition in colorectal cancer cells
No full textKolorektaler Krebs (CRC) gehört zu den häufigsten krebsbedingten Todesursachen und wird häufig durch eine dauerhafte Aktivierung der RAS-RAF-MEK-ERK-Signalkaskade angetrieben. MEK-Inhibitoren zeigen in CRC jedoch nur begrenzte Wirksamkeit, da negative Rückkopplungsschleifen aufgehoben werden und kompensatorische Signalwege wie PI3K/AKT oder alternative MAPK-Kaskaden die Proliferation aufrechterhalten. Viele regulatorisch zentrale, aber niedrig abundant vorkommende Phosphorylierungsereignisse bleiben in Standard-Phosphoproteomik unerfasst. Diese Arbeit etabliert Spike-In Enhanced Detection in DIA (SPIED-DIA), einen Workflow, der synthetische Referenzphosphopeptide in DIA-Messungen einbettet, um vordefinierte Phosphosites gezielt und gleichzeitig im Kontext globaler Phosphoproteomik zu erfassen. Benchmark-Experimente zeigen, dass SPIED-DIA die Nachweiswahrscheinlichkeit und Quantifizierbarkeit kritischer Signalknoten erhöht und zuverlässiger zwischen „niedrig abundant“ und „nicht vorhanden“ unterscheidet, ohne die Breite ungezielter DIA-Analysen einzubüßen.
Die Anwendung von SPIED-DIA auf CRC-Zelllinien unter MEK-Hemmung und Wachstumsfaktorstimulation identifiziert eine synergistische Aktivierung von PI3K/AKT und eine starke, behandlungsabhängige Aktivierung von JNK, insbesondere in KRAS-mutierten HCT116-Zellen. Globale Phosphoproteomik bestätigt diese Muster und offenbart zelllinienspezifische Fluchtstrategien. Funktionelle Assays zeigen, dass die kombinierte Hemmung von MEK und PI3K bzw. MEK und JNK das Zellwachstum synergistisch unterdrücken kann. Insgesamt liefert die Arbeit sowohl einen methodischen Beitrag zur sensitiven, zielgerichteten Phosphoproteomik als auch einen mechanistischen Einblick in JNK-vermittelte Resistenzmechanismen gegenüber MEK-Inhibition in CRC.Colorectal cancer (CRC) remains a leading cause of cancer-related deaths worldwide, largely driven by hyperactive MAPK signaling through the RAS–RAF–MEK–ERK pathway. Therapies targeting this pathway, such as MEK inhibitors, show limited efficacy due to intrinsic and acquired resistance, often resulting from relief of negative feedback loops that activate compensatory pathways like PI3K/AKT. However, low-abundance phosphorylation events critical to understanding these resistance routes often evade standard proteomic workflows. To address this, this thesis introduces Spike-In Enhanced Detection in DIA (SPIED-DIA), which uses heavy-labeled reference peptides to enhance detection and quantification of predefined phosphorylation sites. Through benchmarking in complex lysates and spike-in experiments, SPIED-DIA improves sensitivity and coverage for key signaling nodes while retaining the breadth of global DIA-based methods. Applying SPIED-DIA to a panel of CRC cell lines under MEK inhibition reveals synergistic PI3K/AKT activation in KRAS-mutant HCT116 and DLD-1, plus a prominent role for JNK as an alternative MAPK pathway sustaining proliferation when ERK is blocked. Global phosphoproteomic analyses confirm strong PI3K/AKT and JNK activity in HCT116, but only PI3K/AKT activation in DLD-1. In HCT116, multiple growth factors drive both PI3K/AKT and JNK under MEK inhibition. Growth assays show that co-inhibition of MEK and PI3K or MEK and JNK yields synergistic growth inhibition in HCT116, whereas DLD-1 responds only to dual MEK/PI3K blockade. These findings underscore PI3K/AKT’s central role in bypassing ERK inhibition and highlight JNK as a secondary driver of CRC resistance to MEK inhibition. By integrating targeted and global approaches, SPIED-DIA uncovers low-abundance phosphosites and cell line–specific escape mechanisms, providing both a methodological advance and biological insights with potential to guide more effective combination treatments
High-accuracy and multi-stage mass spectrometry as a tool for quantitative phosphoproteomics
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Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe 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
Full text link“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
Full text linkWe 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
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe 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
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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