PubMed İndeksli Yayınlar Koleksiyonu

Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/397

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Does Your Love Lift Me Higher? A Direct Replication of the Energising Role of Secure Relationships
(John Wiley and Sons Inc, 2026) Lağap, A.C.; Harma, M.
Previous work has revealed that priming people with significant others increases feelings of security and energy, and in turn, boosts exploration motivations. In this preregistered study, we directly replicated Luke et al.'s (2012) Study 2 (N = 281). We found similar results as the replicated study regarding increased security feelings and exploration motivations on the self-report measures after the priming. However, we did not find any support for the increased energy feelings after the attachment security priming. In addition, contrary to Luke et al.'s (2012) results, energy feelings did not mediate the relationship between security priming and exploration motivations. A discussion of null findings, along with the limitations of self-reports and potential misinterpretation of the mediational analyses, follows. We also discuss possible future implications of the current findings. © 2025 International Union of Psychological Science.
Neuroinflammatory Human Brain Organoids Enable Comprehensive Drug Screening Studies: Fingolimod and Its Analogues in Focus
(Bentham Science Publishing Ltd, 2026) Acar, Busra; Pepe, Nihan Aktas; Zivkovic, Aleksandra; Stark, Holger; Sen, Alaattin
Introduction The absence of physiologically relevant models for neuroinflammatory brain disorders, such as multiple sclerosis (MS), highlights the need for improved drug screening platforms. To bridge this gap, this study aimed to develop a human brain organoid (hBO) model incorporating essential neural cell types, including astrocytes, microglia, and oligodendrocytes.Methods hBOs were generated from H9 stem cells, and neuroinflammatory characteristics were elicited by lipopolysaccharide (LPS). The expression of specific neuronal and inflammatory markers was assessed through qRT-PCR, immunofluorescence staining (IFS), and ELISA.Results IFS of mature hBOs with anti-SOX2, anti-SATB2, anti-MAPT, anti-GFAP, anti-MBP, and anti-IBA1 antibodies and images collected with the confocal microscope confirmed the differentiation of H9 cells into cortical neurons, astrocytes, microglia, and oligodendrocyte cell types. Elevated GFAP, IBA1, NF-kappa B, and IL-6 levels, along with reduced CNPase expression with LPS treatment, were considered reflective of MS-like pathology and were used to test fingolimod and its derivatives. Fingolimod and all its derivatives, specifically ST-1505, decreased MAPT (2.1-fold in ELISA, 1.7-fold in IFS), GFAP (1.8-fold in IFS), TNF alpha (5.4-fold in qRT-PCR), and FABP (1.5-fold in ELISA) levels, and increased IL-10 (11-fold in qRT-PCR) and MBP (2.9-fold in IFS) levels.Discussion The present data collectively showed LPS to evoke neuroinflammation in the hBO model, while fingolimod and its derivatives, particularly ST-1505, exhibited significant anti-inflammatory and neuroprotective properties by counteracting these evoked changes in the hBO model.Conclusion The findings supported the applicability of brain organoids as a model system for drug screening studies for neuroinflammatory brain diseases.
A Potential Hemostatic Chitosan/Gelatin Cryogel Impregnated with Verbascum Thapsus Leaf Extract for Noncompressible Hemorrhage Management
(IOP Publishing Ltd, 2025) Uzuner, Hacernur; Yuruk, Adile; Isoglu, Ismail Alper
In this study, we prepared a series of chitosan/gelatin (CS/GEL) cryogels containing Verbascum thapsus (V. thapsus) leaf extract and identified a lead formulation for noncompressible hemorrhage (NCH). Cryogels with average pore diameters ranging from 225 to 478 mu m were fabricated through cryogelation at various CS/GEL ratios. C15 was chosen as the base scaffold due to its homogeneous pore distribution, with a pore size coefficient of variation (CV) of approximately 0.22. Extract loading was 1%, 5%, 10%, and 20% w/v. Functional porosity was reported by the relative accessible void index (RAVI). In PBS, the values relative to neat C15 were 1.00, 0.27, 0.20, 0.13, and 0.09 for concentrations of 0%, 1%, 5%, 10%, and 20% w/v, respectively. In citrated blood, the series was 1.00, 0.29, 0.12, 0.14, and 0.09. After loading, equilibrium swelling decreased and the compressive modulus increased, consistent with partial pore filling in a fixed network. The cryogels maintained an interconnected macroporous network and showed swelling from 300% to 3600% in blood and PBS. Antibacterial activity reached 89% inhibition, and cell viability remained above 80%. Hemolysis was low and within acceptance limits. Clotting improved in whole blood as the blood clotting index decreased from 11.9 to 6.5, and the clotting time was approximately 6 min. The 5% w/v group provided the optimal balance of clotting, antibacterial effects, and biocompatibility. This study presents a novel hemostatic CS/GEL cryogel containing V. thapsus leaf extract that holds strong potential for future applications in NCH management.
Vim-Polyp: Multimodal Colon Polyp Dataset with Video, Histopathology, and Protein Expression
(Nature Portfolio, 2025) Dogan, Refika Sultan; Akay, Ebru; Dogan, Serkan; Yilmaz, Bulent
The dataset in this study includes 202 videos with a total of 422 minutes, reaching Kayseri City Hospital's gastroenterology department as colonoscopy videos and 1903 microscopy images between 2019 and 2021. It includes 399 colonoscopy, microscopy images, and pathological diagnoses of polyps, as well as immunohistochemical staining results for proteins that play an important role in the assessment of cancerous cells, such as staining results for p53 (clone: bp53-11), Ki-67 (clone: 30-9), CD34 (clone: QBend/10), PD-L1 (clone: SP142), BRAF (clone: V600E) and VEGF (clone: SP125). By sharing the data openly, we aim to facilitate benchmarking, exploratory analysis and transfer-learning studies on colorectal polyps and cancer. In combination with external datasets or pretrained models, the resource can help advance data-driven detection and characterisation work. The diverse range of polyps assigned to cancer stages from 201 patients makes this tool valuable for researchers and clinicians in furthering diagnosis and treatment.
Development and Characterization of Starch-Fatty Acid Complexes Produced with Buckwheat Starch and Capric/Stearic Acid Using Different Reaction Conditions
(Elsevier, 2025) Oskaybas-Emlek, Betul; Ozbey, Ayse; Aydemir, Levent Yurdaer; Kahraman, Kevser
The aim of present study was to investigate the impact of reaction parameters on the complex formation between buckwheat starch and capric acid (B-Capric) or stearic acid (B-Stearic). The most effective parameters on complex formation indicator (Complex index (CI) value) were found as reaction temperature (60-90 degrees C) and pH (5-8). Additionally, the effect of these parameters on physicochemical, pasting, and in-vitro digestibility properties of complex samples were evaluated. XRD and FTIR was also used in characterize the complex samples. In general, increasing pH increased the CI values of B-Stearic samples while decreasing those of B-Capric samples. Syneresis of buckwheat starch increased after complexation while paste clarity and swelling power diminished. The pasting properties of native starch significantly changed after complex formation. The FTIR results showed that starch structure changed with complex formation. XRD revealed that buckwheat starch, having an A-type pattern, converted to V-type pattern after complexation. Complex formation of buckwheat starch with capric and stearic acid significantly increased the RS content of buckwheat starch (19.01 %) by up to 36.25 % and 30.60 %, respectively. These results highlight the possibility of using buckwheat starch-capric acid/stearic acid complexes in food formulation to enhance the RS content.
Developing a Label Propagation Approach for Cancer Subtype Classification Problem
(Tubitak Scientific & Technological Research Council Turkey, 2022) Guner, Pinar; Bakir-Gungor, Burcu; Coskun, Mustafa
Cancer is a disease in which abnormal cells grow uncontrollably and invade other tissues. Several types of cancer have various subtypes with different clinical and biological implications. Based on these differences, treatment methods need to be customized. The identification of distinct cancer subtypes is an important problem in bioinformatics, since it can guide future precision medicine applications. In order to design targeted treatments, bioinformatics methods attempt to discover common molecular pathology of different cancer subtypes. Along this line, several computational methods have been proposed to discover cancer subtypes or to stratify cancer into informative subtypes. However, existing works do not consider the sparseness of data (genes having low degrees) and result in an ill-conditioned solution. To address this shortcoming, in this paper, we propose an alternative unsupervised method to stratify cancer patients into subtypes using applied numerical algebra techniques. More specifically, we applied a label propagation based approach to stratify somatic mutation profiles of colon, head and neck, uterine, bladder, and breast tumors. We evaluated the performance of our method by comparing it to the baseline methods. Extensive experiments demonstrate that our approach highly renders tumor classification tasks by largely outperforming the state-of-the-art unsupervised and supervised approaches.
Citation - WoS: 1
Citation - Scopus: 1
Measuring Eudaimonic and Hedonic Wellbeing: Development and Validation of the Holistic Wellbeing Measure
(Routledge, 2025) Arslan, G.; Coşkun, M.
The primary goal of this study was to develop a concise, theoretically grounded tool –the Holistic Wellbeing Measure (HWM)– that captures both hedonic and eudaimonic facets of wellbeing. Items for the HWM were generated through a careful review of existing wellbeing scales and literature, followed by expert consultation, pilot testing, and iterative refinement to ensure conceptual coverage, clarity, and face validity. Data were collected from three distinct samples: adolescents (n = 453), young adults (n = 361), and adults (n = 358). Exploratory and confirmatory factor analyses supported a two-factor structure, with 12 items reflecting independent but related hedonic and eudaimonic wellbeing dimensions. The measure demonstrated strong internal reliability and evidence of convergent, discriminant, and concurrent validity across all age groups. Regression analyses further indicated that the HWM contributed unique variance to the prediction of general health indicators (physical, social, and mental health) and psychological problems (depression, anxiety, and somatization), above the effects of gender, age, and psychological wellbeing. These results suggest that the HWM is a valid and reliable measure for assessing both aspects of wellbeing across age groups and can support strategies aimed at promoting overall mental health. © 2025 Taylor & Francis Group, LLC.
Burg-Aided 2D MIMO Array Extrapolation for Improved Spatial Resolution
(MDPI, 2025) Bekar, Muge; Bekar, Ali; Pirkani, Anum; Baker, Christopher John; Gashinova, Marina
In this paper, the extrapolation of a 2D multiple-input multiple-output (MIMO) array is proposed using the Burg algorithm to achieve higher angular resolution beyond that of the corresponding 2D MIMO virtual array. The main advantage of such an approach is that it allows us to dramatically decrease both the physical size and the number of antenna elements of the MIMO array. The performance and limitations of the Burg algorithm are examined through both simulation and experimentation at 77 GHz. The experimental methodology used to acquire 3D data of range, azimuth and elevation information with the 1D MIMO off-the-shelf radar is described. Using this method, the performance of the proposed array can be tested experimentally, especially at frequencies where it is desired to assess the antenna response prior to fabricating the antenna.
Labyrinthine Microstructures With a High Dipole Moment Boron Complex for Molecular Physically Unclonable Functions
(American Chemical Society, 2025) Yıldız, T.A.; Kiremitler, N.B.; Kayacı, N.; Kalay, M.; Özcan, E.; Deneme, I.; Usta, H.
The design and development of novel molecular-physically unclonable functions (PUFs) with advanced encoding characteristics and ease of fabrication have recently attracted attention in cryptography, secure authentication, and anticounterfeiting. Here, we report the development of a new high dipole-moment small molecule, InIm-BF2, a difluoroborate complex of an indolyl-imine ligand, and the fabrication of unique labyrinthine patterns through a facile two-step thin film process under ambient conditions. The new molecule has a dipolar, coplanar π-backbone and arranges in the solid state with antisymmetric cofacial π-stackings (3.86 Å). These properties, along with short C–H···π contacts (2.74–2.88 Å) and nonclassical C–H···F hydrogen bonds (2.47–2.51 Å) (23.4% and 11.5% of the Hirshfeld surfaces, respectively), drive the formation of amorphous molecular PUF patterns with disordered, short-range interactions. Spin-coating followed by thermal annealing at a moderate temperature produces nanoscopic molecular thin films with intricate labyrinthine patterns. These patterns, characterized by interconnected, irregularly shaped, micron-sized (≈50–100 μm) features, exhibit excellent PUF characteristics, verified through advanced image analysis and computational algorithms. Unlike randomly positioned isolated features in classical binarized keys, the interconnected labyrinthine patterns possess rich entropy and complex features, directly authenticated via deep-learning methodologies. Our work not only demonstrates a facile, promising approach to fabricating unique high-entropy PUF patterns but also provides critical insights into designing advanced molecular materials for next-generation security applications. © 2025 The Authors. Published by American Chemical Society
Effect of Yttrium/Lanthanum-Doped Ultrasonically Assisted Nano-Hydroxyapatite on Remineralization and Bracket Bond Strength in Artificial Enamel Lesions
(BMC, 2025) Ozturk, Taner; Mammadov, Elshan; Bulduk Karakaya, Humeyra; Yagci, Filiz; Dayan, Serkan; Yagci, Ahmet
Background This in vitro study aimed to evaluate the remineralization efficacy of ultrasonically assisted yttrium fluoride-doped (Ult-YF3-nHAP) and lanthanum fluoride-doped (Ult-LaF3-nHAP) nano-hydroxyapatite (nHAP) on artificially induced enamel lesions (aWSLs), and to compare their performance with acidulated phosphate fluoride (APF) gel, fluoride varnish, casein phosphopeptide-amorphous calcium phosphate (CPP-ACP), and resin infiltrant (ICON). Methods This in vitro study followed a four-phase design: enamel lesion creation, application of remineralization agents, a 14-day treatment protocol, and post-treatment analyses using QLF, Micro-CT, SEM-EDX, and SBS testing. This study included 168 extracted human premolars, divided into eight experimental groups (n = 21 per group): (1) Demineralized control (no remineralization treatment), (2) Acidulated phosphate fluoride (APF) gel, (3) Fluoride varnish, (4) Casein phosphopeptide-amorphous calcium phosphate (CPP-ACP), (5) Ultrasonically assisted nHAP (Control nHAP), (6) Ult-YF3-nHAP, (7) Ult-LaF3-nHAP, and (8) Resin infiltrant (ICON). The aWSLs were created under laboratory conditions. Brackets were bonded to the teeth with composite material, and aWSLs were created under laboratory conditions. After lesion formation and at the end of the experimental process, micro-computed tomography (Micro-CT) and laser-assisted quantitative light fluorescence (QLF) analysis were performed to assess lesion progression and remineralization. Additionally, scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX) and shear bond strength (SBS) tests were conducted at the end of the study. Statistical analysis was performed using one-way ANOVA, Kruskal-Wallis, and Mann-Whitney U tests, with a significance level of p < 0.05. Results The bracket bond strength test data showed no significant differences between the groups (p = 0.156). Significant differences were found among groups for QLF fluorescence recovery (Delta F, p < 0.001), with the Ult-YF3-nHAP group showing the greatest increase (median: +0.5, IQR: -1.4 to + 0.7), while the control group showed the greatest decrease (median: -12.1, IQR: -12.4 to -10.2). Micro-CT analysis also revealed significant differences between groups (p = 0.008). The APF Gel group showed values comparable to those of all other experimental groups. The highest remineralization values were recorded in the Ult-YF3-nHAP group (6.87 +/- 3.03 mm(3)), whereas the lowest values were found in the Varnish group. The demineralized control group had significantly higher values than the Varnish group, but lower than the Ult-LaF3-nHAP group. SEM-EDX analysis revealed that fluoride weight was significantly lower in the Tooth Mousse and Varnish groups compared to the other experimental groups (p < 0.001). Ca/P ratio was significantly lower in the demineralized control, Varnish, and Ult-YF3-nHAP groups than in other experimental groups (p = 0.002). Conclusion Ult-YF3-nHAP showed higher efficacy in remineralization of aWSLs compared to fluoride-based treatments, CPP-ACP, and resin infiltrant. The highest remineralization was detected in the Ult-YF3-nHAP group by micro-CT and QLF analysis, while fluoride varnish gave the lowest result.
Pangenome Analysis and Genome-Guided Probiotic Evaluation of Cyclic Dipeptides Producing Levilactobacillus Brevis DY55bre Strain From a Lactic Acid Fermented Shalgam to Assess Its Metabolic, Probiotic Potentials, and Cytotoxic Effects on Colorectal Cancer Cells
(Springer, 2025) Yetiman, Ahmet E.; Horzum, Mehmet; Kanbur, Ertan; Cadir, Mehmet; Bahar, Dilek; Gurbuz, Serife; Akbulut, Mikail
This study investigates the genetic, metabolic, and probiotic characteristics of Levilactobacillus brevis DY55bre, a strain isolated from the traditional Turkish fermented beverage, shalgam. Whole-genome sequencing revealed a circular genome of 2.485 Mb with a GC content of 45.72%, predicted 2791 genes, and multiple CRISPR-Cas systems. Pangenome analysis demonstrated an open structure, with 18.9% core genes and 103 strain-specific genes, highlighting its genetic diversity. The DY55bre exhibits heterofermentative carbohydrate metabolism due to the presence of the araBAD operon and the lack of 1-phosphofructokinase (pfK) and fructose-1,6-bisphosphate aldolase enzymes. Probiotic evaluation revealed firm survival under simulated gastrointestinal conditions, including resistance to acidic pH (as low as 3.0) and bile salts (up to 1%), along with significant adhesion to intestinal epithelial cell lines (HT29;59.3%, Caco-2;87%, and DLD-1;60.8%). The strain exhibited high auto-aggregation (84.55%) and cell surface hydrophobicity (56.69%), essential for gut colonization. Safety assessments confirmed its non-hemolytic nature and absence of horizontally acquired antibiotic resistance genes. Notably, GC-MS analysis identified bioactive cyclic dipeptides, Cyclo(D-Phe-L-Pro) and Cyclo(L-Leu-L-Pro), which demonstrated cytotoxic effects against colorectal cancer cell lines, with IC50 values of 7.71 mg/mL for HT29 and 3.19 mg/mL for DLD-1. The cell-free supernatant exhibited antimicrobial activity against pathogens, likely due to the synergistic effects of cyclic dipeptides, organic acids, and other metabolites. Antioxidant assays revealed significant ABTS+ (76.63%) and DPPH (34.25%) radical scavenging activities, while cholesterol assimilation tests showed a 27.29% reduction. These findings position the DY55bre as a promising candidate for functional foods, nutraceuticals, and therapeutic applications, warranting further in vivo validation.
Correction: Engineering Novel Features for Diabetes Complication Prediction Using Synthetic Electronic Health Records
(Frontiers Media S.A., 2025) Voskergian, Daniel; Bakir-Gungor, Burcu; Yousef, Malik
Citation - WoS: 1
Antifungal Efficacy of 3D-Cultured Palatal Mesenchymal Stem Cells and Their Secreted Factors Against Candida albicans
(American Chemical Society, 2025) Bicer, M.; Öztürk, E.; Sener, F.; Hakki, S.S.; Fidan, O.
Candida albicans is among the life-threatening fungal species and the primary contributor to hospital-acquired systemic infections, accounting for nearly 70% of all fungal infections worldwide. The current treatment primarily relies on azoles, pyrimidine analogs, polyenes, and echinocandins. However, growing antifungal resistance highlights the urgent need for the development of alternative treatments against C. albicans. Mesenchymal stem cells (MSCs) offer huge therapeutic potential for the treatment of C. albicans-associated diseases. In this study, palatal adipose tissue-derived MSCs (PAT-MSCs) and PAT-MSCs cultured in 3D biomaterial using nanofibrillar cellulose were tested against C. albicans strains ATCC 10231 and ATCC MYA 2876 using an in vitro antifungal activity assay. In addition, the conditioned medium from both PAT-MSCs and PAT-MSCs cultured in 3D hydrogel biomaterial (CM-PAT-MSCs-3D) were evaluated for their antifungal activities. The combined effect of PAT-MSCs and their secreted factors was also investigated. The expression of five antimicrobial peptide (AMP)-encoding genes was analyzed by quantitative real-time PCR. The expression of antimicrobial peptides was further confirmed via immunocytochemical staining. PAT-MSCs significantly inhibited the growth of C. albicans strains at varying inoculum concentrations (500 and 2000 CFU). Similarly, a comparable antifungal effect was observed when Candida strains were treated with PAT-MSC secreted factors alone. Statistical analysis revealed significant differences between the antifungal activities of PAT-MSCs and CM-PAT-MSCs. Lastly, the combination of PAT-MSCs and CM-PAT-MSC-3D led to a marked reduction in fungal growth, with inhibition rates of 99.75% and 99.91% for C. albicans ATCC 10231 and ATCC MYA-2876, respectively, at 500 CFU inocula. At 2000 CFU inocula, inhibition rates were 99.54% and 99.91%, respectively (****P ≤ 0.0001). These antifungal activities were further confirmed by using RT-PCR and immunocytochemical analysis. Our findings underscore a perspective on the potent antifungal activity of secreted factors from PAT-MSCs cultured within a 3D hydrogel matrix, specifically against various strains of C. albicans. Particularly, the combination of PAT-MSCs with their secreted factors represents a promising therapeutic platform, potentially offering a safer and more effective alternative to conventional antifungal treatments. © 2025 Elsevier B.V., All rights reserved.
The Joubert syndrome protein CEP41 is excluded from the distal segment of cilia in C. elegans
(2021) Sebiha Cevik; Oktay I Kaplan
Rare diseases are a fundamental issue in today's world, affecting more than 300 million individuals worldwide. According to data from Orphanet and OMIM, about 50-60 new conditions are added to the list of over 6,000 clinically distinct diseases each year, rendering disease diagnosis and treatment even more challenging. Ciliopathies comprise a heterogeneous category of rare diseases made up of over 35 distinct diseases, including Joubert syndrome (JBTS; OMIM 213300), that are caused by functional and structural defects in cilia. JBTS is an autosomal recessive condition characterized by a range of symptoms, including cerebellar vermis hypoplasia and poor muscle tone. There are now a total of 38 genes that cause JBTS, almost all of which encode protein products that are found in cilia and cilia-associated compartments, such as the basal body and transition zone. CEP41 is a JBTS-associated protein that is found in cilia and the basal body of mammals, but its localization in other ciliary organisms remains elusive. C. elegans is an excellent model organism for studying the molecular mechanisms of rare diseases like JBTS. We, therefore, decided to use C. elegans to identify the localization of CEP41. Our microscopy analysis revealed that CEPH-41(CEntrosomal Protein Homolog 41) not only localizes to cilia but is excluded from the distal segment of the amphid and phasmid cilia in C. elegans. Furthermore, we discovered a putative X-box motif located in the promoter of ceph-41 and the expression of ceph-41 is regulated by DAF-19, a sole Regulatory Factor X (RFX) transcription factor.
Subcellular localization of the voltage-gated K+ channel EGL-36 , a member of the KV3 subfamily, in the ciliated sensory neurons in C. elegans
(2021) Sebiha Cevik; Oktay I Kaplan
Delineated as the first cellular organelle in 1675 by Antonie van Leeuwenhoek, cilia did not receive much attention until the 2000s, when it became apparent that cilia played a key role in the development of embryos, a variety of signaling pathways. Therefore, collective efforts by many scientists have led to the identification of many novel ciliopathy and cilia genes, while we are still far from disclosing the complete components of cilia.Here we used the ciliated sensory neurons in C. elegans as a model system that revealed the voltage-gated K+ channel EGL-36 (a member of the Shaw subfamily) as a new component associated with cilia. The confocal microscopy examination of fluorescence tagged EGL-36 together with ciliary (IFT-140) or transition zone (MKS-6) markers reveal that EGL-36 is only expressed in subsets of the ciliated sensory neurons, where it partially overlaps with the basal body signals and predominantly localizes to the periciliary membrane compartment. This expression pattern along with studies of egl-36 gain-of-function variants indicates that egl-36 is not essential for ciliogenesis in C. elegans. Our data identify the voltage-gated K+ channel EGL-36 as a new cilia-associated protein, and future studies should reveal the functional significance of EGL-36 in cilia biogenesis.
On Critical Buckling Loads of Columns under End Load Dependent on Direction
(Hindawi Publishing Corporation, 2014) Başbük, Musa; Eryılmaz, Aytekin; Atay, Mehmet Tarik
Most of the phenomena of various fields of applied sciences are nonlinear problems. Recently, various types of analytical approximate solution techniques were introduced and successfully applied to the nonlinear differential equations. One of the aforementioned techniques is the Homotopy analysis method (HAM). In this study, we applied HAM to find critical buckling load of a column under end load dependent on direction. We obtained the critical buckling loads and compared them with the exact analytic solutions in the literature.
Aerial Swarms: Recent Applications and Challenges
(Springer, 2021) Mohamed Abdelkader; Samet Güler
Purpose of review: Currently, there is a large body of research on multi-agent systems addressing their different system theoretic aspects. Aerial swarms as one type of multi-agent robotic systems have recently gained huge interest due to their potential applications. However, aerial robot groups are complex multi-disciplinary systems and usually research works focus on specific system aspects for particular applications. The purpose of this review is to provide an overview of the main motivating applications that drive the majority of research works in this field, and summarize fundamental and common algorithmic components required for their development._x000D_ _x000D_ Recent findings: Most system demonstrations of current aerial swarms are based on simulations, some have shown experiments using few 10 s of robots in controlled indoor environment, and limited number of works have reported outdoor experiments with small number of autonomous aerial vehicles. This indicates scalability issues of current swarm systems in real world environments. This is mainly due to the limited confidence on the individual robot's localization, swarm-level relative localization, and the rate of exchanged information between the robots that is required for planning safe coordinated motions._x000D_ _x000D_ Summary: This paper summarizes the main motivating aerial swarm applications and the associated research works. In addition, the main research findings of the core elements of any aerial swarm system, state estimation and mission planning, are also presented. Finally, this paper presents a proposed abstraction of an aerial swarm system architecture that can help developers understand the main required modules of such systems.
Citation - WoS: 25
Citation - Scopus: 31
miRmoduleNet: Detecting miRNA-mRNA Regulatory Modules
(Frontiers Media S.A., 2022) Yousef, Malik; Goy, Gokhan; Bakir-Gungor, Burcu
Increasing evidence that MicroRNAs (miRNAs) play a key role in carcinogenesis has revealed the need for elucidating the mechanisms of miRNA regulation and the roles of miRNAs in gene-regulatory networks. A better understanding of the interactions between miRNAs and their mRNA targets will provide a better understanding of the complex biological processes that occur during carcinogenesis. Increased efforts to reveal these interactions have led to the development of a variety of tools to detect and understand these interactions. We have recently described a machine learning approach miRcorrNet, based on grouping and scoring (ranking) groups of genes, where each group is associated with a miRNA and the group members are genes with expression patterns that are correlated with this specific miRNA. The miRcorrNet tool requires two types of -omics data, miRNA and mRNA expression profiles, as an input file. In this study we describe miRModuleNet, which groups mRNA (genes) that are correlated with each miRNA to form a star shape, which we identify as a miRNA-mRNA regulatory module. A scoring procedure is then applied to each module to further assess their contribution in terms of classification. An important output of miRModuleNet is that it provides a hierarchical list of significant miRNA-mRNA regulatory modules. miRModuleNet was further validated on external datasets for their disease associations, and functional enrichment analysis was also performed. The application of miRModuleNet aids the identification of functional relationships between significant biomarkers and reveals essential pathways involved in cancer pathogenesis.
Citation - WoS: 20
Citation - Scopus: 24
miRdisNET: Discovering MicroRNA Biomarkers That Are Associated With Diseases Utilizing Biological Knowledge-Based Machine Learning
(Frontiers Media S.A., 2023) Jabeer, Amhar; Temiz, Mustafa; Bakir-Gungor, Burcu; Yousef, Malik
During recent years, biological experiments and increasing evidence have shown that MicroRNAs play an important role in the diagnosis and treatment of human complex diseases. Therefore, to diagnose and treat human complex diseases, it is necessary to reveal the associations between a specific disease and related miRNAs. Although current computational models based on machine learning attempt to determine miRNA-disease associations, the accuracy of these models need to be improved, and candidate miRNA-disease relations need to be evaluated from a biological perspective. In this paper, we propose a computational model named miRdisNET to predict potential miRNA-disease associations. Specifically, miRdisNET requires two types of data, i.e., miRNA expression profiles and known disease-miRNA associations as input files. First, we generate subsets of specific diseases by applying the grouping component. These subsets contain miRNA expressions with class labels associated with each specific disease. Then, we assign an importance score to each group by using a machine learning method for classification. Finally, we apply a modeling component and obtain outputs. One of the most important outputs of miRdisNET is the performance of miRNA-disease prediction. Compared with the existing methods, miRdisNET obtained the highest AUC value of .9998. Another output of miRdisNET is a list of significant miRNAs for disease under study. The miRNAs identified by miRdisNET are validated via referring to the gold-standard databases which hold information on experimentally verified MicroRNA-disease associations. miRdisNET has been developed to predict candidate miRNAs for new diseases, where miRNA-disease relation is not yet known. In addition, miRdisNET presents candidate disease-disease associations based on shared miRNA knowledge. The miRdisNET tool and other supplementary files are publicly available at: .
Citation - WoS: 26
Citation - Scopus: 31
miRcorrNet: Machine Learning-Based Integration of miRNA and mRNA Expression Profiles, Combined with Feature Grouping and Ranking
(PeerJ Inc., 2021) Yousef, M.; Göy, G.; Mitra, R.; Eischen, C.M.; Jabeer, A.; Bakir-Güngör, B.
A better understanding of disease development and progression mechanisms at the molecular level is critical both for the diagnosis of a disease and for the development of therapeutic approaches. The advancements in high throughput technologies allowed to generate mRNA and microRNA (miRNA) expression profiles; and the integrative analysis of these profiles allowed to uncover the functional effects of RNA expression in complex diseases, such as cancer. Several researches attempt to integrate miRNA and mRNA expression profiles using statistical methods such as Pearson correlation, and then combine it with enrichment analysis. In this study, we developed a novel tool called miRcorrNet, which performs machine learning-based integration to analyze miRNA and mRNA gene expression profiles. miRcorrNet groups mRNAs based on their correlation to miRNA expression levels and hence it generates groups of target genes associated with each miRNA. Then, these groups are subject to a rank function for classification. We have evaluated our tool using miRNA and mRNA expression profiling data downloaded from The Cancer Genome Atlas (TCGA), and performed comparative evaluation with existing tools. In our experiments we show that miRcorrNet performs as good as other tools in terms of accuracy (reaching more than 95% AUC value). Additionally, miRcorrNet includes ranking steps to separate two classes, namely case and control, which is not available in other tools. We have also evaluated the performance of miRcorrNet using a completely independent dataset. Moreover, we conducted a comprehensive literature search to explore the biological functions of the identified miRNAs. We have validated our significantly identified miRNA groups against known databases, which yielded about 90% accuracy. Our results suggest that miRcorrNet is able to accurately prioritize pan-cancer regulating high-confidence miRNAs. miRcorrNet tool and all other supplementary files are available at https://github.com/ malikyousef/miRcorrNet. © 2021 Elsevier B.V., All rights reserved.

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