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A Comprehensive Overview of RNA Deconvolution Methods and Their Application

  • Yebin Im;Yongsoo Kim
    • Molecules and Cells
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    • v.46 no.2
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    • pp.99-105
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    • 2023
  • Tumors are surrounded by a variety of tumor microenvironmental cells. Profiling individual cells within the tumor tissues is crucial to characterize the tumor microenvironment and its therapeutic implications. Since single-cell technologies are still not cost-effective, scientists have developed many statistical deconvolution methods to delineate cellular characteristics from bulk transcriptome data. Here, we present an overview of 20 deconvolution techniques, including cutting-edge techniques recently established. We categorized deconvolution techniques by three primary criteria: characteristics of methodology, use of prior knowledge of cell types and outcome of the methods. We highlighted the advantage of the recent deconvolution tools that are based on probabilistic models. Moreover, we illustrated two scenarios of the common application of deconvolution methods to study tumor microenvironments. This comprehensive review will serve as a guideline for the researchers to select the appropriate method for their application of deconvolution.

Alkaloids from Amaryllidaceae III -Alkaloids from the Bulbs of Pancratium maritimum-

  • Sener, Bilge;Konukol, Sakine;Kruk, Cornelis;Pandit, Upendra K.
    • Natural Product Sciences
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    • v.4 no.3
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    • pp.148-152
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    • 1998
  • The extract from the bulbs of Pancratium maritimum L. afforded 12 alkaloids belonging to the skeletally six different groups of the Amaryllidaceae alkaloids. In this paper, the isolation and identification of (-)-N-demethyl-galanthamine (1), (+)-tazettine (2) and (-)-2-O-demethylmontanine (3) are described. Their structures have been determined by using extensive spectroscopic techniques. This is the first report describing the occurrence of 1 and 3 in this plant.

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The ability of using syringe irrigation and ultrasound irrigation to remove dentin debris from simulated extensions and irregularities in root canals

  • Lee, Se-Joon;Wu, Min-Kai;Wesselink, Paul-R.
    • Proceedings of the KACD Conference
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    • 2003.05a
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    • pp.289-289
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    • 2003
  • I. Objectives Narrow long oval canals usually cannot be instrumented completely and uninstrumented extensions or irregularities usually remain. The aim of this study was to compare the ability of syringe irrigation and ultrasound irrigation to remove dentin debris from simulations of uninstrumented canal extensions and irregularities.(omitted)

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EBM E-learning: Feasible and Effective for Occupational Physicians in Different Countries

  • Hugenholtz, Nathalie I.R.;Slutter, Judith K.;Van Dijk, Frank J.H.;Nieuwenhuijsen, Karen
    • Safety and Health at Work
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    • v.3 no.3
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    • pp.199-208
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    • 2012
  • Objectives: Although evidence-based medicine (EBM) is a useful method for integrating evidence into the decision-making process of occupational physicians, occupational physicians lack EBM knowledge and skills, and do not have the time to learn the EBM method. In order to enable them to educate themselves at the time and place they prefer, we designed an electronic EBM course. We studied the feasibility and utility of the course as well as its effectiveness in increasing EBM knowledge, skills, and behaviour. Methods: Occupational physicians from various countries were included in a within-subjects study. Measurements were conducted on participants' EBM knowledge, skills, behaviour, and determinants of behaviour at baseline, directly after finishing the course and 2 months later (n = 36). The feasibility and utility of the course were evaluated directly after the course (n = 42). Results: The course is applicable as an introductory course on EBM for occupational physicians in various countries. The course is effective in enhancing EBM knowledge and self-efficacy in practising EBM. No significant effect was found on EBM skills, behaviour, and determinants of behaviour. After the course, more occupational physicians use the international journals to solve a case. Conclusion: An electronic introductory EBM course is suitable for occupational physicians. Although it is an effective method for increasing EBM knowledge, it does not seem effective in improving skills and behaviour. We recommend integrating e-learning courses with blended learning, where it can be used side by side with other educational methods that are effective in changing behaviour.

Facilitators and Barriers in the Use of a Checklist by Insurance Physicians during Work Ability Assessments in Depressive Disorder

  • Blok, Sebastiaan;Gouttebarge, Vincent;Slebus, Frans G.;Sluiter, Judith K.;Frings-Dresen, Monique H.W.
    • Safety and Health at Work
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    • v.2 no.4
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    • pp.328-335
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    • 2011
  • Objectives: Depressive disorder (DD) is a complex disease, and the assessment of work ability in patients with DD is also complicated. The checklist depression (CDp) has recently been developed to support such work ability assessments and has been recommended for implementation in insurance medicine, starting with an analysis of the organisational and social contexts. The aim of this study was to identify the potential facilitators and barriers in the use of the CDp by insurance physicians (IPs) during work ability assessments of employees on sick leave due to DD. Methods: A qualitative research was conducted based on semi-structured interviews. The participants were IPs with at least one year of work experience in performing work ability assessments. The interviews were audiotaped, transcribed and analysed qualitatively. Results: Ten IPs (7 males, 3 females; mean 53 years) were interviewed. Important facilitators, which emerged for use of the CDp, were an oral introduction for colleagues and staff, support from management, valuing the increased transparency in work ability assessments with using the CDp, having adequate time for assessments as well as modification of the appearance (colour, plasticised form) and content (clarifying aspects of the examples) of the assessment tool. The fear of the loss of autonomy, lack of added value of the CDp, high workload, inadequate instructions and lack of time were mentioned as barriers. Conclusion: Adequate introduction to the use of CDp and the fear of the loss of autonomy of IPs need special attention in planning its implementation.

Feasibility and Acceptability of Workers' Health Surveillance for Fire Fighters

  • Plat, Marie-Christine J.;Frings-Dresen, Monique H.W.;Sluiter, Judith K.
    • Safety and Health at Work
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    • v.2 no.3
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    • pp.218-228
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    • 2011
  • Objectives: The objective of this study was to test the feasibility and acceptability of a new workers' health surveillance (WHS) for fire fighters in a Dutch pilot-implementation project. Methods: In three fire departments, between November 2007 and February 2009, feasibility was tested with respect to i) worker intent to change health and behavior; ii) the quality of instructions for testing teams; iii) the planned procedure in the field; and iv) future WHS organisation. Acceptability involved i) satisfaction with WHS and ii) verification of the job-specificity of the content of two physical tests of WHS. Fire fighters were surveyed after completing WHS, three testing teams were interviewed, and the content of the two tests was studied by experts. Results: Feasibility: nearly all of the 275 fire fighters intended to improve their health when recommended by the occupational physician. The testing teams found the instructions to be clear, and they were mostly positive about the organisation of WHS. Acceptability: the fire fighters rated WHS at eight points (out of a maximum of ten). The experts also reached a consensus about the optimal job-specific content of the future functional physical tests. Conclusion: Overall, it is feasible and acceptable to implement WHS in a definitive form in the Dutch fire-fighting sector.

The ability of orexin-A to modify pain-induced cyclooxygenase-2 and brain-derived neurotrophic factor expression is associated with its ability to inhibit capsaicin-induced pulpal nociception in rats

  • Shahsavari, Fatemeh;Abbasnejad, Mehdi;Esmaeili-Mahani, Saeed;Raoof, Maryam
    • The Korean Journal of Pain
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    • v.35 no.3
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    • pp.261-270
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    • 2022
  • Background: The rostral ventromedial medulla (RVM) is a critical region for the management of nociception. The RVM is also involved in learning and memory processes due to its relationship with the hippocampus. The purpose of the present study was to investigate the molecular mechanisms behind orexin-A signaling in the RVM and hippocampus's effects on capsaicin-induced pulpal nociception and cognitive impairments in rats. Methods: Capsaicin (100 g) was applied intradentally to male Wistar rats to induce inflammatory pulpal nociception. Orexin-A and an orexin-1 receptor antagonist (SB-334867) were then microinjected into the RVM. Immunoblotting and immunofluorescence staining were used to check the levels of cyclooxygenase-2 (COX-2) and brain-derived neurotrophic factor (BDNF) in the RVM and hippocampus. Results: Interdental capsaicin treatment resulted in nociceptive responses as well as a reduction in spatial learning and memory. Additionally, it resulted in decreased BDNF and increased COX-2 expression levels. Orexin-A administration (50 pmol/1 µL/rat) could reverse such molecular changes. SB-334867 microinjection (80 nM/1 µL/rat) suppressed orexin's effects. Conclusions: Orexin-A signaling in the RVM and hippocampus modulates capsaicin-induced pulpal nociception in male rats by increasing BDNF expression and decreasing COX-2 expression.