Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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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, CemalThe 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.Article Citation - WoS: 6Citation - Scopus: 4Early 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, EfeIntroduction: 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: 11Citation - Scopus: 10Molecular Evolution and Population Genetics of Glutamate Decarboxylase Acid Resistance Pathway in Lactic Acid Bacteria(Frontiers Media S.A., 2023) Sezgin, Efe; Tekin, BurcuGlutamate 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: 1Aso 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, EfeThe 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.Article Citation - WoS: 6Citation - Scopus: 8Intervention 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, EfeBackground: 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: 8Citation - Scopus: 10Factors 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, YersultanObjective: 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.Article Citation - WoS: 4Citation - Scopus: 7Adding Pneumatic Compression Therapy in Lower Extremity Lymphedema Increases Compliance of Treatment, While Decreasing the Infection Rate(Mary Ann Liebert, Inc, 2022) Soran, Atilla; Toktaş, Osman; Grassi, Ariel; Sezgin, EfeBackground: Lymphedema (LE) is a chronic condition that requires lifelong treatment. Although pneumatic compression therapy (PCT) is one treatment option, current algorithms consider it as an adjunct to standard LE. The purpose of this study is to evaluate the importance of adapting PCT for lower extremity LE (LEL) in relation to patient compliance and rate of infection.</p> Materials and Methods: Patients diagnosed with LEL were followed prospectively. Patient demographics, comorbidities, treatment modality, compliance, infection due to LE, and hospitalization were recorded. LEL patients with no-PCT were also recorded in the same time period to evaluate the treatment compliance and the need for physical therapy visits. The no-PCT group received the standard LE care, whereas the PCT group received the standard LE care plus a new-generation pneumatic compression device.</p> Results: A total of 69 patients were enrolled in this study. The PCT group had 50 patients and no-PCT group had 19 patients. The PCT group had median 58.5 months of LE symptoms, while non-PCT patients had median 23 months of LE symptoms (p = 0.11). Infection rates decreased by 32% and hospitalizations due to infection decreased by 14% after PCT treatment had been initiated. Physical therapy needs decreased by 24% after PCT use. At median 18 months, follow-up compliance for PCT was 84%, but compliance for manual lymphatic drainage was almost half (53%) in no-PCT group.</p> Conclusions: PCT leads to a decrease in infection rate, hospital admissions, and physical therapy (PT) visits in clinically significant LEL. Although there is no cost calculation in this study, it can be correlated to significant cost savings due to a reduction of infection and hospitalization and the need for PT visits. Adoption of PCT offers a superior value proposition to not only patients but also the health care system. Cost analysis should be followed.</p>Article Citation - WoS: 34Citation - Scopus: 32Lymphedema After Sentinel Lymph Node Biopsy: Who Is at Risk?(Mary Ann Liebert, Inc., 2021) Işık, Arda; Soran, Atilla; Grasi, Ariel; Barry, Noran; Sezgin, EfeAim: Sentinel lymph node biopsy (SLNB) is the accepted approach to stage the clinically negative axilla. The incidence of lymphedema (LE) after SLNB is about 5%. We hypothesize that patients undergoing axillary excision of >5 lymph nodes (LNs) are at increased risk of developing LE. Methods and Results: A single institution prospective breast cancer database was retrospectively reviewed from January 2013 to December 2017, to identify patients who underwent SLNB and were diagnosed with LE. Inclusion criteria was (1) de novo breast cancer, (2) SLNB in clinically node negative patients, and (3) no preoperative diagnosis LE of an extremity. Exclusion criteria was history of axillary lymph node dissection. Age, body mass index, tumor-node-metastasis status, surgery type, neoadjuvant or adjuvant chemotherapy, radiotherapy, and hormone therapy were analyzed. Of the 3325 patients identified, 2940 patients met the inclusion criteria and were included in the final analysis. Median follow-up time was 24 months. Forty-seven (2%) patients were diagnosed with LE, and nine patients (19%) had >5 LNs excised. LE was diagnosed in 3.7% of patients who had >5 LNs excised versus 1.4% of patients with <= 5 LNs excised. Incidence of LE was higher in patients with >5 LNs excision (p = 0.006). Conclusion: Our study showed that patients have a higher likelihood of developing LE when >5 LNs are excised.Article Citation - WoS: 63Citation - Scopus: 63The Effect of Primary Surgery in Patients With De Novo Stage Iv Breast Cancer With Bone Metastasis Only (protocol Bomet Mf 14-01): a Multi-Center, Prospective Registry Study(Springer, 2021) Soran, Atilla; Doğan, Lütfi; Işık, Arda; Özbaş, Serdar; Trabulus, Didem Can; Demirci, Umut; Sezgin, EfeBackground More evidence shows that primary surgery for de novo metastatic breast cancer (BC) prolongs overall survival (OS) in selected cases. The aim of this study was to evaluate the role of locoregional treatment (LRT) in BC patients with de novo stage IV bone only metastasis (BOM). Methods The prospective, multicenter registry study BOMET MF14-01 was initiated in May 2014. Patients with de novo stage IV BOM BC were divided into two groups: those receiving systemic treatment (ST group) and those receiving LRT (LRT group). Patients who received LRT were further divided into two groups: ST after LRT (LRT + ST group) and ST before LRT (ST + LRT group). Results We included 505 patients in this study; 240 (47.5%) patients in the ST group and 265 (52.5%) in the LRT group. One hundred and thirteen patients (26.3%) died in the 34-month median follow-up, 85 (35.4%) in the ST group and 28 (10.5%) in LRT group. Local progression was observed in 39 (16.2%) of the patients in the ST group and 18 (6.7%) in the LRT group (p = 0.001). Hazard of death was 60% lower in the LRT group compared with the ST group (HR 0.40, 95% CI 0.30-0.54, p < 0.0001). Conclusion In this prospectively maintained registry study, we found that LRT prolonged survival and decreased locoregional recurrence in the median 3-year follow-up. Timing of primary breast surgery either at diagnosis or after ST provided a survival benefit similar to ST alone in de novo stage IV BOM BC patients.Letter Citation - Scopus: 3Reply: the Effect of Primary Surgery in Patients With Stage Iv Breast Cancer With Bone Metastasis Only (protocol Bomet Mf 14-01): a Multi-Center, Registry Study(Springer, 2021) Soran, Atilla; Sezgin, Efe; Özbaş, Serdar; Doğan, LütfiDear Editor, We’d like to thank Drs. Ishizuka and Horimoto for their letter to the editor. We’re glad to see their interest to our prospective study. Regarding their recommendation that univariate Kaplan–Meier analysis does not eliminate confounding factors, such as age, tumor size, number of bone metastasis, etc., we employed propensity score methods for the results, including Fig. 1.