Browsing by Subject "Review"
Now showing 1 - 20 of 22
Results Per Page
Sort Options
Item Restricted Arts and letters : the golden compass needle(1959) Nemerov, HowardItem Open Access Biological properties of extracellular vesicles and their physiological functions(Taylor & Francis, 2015) Yáñez-Mó, M.; Siljander, P. R. M.; Andreu, Z.; Zavec, A. B.; Borràs, F. E.; Buzas, E. I.; Buzas, K.; Casal, E.; Cappello, F.; Carvalho, J.; Colás, E.; Cordeiro-Da, S. A.; Fais, S.; Falcon-Perez, J. M.; Ghobrial, I. M.; Giebel, B.; Gimona, M.; Graner, M.; Gursel, I.; Gursel, M.; Heegaard, N. H. H.; Hendrix, A.; Kierulf, P.; Kokubun, K.; Kosanovic, M.; Kralj-Iglic, V.; Krämer-Albers, E. M.; Laitinen, S.; Lässer, C.; Lener, T.; Ligeti, E.; Line, A.; Lipps, G.; Llorente, A.; Lötvall, J.; Manček-Keber, M.; Marcilla, A.; Mittelbrunn, M.; Nazarenko, I.; Nolte-'t Hoen, E. N. M.; Nyman, T. A.; O'Driscoll, L.; Olivan, M.; Oliveira, C.; Pállinger, E.; Del Portillo, H. A.; Reventós, J.; Rigau, M.; Rohde, E.; Sammar, M.; Sánchez-Madrid, F.; Santarém, N.; Schallmoser, K.; Ostenfeld, M. S.; Stoorvogel, W.; Stukelj, R.; Grein V. D. S.G.; Helena,ü V. M.; Wauben, M. H. M.; De Wever, O.In the past decade, extracellular vesicles (EVs) have been recognized as potent vehicles of intercellular communication, both in prokaryotes and eukaryotes. This is due to their capacity to transfer proteins, lipids and nucleic acids, thereby influencing various physiological and pathological functions of both recipient and parent cells.While intensive investigation has targeted the role of EVs in different pathological processes, for example, in cancer and autoimmune diseases, the EV-mediated maintenance of homeostasis and the regulation of physiological functions have remained less explored. Here, we provide a comprehensive overview of the current understanding of the physiological roles of EVs, which has been written by crowd-sourcing, drawing on the unique EV expertise of academia-based scientists, clinicians and industry based in 27 European countries, the United States and Australia. This review is intended to be of relevance to both researchers already working on EV biology and to newcomers who will encounter this universal cell biological system. Therefore, here we address the molecular contents and functions of EVs in various tissues and body fluids from cell systems to organs. We also review the physiological mechanisms of EVs in bacteria, lower eukaryotes and plants to highlight the functional uniformity of this emerging communication system.Item Open Access The BioPAX community standard for pathway data sharing(Nature Publishing Group, 2010-09) Demir, Emek; Cary, M. P.; Paley, S.; Fukuda, K.; Lemer, C.; Vastrik, I.; Wu, G.; D'Eustachio, P.; Schaefer, C.; Luciano, J.; Schacherer, F.; Martinez-Flores, I.; Hu, Z.; Jimenez-Jacinto, V.; Joshi-Tope, G.; Kandasamy, K.; Lopez-Fuentes, A. C.; Mi, H.; Pichler, E.; Rodchenkov, I.; Splendiani, A.; Tkachev, S.; Zucker, J.; Gopinath, G.; Rajasimha, H.; Ramakrishnan, R.; Shah, I.; Syed, M.; Anwar, N.; Babur, Özgün; Blinov, M.; Brauner, E.; Corwin, D.; Donaldson, S.; Gibbons, F.; Goldberg, R.; Hornbeck, P.; Luna, A.; Murray-Rust, P.; Neumann, E.; Reubenacker, O.; Samwald, M.; Iersel, Martijn van; Wimalaratne, S.; Allen, K.; Braun, B.; Whirl-Carrillo, M.; Cheung, Kei-Hoi; Dahlquist, K.; Finney, A.; Gillespie, M.; Glass, E.; Gong, L.; Haw, R.; Honig, M.; Hubaut, O.; Kane, D.; Krupa, S.; Kutmon, M.; Leonard, J.; Marks, D.; Merberg, D.; Petri, V.; Pico, A.; Ravenscroft, D.; Ren, L.; Shah, N.; Sunshine, M.; Tang R.; Whaley, R.; Letovksy, S.; Buetow, K. H.; Rzhetsky, A.; Schachter, V.; Sobral, B. S.; Doğrusöz, Uğur; McWeeney, S.; Aladjem, M.; Birney, E.; Collado-Vides, J.; Goto, S.; Hucka, M.; Novère, Nicolas Le; Maltsev, N.; Pandey, A.; Thomas, P.; Wingender, E.; Karp, P. D.; Sander, C.; Bader, G. D.Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery. © 2010 Nature America, Inc. All rights reserved.Item Restricted Bir edebiyat devi... Yaşar Kemal(1996) Gürsel, NedimItem Open Access Can accessing much data reshape the theory? Inventory theory under the challenge of data-driven systems(Elsevier, 2022-08-24) Erkip, Nesim KohenIn this review, we discuss the data-driven systems and their effects on the implementation of the inventory theory. After overviewing the theory briefly, we group the data-driven approaches to simplify exposition. We consider the use of available data to estimate the parameters of more complex models, and propose developing the theory in that direction, as well. As a pedagogical example, an extension of the standard EOQ model with heterogenous customers is presented. The review proposes a research agenda for inventory problems and concludes with discussing challenges for the future.Item Open Access Carving event and episodic memory at their Joints(Cambridge University Press, 2018) Keven, NazımMahr & Csibra (M&C) argue that event and episodic memories share the same scenario construction process. I think this way of carving up the distinction throws the baby out with the bathwater. If there is a substantive difference between event and episodic memory, it is based on a difference in the construction process and how they are organized, respectively.Item Open Access Dopamine replacement therapy, learning and reward prediction in Parkinson’s disease: Implications for rehabilitation(Frontiers Research Foundation, 2016) Ferrazzoli, D.; Carter, A.; Ustun, F. S.; Palamara, G.; Ortelli, P.; Maestri, R.; Yucel, M.; Frazzitta, G.The principal feature of Parkinson’s disease (PD) is the impaired ability to acquire and express habitual-automatic actions due to the loss of dopamine in the dorsolateral striatum, the region of the basal ganglia associated with the control of habitual behavior. Dopamine replacement therapy (DRT) compensates for the lack of dopamine, representing the standard treatment for different motor symptoms of PD (such as rigidity, bradykinesia and resting tremor). On the other hand, rehabilitation treatments, exploiting the use of cognitive strategies, feedbacks and external cues, permit to “learn to bypass” the defective basal ganglia (using the dorsolateral area of the prefrontal cortex) allowing the patients to perform correct movements under executive-volitional control. Therefore, DRT and rehabilitation seem to be two complementary and synergistic approaches. Learning and reward are central in rehabilitation: both of these mechanisms are the basis for the success of any rehabilitative treatment. Anyway, it is known that “learning resources” and reward could be negatively influenced from dopaminergic drugs. Furthermore, DRT causes different well-known complications: among these, dyskinesias, motor fluctuations, and dopamine dysregulation syndrome (DDS) are intimately linked with the alteration in the learning and reward mechanisms and could impact seriously on the rehabilitative outcomes. These considerations highlight the need for careful titration of DRT to produce the desired improvement in motor symptoms while minimizing the associated detrimental effects. This is important in order to maximize the motor re-learning based on repetition, reward and practice during rehabilitation. In this scenario, we review the knowledge concerning the interactions between DRT, learning and reward, examine the most impactful DRT side effects and provide suggestions for optimizing rehabilitation in PD.Item Open Access Early outcomes after transoral CO2 laser resection of laryngeal and hypopharyngeal squamous cell carcinoma: One centre's experience(Cambridge University Press, 2010) Leong, S. C.; Kathan, C.; Mortimore, S.Objectives: To review early oncological outcomes following transoral CO2 laser resection of laryngeal and hypopharyngeal squamous cell carcinoma. Design: Retrospective review of hospital electronic database. Setting: Large district general hospital in England, UK.Main outcome measures: Patients' three-year disease-specific survival and disease-free survival were evaluated, including post-operative complications, voice quality and swallowing status. Results: Seventy-seven patients (16 women and 61 men) were identified. Transoral laser excision of squamous cell carcinoma of the larynx was undergone by 65 patients, and the same procedure in the hypopharynx by 12. Patients with laryngeal cancer had statistically better disease-specific survival than those with hypopharyngeal cancer (p=0.021), although the cumulative disease-free survival probability was 0.71 for both larynx and hypopharynx groups. Patients who underwent laryngectomy following failed laser treatment or as a salvage procedure had poorer outcomes.Conclusions: The overall results of this study were comparable with those of other, larger studies. At three-year follow up, cumulative disease-specific survival probabilities were 0.92 and 0.71 for laryngeal and hypopharyngeal squamous cell carcinoma, respectively. Copyright © JLO (1984) Limited 2009.Item Embargo Facility location decisions for drone delivery: A literature review(Elsevier BV, 2023-10-30) Dükkancı, Okan; Campbell, James F.; Yetiş Kara, BaharThis study presents a comprehensive literature survey on facility location problems for drone (uncrewed vehicle) delivery, where either (i) drones are the only vehicles, or (ii) drones and other vehicles (e.g., trucks) work together for delivery, but drones do not ride in or on the other vehicles. The main goals of this review are to identify and categorize fundamental facility location problems associated with drone delivery, to document the large volume of research in this area, to provide a connection between the studies from different research fields that consider similar location problems, and to highlight promising areas for future research. We first discuss and classify the functions of drones and the various types of facilities used for drone and hybrid vehicle-drone (e.g., truck and drone, or transit and drone) delivery systems, including drone bases (fixed or temporary), other vehicle bases, recharging stations, (re)supply points, and platooning points. The literature is reviewed and categorized based on the types of vehicles involved and their interactions, the types of facilities located, the types of drones and the location space (discrete or continuous). Each category is analyzed in terms of the modeling approach, decision(s), the objective function(s), constraint(s) and additional feature(s). The paper concludes with some promising future research directions.Item Open Access Injectable in situ forming microparticles: A novel drug delivery system(2012) Yapar, E. A.; Inal, Ö.; Özkan, Y.; Baykara, T.Pharmaceutical formulation research has recently been focusing on delivery systems which provide long therapeutic effects and reduced side effects, and involving simplified production stages and facilitated application process. In situ forming microparticle (ISM) systems, one of the latest approach in this field, offer a new encapsulation technique and meet the objectives stated above. Factors such as the carrier used to form the multiparticles, amount and type of drug and the vehicle type can be taken as the main performance criteria for these systems. Ongoing studies have shown that this new multiparticulate drug delivery system is suitable for achieving new implant delivery system with low risk of dose-dumping, capable of being modulated to exhibit varying release patterns, reproducible, easily applicable and welltolerated compared with classically surgical implants.Item Open Access Judgemental forecasting: a review of progress over the last 25 years(Elsevier, 2006) Lawrence, M.; Goodwin, P.; O'Connor, M.; Önkal D.The past 25 years has seen phenomenal growth of interest in judgemental approaches to forecasting and a significant change of attitude on the part of researchers to the role of judgement. While previously judgement was thought to be the enemy of accuracy, today judgement is recognised as an indispensable component of forecasting and much research attention has been directed at understanding and improving its use. Human judgement can be demonstrated to provide a significant benefit to forecasting accuracy but it can also be subject to many biases. Much of the research has been directed at understanding and managing these strengths and weaknesses. An indication of the explosion of research interest in this area can be gauged by the fact that over 200 studies are referenced in this review.Item Open Access miR-200c: a versatile watchdog in cancer progression, EMT, and drug resistance(Springer Verlag, 2016-06) Mutlu, M.; Raza, U.; Saatci, Ö.; Eyüpoğlu, E.; Yurdusev, E.; Şahin, Ö.MicroRNAs (miRNAs) are 20–22-nucleotide small endogenous non-coding RNAs which regulate gene expression at post-transcriptional level. In the last two decades, identification of almost 2600 miRNAs in human and their potential to be modulated opened a new avenue to target almost all hallmarks of cancer. miRNAs have been classified as tumor suppressors or oncogenes depending on the phenotype they induce, the targets they modulate, and the tissue where they function. miR-200c, an illustrious tumor suppressor, is one of the highly studied miRNAs in terms of development, stemness, proliferation, epithelial-mesenchymal transition (EMT), therapy resistance, and metastasis. In this review, we first focus on the regulation of miR-200c expression and its role in regulating EMT in a ZEB1/E-cadherin axis-dependent and ZEB1/E-cadherin axis-independent manner. We then describe the role of miR-200c in therapy resistance in terms of multidrug resistance, chemoresistance, targeted therapy resistance, and radiotherapy resistance in various cancer types. We highlight the importance of miR-200c at the intersection of EMT and chemoresistance. Furthermore, we show how miR-200c coordinates several important signaling cascades such as TGF-β signaling, PI3K/Akt signaling, Notch signaling, VEGF signaling, and NF-κB signaling. Finally, we discuss miR-200c as a potential prognostic/diagnostic biomarker in several diseases, but mainly focusing on cancer and its potential application in future therapeutics.Item Open Access Oligonucleotide-based label-free detection with optical microresonators: strategies and challenges(Royal Society of Chemistry, 2016) Toren, P.; Ozgur E.; Bayındır, MehmetThis review targets diversified oligonucleotide-based biodetection techniques, focusing on the use of microresonators of whispering gallery mode (WGM) type as optical biosensors mostly integrated with lab-on-a-chip systems. On-chip and microfluidics combined devices along with optical microresonators provide rapid, robust, reproducible and multiplexed biodetection abilities in considerably small volumes. We present a detailed overview of the studies conducted so far, including biodetection of various oligonucleotide biomarkers as well as deoxyribonucleic acids (DNAs), ribonucleic acids (RNAs) and proteins. We particularly advert to chemical surface modifications for specific and selective biosensing.Item Open Access Operational research: methods and applications(Taylor and Francis Ltd., 2023-12-27) Petropoulos, F.; Laporte, G.; Aktas, E.; Alumur, S.; Archetti, C.; Ayhan, H.; Battarra, M.; Bennell, J.; Bourjolly, J.; Boylan, J. E.; Breton, M.; Canca, D.; Charlin, L.; Chen, B.; Cicek, C.; Cox, L.; Currie, C. S.M.; Demeulemeester, E.; Ding, L.; Disney, S. M.; Ehrgott, M.; Eppler, M. J.; Erdoğan, G.; Fortz, B.; Franco, L. A.; Frische, J.; Greco, S.; Gregory, A. J.; Hämäläinen, R. P.; Herroelen, W.; Hewitt, M.; Holmström, J.; Hooker, J. N.; Işık, T.; Johnes, J.; Kara, B. Y.; Karsu, Özlem; Kent, K.; Köhler, C.; Kunc, M.; Kuo, Y.; Letchford, A. N.; Leung, J.; Li, D.; Li, H.; Lienert, J.; Ljubić, I.; Lodi, A.; Lozano, S.; Lurkin, V.; Martello, S.; McHale, I. G.; Midgley, G.; Morecroft, J. D.W.; Mutha, A.; Oğuz, C.; Petrovic, S.; Pferschy, U.; Psaraftis, H. N.; Rose, S.Throughout its history, Operational Research has evolved to include methods, models and algorithms that have been applied to a wide range of contexts. This encyclopedic article consists of two main sections: methods and applications. The first summarises the up-to-date knowledge and provides an overview of the state-of-the-art methods and key developments in the various subdomains of the field. The second offers a wide-ranging list of areas where Operational Research has been applied. The article is meant to be read in a nonlinear fashion and used as a point of reference by a diverse pool of readers: academics, researchers, students, and practitioners. The entries within the methods and applications sections are presented in alphabetical order. The authors dedicate this paper to the 2023 Turkey/Syria earthquake victims. We sincerely hope that advances in OR will play a role towards minimising the pain and suffering caused by this and future catastrophes.Item Open Access Purinergic regulation of the immune system(Nature Publishing Group, 2016) Cekic, C.; Linden, J.Cellular stress or apoptosis triggers the release of ATP, ADP and other nucleotides into the extracellular space. Extracellular nucleotides function as autocrine and paracrine signalling molecules by activating cell-surface P2 purinergic receptors that elicit pro-inflammatory immune responses. Over time, extracellular nucleotides are metabolized to adenosine, leading to reduced P2 signalling and increased signalling through anti-inflammatory adenosine (P1 purinergic) receptors. Here, we review how local purinergic signalling changes over time during tissue responses to injury or disease, and we discuss the potential of targeting purinergic signalling pathways for the immunotherapeutic treatment of ischaemia, organ transplantation, autoimmunity or cancer.Item Open Access Quantum dot integrated LEDs using photonic and excitonic color conversion(Elsevier, 2011-11-23) Demir, Hilmi Volkan; Nizamoglu, S.; Erdem, T.; Mutlugun, E.; Gaponik N.; Eychmüller A.This review summarizes advantages, recent progress and challenges related to the quickly evolving research field of colloidal quantum dot integrated LEDs based on color conversion. We start with presenting a short general introduction to the field of solid state lighting and color conversion phenomena, which are essential for defining the requirements for high-quality general lighting. Subsequently we continue with a brief description of the synthesis of nanocrystal quantum dots and their optical properties together with the advantages of utilizing them in LEDs as color convertors. Following this basic background, we review the recent efforts on quantum dot integrated color-conversion LEDs, Förster resonance energy transfer (FRET) converted LEDs and FRET-enhanced LEDs. Finally, we conclude with a future outlook on semiconductor lighting and quantum dot integrated LEDs.Item Open Access Retinal proteins as model systems for membrane protein folding(Elsevier BV, 2014) Tastan, O.; Dutta, A.; Booth, P.; Klein-Seetharaman, J.Experimental folding studies of membrane proteins are more challenging than water-soluble proteins because of the higher hydrophobicity content of membrane embedded sequences and the need to provide a hydrophobic milieu for the transmembrane regions. The first challenge is their denaturation: due to the thermodynamic instability of polar groups in the membrane, secondary structures in membrane proteins are more difficult to disrupt than in soluble proteins. The second challenge is to refold from the denatured states. Successful refolding of membrane proteins has almost always been from very subtly denatured states. Therefore, it can be useful to analyze membrane protein folding using computational methods, and we will provide results obtained with simulated unfolding of membrane protein structures using the Floppy Inclusions and Rigid Substructure Topography (FIRST) method. Computational methods have the advantage that they allow a direct comparison between diverse membrane proteins. We will review here both, experimental and FIRST studies of the retinal binding proteins bacteriorhodopsin and mammalian rhodopsin, and discuss the extension of the findings to deriving hypotheses on the mechanisms of folding of membrane proteins in general. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.Item Open Access TP53 mutations in familial breast cancer: Functional aspects(John Wiley & Sons, Inc., 2003) Gasco, M.; Yulug, I. G.; Crook, T.Mutation in p53 (TP53) remains one of the most commonly described genetic events in human neoplasia. The occurrence of mutations is somewhat less common in sporadic breast carcinomas than in other cancers, with an overall frequency of about 20%. There is, however, evidence that p53 is mutated at a significantly higher frequency in breast carcinomas arising in carriers of germ-line BRCA1 and BRCA2 mutations. Some of the p53 mutants identified in BRCA1 and BRCA2 mutation carriers are either previously undescribed or infrequently reported in sporadic human cancers. Functional characterization of such mutants in various systems has revealed that they frequently possess properties not commonly associated with those occurring in sporadic cases: they retain apoptosis-inducing, transactivating, and growth-inhibitory activities similar to the wild-type protein, yet are compromised for transformation suppression and also possess an independent transforming phenotype. The occurrence of such mutants in familial breast cancer implies the operation of distinct selective pressures during tumorigenesis in BRCA-associated breast cancers.Item Restricted Trajectors of the Russian spirit(1967) Morral, FrankItem Open Access Universal product design involving elderly users: a participatory design model(Elsevier, 2004-07) Demirbilek, O.; Demirkan, H.Recent studies have shown that people prefer to age in their familiar environments, thus guiding designers to provide a safe and functionally appropriate environment for ageing people, regardless of their physical conditions or limitations. Therefore, a participatory design model is proposed where human beings can improve their quality of life by promoting independence, as well as safety, useability and attractiveness of the residence. Brainstorming, scenario building, unstructured interviews, sketching and videotaping are used as techniques in the participatory design sessions. Quality deployment matrices are employed to find the relationships between the elderly user's requirements and design specifications. A case study was devised to apply and test the conceptual model phase of the proposed model.