Researcher:
Yılmaz, Özlem

Profile Picture
ORCID

Job Title

Doctor

First Name

Özlem

Last Name

Yılmaz

Name

Name Variants

Yılmaz, Özlem

Email Address

Birth Date

Filters

Advanced Search

Filter by

Settings

Researcher Of Publications: search.filters.isAuthorOfPublication.7e1f77e4-df86-413c-a3e0-e5f5be697c69

Search Results

Now showing 1 - 9 of 9
  • Placeholder
    PublicationMetadata only
    Prediction of secondary structures of proteins using a two-stage method
    (Pergamon-Elsevier Science Ltd, 2008) Department of Industrial Engineering; N/A; Department of Industrial Engineering; Yüksektepe, Fadime Üney; Yılmaz, Özlem; Türkay, Metin; Researcher; Master Student; Faculty Member; Department of Industrial Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 24956
    Protein structure determination and prediction has been a focal research subject in life sciences due to the importance of protein structure in understanding the biological and chemical activities of organisms. The experimental methods used to determine the structures of proteins demand sophisticated equipment and time. A host of computational methods are developed to predict the location of secondary structure elements in proteins for complementing or creating insights into experimental results. However, prediction accuracies of these methods rarely exceed 70%. In this paper, a novel two-stage method to predict the location of secondary structure elements in a protein using the primary structure data only is presented. In the first stage of the proposed method, the folding type of a protein is determined using a novel classification approach for multi-class problems. The second stage of the method utilizes data available in the Protein Data Bank and determines the possible location of secondary structure elements in a probabilistic search algorithm. It is shown that the average accuracy of the predictions is 74.1 % on a large structure dataset.
  • Placeholder
    PublicationMetadata only
    Prediction of folding type of proteins using mixed-integer linear programming
    (Elsevier Science Bv, 2005) Department of Industrial Engineering; Department of Industrial Engineering; N/A; Türkay, Metin; Yüksektepe, Fadime Üney; Yılmaz, Özlem; Faculty Member; Researcher; Master Student; Department of Industrial Engineering; College of Engineering; College of Engineering; Graduate School of Sciences and Engineering; 24956; N/A; N/A
    Proteins are classified into four main structural classes by considering their amino acid compositions. Traditional approaches that use hyperplanes to partition data sets into two groups perform poorly due to the existence of four classes. Therefore, a novel method that uses mixed-integer programming is developed to overcome difficulties and inconsistencies of these traditional approaches. Mixed-integer programming (MIP) allows the use of hyper-boxes in order to define the boundaries of the sets that include all or some of the points in that class. For this reason, the efficiency and accuracy of data classification with MIP approach can be improved dramatically compared to the traditional methods. The efficiency of the proposed approach is illustrated on a training set of 120 proteins (30 from each type). The prediction results and their validation are also examined.
  • Placeholder
    PublicationMetadata only
    A case with acute baked milk protein-induced enterocolitis syndrome
    (Wiley, 2019) N/A; N/A; N/A; Saçkesen, Cansın; Yılmaz, Özlem; Demirkol, Demet; Faculty Member; Doctor; Faculty Member; School of Medicine; School of Medicine; School of Medicine; 182537; 140706; 108964
    N/A
  • Placeholder
    PublicationMetadata only
    Investigation of the effects of tumor necrosis factor-alpha, H2o2, ethanol and butyrate on intestinal epithelial cell permeability
    (Wiley, 2019) Yazıcı, Duygu; Süer, Hande; Yılmaz, Özlem; Karahüseyinoğlu, Serçin; Saçkesen, Cansın; PhD Student; PhD Student; Master Student; Faculty Member; Faculty Member; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Health Sciences; Graduate School of Health Sciences; Graduate School of Sciences and Engineering; School of Medicine; School of Medicine; N/A; N/A; N/A; 110772; 182537
    N/A 
  • Placeholder
    PublicationMetadata only
    A possibly fatal outcome of oral contraceptive therapy: estrogen triggered hereditary angioedema attack in an adolescent
    (Galenos Yayınevi, 2021) Demirkol, Demet; Birben, Esra; Soyer, Özge; N/A; Balkancı, Uğur Berkay; Yeşiltepe Mutlu, Rahime Gül; Yılmaz, Özlem; Saçkesen, Cansın; Undergraduate Student; Faculty Member; Doctor; Faculty Member; School of Medicine; School of Medicine; N/A; School of Medicine; Koç University Hospital; Koc University Hospital; N/A; 153511; 140706; 182537
    Hereditary angioedema (HAE) is characterized by recurrent angioedema attacks with no urticaria. This disease has a high mortality due to asphyxia. Level of complement 4 (C4), C1 esterase inhibitor (C1-INH) level and function, and genetic mutations determine different endotypes of HAE. Clinical presentation and the triggers of vasogenic edema may change according to the endotypes. An adolescent girl with oligomenorrhea, obesity, hirsutism, and acanthosis nigricans was diagnosed with polycystic ovary syndrome (PCOS) and prescribed ethinyl estradiol & cyproterone acetate containing oral contraceptive (OC). On the 16th day of treatment, she developed angioedema on the face, neck, and chest leading to dyspnea. Adrenaline, antihistamine, and corticosteroid treatments were ineffective. In the family history, the patient's mother and two cousins had angioedema attacks. C1-INH concentrate was administered with a diagnosis of HAE. C4, and C1-INH level and activity were normal. Genetic analysis identified a mutation of Factor XII (F12) gene, and the diagnosis of Factor 12 (F12)-related HAE was made. OC treatment discontinued. She has had no additional angioedema attacks in the follow-up period of two years. OC containing estrogen may induce the life-threatening first attack of F12-related HAE even in children. Recurring angioedema attacks in the family should be asked before prescribing estrogen-containing OC pills.
  • Placeholder
    PublicationMetadata only
    IgE and IgG4 binding to lentil epitopes in children with red and green lentil allergy
    (Wiley, 2020) Gimenez, Gustavo; Grishina, Galina; Yavuz, Süleyman T.; Şahiner, Ümit Murat; Büyüktiryaki, Betül; Yılmaz, Ebru Arık; Cavkaytar, Özlem; Sampson, Hugh A.; N/A; N/A; N/A; Saçkesen, Cansın; Erman, Baran; Yılmaz, Özlem; Faculty Member; Researcher; Doctor; School of Medicine; School of Medicine; School of Medicine; 182537; 268521; 140706
    Background: The consumption of lentil is common in the Mediterranean area and is one of the causes of IgE-mediated food allergy in many countries. Len c 1 is a well-defined allergen of lentil and approximately 80% of the patients with lentil allergy recognize the purified Len c 1 protein. We sought to identify IgE and IgG4 sequential epitopes of Len c 1 in patients with red and/or green lentil allergy. We also aimed to determine IgE and IgG4 binding differences between those patients who had outgrown or remained reactive to lentil. Methods: Children with IgE-mediated lentil allergy were included in the study. We applied a microarray immunoassay to determine the characterization of positive IgE and IgG4 binding to Len c 1 epitopes in the patients' sera. Results The peptides specifically recognized by IgE and IgG4 antibodies were mainly detected between peptides 107 and 135 of Len c 1. The signal intensities of positive epitopes were significantly greater in reactive patients than tolerant ones (P = .008 for IgE and P = .002 for IgG4). Moreover, IgE and IgG4 antibodies bound largely the same sequential epitopes in patients who remained reactive or outgrew their allergy. Conclusion: IgG4-binding epitopes in lentil allergy were identified and IgE and IgG4 binding to epitopes in both red and green lentils was compared. Our data regarding signal intensity differences between reactive and outgrown patients and overlap binding of IgE and IgG4 antibodies may be important for the development of more accurate diagnostic tests and understanding of natural tolerance development.
  • Placeholder
    PublicationMetadata only
    Prediction of secondary structures of proteins using a two-stage method
    (Elsevier Science Bv, 2006) Department of Industrial Engineering; N/A; N/A; Türkay, Metin; Yılmaz, Özlem; Yüksektepe, Fadime Üney; Faculty Member; Master Student; PhD Student; Department of Industrial Engineering; College of Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; 24956; N/A; N/A
    Protein structure determination and prediction has been a focal research subject in life sciences due to the importance of protein structure in understanding the biological and chemical activities in any organism. the experimental methods used to determine the structures of proteins demand sophisticated equipment and time. in order to overcome the shortcomings of the experimental methods, A host of algorithms aimed at predicting the location of secondary structure elements using statistical and computational methods are developed. However, prediction accuracies of these methods rarely exceeded 70%. in this paper a novel two-stage method to predict the location of secondary structure elements in a protein using the primary structure data only is presented. in the first stage of the proposed method, folding type of a protein is determined using a novel classification model for multi-class problems. the second stage of the method utilizes data available in the Protein Data Bank and determines the possible location of secondary structure elements in a probabilistic search algorithm. It is shown that the average accuracy of the predictions increased to 74.1%.
  • Placeholder
    PublicationMetadata only
    The relationship between dietary elimination and maternal psychopathology in breastfeeding mothers of infants with food allergy
    (Wiley, 2022) Can, Ceren; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; Yılmaz, Özlem; Saçkesen, Cansın; Kaçar, Anıl Şafak; Göğebakan, Emre; Necef, Işıl; Mutluer, Tuba; Taşkıran, Ali Sarper; Kızılkan, Nuray Uslu; Doctor; Faculty Member; PhD Student; Undergraduate Student; Faculty Member; Faculty Member; Other; Faculty Member; N/A; School of Medicine; Graduate School of Health Sciences; School of Medicine; School of Medicine; School of Medicine; School of Medicine; School of Medicine; Koç University Hospital; N/A; N/A; N/A; N/A; N/A; N/A; N/A; 140706; 182537; N/A; N/A; N/A; 305311; 195168; 221274
    Background: There has been no study evaluating the psychopathology in breastfeeding mothers of infants with food allergy (FA). Objective: The aim of the study was to investigate the relationship between dietary elimination and maternal psychopathology, specifically anxiety, depression, and mother-to-infant bonding, in breastfeeding mothers of infants with food allergy. Methods: Breastfeeding mothers following an elimination diet due to FA in their children aged 1-to-12 months were compared with the healthy controls. The physician-diagnosed FA group was divided into IgE-, non-IgE-mediated, and infants with some minor symptoms which were not enough to make the diagnosis of FA were classified as Indecisive symptoms for FA group. Mothers completed standardized questionnaires including Symptom Checklist 90R, Beck Depression/Anxiety Inventories (BDI/BAI), Postpartum Bonding Questionnaire (Bonding). Results: Of 179 mother and infants, 64 were healthy, 89 were FA, 16 were indecisive symptoms for FA. The mean age of the mothers and infants were 31.1 ± 4.7 years and 6.3 ± 3.6 months, respectively. The physician-diagnosed FA groups had higher scores for anxiety (p = .008), anger (p = .042), depression (p < .001), obsession (p = .002), phobia (p = .008), somatization (p = .002), general symptom index (GSI) (p = .001), BDI (p < .001), BAI (p = .008), and Bonding (attachment [p = .001], anger [p = .019], and total [p = .036]) than the healthy ones. The indecisive symptoms for FA group had a similar score pattern to physician-diagnosed FA, except interpersonal sensitivity, BDI, and attachment. Conclusion: Breastfeeding mothers of infants with FA were more anxious, with higher depression scores than controls, and had many psychopathologies which affected bonding. Interventions targeting negativity in caregivers' social relationships are urgently needed.
  • Placeholder
    PublicationMetadata only
    Negative psychosocial effect of dietary elimination on breastfeeding mothers having infants with and without food allergy
    (Wiley-Blackwell, 2019) Can, Ceren; N/A; Kaçar, Anıl Şafak; Yılmaz, Özlem; Göğebakan, Emre; Necef, Işıl; Mutluer, Tuba; Kızılkan, Nuray Uslu; Taşkıran, Ali Sarper; Saçkesen, Cansın; PhD Student; Doctor; Undergraduate Student; Faculty Member; Faculty Member; Faculty Member; Other; Faculty Member; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Health Sciences; N/A; School of Medicine; School of Medicine; School of Medicine; School of Medicine; School of Medicine; School of Medicine; N/A; Koç University Hospital; N/A; Koç University Hospital; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; 305311; 221274; 195168; 182537
    Background: There has been no trial evaluating the psychopathology in breastfeeding mothers of infants with food allergy (FA). Objective: To investigate the effect of dietary elimination on maternal psychopathology, specifically stress/anxiety and mother-to-infant bonding and explore the importance of sociodemographic features on these variables. Methods: Breastfeeding mothers following an elimination diet due to FA in their children aged 1-to-12 months were compared with the healthy controls. Physician-diagnosed FA group were divided into IgE-, non-IgE-mediated and infants with some minor symptoms which were not enough to make the diagnosis of FA were classified as Indecisive symptoms for FA group. Mothers completed standardized questionnaires including Symptom Checklist 90R, Beck Depression/Anxiety Inventories (BDI/BAI), Postpartum Bonding Questionnaire (Bonding). Results: Of 179 mother-infants, 64 were healthy, 89 were FA, 16 were indecisive symptoms for FA. The mean age of the mothers and infants were 31.1±4.7 years and 6.3±3.6 months. The physician diagnosed FA groups had higher scores for anxiety (p=0.008), anger (p=0.042), depression (p