Publications by authors named "Merve Arslan"

11 Publications

  • Page 1 of 1

A short course of antimicrobial therapy for asymptomatic bacteriuria is safe and effective before urologic procedures.

J Infect Dev Ctries 2021 05 31;15(5):742-746. Epub 2021 May 31.

Department of Urology, Pamukkale University School of Medicine, Denizli, Turkey.

Introduction: In the presence of asymptomatic bacteriuria (ASB) before the urological procedure, the duration of antimicrobial treatment is controversial. This study aims to evaluate whether a short course of antimicrobial therapy is safe and effective in cases with ASB before urological procedures.

Methodology: We retrospectively reviewed adult patients who had ASB before undergoing several urological procedures between 2011 and 2019. The patients received a single dose of an appropriate parenteral antibiotic, determined by antimicrobial sensitivity testing, 30 to 60 minutes before the urological procedure. If a urinary catheter was placed post-procedure, a second dose was given.

Results: A total of 293 patients who had ASB before undergoing several urological procedures were included in the study. The total number of procedures was 328. Female/male ratio was 92 (31.4%)/201 (68.6%). The mean age was 63.7 ± 14.9 years. The most common isolated microorganisms were Escherichia coli (155 [47%]), Klebsiella pneumoniae (38 [11.6%]), and Pseudomonas aeruginosa (28 [8.5%]). The most common antimicrobial used was ertapenem. A second dose antimicrobial was given for 290 procedures due to a urinary catheter after a urological procedure. The mean hospitalization time was 3.97 ± 3.42 days. None of the patients developed infectious complications.

Conclusions: This study has demonstrated that a single dose of parenteral antimicrobial drug administered 30-60 minutes before the urologic procedures and a second dose in the presence of a post-procedure catheter, was adequate to prevent post-procedure septicemia and urinary tract infection.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3855/jidc.14377DOI Listing
May 2021

Repair bond strength and surface topography of resin-ceramic and ceramic restorative blocks treated by laser and conventional surface treatments.

Microsc Res Tech 2021 Jun 8;84(6):1145-1154. Epub 2020 Dec 8.

Department of Dental Prosthetics Technology, Vocational School of Health Services, Kırıkkale University, Kırıkkale, Turkey.

This study intended to compare the repair bond strength of computer-aided design/computer-aided manufacturing (CAD/CAM) blocks consisting of resin and feldspathic ceramics following different surface treatments using the microtensile bond strength (μTBS) test. Ten specimens were prepared with 4 mm height for Vita Enamic (VE), Lava Ultimate (LU), Vita Mark II (VM), and thermocycled (10,000 cycle, 5-55°C). Each material was categorized into one of five subgroups according to following surface treatments: (a) bur grinding (BG), (b) hydrofluoric acid etching (HF), (c) neodymium-doped yttrium aluminum garnet (Nd:YAG or NY), (d) erbium-doped yttrium aluminum garnet (Er:YAG or EY), and (e) erbium, chromium-doped yttrium, scandium, gallium, and garnet (Er,Cr:YSGG or ECY) laser conditioning. After surface treatment procedures, specimens were properly restored to 4 mm high with a micro-hybrid composite resin. Bar specimens (1 × 1 × 8 mm) were obtained using a low-speed cutting machine and then thermocycled (10,000 cycle, 5-55°C). The μTBS was tested at 1 mm/min crosshead speed, and failure modes were evaluated. Data were analyzed with two-way ANOVA and post hoc Tukey tests. LU-BG showed significantly higher μTBS (32.94 ± 5.80 MPa) compared to LU-laser groups (p < .05). VE-BG showed significantly higher μTBS (22.06 ± 4.26 MPa) compared to other VE groups (p < .05). Among the laser groups, the NY laser produced the lowest (p < .05) μTBS for LU (13.42 ± 3.44 MPa) and VE (2.27 ± 0.85 MPa), while EY showed the highest (p < .05). Laser-treated VM groups were all prefailured. VM-HF produced a higher μTBS (18.73 ± 3.75 MPa) than VM-BG (5.05 ± 1.76 MPa) (p < .05).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/jemt.23672DOI Listing
June 2021

CENP-A Nucleosome is a Sensitive Allosteric Scaffold for DNA and Chromatin Factors.

J Mol Biol 2021 03 31;433(6):166789. Epub 2020 Dec 31.

Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, Balçova, Izmir 35330, Turkey. Electronic address:

Centromeric loci of chromosomes are defined by nucleosomes containing the histone H3 variant CENP-A, which bind their DNA termini more permissively than their canonical counterpart, a feature that is critical for the mitotic fidelity. A recent cryo-EM study demonstrated that the DNA termini of CENP-A nucleosomes, reconstituted with the Widom 601 DNA sequence, are asymmetrically flexible, meaning one terminus is more clearly resolved than the other. However, an earlier work claimed that both ends could be resolved in the presence of two stabilizing single chain variable fragment (scFv) antibodies per nucleosome, and thus are likely permanently bound to the histone octamer. This suggests that the binding of scFv antibodies to the histone octamer surface would be associated with CENP-A nucleosome conformational changes, including stable binding of the DNA termini. Here, we present computational evidence that allows to explain at atomistic level the structural rearrangements of CENP-A nucleosomes resulting from the antibody binding. The antibodies, while they only bind the octamer façades, are capable of altering the dynamics of the nucleosomal core, and indirectly also the surrounding DNA. This effect has more drastic implications for the structure and the dynamics of the CENP-A nucleosome in comparison to its canonical counterpart. Furthermore, we find evidence that the antibodies bind the left and the right octamer façades at different affinities, another manifestation of the DNA sequence. We speculate that the cells could use induction of similar allosteric effects to control centromere function.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmb.2020.166789DOI Listing
March 2021

Fracture load and microcrack comparison of crowns manufactured from tooth-shaped and traditional blocks.

Microsc Res Tech 2021 Jan 26;84(1):111-118. Epub 2020 Aug 26.

Department of Prosthodontics, Faculty of Dentistry, Çanakkale Onsekiz Mart University, Çanakkale, Turkey.

This study intended to analyze microcracks and fractographic markings on the surface of all ceramic crowns after milling and compare the fracture loads. 90 crowns were manufactured from two feldspathic (Priticrown-Pr and Vita Mark II-Vi) and a lithium disilicate (EmaxCAD-Em) blocks (n = 30). Two groups (n = 15) were prepared for each ceramic. In the first group, crowns were analyzed twice via the fluorescent penetrant method for microcrack detection, after the manufacturing process and thermal cycles. The load to fracture test was applied at a crosshead speed of 0.5 mm/min until catastrophic failure. Second group crowns were directly cemented onto the Co-Cr dies following the manufacturing process and loaded to fracture. Fractographic markings were analyzed through scanning electron microscope. Spearman correlation analysis, Kruskal-Wallis H test, Mann-Whitney U test, and Wilcoxon Signed Rank test were applied (α = .05). Fracture loads of Em crowns were higher than other groups (p < .05), with and without the aging procedure. Except for second group Pr (r = -.532), no significant relationship was found between microcrack numbers and fracture loads (p > .05). Thermal cycling did not affect microcrack numbers and fracture loads (p > .05). Tooth-shaped multilayered Pr blocks did not provide an advantage in terms of microcrack and fracture loads.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/jemt.23571DOI Listing
January 2021

Effect of dentin and fiber post surface treatments with fumaric acid on the bonding ability of fiber posts.

Microsc Res Tech 2020 Oct 12;83(10):1290-1296. Epub 2020 Aug 12.

Vocational School of Health Services, Kirikkale University, Kirikkale, Turkey.

This study investigated the effects of fumaric acid on push-out bond strength when applied to dentin surfaces and fiber posts. The root canals of 60 mandibular premolar teeth were instrumented and obturated. After removing two thirds of filling material, teeth were prepared according to six randomized groups (n = 10/group) defined by two fiber post surface treatments (0.7% fumaric acid or 9% hydrofluoric acid) and three dentin conditioning treatments [control (no conditioning); 17% ethylenediamine tetraacetic acid (EDTA); or 0.7% fumaric acid]. After fiber post-cementation, three 1-mm thick discs were obtained from each tooth by transverse sectioning, and each disc underwent push-out bond strength testing. Data were analyzed with a one-way analyses of variance (anova) and t tests; p < .05 was considered statistically significant. Failure modes were determined by stereomicroscopy, and the surface characteristics of dentin and fiber posts were observed by scanning electron microscopy. Push-out bond strength was greater for the group in which the post surface treated with hydrofluoric acid and the dentin surface treated with fumaric acid than the nontreated dentin and hydrofluoric acid-treated post group (p < .05). There were no significant differences between other comparison pairs (p > .05). A combination of fumaric acid dentin conditioning and hydrofluoric acid fiber post treatment strengthened the bonding ability of fiber posts.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/jemt.23562DOI Listing
October 2020

Conformational changes in a Vernier zone region: Implications for antibody dual specificity.

Proteins 2020 11 3;88(11):1447-1457. Epub 2020 Jul 3.

Izmir Biomedicine and Genome Center, Izmir, Turkey.

Understanding the determinants of antibody specificity is one of the challenging tasks in antibody development. Monospecific antibodies are still dominant in approved antibody therapeutics but there is a significant body of work to show that multispecific antibodies can increase the overall therapeutic effect. Dual-specific or "Two-in-One" antibodies can bind to two different antigens separately with the same antigen-binding site as opposed to bispecifics, which simultaneously bind to two different antigens through separate antigen-binding units. These nonstandard dual-specific antibodies were recently shown to be promising for new antibody-based therapeutics. Here, we physicochemically and structurally analyzed six different antibodies of which two are monospecific and four are dual-specific antibodies derived from monospecific templates to gain insight about dual-specificity determinants. These dual-specific antibodies can target both human epidermal growth factor receptor 2 and vascular endothelial growth factor at different binding affinities. We showed that a particular region of clustered Vernier zone residues might play key roles in gaining dual specificity. While there are minimal intramolecular interactions between a certain Vernier zone region, namely LV4 and LCDR1 of monospecific template, there is a significant structural change and consequently close contact formation between LV4-LCDR1 loops of derived dual-specific antibodies. Although Vernier zone residues were previously shown to be important for humanization applications, they are mostly underestimated in the literature. Here, we also aim to resurrect Vernier zone residues for antibody engineering efforts.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/prot.25964DOI Listing
November 2020

Physicochemical determinants of antibody-protein interactions.

Adv Protein Chem Struct Biol 2020 19;121:85-114. Epub 2019 Nov 19.

Izmir Biomedicine and Genome Center, İzmir, Turkey.

Antibodies are specialized proteins generated by immune system for high specificity and affinity binding to target antigens. Because of their essential roles in immune system, antibodies have been successfully developed and engineered as biopharmaceuticals for treatment of various diseases. Analysis of antibody-protein interactions is always required to get detailed information on effectivity of such antibody-based therapeutics. Although physicochemical rules cannot be generalized for every antibody-protein interaction, there are some features which should be taken into account during antibody development and engineering efforts. In this chapter, physicochemical analysis of antibody paratope-protein epitope interactions will be discussed to highlight important characteristics. First, paratope and non-paratope regions of antibodies will be described and important roles of these regions on binding and biophysical features of antibodies will be discussed. Then, general features of epitope regions of protein antigens will be introduced along with several computational/experimental tools to identify them. Lastly, a rising star of antibody biopharmaceuticals, nanobodies, will be described to show importance of next-generation antibody fragment based biopharmaceuticals in drug development.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/bs.apcsb.2019.08.011DOI Listing
January 2021

Protein engineering approaches for antibody fragments: directed evolution and rational design approaches.

Turk J Biol 2019 7;43(1):1-12. Epub 2019 Feb 7.

İzmir Biomedicine and Genome Center , İzmir , Turkey.

The number of therapeutic antibodies in preclinical, clinical, or approved phases has been increasing exponentially, mostly due to their known successes. Development of antibody engineering methods has substantially hastened the development of therapeutic antibodies. A variety of protein engineering techniques can be applied to antibodies to improve their afinity and/or biophysical properties such as solubility and stability. Antibody fragments (where all or some parts of constant regions are eliminated while the essential antigen binding region is preserved) are more suitable for protein engineering techniques because there are many in vitro screening technologies available for antibody fragments but not full-length antibodies. Improvement of biophysical characteristics is important in the early development phase because most antibodies fail at the later stage of development and this leads to loss of resources and time. Here, we review directed evolution and rational design methods to improve antibody properties. Recent developments in rational design approaches and antibody display technologies, and especially phage display, which was recently awarded the 2018 Nobel Prize, are discussed to be used in antibody research and development.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3906/biy-1809-28DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6426644PMC
February 2019

Effect of different framework materials of resin-bonded bridges on load to fracture values and stress distribution.

Niger J Clin Pract 2018 Dec;21(12):1585-1589

Department of Prosthodontics, Kırıkkale University Faculty of Dentistry, Kırıkkale, Turkey.

Purpose: The aim of this study was to compare in vitro fracture strengths (FSs) of metal- and fiber-reinforced frameworks of resin-bonded bridges and to evaluate stress distribution with finite element analysis (FEA).

Materials And Methods: Totally 80 extracted maxillary central and maxillary canine teeth were used for in vitro part of this study as two groups; metal-reinforced framework (n = 20) [(metal-supported resin-bonded bridge (MR-RB)] and fiber-reinforced frameworks (n = 20) [fiber-reinforced resin-bonded bridge (FR-RB) were prepared for three unit resin-bonded bridges. All bridges were loaded from lateral pontic at 1 mm/min crosshead speed and fracture values were recorded. Mann-Whitney U-test was used for statistical analysis, and fracture patterns were evaluated visually. FEA was carried out in the second part of the study, and stress distribution of MR-RB and FR-RB structures was analyzed using one of the models from in vitro specimens as main model.

Results: The mean FSs of MR-RB and FR-RB were 637.47 ± 151.91 N and 224.86 ± 80.97 N, respectively. Fiber-reinforced specimens were found to distribute stress more homogeneous and connectors in each framework were the regions where stress concentrated mostly.

Conclusion: In vitro FSs of MR-RB and the stress concentration of the point that the forces were applied were higher as compared to other parts of the restoration. Furthermore, in contrast to FR-RB specimens, retainer tooth fractures were observed in MR-RB specimens.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.4103/njcp.njcp_281_18DOI Listing
December 2018

Effects of staining liquids and finishing methods on translucency of a hybrid ceramic material having two different translucency levels.

J Adv Prosthodont 2017 Oct 16;9(5):387-393. Epub 2017 Oct 16.

Department of Prosthodontics, Faculty of Dentistry, Akdeniz University, Antalya, Turkey.

Purpose: Beverages may affect the translucency of esthetic dental restorative materials. The aim of the present study was to investigate the effects of coffee and red wine on the translucency of a PICN material with two translucency levels, and finished with different methods.

Materials And Methods: 2M2 high translucent and translucent VITA Enamic hybrid ceramic blocks were investigated. Rectangular specimens with the dimensions of 12 mm × 14 mm × 2 mm were prepared. The specimens were finished and polished with different methods as suggested by the manufacturer. The translucency parameters of the specimens were evaluated before and after 24 hours, 7 days, and 28 days immersion in distilled water, coffee and red wine. Translucency parameters were measured using a portable spectrophotometer.

Results: At the end of 28 days, there was no statistically significant difference between the groups of specimens kept in coffee (>.05). In the red wine groups, there was a statistically significant difference between the control group and all other groups (<.05) at the end of 28 days.

Conclusion: The translucency of hybrid ceramic for a restoration may not be important regarding the effects of coffee on translucency change because the specimens with different translucencies and finishing methods that were immersed to coffee had similar translucency parameters at the end of 28 days. The translucency of hybrid ceramic may be important in the case of red wine, however, since the results showed that highly translucent specimens exposed to red wine demonstrated better translucency parameters than specimens made from translucent blocks at the end of 28 days.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.4047/jap.2017.9.5.387DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5673616PMC
October 2017

Effects of different surface finishing procedures on the change in surface roughness and color of a polymer infiltrated ceramic network material.

J Adv Prosthodont 2016 Feb 23;8(1):16-20. Epub 2016 Feb 23.

Department of Prosthodontics, Faculty of Dentistry, Akdeniz University, Antalya, Turkey.

Purpose: Polymer infiltrated ceramic network (PICN) materials, also called hybrid ceramics, are new materials in dental market. The manufacturer of the PICN material VITA Enamic suggests 3 different finishing procedures for this new material. In the present study, surface roughness and color differences caused from different finishing procedures of VITA Enamic were investigated.

Materials And Methods: 120 specimens were prepared in dimensions 2 × 10 × 12 mm from VITA Enamic hybrid ceramic blocks with 'high translucency' and 'translucency 2M2' shades. The specimens were divided into 8 groups. For each group, different finishing procedures suggested by the manufacturer were performed. Surface roughness values were determined by a tactile portable profilometer. Color changes were evaluated using a clinical spectrophotometer. The data were analyzed using one-way ANOVA and Tukey's post-hoc comparison. The significance level was set at α=0.05.

Results: The roughest surfaces were observed in Glaze Groups. Their surface roughness values were similar to that of the control group. Clinical Kit and Technical Kit groups did not show a statistically significant difference regarding surface roughness (P>.05). The largest color difference regarding ΔE00 was observed in Clinical Kit finishing groups. There were also statistically significant color changes between the groups (P<.05). However, all the groups showed clinically acceptable color change (ΔE00<2.25) except Clinical Kit Groups (ΔE00>2.25).

Conclusion: Within the limitations of the present study, it may be suggested that finishing the VITA Enamic restorations by Technical Kit instead of Glaze and Clinical Kit gives better clinical performance in regard to surface roughness and shade matching.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.4047/jap.2016.8.1.16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4769885PMC
February 2016
-->