WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection

Permanent URI for this collectionhttps://hdl.handle.net/11147/7150

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Now showing 1 - 10 of 24
  • Article
    Mitotyping of Random Bred Cats and Pure Breed Cats (turkish Angora and Turkish Van) Using Non-Repetitive Mitochondrial Dna Control Region
    (Elsevier, 2024) Bilgen, Nuket; Guvendi, Mervenur; Sezgin, Efe; Can, Huseyin; Koseoglu, Ahmet Efe; Alak, Sedef Erkunt; Un, Cemal
    The Fertile Crescent appears to be the most plausible region where the domestication of cats commenced through a mutually beneficial relationship between wild cats and early agrarian societies. These domesticated cats then journeyed across the globe mirroring the paths of human migration. An examination of mitochondrial DNA (mtDNA) control region-based mitotyping suggested that a significant majority, exceeding 80%, of globally sampled random-bred and pure-bred cats could be categorized into 12 predominant mitotypes. However, the extent of mitotype diversity within random-bred cats from regions proximate to the Fertile Crescent remains inadequately explored. In light of this we aimed to investigate the mitotype diversity in random bred cats sampled from various regions across Turkey. Additionally, we sought to establish a comparison with the mito-type profiles of locally recognized pure breeds, namely the Turkish Angora and Turkish Van. To unravel their evolutionary narratives, we engaged in comprehensive population genetics analyses at both the individual and mitotype-based levels. Our study encompassed a sample size of 240 specimens, forming the basis for both mitotyping and population genetics scrutiny. Our analysis yielded the identification of nine 'universal' mitotypes (A-J), alongside an 'outlier' mitotype group I. Notably mitotypes A and D emerged as particularly prevalent in contrast to the lesser occurrence mitotypes C, G, and H. With the realm of random bred cats the structure of haplotypes exhibited remarkable diversity presenting distinctions from Turkish Angora and Van breeds. Nucleotide diversity was higher compared to previous reports from Turkey and was one of the highest among reported world cat population estimates. Intriguingly, our investigations did not unveil any pronounced instances of strong selection, population expansions or contractions within any specific population or mitotype. To conclude, our study represents a pioneering effort in uncovering the mitotype profiles and haplotype structures inherent to both random-bred and pure breed cats in Turkey. This endeavor not only broadens our understanding of the feline genetic landscape within the region but also lays the foundation for future inquiries into the evolutionary trajectories and genetic legacies of these feline populations.
  • Conference Object
    Decision Making on Postmastectomy Radiation Therapy for Patients With T3n0m0 Luminal Breast Cancer
    (Springer, 2023) King, Caleb; Vargo, John; Bhargava, Rohit; Diego, Emilia J.; Cowher, Michael; Johnson, Ronald; Sezgin, Efe
    [No abstract available]
  • Conference Object
    Locoregional Treatment Improves Survival in De Novo Bone-Only Metastatic Breast Cancer: Long-Term Results of the Prospective, Multi-Institutional Study - Protocol Bomet Mf14-01
    (Springer, 2023) Soran, Atilla; Doğan, Lütfi; Işık, Arda; Özbaş, Serdar; Can Trabulus, Didem; Demirci, Umut; Karanlık, Hasan; Sezgin, Efe
    [No abstract available]
  • Article
    Citation - WoS: 6
    Citation - Scopus: 4
    Early Detection of Breast Cancer-Related Lymphedema: Accuracy of Indocyanine Green Lymphography Compared With Bioimpedance Spectroscopy and Subclinical Lymphedema Symptoms
    (Mary Ann Liebert, 2023) Soran, Atilla; Bengur, Fuat Barış; Rodriguez, Wendy; Chroneos, Maria Z.; Sezgin, Efe
    Introduction: The reported incidences of breast cancer-related lymphedema (LE) affecting the arms vary greatly. Reason for this variability includes different diagnostic techniques used across studies. In the current study, we compared the accuracy of indocyanine green lymphography (ICG_L) and bioimpedance spectroscopy (BIS) in detecting LE before presentation of clinical signs.Methods and Results: Patients with no initial detectable signs of clinical LE of their arms after axillary lymph node dissection or removal of >5 lymph nodes on sentinel lymph node biopsy were included. Subclinical LE was defined as BIS values outside the normal range [(>= 7 units (or >10 units)] or a 7-unit (or 10 unit) change between two measurements. We tracked ICG_L and BIS measurements for 133 potentially affected arms (n = 123). ICG_L detected signs of lymphatic flow disruption in 63 arms (47%). Based on the BIS value of 7 units, 60 arms (45%) had values outside the normal range. When using ICG_L-identified LE cases as true positives, BIS had a 54% accuracy (area under the curve [AUC] = 0.54) in detecting LE. Accuracy was 61% for subclinical LE symptoms when compared with ICG_L (AUC = 0.62). Both BIS and subclinical LE symptoms had <0.70 AUC-receiver characteristic operator curve, suggesting that BIS and development of subclinical LE symptoms are not adequate for identifying patients with subclinical LE.Conclusion: ICG_L is a reliable diagnostic tool for detecting early signs of lymphatic flow disruption in subclinical LE. Utilizing ICG_L to diagnose subclinical LE followed by a personalized treatment plan may provide patients the best chance of preventing disease progression.
  • Article
    Citation - WoS: 11
    Citation - Scopus: 10
    Molecular Evolution and Population Genetics of Glutamate Decarboxylase Acid Resistance Pathway in Lactic Acid Bacteria
    (Frontiers Media S.A., 2023) Sezgin, Efe; Tekin, Burcu
    Glutamate decarboxylase (GAD) pathway (GDP) is a major acid resistance mechanism enabling microorganisms’ survival in low pH environments. We aimed to study the molecular evolution and population genetics of GDP in Lactic Acid Bacteria (LAB) to understand evolutionary processes shaping adaptation to acidic environments comparing species where the GDP genes are organized in an operon structure (Levilactobacillus brevis) versus lack of an operon structure (Lactiplantibacillus plantarum). Within species molecular population genetic analyses of GDP genes in L. brevis and L. plantarum sampled from diverse fermented food and other environments showed abundant synonymous and non-synonymous nucleotide diversity, mostly driven by low frequency changes, distributed throughout the coding regions for all genes in both species. GAD genes showed higher level of replacement polymorphism compared to transporter genes (gadC and YjeM) for both species, and GAD genes that are outside of an operon structure showed even higher level of replacement polymorphism. Population genetic tests suggest negative selection against replacement changes in all genes. Molecular structure and amino acid characteristics analyses showed that in none of the GDP genes replacement changes alter 3D structure or charge distribution supporting negative selection against non-conservative amino acid changes. Phylogenetic and between species divergence analyses suggested adaptive protein evolution on GDP genes comparing phylogenetically distant species, but conservative evolution comparing closely related species. GDP genes within an operon structure showed slower molecular evolution and higher conservation. All GAD and transporter genes showed high codon usage bias in examined LAB species suggesting high expression and utilization of acid resistance genes. Substantial discordances between species, GAD, and transporter gene tree topologies were observed suggesting molecular evolution of GDP genes do not follow speciation events. Distribution of operon structure on the species tree suggested multiple independent gain or loss of operon structure in LABs. In conclusion, GDP genes in LABs exhibit a dynamic molecular evolutionary history shaped by gene loss, gene transfer, negative and positive selection to maintain its active role in acid resistance mechanism, and enable organisms to thrive in acidic environments.
  • Article
    Citation - WoS: 1
    Aso Visual Abstract: Intervention for Hepatic and Pulmonary Metastases in Breast Cancer Patients-Prospective, Multi-Institutional Registry Study: Imet; Protocol Mf 14-02
    (Springer, 2022) Soran, Atilla; Özbaş, Serdar; Özçınar, Beyza; Işık, Arda; Doğan, L.; Şenol, Kazım; Dağ, Ahmet; Karanlık, Hasan; Aytaç, Özgür; Karadeniz Çakmak, Güldeniz; Dalcı, Kubilay; Doğan, Mutlu; Sezer, Atakan Y.; Gökgöz, Şehsuvar; Özyar, Enis; Sezgin, Efe
    The aim of our prospective, multicenter registry study was to investigate the importance of interventions for operable lung and/or liver metastasis for breast cancer (BC) survival (https://doi.org/10.1245/s10434-022-12239-z). The results reveal that surgical resection or ablative interventions may contribute to survival in patients with BC with limited number and operable metachronous hepatic/pulmonary metastases. Ultimately, randomized studies will determine whether intervention on lung and liver metastatic sites should be performed. In the meantime, such interventions can be considered on select patients.
  • Conference Object
    Intervention To Hepatic and Pulmonary Metastases in Breast Cancer Patients: Prospective, Multi-Institutional Registry Study-Imet; Protocol Mf 14-02
    (Springer, 2022) Soran, Atilla; Özbaş, Serdar; Özçınar, Beyza; Işık, Arda; Doğan, Lütfi; Şenol, Kazım; Dağ, Ahmet; Karanlık, Hasan; Aytaç, Özgür; Karadeniz Çakmak, Güldeniz; Dalcı, Kubilay; Doğan, Mutlu; Sezer, Atakan Y.; Gökgöz, Şehsuvar; Özyar, Enis; Sezgin, Efe
    Background/Objective: One‐fourth of early‐stage breast cancer (BC) becomes metastatic at follow‐up. Limited metastases represents a clinical state of metastatic disease that is limited in the number of metastatic sites and extent of disease, and amenable to metastasis‐directed intervention. The aim of this prospective study is to evaluate intervention to limited metastases in lung and/or liver.
  • Conference Object
    Survival Impact of Intervention To Distant Metastatic Lesions in Patients With Breast Cancer
    (Springer, 2022) Abidi, Hira; Ayoade, Oluwaseun; McAuliffe, Priscilla; Johnson, Ronald; Lee, Joanna; Keenan, Donald; Steiman, Jennifer; Sezgin, Efe; Soran, Atilla
    INTRODUCTION: Approximately 25% of patients (pts) with stage I - III breast cancer (BC) develop distant metastatic disease, a significant cause of mortality. The aim of this study is to evaluate whether intervention to metastatic lesions, in pts initially presenting with stage I–III BC, impacts overall survival (OS) and post-distant recurrence survival (PDRS). METHODS: This is a singleinstitution retrospective study of 201 pts with stage I–III BC, who subsequently develop metastatic lesions to the liver, lung, and/or bone, from 2006-2016. The cohorts included pts receiving intervention to their metastases (IM, n=100) versus no intervention to their metastases (NI, n=101). Two pts in the IM group were lost to follow up and excluded from the survival analysis. The primary study outcomes are OS and PDRS. The characteristics of the pts were compared with X2 test. OS curves were calculated by Kaplan-Meier method and multivariable analysis by Cox regression. Statistical significance was set at p< 0.05.
  • Article
    Citation - WoS: 6
    Citation - Scopus: 8
    Intervention for Hepatic and Pulmonary Metastases in Breast Cancer Patients: Prospective, Multi-Institutional Registry Study-Imet, Protocol Mf 14-02
    (Springer, 2022) Soran, Atilla; Özbaş, Serdar; Özçınar, Beyza; Işık, Arda; Doğan, Lütfi; Şenol, Kazım; Dağ, Ahmet; Karanlık, Hasan; Aytaç, Özgür; Karadeniz Çakmak, Güldeniz; Dalcı, Kubilay; Doğan, Mutlu; Sezer, Atakan Y.; Gökgöz, Şehsuvar; Özyar, Enis; Sezgin, Efe
    Background: One fourth of early-stage breast cancer cases become metastatic during the follow-up period. Limited metastasis is a metastatic disease condition in which the number of metastatic sites and the extent of the disease both are limited, and the disease is amenable to metastatic intervention. This prospective study aimed to evaluate intervention for limited metastases in the lung, liver, or both. Methods: The study enrolled luminal A/B and/or human epidermal growth factor receptor 2 (HER2)-neu+ patients with operable lung and/or liver metastases in the follow-up assessment after completion of primary breast cancer treatment and patients with a diagnosis of metastasis after 2014. Demographic, clinical, tumor-specific, and metastasis detection-free interval (MDFI) data were collected. Bone metastasis in addition to lung and liver metastases also was included in the analysis. The patients were divided into two groups according to the method of treatment for metastases: systemic therapy alone (ST) group or intervention (IT) group.
  • Article
    Citation - WoS: 8
    Citation - Scopus: 10
    Factors Associated With the Occurrence and Healing of Umbilical Pilonidal Sinus: a Rare Clinical Entity
    (Lippincott Williams and Wilkins Ltd., 2022) Işık, Arda; Wysocki, Arkadiusz Peter; Memiş, Ufuk; Sezgin, Efe; Yezhikova, Assel; Islambekov, Yersultan
    Objective: Pilonidal sinus disease (PSD) is a chronic inflammatory condition of skin that is thought to be related to implanted loose hair. Although PSD is most frequently seen in the sacrococcygeal region, it can also occur at the axilla, perineum, suprapubic regions, hands, and umbilicus. The aim of this project was to find factors influencing the development and treatment of umbilical PSD. Methods: In this retrospective study, the authors evaluated 82 patients (19 women, 63 men) with a history of umbilical PSD between 2012 and 2020 to determine predisposing factors and treatment modalities. Results: There was a 20% concordance with intergluteal PSD. Smoking was the only modifying factor for recurrence. The three different treatment methods studied (conservative treatment, surgical treatment, silver nitrate) did not differ in recurrence rate (P =.57). Conclusions: Because of its rare nature, umbilical PSD can be misdiagnosed or underdiagnosed. Key aspects of treatment include smoking cessation and a conservative approach.