Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection

Permanent URI for this collectionhttps://hdl.handle.net/11147/7148

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  • Article
    Citation - Scopus: 10
    Visualization and Analysis of Mirnas Implicated in Amyotrophic Lateral Sclerosis Within Gene Regulatory Pathways
    (IOS Press, 2018) Hamzeiy, Hamid; Allmer, Jens; Suluyayla, Rabia; Brinkrolf, Christoph; Janowski, Sebastian Jan; Hofestadt, Ralf; Allmer, Jens
    MicroRNAs (miRNAs), approximately 22 nucleotides long, post-transcriptionally active gene expression regulators, play active roles in modulating cellular processes. Gene regulation and miRNA regulation are intertwined and the main aim of this study is to facilitate the analysis of miRNAs within gene regulatory pathways. VANESA enables the reconstruction of biological pathways and supports visualization and simulation. To support integrative miRNA and gene pathway analyses, a custom database of experimentally proven miRNAs, integrating data from miRBase, TarBase and miRTarBase, was added to DAWIS-M.D., which is the main data source for VANESA. Analysis of human KEGG pathways within DAWIS-M.D. showed that 661 miRNAs (~1/3 recorded human miRNAs) lead to 65,474 interactions. hsa-miR-335-5p targets most genes in our system (2,544); while the most targeted gene (with 71 miRNAs) is NUFIP2 (Nuclear Fragile X Mental Retardation Protein Interacting Protein 2). Amyotrophic Lateral Sclerosis (ALS), a complex neurodegenerative disease, was chosen as a proof of concept model. Using our system, it was possible to reduce the initially several hundred genes and miRNAs associated with ALS to eight genes, 19 miRNAs and 31 interactions. This highlights the effectiveness of the implemented system to distill important information from otherwise hard to access, highly convoluted and vast regulatory networks.
  • Article
    Citation - Scopus: 37
    The Impact of Onco Type Dx® Recurrence Score of Paraffin-Embedded Core Biopsy Tissues in Predicting Response To Neoadjuvant Chemotherapy in Women With Breast Cancer
    (IOS Press, 2016) Soran, Atilla; Bhargava, Rohit; Johnson, Ronald; Ahrendt, Gretchen; Bonaventura, Marguerite; Diego, Emilia; McAuliffe, Priscilla F.; Serrano, Merida; Menekşe, Ebru; Sezgin, Efe; McGuire, Kandace P.
    BACKGROUND: Oncotype DX® test is beneficial in predicting recurrence free survival in estrogen receptor positive (ER+) breast cancer. Ability of the assay to predict response to neoadjuvant chemotherapy (NCT) is less well-studied. OBJECTIVE: We hypothesize a positive association between the Oncotype DX® recurrence score (RS) and the percentage tumor response (%TR) after NCT. METHODS: Pre-therapy RS was measured on core biopsies from 60 patients with ER+, HER2.. invasive breast cancer (IBC) who then received NCT. Pre-therapy tumor size was measured using imaging. %TR, partial response (PR; 50%), pathologic complete response (PCR) and breast conserving surgery (BCS) rates were measured. RESULTS: Median RS was 20 (2 69). Median %TR was 42 (0 97)%. PR was observed in 43% of patients. There was no association between %TR and pre-NCT tumor size, age, Nottingham score or nodal status (p 0:05). No statistically significant association with %TR was seen with RS as a categorical or continuous variable (p = 0:21 and 0.7, respectively). Response to NCT improved as ER (p = 0:02) by RT-PCR decreased. Lower ER expression by IHC correlated with response (p = 0:03). CONCLUSIONS: In patients with ER+ IBC receiving NCT, RS did not predict response to NCT using %TR. The benefit of the assay prior to NCT requires further study.
  • Article
    Citation - WoS: 3
    Citation - Scopus: 3
    Tensile Adhesion of Type I Collagen To Titanium Alloy and Calcium Phosphate Coated Surfaces With Different Roughness Values
    (IOS Press, 2002) Özerdem, Barış
    The purpose of total joint arthroplasty is to reduce pain and restore function. Its success depends on the formation of a new bone that stabilizes the prosthesis. The proposed solution for this important problem is to have bio-coated implant surfaces which are more conductive to bone growth. Additionally, collagen has long been used as a matrix for medical applications, because of its biocompatibility and adaptability. In this study, a test method for measuring the tensile adhesion strength of collagen to titanium alloy and calcium phosphate coated surfaces with different roughness values was developed, in order to evaluate how well the collagen adheres to the metallic and bio-coated surfaces. A precision motion system was used to stretch gels that were adherent to the plate surfaces. The tests were done in DMEM solution. The adhesive strength between the collagen gel and plate was significantly higher for calcium phosphate coated surfaces. Adhesive strength was highest in the sample with the highest roughness value.