Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection

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

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Now showing 1 - 6 of 6
  • Article
    Citation - WoS: 8
    Citation - Scopus: 8
    Strain Tunable Band Structure of a New 2d Carbon Allotrope C-568
    (IOS Press, 2020) Gao, Qiang; Kang, Jun; Şahin, Hasan
    Recently, C(568)has emerged as a new carbon allotrope, which shows semiconducting properties with a band gap around 1 eV and has attracted much attention. In this work, the external strain effects on the electronic properties of C(568)have been studied theoretically through first-principle calculations. The numerical results show that while in-plane uniaxial and biaxial strains both reduces the band gap of C(568)in case of tensile strain, their effects are quite different in the case of compressive strain. With increasing compressive uniaxial strain, the band gap of C(568)first increases, and then dramatically decreases. In contrast, the application of compressive biaxial strain up to -10% only leads to a slight increase of band gap. Moreover, an indirect-to-direct gap transition can be realized under both types of compressive strain. The results also show that the optical anisotropy of C(568)can be induced under uniaxial strain, while biaxial strain does not cause such an effect. These results indicate good strain tunability of the band structure of C-568, which could be helpful for the design and optimization of C-568-based nanodevices.
  • Conference Object
    Citation - WoS: 2
    Citation - Scopus: 2
    Dynamic Itemset Mining Under Multiple Support Thresholds
    (IOS Press, 2016) Abuzayed, Nourhan; Ergenç Bostanoğlu, Belgin; Ergenç, Belgin
    Handling dynamic aspect of databases and multiple support threshold requirements of items are two important challenges of frequent itemset mining algorithms. Existing dynamic itemset mining algorithms are devised for single support threshold whereas multiple support threshold algorithms assume that the databases are static. This paper focuses on dynamic update problem of frequent itemsets under MIS (Multiple Item Support) thresholds and introduces Dynamic MIS algorithm. It is i) tree based and scans the database once, ii) considers multiple support thresholds, and iii) handles increments of additions, additions with new items and deletions. Proposed algorithm is compared to CFP-Growth++ and findings are; in dynamic database 1) Dynamic MIS performs better than CFP-Growth++ since it runs only on increments and 2) Dynamic MIS can achieve speed-up up to 56 times against CFP-Growth++.
  • 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
    Determination of the Effects of Biomaterials on Human Peripheral Blood Mononuclear Cells (pbmc)
    (IOS Press, 2002) Sudağıdan, Mert; Güneş, Hatice; Harsa, Şebnem
  • 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.