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Characterization Of Tfiie-Regulated Genes By Transcriptome Analysis, Serdar Baysal

Turkish Journal of Biology

RETRACTED: This article has been retracted. Please see the Retraction Notice for details. An Expression of Concern was previously published.

Previous studies on GTF2E showed that it has association with certain group of diseases such as colon cancer and trichothiodystrophy but what is the global effect of GTF2E on cellular processes is not widely characterized. In this regard, this study aimed to investigate and characterize the affect of GTF2E on transcription level of genes and identify the cellular processes and diseases associated with GTF2E. The HCT116 cell line was used in the study and transfected at 30 nM concentration with …

Cover And Contents

Turkish Journal of Chemistry

No abstract provided.

Synthesis, Characterization, And Investigation Of Photochemical And In Vitro Properties Of Novel Zn(Ii) Phthalocyanine, Yasemi̇n Bayğu Yildiz, Ni̇lgün Kabay, Burak Yildiz, İpek Ömeroğlu, Mahmut Durmuş, E. Riza Karagür, Hakan Akça, Çağri Ergi̇n, Yaşar Gök

Turkish Journal of Chemistry

In our work, a new non-peripheral zinc(II) phthalocyanine bearing octa carboxylic acid ethyl ester derivative substituted triazole attached propylmercaptothiobenzylmercapto derivative was synthesized by the tetramerization reaction of phthalonitrile. The photochemical in vitro photodynamic activity of zinc(II) phthalocyanine (ZnPc-I), such as human non-small cell lung carcinoma cell lines, was investigated in this study. The singlet oxygen generation property of novel zinc(II) phthalocyanine (ZnPc-I) was also examined due to the significantly high singlet oxygen quantum yield of ZnPc-I (ΦΔ = 0.66). The antiproliferative effects of ZnPc-I were also investigated on A549 and H1299 cell lines, our results demonstrate that the ZnPc-I has …

Synthesis, Structure, Hirshfeld Surface Analysis, And Molecular Docking Studies Of The Cocrystal Between The Cu(Ii) Complex Of Salicylic Acid And Uncoordinated Piracetam, Nazokat N. Yuldasheva, Ikram I. Abdullaev, Oybek I. Khudoyberganov, Lola A. Gandjaeva, Pirnazar K. Kodamboev, Elyor Sh. Samandarov, Adkhamjon S. Normamatov, Abror Kh. Ruzmetov, Yuldosh Y. Yakubov, C. Balakrishnan, Bakhtiyar T. Ibragimov, Aziz Bakhti̇yarovich Ibragimov

Turkish Journal of Chemistry

The cocrystal or supramolecular complex between Cu(II) complex of salicylic acid and uncoordinated piracetam has been synthesized. Its structure is characterized by element analysis, FT-IR, UV-Visible spectroscopy and X-ray crystallography. Spectroscopic methods confirm the formation of the metal complex while X-ray crystallography establishes molecular and crystal structure of the obtained compound. Binuclear Cu(II) complex of salicylic acid (complex molecule) is in the form of “Chinese lantern” and it interacts with uncoordinated piracetam by complicated system of H-bonds. However, according to the Hirshfeld surface analysis a contribution of the O•••H/H•••O contacts is only 24.9% while H•••H and H•••C/C•••H contacts account for …

Preparation Of Manganese-Doped Carbon Quantum Dots@Halloysite Nanotubes Composites Films For Advanced Uv Shielding Properties, Xiao Zhang, Bin Wang

Turkish Journal of Chemistry

The development of Ultraviolet (UV) shielding materials are of great importance to protect human's health concerns and prevent the degradation of organic matters. However, the synthesis of highly efficient UV shielding polymer nanocomposites is currently limited by the agglomeration of inorganic anti-UV nanoparticles (NPs) within the polymer matrix and limited absorption spectrum of UV shielding agents. In this study, highly effective manganese doped carbon quantum dots@halloysite nanotubes composites (Mn-CDs@HNTs/PAS) were successfully synthesized by loading manganese doped carbon quantum dot (Mn-CDs) into UV shielding effective halloysite nanotubes (HNTs) via solvothermal method, followed by polymerization modification. The results show that inorganic NPs …

A Fast And Responsive Turn-On Fluorescent Probe Based On A Quinone Conjugated Alkoxy Derivative For Biothiols And A Cellular Imaging Study, Ulviyye Nemetova, Ayşe Nur Önem, Alev Er, Sefa Çeli̇k, Ayşen E. Özel, Sevi̇m Akyüz, Mustafa Özyürek, Si̇bel Şahi̇nler Ayla

Turkish Journal of Chemistry

Detection of intracellular biothiols (cysteine (CYS), N-acetyl cysteine (NAC) and glutathione (GSH)) with high-selectivity and sensitivity is important to reveal biological functions. In this study, 2-(2-methoxy-4-methylphenoxy)-3-chloro-5,8-dihydroxynaphthalene-1,4-dione (3) (DDN-O) compound was newly synthesized and used as a fluorogenic probe (detector molecule) in the fluorometric method for the rapid, highly selective and sensitive determination of biothiols. The intensity values (λex = 260 nm, λem = 620 nm) of the product were measured by adding biotihols to the reaction medium at varying concentrations and the glutathione equivalent thiol content (GETC) values of each biotiol were calculated. Using the compoud (3), the reference biotiol …

Understanding Ammonia's Role In Mitigating Concentration Polarization In Anion-Exchange Membrane Electrodialysis, Abdallah Timmaoui, Mahmoud Ferhat, Nesri̇ne Souad Ferhat, Ahmed Hamdi

Turkish Journal of Chemistry

In processes such as electrodialysis, the applied electrical potential is constrained by concentration polarization at the membrane/solution interface. This polarization, which intensifies at higher current densities, impedes ion transport efficiency and may lead to problems such as salt precipitation, membrane degradation, and increased energy consumption. Therefore, understanding concentration polarization is essential for enhancing membrane performance, improving efficiency, and reducing operational costs. This study investigates the impact of ammonia buffer (NH₄⁺/NH₃) on sulfate ion transport through anion-exchange membranes, with a particular focus on limiting current density and concentration polarization under constant current conditions. Our findings demonstrate that ammonia effectively eliminates concentration …

New Naphthalene-Linked Pyrazoline-Thiazole Hybrids As Prominent Antilung And Antibreast Cancer Inhibitors, Hali̇li̇brahi̇m Çi̇ftçi̇, Masami Otsuka, Mikako Fujita, Belgi̇n Sever

Turkish Journal of Chemistry

Epidermal growth factor receptor (EGFR) and HER2, pioneer members of the receptor tyrosine kinase subfamily, are frequently mutated and/or overexpressed in several types of human cancers, including non-small cell lung cancer (NSCLC) and breast cancer, which are leading causes of cancer-related deaths worldwide. EGFR and HER2-focused anti-NSCLC and anti-breast cancer studies encouraged us to search for new potential agents. For this purpose, in the current work, naphthalene-linked pyrazoline-thiazole hybrids (BTT1-10 and BTP1-10) were synthesized and examined for their antiproliferative effects on A549 NSCLC and MCF-7 breast cancer cell lines. According to the results, MTT assay showed that BTT-5 induced strong …

Analysis And Optimization Of The Adsorption Of Lead Ions On A New Material Based On Silica Synthesized From Blast Furnace Slag, Toufik Chouchane, Ouahida Khireddine, Sabiha Chouchane, Mohamed Tayeb Abedghars, Hazem Meradi

Turkish Journal of Chemistry

A novel silica-based material (SBM), synthesized from chemically, thermally, and mechanically treated blast furnace slag (TBFS), was examined for its batch-mode lead adsorption capacity, based on various parameters. Physico-chemical examinations revealed that the formulation of the new material (SBM) consists mainly of silica, which represents 81.79% of its total composition. After modification, the measured specific surface area changed significantly, from 275.8 to 480.13 m2/g, with a point of zero charge (PZC) of approximately 3.4 on the pH scale. The experiment revealed that the driving factors (contact time, stirring speed, solution pH, temperature, and initial concentration) greatly influenced the improvement of …

Investigation And Computational Analysis Of The Iqd Gene Family In Common Bean (Phaseolus Vulgaris L.): Expression Profiling Under Salt Stress, Tarik Kirlioğlu, Aybüke Okay, Emi̇ne Sümer Aras, İlker Büyük

Turkish Journal of Botany

Common bean is one of the most nutritionally important legumes because of its high-quality protein content. While its genome has been widely studied however, the IQD gene family has not been extensively investigated in common bean to date. The IQD proteins (IQ-67 domain), a type of calmodulin-binding protein, are involved in plant growth and development, as well as the plant's response to environmental stressors. In this study, thirty-six PvIQD genes were discovered and their proteins were found to be classified into four groups according to the phylogenetic tree. The proteins which are encoded by PvIQD genes with similar exon-intron pattern …

Primary Distribution And Rt-Pcr-Based Detection Of Citrus Dwarfing Viroid (Cdvd) In Citrus Cultivars Of Pakistan, Zia Ul Haq, Amjad Ali, Syed A.H. Naqvi, Faheem Shehzad Baloch, Ummad U.D. Umar

Turkish Journal of Botany

Viroid diseases have emerged as a significant threat to citrus orchards globally. In Pakistan, viroid infections have rapidly spread across different citrus cultivar, posing serious challenges to the survival of orchards. This study encompasses the determination of the prevalence and detection of Citrus dwarfing viroid (CDVd) in both reported and newly introduced citrus cultivars in Pakistan using RT-PCR. RNA was extracted from 122 infected citrus samples and examined for the presence of viroids following the successful optimization of newly designed CDVd primers (CDVd AF1/AR1). This led to the confirmation of CDVd in 72 samples (59.01%).. Biological indexing was performed using …

Functional Characterization Of Haloarchaeal Udp-Glucose 4-Epimerase And 3-Hydroxybutyryl-Coa Dehydrogenase Genes In Nicotiana Tabacum, Çi̇ğdem Otur, Sezer Okay, Aslihan Kurt Kizildoğan

Turkish Journal of Botany

The objective of the studyAbiotic stress poses a significant threat to plant survival. In response to the challenging conditions, plants have evolved various resistance mechanisms. Recently, genetic strategies have become increasingly prevalent in efforts to enhance abiotic stress tolerance and develop stress-resistant plant varieties. In this study, we employed heterologous expression of two metabolism-related haloarchaeal genes in the Nicotiana tabacum genome to improve its mechanism for salt and drought tolerance.Experimental procedure(s)The U2642 and CL165 genes encoding 3-hydroxybutyryl-CoA dehydrogenase and UDP-glucose 4-epimerase, respectively, were subcloned into the pIPKb004 vector under the control of Cauliflower mosaic virus 35S (CaMV35S) promoter using the …

Genome-Wide Identification And Characterization Of The Lea Gene Family In Common Bean And The Role Of The Dehydrin Gene Pvhdn3 In Enhancing Salt And Drought Tolerance In Transgenic Tobacco Plant., Gökhan Gökdemi̇r, Zafer Seçgin, Karam Mostafa, Mohamed Farah Abdulla, Musa Kavas

Turkish Journal of Botany

Global climate change exposes crops to numerous abiotic and biotic stress factors, significantly threatening their growth, development, and overall productivity. Among the various abiotic stresses, salt and drought are the most detrimental, having a severe impact on yield stability. Late Embryogenesis Abundant proteins (LEA) represent a broad and varied class of polypeptides that accumulate in response to cellular dehydration across diverse organisms. Nonetheless, there has been a scarcity of studies on this protein family in common beans prior to this investigation. In this study, we identified 69 members of the LEA gene family in common bean, characterized by conserved LEA …

Phylogenomics Of The Tribe Leonureae Reveals A New Genus: Paraleonurus (Lamiaceae, Lamioideae), Mei-Lin Qian, Ya-Ping Chen, Tuncay Di̇rmenci̇, Yue Zhao, Guo-Xiong Hu, Fei Zhao, Ferhat Celep, Bo Li, Chunlei Xiang

Turkish Journal of Botany

With approximately 80 species across six genera (Leonurus, Lagopsis, Panzerina, Lagochilus, Chaiturus, and Loxocalyx), the tribe Leonureae represents one of the most morphologically diverse tribes within the subfamily Lamioideae of Lamiaceae. Previous studies indicated that Leonurus and Lagopsis are not monophyletic, and relationships among and within these genera remain unclear due to limited sampling and DNA markers. In this study, we present the most comprehensive phylogenomic analyses of Leonureae based on complete plastome sequences and 127 nuclear loci retrieved from next-generation sequencing data. Our results provide strong evidence for the monophyly of Leonureae, which can be further divided into six …

Heterologous Expression Of Haloarchaeal Transporter Genes In Nicotiana Tabacum Under Salt And Drought Stresses, Çi̇ğdem Otur, Musa Kavas, Aslihan Kurt Kizildoğan

Turkish Journal of Botany

The objective of the study: Climate change and human activities impose severe biotic and abiotic stresses that threaten plant survival. To cope with these extreme conditions, plants have evolved various resistance mechanisms. In recent years, genetic approaches have been increasingly employed to enhance abiotic stress tolerance and develop stress-resistant plants. In this study, we introduced three transporter-related genes from extreme haloarchaea, which thrive in saturated NaCl environments, into the Nicotiana tabacum genome to improve its salt and drought tolerance mechanisms.E xperimental procedure(s) : The U2845, U3508, and CL165 genes were subcloned into the pIPKb004 vector, which includes the cauliflower mosaic …

Innovations In Plant Genome Editing And Biotechnology: Addressing Global Agricultural Challenges, Bayram Ali̇ Yerli̇kaya, Karam Mostafa, Abdullah Aydin, Seher Yerli̇kaya, Momna Mehmood, Ni̇sa Nur Yilmaz, Kubi̇lay Yildirim, Musa Kavas

Turkish Journal of Botany

Developments in genome editing and plant biotechnology in recent years, especially CRISPR-Cas9 and RNA interference (RNAi) technologies, offer essential tools for solving global agricultural problems that are worsened by climate change and the increasing food demand caused by the rising world population. This review focuses on the urgent need to feed a growing global population. It explores how key biotechnological tools can enhance crop resilience and nutritional quality amid climate variability and extreme weather. The applicability of CRISPR-Cas technologies in the development of climate-friendly, more nutritious, and higher-yielding crops has opened a biotechnological avenue for the development of both transgenic …

Advancements In Qtl Mapping And Gwas Application In Plant Improvement, Muhammad Tanveer Altaf, Muhammed Tatar, Amjad Ali, Waqas Liaqat, Parnaz Mortazvi, Ceyhun Kayihan, Fati̇h Ölmez, Muhammad Azhar Nadeem, Jazib Javed, Jin-Ying Gou, Meng-Lu Wang, Ummad Ud Din Umar, Hayri̇ye Yildiz Daşgan, Cemal Kurt, Mehtap Yildiz, Sheikh Mansoor, Abdelfattah A. Dababat, Nafiz Çeli̇ktaş, Faheem Shehzad Baloch

Turkish Journal of Botany

Molecular markers play a crucial role in modern plant breeding by enabling the precise identification of genetic loci associated with important agronomic traits. This article focuses on the advancements in Quantitative Trait Locus (QTL) mapping and Genome-Wide Association Studies (GWAS), which are pivotal in identifying and dissecting complex traits such as stress tolerance, yield improvement, and nutrient efficiency. Through QTL mapping, significant genetic regions linked to desired traits are identified, while GWAS leverages larger populations for higher resolution in genetic association studies. The integration of next-generation sequencing, CRISPR, and transcriptomics technologies has revolutionized the precision and efficiency of these methods, …

Identification Of Genes Associated With Zinc And Copper Concentrations In Walnut (Juglans Regia L.) By Gwas Analysis, Berfi̇n Nazlican Kaman, Bülent Yağmur, Erdal Orman, Muhammed Bahatti̇n Tanyolaç, Duygu Ateş

Turkish Journal of Botany

154 walnut genotypes from various geographic regions were analyzed in the study. Micronutrient concentrations of zinc (Zn) ranged from 1.61 to 8.98 mg/100 g, and the concentrations of copper (Cu) varied between 0.12 and 0.38 mg/100 g. 16,473 SNPs were generated using Diversity Array Technology (DArT) for genome-wide association (GWAS) studies. The Mixed Linear Model (MLM) utilizing the Q + K model revealed seven associated markers for the element Zn in 2021 and four in 2022. The MLM (Q + K) model indicated two associated markers for the element Cu in 2021 and three in 2022. The markers found in …

Gene Expression Changes In The Seagrass Cymodocea Nodosa Individuals In Response To Aquatic Acidification, Enes Göksal, Esra Öztürk Yi̇ği̇t

Turkish Journal of Botany

Human activities have caused a rise in atmospheric carbon dioxide (CO2) levels, leading to greater absorption of CO2 by oceans and causing ocean acidification. This phenomenon, marked by a reduction in pH, represents substantial risks to marine ecosystems, including seagrass meadows. Seagrasses are vital elements of coastal ecosystems, performing important functions in carbon storage, stabilizing shorelines, and preserving biodiversity; however, reactions to ocean acidification are not well understood, especially in terms of molecular.This research study examined alterations in gene expression within seagrass meadows, namely the species Cymodocea nodosa, in reaction to simulated ocean acidification conditions. Climate chamber system to adjust …

Exploring The Population Structure And Genetic Diversity In Apple Germplasm Using Ipbs-Retrotransposon Markers, Aigul Madenova, Angsagan Kuan, Amjad Ali, Muhammad Azhar Nadeem, Muhammad Tanveer Altaf, Balnur Kabylbekova, Dinara Kaldybaeva, Ti̇mur Turdi̇yev, Faheem Shahzad Baloch

Turkish Journal of Botany

The apple (Malus domestica [Suckow] Borkh) is economically and culturally significant worldwide, thriving in temperate regions. This study examined genetic variations among 52 apple accessions from three research centers in Kazakhstan using the iPBS-retrotransposons marker system. Out of 35 screened markers, 12 highly polymorphic markers were selected for PCR amplification, resulting in 280 bands, 279 of which were polymorphic, yielding a 99.64% polymorphism rate. Genetic diversity indices showed substantial variation: effective number of alleles (ne=1.655), Shannon's information index (I=0.373), gene diversity (h=0.549), and an average genetic distance of 1.2. The analysis of molecular variance (AMOVA) indicated that 98.80% of the …

Role Of Sulfur Metabolism In Acquiring Of Boron Tolerance In Arabidopsis Thaliana, Seda Yi̇rmi̇beş, Ceyhun Kayihan, Nuran Çi̇çek, Yasemi̇n Ekmekçi̇

Turkish Journal of Botany

The purpose of this study was to assess whether sulfate applications (pre- and combined) caused the changes of tolerance against boron (B) toxicity in Arabidopsis thaliana at physiological, biochemical and molecular levels. Plants were germinated and grown on MS medium for 12 days, and then, sulfate pre-treatment groups (PS-B) were transferred to sulfate-containing media for 3 days. Subsequently, PS-B, combined (S+B) and un-treated application groups were transferred to medium containing 3 and 5 mM B for 10 days. Leaf area, plant biomass and total chlorophyll content decreased significantly depending on the accumulation of B. Toxic levels of B adversely affected …

Cover And Contents

Turkish Journal of Botany

No abstract provided.

Selective Indel Marker Identification Across The Peanut (Arachis Hypogaea L.) Genome Using Ddradseq, Moin Qureshi, Bi̇rgül Guden, Hi̇lal Şule Tosun, Mojtaba Kordrostami, Sunil Shiwaji Gangurde, Bülent Uzun, Engi̇n Yol

Turkish Journal of Botany

The advent of next-generation sequencing technologies, mainly double digest restriction site-associated DNA sequencing (ddRADSeq), has significantly advanced the development of molecular markers for crop genetics. This study used ddRADSeq to identify and develop insertion-deletion (InDel) markers in 25 peanut genotypes from diverse geographic regions. The bioinformatic analysis unveiled 62728 InDels across the peanut genome, predominantly between 1-5 bp, which constituted 96% of the total, while InDels of ≥ 6 bp accounted for 3.96%. We focused on 1013 InDels of at least 10 bp for further analysis, representing 1.61% of the total reads, with a distribution of 832 insertions and 181 …

Thyroid And Cardiovascular Diseases, Si̇nem Başak Tan Öksüz, Mustafa Şahi̇n

Turkish Journal of Medical Sciences

The thyroid gland is one of the major regulator organs of hemostasis in the human body, controlling the function of numerous systems. Thyroid hormones exert a modulating effect on particularly cardiovascular system, ensuring optimal functioning within the normal range. Triiodothyronine (T3), as an active form of thyroid hormones, is mainly responsible for this effect via both genomic and non-genomic mechanisms. It has been reported that overt thyroid disorders are associated with a number of cardiovascular diseases and cardiac mortality. While hyperthyroidism appears to be related to atrial fibrillation and heart failure, the most pronounced cardiovascular complication of hypothyroidism seems to …

Cardiac Effects And Comorbidities Of Neurological Diseases, Bi̇lgi̇n Öztürk

Turkish Journal of Medical Sciences

Neurological disorders encompass a complex and heterogeneous spectrum of diseases affecting the brain, spinal cord, and peripheral nervous system, each presenting unique challenges that extend well beyond primary neurological symptoms. These disorders profoundly impact cardiovascular health, prompting an intensified exploration into the intricate interconnections between the neurological and cardiovascular systems. This review synthesizes current insights and research on cardiovascular comorbidities associated with major neurological conditions, including stroke, epilepsy, Parkinson’s disease, multiple sclerosis (MS), and Alzheimer’s disease.The cardiovascular sequelae of these neurological disorders are multifactorial. For instance, strokes not only predispose individuals to arrhythmia and heart failure but also exacerbate pre-existing …

Hematological Diseases And Heart, Ferda Can

Turkish Journal of Medical Sciences

The heart, main part of the circulatory system, is one of the organs that frequently affected in hematological diseases. Cardiac problems may develop during the course and treatment of benign and malign hematological diseases. Determining cardiac approaches in hematological diseases with knowledge and experience about the development of cardiac involvements with pathophysiological conditions has an important role in the diagnosis and treatment process of patients. In this section, information about hematological diseases and the heart is included, and key points that will help in the diagnosis and treatment process are mentioned.

Cover And Contents

Turkish Journal of Medical Sciences

No abstract provided.

Factors Associated With Morbidity Of Totally Implantable Venous Access Device In Patients With Breast Cancer, Burak İlhan, Berkay Kiliç

Turkish Journal of Medical Sciences

Background/aim: To investigate the possible morbidities associated with the implantation of a totally implantable venous access device (TIVAD) in breast cancer (BC) patients.Materials and methods: Clinical data and developed complications in 546 BC patients with TIVAD between 2017 and 2021 were analyzed retrospectively. Among these patients, 524 (96.0%) patients who underwent TIVAD implantation via the right subclavian vein (SCV) route were examined separately.Results: The mean patient age was 56.1±11.4 years, and the mean patient body mass index was 25.3±6.5. The incidence of early complications was 2.3% (12 cases), and late complications were 2.6% (14 cases). Among these complications, 10 (1.9%) …

Rare Stat3 Haplotypes Cause A Predisposition To Develop Congenital Anomalies Of The Kidney And Urinary Tract Disorder, Mert Polat, Feri̇de Şahi̇n, Esra Baskin, Uğur Toprak, Kaan Gülleroğlu, Mehmet Haberal, Yunus Terzi̇

Turkish Journal of Medical Sciences

Background/aimCongenital anomalies of the kidney and urinary tract (CAKUT) are characterized by renal developmental disorders in the embryonic period. STAT3 is a member of the STAT protein family. The members of this protein family play roles in various cellular mechanisms, such as the early stages of embryonic development, kidney development, and renal diseases. This study aims to determine the frequency of STAT3 rs1053004, rs744166, rs3816769, and rs4796793 polymorphisms in individuals with CAKUT disease.Materials and methodsTwo of the four polymorphisms, rs744166 (c.-1-13666T>C, NM_001369512.1) and rs4796793 ( c.-1915C>G, NM_001369512.1), were analyzed by a polymerase chain reaction and restriction fragment length …

Evaluation Of The Update On Screening For Retinopathy Of Prematurity In A Tertiary Care Center In Türkiye With Retrospective Cohort, Emi̇ne Kaya Güner, Duygu İnci̇ Bozbiyik

Turkish Journal of Medical Sciences

Background/aim: In Turkey, recommendations for screening for retinopathy of prematurity (ROP) have been updated in 2021. Herein, we aimed to present detailed data on the infants included in the screening according to the new criteria and evaluate whether these changes benefit in detecting severe ROP.Materials and Methods: Our hospital's medical records of babies screened for ROP between July 2019 - July 2021 and August 2021 - August 2023 were retrospectively examined. Gestational age (GA), birth weight (BW), gender of the babies, whether there was a multiple pregnancy, ROP examination results, the most advanced ROP level and time, and ROP treatment …