Akademik Çıktılar
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Article Citation Count: 2252019 EACTS Expert Consensus on long-term mechanical circulatory support(European Association for Cardio-Thoracic Surgery, 2019) Potapov,E.V.; Antonides,C.; Crespo-Leiro,M.G.; Combes,A.; Färber,G.; Hannan,M.M.; Gustafsson,F.Long-term mechanical circulatory support (LT-MCS) is an important treatment modality for patients with severe heart failure. Different devices are available, and many - sometimes contradictory - observations regarding patient selection, surgical techniques, perioperative management and follow-up have been published. With the growing expertise in this field, the European Association for Cardio-Thoracic Surgery (EACTS) recognized a need for a structured multidisciplinary consensus about the approach to patients with LT-MCS. However, the evidence published so far is insufficient to allow for generation of meaningful guidelines complying with EACTS requirements. Instead, the EACTS presents an expert opinion in the LT-MCS field. This expert opinion addresses patient evaluation and preoperative optimization as well as management of cardiac and non-cardiac comorbidities. Further, extensive operative implantation techniques are summarized and evaluated by leading experts, depending on both patient characteristics and device selection. The faculty recognized that postoperative management is multidisciplinary and includes aspects of intensive care unit stay, rehabilitation, ambulatory care, myocardial recovery and end-of-life care and mirrored this fact in this paper. Additionally, the opinions of experts on diagnosis and management of adverse events including bleeding, cerebrovascular accidents and device malfunction are presented. In this expert consensus, the evidence for the complete management from patient selection to end-of-life care is carefully reviewed with the aim of guiding clinicians in optimizing management of patients considered for or supported by an LT-MCS device. © 2019 The Author(s).Article Citation Count: 487Advanced heart failure: a position statement of the Heart Failure Association of the European Society of Cardiology(John Wiley and Sons Ltd, 2018) Crespo-Leiro,M.G.; Metra,M.; Lund,L.H.; Milicic,D.; Costanzo,M.R.; Filippatos,G.; Ruschitzka,F.This article updates the Heart Failure Association of the European Society of Cardiology (ESC) 2007 classification of advanced heart failure and describes new diagnostic and treatment options for these patients. Recognizing the patient with advanced heart failure is critical to facilitate timely referral to advanced heart failure centres. Unplanned visits for heart failure decompensation, malignant arrhythmias, co-morbidities, and the 2016 ESC guidelines criteria for the diagnosis of heart failure with preserved ejection fraction are included in this updated definition. Standard treatment is, by definition, insufficient in these patients. Inotropic therapy may be used as a bridge strategy, but it is only a palliative measure when used on its own, because of the lack of outcomes data. Major progress has occurred with short-term mechanical circulatory support devices for immediate management of cardiogenic shock and long-term mechanical circulatory support for either a bridge to transplantation or as destination therapy. Heart transplantation remains the treatment of choice for patients without contraindications. Some patients will not be candidates for advanced heart failure therapies. For these patients, who are often elderly with multiple co-morbidities, management of advanced heart failure to reduce symptoms and improve quality of life should be emphasized. Robust evidence from prospective studies is lacking for most therapies for advanced heart failure. There is an urgent need to develop evidence-based treatment algorithms to prolong life when possible and in accordance with patient preferences, increase life quality, and reduce the burden of hospitalization in this vulnerable patient population. © 2018 The Authors. European Journal of Heart Failure © 2018 European Society of CardiologyBook Citation Count: 15Advanced Sensor and Detection Materials(Wiley Blackwell, 2014) Tiwari A.; Demir, M.M.Presents a comprehensive and interdisciplinary review of the major cutting-edge technology research areas-especially those on new materials and methods as well as advanced structures and properties-for various sensor and detection devices. The development of sensors and detectors at macroscopic or nanometric scale is the driving force stimulating research in sensing materials and technology for accurate detection in solid, liquid, or gas phases; contact or non-contact configurations; or multiple sensing. The emphasis on reduced-scale detection techniques requires the use of new materials and methods. These techniques offer appealing perspectives given by spin crossover organic, inorganic, and composite materials that could be unique for sensor fabrication. The influence of the length, composition, and conformation structure of materials on their properties, and the possibility of adjusting sensing properties by doping or adding the side-groups, are indicative of the starting point of multifarious sensing. The role of intermolecular interactions, polymer and ordered phase formation, as well as behavior under pressure and magnetic and electric fields are also important facts for processing ultra-sensing materials. The 15 chapters written by senior researchers in Advanced Sensor and Detection Materials cover all these subjects and key features under three foci: 1) principals and perspectives, 2) new materials and methods, and 3) advanced structures and properties for various sensor devices. © 2014 Scrivener Publishing LLC. All rights reserved.Book Part Citation Count: 4Advances in Model-Based Testing of Graphical User Interfaces(Elsevier Academic Press inc, 2017) Belli, Fevzi; Beyazit, Mutlu; Budnik, Christof J.; Tuglular, Tugkan; Tuğlular, Tuğkan; Bilgisayar Mühendisliği BölümüGraphical user interfaces (GUIs) enable comfortable interactions of the computer-based systems with their environment. Large systems usually require complex GUIs, which are commonly fault prone and thus are to be carefully designed, implemented, and tested. As a thorough testing is not feasible, techniques are favored to test relevant features of the system under test that will be specifically modeled. This chapter summarizes, reviews, and exemplifies conventional and novel techniques for model-based GUI testing.Article Citation Count: 15Aggregation of fillers blended into random elastomeric networks: Theory and comparison with experiments(2006) Demir M.M.; Menceloglu Y.Z.; Erman, B.A theoretical model describing aggregation of filler particles in amorphous elastomers is proposed. The model is based on a counting technique originally used in genome analysis to characterize the size and distribution of overlapping segments randomly placed on a DNA molecule. In the present model, the particles are first assumed to aggregate randomly upon mixing into the elastomer and then-sizes are calculated. The sizes and distributions of aggregates are also studied in the presence of attractive interparticle forces. Results of the proposed model are compared with experimental data on silica-filled end-linked poly(dimethyl-siloxane) networks. Comparison of the theory and experiment shows that the random aggregation assumption where no attractive forces exist between the particles is not valid and a significant attraction between the silica particles is needed in the theory to justify the experimental data obtained using atomic force microscopy. For filler content below 1.45 vol.-%, the model agrees, qualitatively, with experiment and shows the increase in cluster size with increasing amount of filler. It also explains the increase in the dispersion of aggregate sizes with increasing amount of filler. © 2006 WILEY-VCH Verlag GmbH & Co. KGaA.Article Citation Count: 0AMWC 2013: Advanced Materials World Congress (izmir, Turkey, September 16-19, 2013)(2013) Demir, M.M.[No abstract available]Article Citation Count: 17Apoptotic effects of non-edible parts of Punica granatum on human multiple myeloma cells(Sage Publications Ltd, 2016) Kiraz, Yagmur; Neergheen-Bhujun, Vidushi S.; Rummun, Nawraj; Baran, Yusuf; Baran, YusufMultiple myeloma is of great concern since existing therapies are unable to cure this clinical condition. Alternative therapeutic approaches are mandatory, and the use of plant extracts is considered interesting. Punica granatum and its derived products were suggested as potential anticancer agents due to the presence of bioactive compounds. Thus, polypenolic-rich extracts of the non-edible parts of P. granatum were investigated for their antiproliferative and apoptotic effects on U266 multiple myeloma cells. We demonstrated that there were dose-dependent decreases in the proliferation of U266 cells in response to P. granatum extracts. Also, exposure to the extracts triggered apoptosis with significant increases in loss of mitochondrial membrane potential in U266 cells exposed to the leaves and stem extracts, while the flower extract resulted in slight increases in loss of MMP. These results were confirmed by Annexin-V analysis. These results documented the cytotoxic and apoptotic effects of P. granatum extracts on human U266 multiple myeloma cells via disruption of mitochondrial membrane potential and increasing cell cycle arrest. The data suggest that the extracts can be envisaged in cancer chemoprevention and call for further exploration into the potential application of these plant parts.Article Citation Count: 20Apoptotic effects of non-edible parts of Punica granatum on human multiple myeloma cells(Springer Science and Business Media B.V., 2016) Baran, Yusuf; Neergheen-Bhujun,V.S.; Rummun,N.; Baran,Y.Multiple myeloma is of great concern since existing therapies are unable to cure this clinical condition. Alternative therapeutic approaches are mandatory, and the use of plant extracts is considered interesting. Punica granatum and its derived products were suggested as potential anticancer agents due to the presence of bioactive compounds. Thus, polypenolic-rich extracts of the non-edible parts of P. granatum were investigated for their antiproliferative and apoptotic effects on U266 multiple myeloma cells. We demonstrated that there were dose-dependent decreases in the proliferation of U266 cells in response to P. granatum extracts. Also, exposure to the extracts triggered apoptosis with significant increases in loss of mitochondrial membrane potential in U266 cells exposed to the leaves and stem extracts, while the flower extract resulted in slight increases in loss of MMP. These results were confirmed by Annexin-V analysis. These results documented the cytotoxic and apoptotic effects of P. granatum extracts on human U266 multiple myeloma cells via disruption of mitochondrial membrane potential and increasing cell cycle arrest. The data suggest that the extracts can be envisaged in cancer chemoprevention and call for further exploration into the potential application of these plant parts. © 2015, International Society of Oncology and BioMarkers (ISOBM).Article Citation Count: 19Apoptotic Effects of Resveratrol, a Grape Polyphenol, on Imatinib-Sensitive and Resistant K562 Chronic Myeloid Leukemia Cells(int inst Anticancer Research, 2012) Can, Geylani; Cakir, Zeynep; Kartal, Melts; Gunduz, Ufuk; Baran, Yusuf; Baran, YusufAim: To examine the antiproliferative and apoptotic effects of resveratrol on imatinib-sensitive and imatinib-resistant K562 chronic myeloid leukemia cells. Materials and Methods: Antiproliferative effects of resveratrol were determined by the 3-Bis[2-methoxy-4-nitro-5-sulphophenyl]-2H-tetrazolium-5-carboxanilide inner salt (XTT) cell proliferation assay. Apoptotic effects of resveratrol on sensitive K562 and resistant K562/IMA-3 cells were determined through changes in caspase-3 activity, loss of mitochondrial membrane potential (MMP), and apoptosis by annexin V-(FITC). Results: The concentrations of resveratrol that inhibited cell growth by 50% (IC50) were calculated as 85 and 122 mu M for K562 and K562/IMA-3 cells, respectively. There were 1.91-, 7.42- and 14.73-fold increases in loss of MMP in K562 cells treated with 10, 50, and 100 mu M resveratrol, respectively. The same concentrations of resveratrol resulted in 2.21-, 3.30- and 7.65-fold increases in loss of MMP in K562/IMA3 cells. Caspase-3 activity increased 1.04-, 2.77- and 4.8-fold in K562 and 1.02-, 1.41- and 3.46-fold in K562/IMA3 cells in response to the same concentrations of resveratrol, respectively. Apoptosis was induced in 58.7%- and 43.3% of K562 and K562/IMA-3 cells, respectively, in response to 100 mu M resveratrol. Conclusion: Taken together these results may suggest potential use of resveratrol in CML, as well as in patients with primary and/or acquired resistance to imatinib.Article Citation Count: 0Application of the Law of Minimum and Dissimilarity Analysis to Regression Test Case Prioritization(Ieee-inst Electrical Electronics Engineers inc, 2023) Ufuktepe, Ekincan; Tuglular, Tugkan; Tuğlular, Tuğkan; Bilgisayar Mühendisliği BölümüRegression testing is one of the most expensive processes in testing. Prioritizing test cases in regression testing is critical for the goal of detecting the faults sooner within a large set of test cases. We propose a test case prioritization (TCP) technique for regression testing called LoM-Score inspired by the Law of Minimum (LoM) from biology. This technique calculates the impact probabilities of methods calculated by change impact analysis with forward slicing and orders test cases according to LoM. However, this ordering doesn't consider the possibility that consecutive test cases may be covering the same methods repeatedly. Thereby, such ordering can delay the time of revealing faults that exist in other methods. To solve this problem, we enhance the LoM-Score TCP technique with an adaptive approach, namely with a dissimilarity-based coordinate analysis approach. The dissimilarity-based coordinate analysis uses Jaccard Similarity for calculating the similarity coefficients between test cases in terms of covered methods and the enhanced technique called Dissimilarity-LoM-Score (Dis-LoM-Score) applies a penalty with respective on the ordered test cases. We performed our case study on 10 open-source Java projects from Defects4J, which is a dataset of real bugs and an infrastructure for controlled experiments provided for software engineering researchers. Then, we hand-seeded multiple mutants generated by Major, which is a mutation testing tool. Then we compared our TCP techniques LoM-Score and Dis-LoM-Score with the four traditional TCP techniques based on their Average Percentage of Faults Detected (APFD) results.Article Citation Count: 5Bioactive Sphingolipids in Response to Chemotherapy: A Scope on Leukemias(Bentham Science Publ Ltd, 2011) Ekiz, Huseyin Atakan; Baran, Yusuf; Baran, YusufSphingolipids are major constituents of the cells with emerging roles in the regulation of cellular processes. Deregulation of sphingolipid metabolism is reflected as various pathophysiological conditions including metabolic disorders and several forms of cancer. Ceramides, ceramide-1-phosphate (C1P), glucosyl ceramide (GluCer), sphingosine and sphingosine-1-phosphate (S1P) are among the bioactive sphingolipid species that have important roles in the regulation of cell death, survival and chemotherapeutic resistance. Some of those species are known to accumulate in the cells upon chemotherapy while some others are known to exhibit an opposite pattern. Even though the length of fatty acid chain has a deterministic effect, in general, upregulation of ceramides and sphingosine is known to induce apoptosis. However, S1P, C1P and GluCer are proliferative for cells and they are involved in the development of chemoresistance. Therefore, sphingolipid metabolism appears as a good target for the development of novel therapeutics or supportive interventions to increase the effectiveness of the chemotherapeutic drugs currently in hand. Some approaches involve manipulation of the synthesis pathways yielding the increased production of apoptotic sphingolipids while the proliferative ones are suppressed. Some others are trying to take advantage of cytotoxic sphingolipids like short chain ceramide analogs by directly delivering them to the malignant cells as a distinct chemotherapeutic intervention. Numerous studies in the literature show the feasibility of those approaches especially in acute and chronic leukemias. This review compiles the current knowledge about sphingolipids and their roles in chemotherapeutic response with the particular attention to leukemias.Article Citation Count: 25Caffeic acid phenethyl ester triggers apoptosis through induction of loss of mitochondrial membrane potential in CCRF-CEM cells(Springer, 2011) Avci, Cigir Biray; Gunduz, Cumhur; Baran, Yusuf; Sahin, Fahri; Yilmaz, Sunde; Dogan, Zeynep Ozlem; Saydam, Guray; Baran, YusufCAPE (caffeic acid phenethyl ester) is one of the most valuable and investigated component of propolis which is composed by honeybees. In the current study, we aimed at examining apoptotic effects of CAPE on CCRF-CEM leukemic cells and at determining the roles of mitochondrial membrane potential (MMP) in cell death. Trypan blue and XTT methods were used to evaluate the cytotoxicity. Apoptosis was examined by ELISA-based oligonucleotide and acridine orange/ethidium bromide dye techniques. Loss of mitochondrial membrane potential was evaluated using JC-1 dye by flow cytometric analysis and under fluorescent microscope. We detected the time- and dose-dependent increases in cytotoxic effect of CAPE on CCRF-CEM cells. ELISA and acridine orange/ethidium bromide results showed that apoptotic cell population increased significantly in CCRF-CEM cells exposed to increasing concentrations of CAPE. On the other hand, there was significant loss of MMP determined in response to CAPE in CCRF-CEM cells. This in vitro data by being supported with clinical data may open the way of the potential use of CAPE for the treatment of leukemia.Article Citation Count: 8The case of a cyst hydatid localized within the interatrial septum(2004) Karabay,Ö.; Önen,A.; Yildiz,F.; Yilmaz,E.; Erdal,A.C.; Şanli,A.; Açikel,Ü.The ratio of cardiac involvement of Echinoccocus granulosus is 0.02-2% and although seen rarely, involvement of the interatrial septum has also been reported in the published literature. The present case was a 19-year-old male university student admitted to hospital with complaints of headache and dizziness. Computerized tomography of the cranium revealed a cystic mass located at the frontal region and enucleation of the cyst was performed during surgery. A cystic lesion 5 × 4 cm in size was detected within the interatrial septum on two-dimensional transthoracic echocardiography during the postoperative period and the patient was referred to our clinic. Open heart surgery was performed and a hydatid cyst that involved the interatrial septum was enucleated. The cyst wall was sutured to the interatrial septum. No complications developed during the postoperative period. The patient was discharged on the fifth day of hospitalization and medical therapy was started with albendazole. Copyright © 2004 by the Japanese Heart Journal.Review Citation Count: 255Cell proliferation and cytotoxicity assays(Bentham Science Publishers B.V., 2016) Baran, Yusuf; Kiraz,Y.; Baran,Y.Cell viability is defined as the number of healthy cells in a sample and proliferation of cells is a vital indicator for understanding the mechanisms in action of certain genes, proteins and pathways involved cell survival or death after exposing to toxic agents. Generally, methods used to determine viability are also common for the detection of cell proliferation. Cell cytotoxicity and proliferation assays are generally used for drug screening to detect whether the test molecules have effects on cell proliferation or display direct cytotoxic effects. Regardless of the type of cell-based assay being used, it is important to know how many viable cells are remaining at the end of the experiment. There are a variety of assay methods based on various cell functions such as enzyme activity, cell membrane permeability, cell adherence, ATP production, co-enzyme production, and nucleotide uptake activity. These methods could be basically classified into different categories: (I) dye exclusion methods such as trypan blue dye exclusion assay, (II) methods based on metabolic activity, (III) ATP assay, (IV) sulforhodamine B assay, (V) protease viability marker assay, (VI) clonogenic cell survival assay, (VII) DNA synthesis cell proliferation assays and (V) raman micro-spectroscopy. In order to choose the optimal viability assay, the cell type, applied culture conditions, and the specific questions being asked should be considered in detail. This particular review aims to provide an overview of common cell proliferation and cytotoxicity assays together with their own advantages and disadvantages, their methodologies, comparisons and intended purposes. © 2016 Bentham Science Publishers.Review Citation Count: 47Challenges in the preparation of optical polymer composites with nanosized pigment particles: A review on recent efforts(2012) Demir M.M.; Wegner, G.Blends of nanosized pigment particles and polymers are widely believed to offer the potential for the design of novel or at least improved materials. This review critically evaluates the recent literature with regard to the following issues: (a) why and how does the size of the particles matter, (b) what are the requirements to create compatibility between amorphous polymers and nanoparticles, (c) carbon allotropes as nanosized pigments, (d) bulk polymerization of monomer/pigment mixtures, (e) interaction of growing chains with the particles in the polymerization, (f) depletion flocculation as a mechanism to counteract homogeneous distribution of the particles in the polymer matrix and ways to suppress the undesirable flocculation, and (g) optical properties of the blends as well as methods of optical characterization. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.Review Citation Count: 17Changes in molecular biology of chronic myeloid leukemia in tyrosine kinase inhibitor era(E-century Publishing Corp, 2013) Comert, Melda; Baran, Yusuf; Saydam, Guray; Baran, YusufChronic myeloid leukemia (CML) is a clonal myeloproliferative disease characterized by a reciprocal translocation between long arms of chromosomes 9 and 22 t(9; 22) that generates the BCR-ABL fusion gene. If left untreated, newly diagnosed chronic phase CML patients finally progress to accelerated and blastic phase. After the introduction of tyrosine kinase inhibitors (TKIs), treatment strategies of CML changed dramatically. However, the development of resistance to TKIs started to create problems over time. In this review, the current information about CML biology before and after imatinib mesylate treatment is summarized.Article Citation Count: 7Characterization of Sb scaling and fluids in saline geothermal power plants: A case study for Germencik Region (Büyük Menderes Graben, Turkey)(Elsevier Ltd, 2021) Tonkul S.; Baba A.; Demir M.M.; Regenspurg, S.Turkey is located on the seismically active Alpine-Himalayan belt. Although tectonic activity causes seismicity in the Anatolian plate, it also constitutes an important geothermal energy resource. Today, geothermal energy production is heavily concentrated in Turkey's Western Anatolia region. Graben systems in this region are very suitable for geothermal resources. The Büyük Menderes Graben (BMG) is an area of complex geology with active tectonics and high geothermal potential power. Germencik (Aydın) is located in the BMG, where the geothermal waters include mainly Na-Cl-HCO3 water types. This study examined the stibnite scaling formed in the preheater system of the Germencik Geothermal Field (GGF). The formation of the stibnite scaling on the preheater system dramatically reduces the energy harvesting of the GGF. Considering the stibnite scaling in the surface equipment, the optimum reinjection temperature was determined as 95 °C to prevent stibnite scaling in the GGF. © 2021 Elsevier LtdArticle Citation Count: 101Chitosan fiber-supported zero-valent iron nanoparticles as a novel sorbent for sequestration of inorganic arsenic(Royal Soc Chemistry, 2013) Horzum, Nesrin; Demir, Mustafa M.; Nairat, Muath; Shahwan, Talal; Demir, MustafaThis study proposes a new sorbent for the removal of inorganic arsenic from aqueous solutions. Monodispersed nano zero-valent iron (nZVI) particles were nucleated at the surface of electrospun chitosan fibers (average fiber diameter of 195 +/- 50 nm) by liquid phase reduction of FeCl3 using NaBH4. The material was characterized using SEM, TGA, XPS, XRD, and FTIR. The diameter of iron nanoparticles was found to vary between 75-100 nm. A set of batch experiments were carried out to elucidate the efficiency of the composite sorbent toward fixation of arsenite and arsenate ions. The ion concentrations in the supernatant solutions were determined using inductively coupled plasma-mass spectrometry (ICP-MS). The results revealed that the chitosan fiber supported nZVI particles is an excellent sorbent material for inorganic arsenic uptake at concentrations ranging from 0.01 to 5.00 mg L-1 over a wide range of pH values. Based on XPS analysis, As(III) was found to undergo oxidation to As(V) upon sorption, while As(V) retained its oxidation state. By virtue of the successful combination of the electrospun fibers' mechanical integrity and the large reactivity of dispersed nZVI particles, the applicability of the resulting sorbent material in arsenic sorption holds broad promise.Article Citation Count: 38Clinical and laboratory features, complications and treatment outcome of brucellosis in childhood and review of the literature(2011) Uluǧ,M.; Yaman,Y.; Yapici,F.; Can-Uluǧ,N.Brucellosis, whether in an endemic region or not, remains a diagnostic puzzle due to occasional misleading unusual presentations and non-specific symptoms. The aim of this study was to evaluate the clinical and laboratory findings, complications and treatment outcome of brucellosis in children in southeastern Anatolia, Turkey. This study focuses on the frequency of clinical and laboratory findings and complications in cases with brucellosis. Of 22 patients, 8 (36.3%) were female and 14 (63.7%) were male. Fever, malaise, lack of appetite, arthralgia, and night sweating were the main presenting symptoms overall. Hematologic complications (n=13, 59.1%) were most common, followed by skeletal (n=7, 31.8%) and cutaneous system (n=1, 4.5%). Brucellosis may affect any organ system and imitate a variety of clinical entities. Diagnosis of brucellosis should be considered whenever there is a febrile illness associated with rheumatological complaints. Consequently, early recognition of the infection, prolonged antibiotic treatment and careful long-term follow-up should improve the patient outcome.Article Citation Count: 12Colloidal films of SiO2 in elastomeric polyacrylates by photopolymerization: A strain sensor application(Elsevier Science Sa, 2020) Inci, Ezgi; Topcu, Gokhan; Demir, Mustafa M.; Demir, MustafaThin layer SiO2 colloidal films show angle-dependent coloration (iridescence) based on constructive interference, rather than absorption, without the existence of pigments. The transfer of thin layered colloidal film into a transparent elastomeric matrix maintaining its color may allow the fabrication of colorimetric strain sensors. In this study, trilayer SiO2 colloidal films were prepared by Langmuir-Blodgett deposition using a binary solvent system (chloroform/methanol) and this structure is successfully transferred into poly(ethylene glycol) phenyl ether acrylate elastomer via lateral capillary force. The resulting composite films exhibit iridescence depending on the particle size, therefore, film thickness as similar in mere colloidal films with a slight difference due to change in efficient refractive index (neff). Uniaxial extension of the composite film up to 50 % strain causes a remarkable linear shift in reflection signal from 568 to 496 nm. The change in thickness of the composite film accordingly intercolloidal distance normal to the application of mechanical stretching causes variation of the reflection of light.
