Retraction Note: Efficiency analysis of the dynamic traffic control for an urban highway

The authors and the Editor-in-Chief have agreed to retract this article [1] due to excessive overlap with previously published content. Moreover, no proper reference was given to the respective sources.Publisher's Versio

In silico analysis of biomarker potentials of miRNA-mediated ceRNAs in prostate cancer

Objective: The objective of this study is to define novel biomarkers for Prostate Cancer (PCa) via in silico analysis that takes PCa-specific miRNAs, finds their combinatorial target genes (potential ceRNAs), selects ones containing Transcribed Ultra Conserved Region (T-UCR) among them and potentiates their relevance with PCa. Methods: Thirty-four miRNAs of which clinical relevances with PCa were proved experimentally were exported via miRWalk database.Using the ComiR database, 859 genes targeted by these 34 miRNAs simultaneously were identified. Genes with ComiR score above 0.911 were taken into account. Genes containing T-UCR and showing potential ceRNA activity were extracted. Among PCa-associated ceRNAs including T-UCR, we identified genes with significant expression differences between PCa and normal prostate tissue using the GEPIA database. The statistical evaluation of the association of NFAT5 and PTBP2 genes with PCa was performed by Spearman correlation test in GEPIA database. Results: PCa-associated ceRNAs cross-matching with genes including T-UCR in their exonic regions were NFAT5, CLK3, PTBP2, CPEB4, MIPOL1 and TCF4. We identified genes with significant expression differences between PCa and normal prostate tissues among PCa-associated ceRNAs including T-UCR. According to this analysis, NFAT5 and PTBP2 genes were significantly less expressed in PCa than in normal prostate tissue while the others didn’t show any significant differential expression pattern. NFAT5 and PTBP2 genes were found to be significantly associated with PCa (p=0.000012; R=0.72). Conclusion: All in all, this is the study associating NFAT5 and PTBP2 genes with PCa and giving them tumor suppressive potential for PCa. Still, larger and more comprehensive studies are needed on this issue

Clinically informative microRNAs for SARS-CoV-2 infection

COVID-19 is a viral respiratory infection induced by the newly discovered coronavirus SARS-CoV-2. miRNA is an example of a strong and direct regulator of a gene's transcriptional activity. The interaction between miRNAs and their target molecules is responsible for homeostasis. Virus-derived and host-derived miRNAs are involved in the activity of hiding from immune system cells, inducing the inflammatory reaction through interplay with associated genes, during SARS-COV-2 infection. Interest in miRNAs has raised the comprehension of the machinery and pathophysiology of SARS-COV-2 infection. In this review, the effects and biological roles of miRNAs on SARS-CoV-2 pathogenicity and life cycle are described. The therapeutic potential of miRNAs against SARS-CoV-2 infection are also mentioned

An automatic calibration procedure of driving behaviour parameters in the presence of high bus volume

Most of the microscopic traffic simulation programs used today incorporate car-following and lane-change models to simulate driving behaviour across a given area. The main goal of this study has been to develop an automatic calibration process for the parameters of driving behaviour models using metaheuristic algorithms. Genetic Algorithm (GA), Particle Swarm Optimization (PSO), and a combination of GA and PSO (i.e. hybrid GAPSO and hybrid PSOGA) were used during the optimization stage. In order to verify our proposed methodology, a suitable study area with high bus volume on-ramp from the 0-1 Highway in Istanbul has been modelled in VISSIM. Traffic data have been gathered through detectors. The calibration procedure has been coded using MATLAB and implemented via the VISSIM-MATLAB COM interface. Using the proposed methodology, the results of the calibrated model showed that hybrid GAPSO and hybrid PSOGA techniques outperformed the GA-only and PSO-only techniques during the calibration process. Thus, both are recommended for use in the calibration of microsimulation traffic models, rather than GA-only and PSO-only techniques.This study is a part of Ph.D. thesis of the corresponding author from the Istanbul Technical University, Turkey. We would like to thank Prof. Dr. Toma? Maher and Assist. Dr. Rok Marseti? from the Traffic Technical Institute of Civil and Geodetic Engineering Faculty, University of Ljubljana, Slovenia, for their kind support, valuable comments, and helpful suggestions. The authors are also thankful to the PTV-AG Karlsruhe Company for their support in providing a thesis-based unlimited version of VISSIM softwarePublisher's Versio

Hypericum perforatum L. extracts exert cytotoxic effects and show different miRNA signatures in PC-3 and DU 145 prostate cancer cells

Phytochemicals and bioactive substances derived from a wide range of plant extracts have been reported to exert various anticancer effects. Prostate cancer is one of the leading causes of cancer-related deaths within the male population. Prostate cancer-specific miRNA signatures were associated with cancer formation and progression, with various subtypes, and response to therapy. MicroRNA levels of expression were shown to change after the treatment of various compounds and substances extracted from natural products. Natural herbal compounds were shown to induce variations in miRNA expression levels in cancer cells. The aims of this study were to investigate the cytotoxic effects of methanol, ethyl-acetate, and hexane extracts obtained from branch-body part and flowers of Hypericum perforatum L. against humane PC-3 and DU 145 and to test potential miRNA-128/133b/155/193a/206/21/335 signature changes and differences between the two prostate cancer cell lines. Cytotoxic activity of H. perforatum extracts, their effects on cell cycle distribution, and miRNA expression levels were examined in humane PC-3 and DU 145 prostate cancer cells by MTT cell survival assay, flow cytometry, and quantitative real-time PCR. Hexane extract of flowers showed the strongest intensity of cytotoxic activity against PC-3 and DU 145 cells. The highest increase in the percentage of PC-3 cells in the subG1 phase was observed in cell samples treated with hexane extract of flowers and branch-body part. Significant differences in miRNA-128/133b/155/193a/206/21/335 levels were observed between PC-3 and DU 145 cell lines, especially in samples treated with flower extracts compared with the branch-body part. Conclusions: Investigated extracts have significant anticancer potential not only from the aspects of cytotoxicity and cell cycle effects but also from the aspect of lowering oncogenic or increasing tumor-suppressive miRNAs. The best effect might be the increase of tumor-suppressive miR-128 (accompanied by miR-193a) induced by the hexane extract of the flowers, which also exerted the highest cytotoxic activity. Hexane extract of flowers may be the candidate for further investigation for improving the efficiency of standard therapies for PCa. A miRNA signature might be cell-type specific after the treatment with H. perforatum extracts

İstabul Üniversitesi gözlemevi odak düzlemi aygıtı test ve karakterizasyon laboratuvarı

Doğu Anadolu Gözlemevi Odak Düzlemi Aygıtları ve Adaptif Optik Sistemi başlıklı, 2016K121370 numaralı T.C. Kalkınma Bakanlığı projesi ve İstanbul Üniversitesi Rektörlüğü desteğinde yürüyen çalışmalar kapsamında İstanbul Üniversitesi Astronomi ve Uzay Bilimleri Bölümü’nde teleskop odak düzlemi aygıtı test ve karakterizasyon laboratuvarı kurulum çalışmaları başlatılmıştır. Başta DAG Teleskobu olmak üzere ülkemizdeki tüm gözlemevlerine hizmet verebilecek şekilde tasarlanan laboratuvar, CCD kamera, filtre ve odak düzlemi aygıtları için bir test masasına sahip olacaktır. Bu sunumda, laboratuvarın kurulumu ve alımlarında gelinen son noktanın yanı sıra, İstanbul Üniversitesi Fizik Bölümü Nano-Optoelektronik Araştırma Laboratuvarları ile birlikte yapılması planlanan çalışmalar sunulacaktır.Publisher's Versio

Unpublished Mediterranean records of marine alien and cryptogenic species

Good datasets of geo-referenced records of alien species are a prerequisite for assessing the spatio-temporal dynamics of biological invasions, their invasive potential, and the magnitude of their impacts. However, with the exception of first records on a country level or wider regions, observations of species presence tend to remain unpublished, buried in scattered repositories or in the personal databases of experts. Through an initiative to collect, harmonize and make such unpublished data for marine alien and cryptogenic species in the Mediterranean Sea available, a large dataset comprising 5376 records was created. It includes records of 239 alien or cryptogenic taxa (192 Animalia, 24 Plantae, 23 Chromista) from 19 countries surrounding the Mediterranean Sea. In terms of records, the most reported Phyla in descending order were Chordata, Mollusca, Chlorophyta, Arthropoda, and Rhodophyta. The most recorded species was Caulerpa cylindracea, followed by Siganus luridus, Magallana sp. (cf. gigas or angulata) and Pterois miles. The dataset includes records from 1972 to 2020, with the highest number of records observed in 2018. Among the records of the dataset, Dictyota acutiloba is a first record for the Mediterranean Sea. Nine first country records are also included: the alga Caulerpa taxifolia var. distichophylla, the cube boxfish Ostracion cubicus, and the cleaner shrimp Urocaridella pulchella from Israel; the sponge Paraleucilla magna from Libya and Slovenia; the lumpfish Cyclopterus lumpus from Cyprus; the bryozoan Celleporaria vermiformis and the polychaetes Prionospio depauperata and Notomastus aberans from Malta

Unpublished Mediterranean and Black Sea records of marine alien, cryptogenic, and neonative species

To enrich spatio-temporal information on the distribution of alien, cryptogenic, and neonative species in the Mediterranean and the Black Sea, a collective effort by 173 marine scientists was made to provide unpublished records and make them open access to the scientific community. Through this effort, we collected and harmonized a dataset of 12,649 records. It includes 247 taxa, of which 217 are Animalia, 25 Plantae and 5 Chromista, from 23 countries surrounding the Mediterranean and the Black Sea. Chordata was the most abundant taxonomic group, followed by Arthropoda, Mollusca, and Annelida. In terms of species records, Siganus luridus, Siganus rivulatus, Saurida lessepsianus, Pterois miles, Upeneus moluccensis, Charybdis (Archias) longicollis, and Caulerpa cylindracea were the most numerous. The temporal distribution of the records ranges from 1973 to 2022, with 44% of the records in 2020–2021. Lethrinus borbonicus is reported for the first time in the Mediterranean Sea, while Pomatoschistus quagga, Caulerpa cylindracea, Grateloupia turuturu, and Misophria pallida are first records for the Black Sea; Kapraunia schneideri is recorded for the second time in the Mediterranean and for the first time in Israel; Prionospio depauperata and Pseudonereis anomala are reported for the first time from the Sea of Marmara. Many first country records are also included, namely: Amathia verticillata (Montenegro), Ampithoe valida (Italy), Antithamnion amphigeneum (Greece), Clavelina oblonga (Tunisia and Slovenia), Dendostrea cf. folium (Syria), Epinephelus fasciatus (Tunisia), Ganonema farinosum (Montenegro), Macrorhynchia philippina (Tunisia), Marenzelleria neglecta (Romania), Paratapes textilis (Tunisia), and Botrylloides diegensis (Tunisia).peer-reviewe

RETRACTED ARTICLE: Efficiency analysis of the dynamic traffic control for an urban highway

In this study, dynamic traffic control strategies, namely dynamic ramp metering and dynamic speed limit control, have been examined through microscopic traffic simulation based on site measurements. In this context, the traffic flow data at a particular highway intersection have been analyzed to determine the pattern of the traffic. Then, the traffic model has been built in a traffic micro-simulation software and calibrated with the field data. The foci of the study are to measure the efficiency of the dynamic traffic control strategies and to compare it with the uncontrolled case considering various performance indicators such as total travel time, average delay time per vehicle, and average number of stops per vehicle. For the dynamic ramp metering strategies, the ALINEA (Asservissement Lineaire d'Entree Autoroutiere - French for Linear Utilization for Highway Entrances) control algorithm is implemented with different fixed-time cycle lengths. It has been observed that various ramp metering implementations decreased the average delay time per vehicle up to 30%. The dynamic speed limit control strategies are set according to the occupancy rates that are measured at the bottleneck downstream. The examined speed limit control strategies decreased the average delay time per vehicle to around 7%. The results also revealed that the implemented dynamic traffic control strategies help alleviate congestion by increasing the capacity of the bottleneck section.Ministry of Education, Culture, Sports, Science & Technology of JapanThe first author would like to thank PTV Japan for providing the license key of PTV VISSIM. The Ministry of Education, Culture, Sports, Science & Technology of Japan supported the PhD research of the first author.Publisher's Versio