Decoding dynamic miRNA:ceRNA interactions unveils therapeutic insights and targets across predominant cancer landscapes.

Competing endogenous RNAs play key roles in cellular molecular mechanisms through cross-talk in post-transcriptional interactions. Studies on ceRNA cross-talk, which is particularly dependent on the abundance of free transcripts, generally involve large- and small-scale studies involving the integration of transcriptomic data from tissues and correlation analyses. This abundance-dependent nature of ceRNA interactions suggests that tissue- and condition-specific ceRNA dynamics may fluctuate. However, there are no comprehensive studies investigating the ceRNA interactions in normal tissue, ceRNAs that are lost and/or appear in cancerous tissues or their interactions. In this study, we comprehensively analyzed the tumor-specific ceRNA fluctuations observed in the three highest-incidence cancers, LUAD, PRAD, and BRCA, compared to healthy lung, prostate, and breast tissues, respectively. Our observations pertaining to tumor-specific competing endogenous RNA (ceRNA) interactions revealed that, in the cases of lung adenocarcinoma (LUAD), prostate adenocarcinoma (PRAD), and breast invasive carcinoma (BRCA), 3,204, 1,233, and 406 ceRNAs, respectively, engage in post-transcriptional intercommunication within tumor tissues, in contrast to their absence in corresponding healthy samples. We also found that 90 ceRNAs are shared by the three cancer types and that these ceRNAs participate in ceRNA interactions in tumor tissues compared to those in normal tissues. Among the 90 ceRNAs that directly interact with miRNAs, we uncovered a core network of 165 miRNAs and 63 ceRNAs that should be considered in RNA-targeted and RNA-mediated approaches in future studies and could be used in these three aggressive cancer types. More specifically, in this core interaction network, ceRNAs such as GALNT7, KLF9, and DAB2 and miRNAs like miR-106a/b-5p, miR-20a-5p, and miR-519d-3p may have potential as common targets in the three critical cancers. In contrast to conventional methods that construct ceRNA networks using differentially expressed genes compared to normal tissues, our proposed approach identifies ceRNA players by considering their context within the ceRNA:miRNA interactions. Our results have the potential to reveal distinct and common ceRNA interactions in cancer types and to pinpoint critical RNAs, thereby paving the way for RNA-based strategies in the battle against cancer.

Carcass characteristics and meat quality of goat kids according to the Colomer - Rocher carcass fatness and conformation classes.

Classifying kid carcasses according to their fatness and conformation scores guides producers toward higher quality and income-generating production methods and determines the ideal slaughter time. This study aimed to determine the effects of Colomer-Rocher fatness and conformation classes on carcass and meat quality characteristics in goat kids. A total of 102 male kid carcasses were used in the study. Carcasses were divided into fatness (1-, 1, 1+, 2-) and conformation (P-, P, P+; O-) classes according to the Colomer-Rocher classification, and these groups were accepted as the experimental group. Hierarchical clustering analysis divided the kid carcasses into 5 clusters using certain carcass characteristics. Differences between clusters in most of the carcass characteristics were significant. The difference between the cluster groups in terms of meat colour and sensory characteristics was also significant. Fatness and conformation classes significantly affected most characteristics except kidney knob and channel fat (KKCF) percentages and carcass joints percentages. The Colomer-Rocher conformation classification was found to be more discriminatory in terms of meat quality than the fatness classification.

Biofabrication of Acer palmatum-Mediated Multifunctional CuO Nanoparticles for Dye Removal, Antibacterial-Antifungal Activity, and Molecular Docking.

Copper oxide nanoparticles (CuONPs) are used in many fields from electronics to medicine due to their multifunctionality, and therefore, their production with environmentally friendly methods is a current issue. In this study, biofabricated CuONPs were obtained by using the leaf extract of Acer palmatum plant originating from the Far East to enlighten the characteristics of the novel nanoparticles differentiating from those existing in the literature. Multifunctional nature of the CuONPs was evaluated by the antibacterial, antifungal, and decolorative applications and also by performing molecular docking analysis. The fabricated CuONPs were characterized using ultraviolet-visible spectroscopy (UV-vis), Fourier-transform infrared spectroscopy (FT-IR), scanning electron microscopy (SEM), and dynamic light scattering (DLS). The absorbance seen at 270 nm in the SPR band obtained by UV-vis spectroscopy proved the presence of CuONPs, while the 602, 560, and 540 cm-1 vibrations obtained in the FT-IR spectroscopy indicated the same result. SEM images proved that the nanoparticles were in spherical form with sizes ranging from 140 to 225 nm. The result of DLS analysis showed that the average particle size was 229 nm in diameter, and CuONPs had monodisperse systems (polydispersity index, 0.184). The dye removal potency of CuONPs was also investigated by using remazol brilliant blue R (RBBR) and napthol blue black (NBB). Decolorizations (74 and 86%) of RBBR and NBB were obtained in 90 min at 50 °C, respectively. The strong antibacterial properties of the synthesized CuONPs were observed on both Gram (-) and Gram (+) bacterial strains by disk diffusion and optical analyses, and their antifungal activity was close to that of Amphotericin B, which was applied as a positive control. Molecular docking analysis was performed with Escherichia coli dihydrofolate reductase and Staphylococcus aureus DNA Gyrase B to analyze the antibacterial mechanisms of CuONP and observed that they exhibit good interactions with their targets with binding energies of -12.562 and -8.797 kcal/mol, respectively. Our findings suggested that CuONPs are crucial in the mechanisms of folate metabolism and DNA replication associated with bacterial proliferation. This work will provide significant guidance for the biofabrication of CuONPs and their medical and industrial applications.

Evaluation of retina and choroid perfusion with optical coherence tomography angiography in patients with retinitis pigmentosa.

PURPOSE: In this study, we aimed to evaluate macular perfusion with optical coherence tomography angiography (OCTA) and to investigate the correlation between OCTA quantitative data and visual acuity (VA) in patients with retinitis pigmentosa (RP). METHODS: This retrospective single-center study was conducted on 60 eyes of 30 RP patients and 52 healthy eyes. The vessel density (VD) of the superficial capillary plexus (SCP) and deep capillary plexus (DCP) of the macula, the size of foveal avascular zone (FAZ), choriocapillary flow density (FD) were measured using OCTA. Quantitative data obtained with OCTA were compared between the two groups. In addition, the correlation between the OCTA measurements and VA was examined. RESULTS: In patients with RP, the choriocapillary FD was decreased (p = 0.001), the FAZ area was enlarged (p = 0.010), and the VDs of the SCP and DCP were decreased in all areas (p = 0.001). Correlation was found between VA and SCP VD, whole image (p = 0.011, rho = -0.327) and parafoveal (p = 0.001, rho = -0.444) areas. CONCLUSION: Quantitative data from OCTA showed reduced macular perfusion in patients with RP compared to healthy controls. There was also a correlation between the quantitative OCTA data and VA.

Subgraph Learning for Topological Geolocalization with Graph Neural Networks.

One of the challenges of spatial cognition, such as self-localization and navigation, is to develop an efficient learning approach capable of mimicking human ability. This paper proposes a novel approach for topological geolocalization on the map using motion trajectory and graph neural networks. Specifically, our learning method learns an embedding of the motion trajectory encoded as a path subgraph where the node and edge represent turning direction and relative distance information by training a graph neural network. We formulate the subgraph learning as a multi-class classification problem in which the output node IDs are interpreted as the object's location on the map. After training using three map datasets with small, medium, and large sizes, the node localization tests on simulated trajectories generated from the map show 93.61%, 95.33%, and 87.50% accuracy, respectively. We also demonstrate similar accuracy for our approach on actual trajectories generated by visual-inertial odometry. The key benefits of our approach are as follows: (1) we take advantage of the powerful graph-modeling ability of neural graph networks, (2) it only requires a map in the form of a 2D graph, and (3) it only requires an affordable sensor that generates relative motion trajectory.

Automated rolling shutter calibration with an LED panel.

Cameras with rolling shutters (RSs) dominate consumer markets but are subject to distortions when capturing motion. Many methods have been proposed to mitigate RS distortions for applications such as vision-aided odometry and three-dimensional (3D) reconstruction. They usually need known line delay d between successive image rows. To calibrate d, several methods have been proposed that often involve complex procedures. This Letter proposes an easy RS calibration method by using an off-the-shelf light-emitting diode (LED) panel, using the fact that the RS causes the blinking LED columns to appear slanted in images by a static camera. The calibration starts with extracting the LED lights and then rectifies the images to remove the lens distortion and misalignment between the camera and the LED panel. Next, blocks of slanted bright LEDs are recognized and their inclination leads to the line delay estimate. Our method needs not to move the camera, adjust the ambient light, or calibrate camera intrinsic parameters beforehand, and it can usually estimate the line delay given two LED panel images in one second. Extensive tests with industrial cameras and consumer cameras of wide-angle and fish-eye lenses validate its competitive accuracy relative to the established methods.

PGT for structural chromosomal rearrangements in 300 couples reveals specific risk factors but an interchromosomal effect is unlikely.

RESEARCH QUESTION: What factors affect the proportion of chromosomally balanced embryos in structural rearrangement carriers? Is there any evidence for an interchromosomal effect (ICE)? DESIGN: Preimplantation genetic testing outcomes of 300 couples (198 reciprocal, 60 Robertsonian, 31 inversion and 11 complex structural rearrangement carriers) were assessed retrospectively. Blastocysts were analysed either by array-comparative genomic hybridization or next-generation sequencing techniques. ICE was investigated using a matched control group and sophisticated statistical measurement of effect size (φ). RESULTS: 300 couples underwent 443 cycles; 1835 embryos were analysed and 23.8% were diagnosed as both normal/balanced and euploid. The overall cumulative clinical pregnancy and live birth rates were 69.5% and 55.8%, respectively. Complex translocations and female age (≥35) were found to be risk factors associated with lower chance of having a transferable embryo (P < 0.001). Based on analysis of 5237 embryos, the cumulative de-novo aneuploidy rate was lower in carriers compared to controls (45.6% versus 53.4%, P < 0.001) but this was a 'negligible' association (φ < 0.1). A further assessment of 117,033 chromosomal pairs revealed a higher individual chromosome error rate in embryos of carriers compared to controls (5.3% versus 4.9%), which was also a 'negligible' association (φ < 0.1), despite a P-value of 0.007. CONCLUSIONS: These findings suggest that rearrangement type, female age and sex of the carrier have significant impacts on the proportion of transferable embryos. Careful examination of structural rearrangement carriers and controls indicated little or no evidence for an ICE. This study helps to provide a statistical model for investigating ICE and an improved personalized reproductive genetics assessment for structural rearrangement carriers.

Robust and rigorous identification of tissue-specific genes by statistically extending tau score.

OBJECTIVES: In this study, we aimed to identify tissue-specific genes for various human tissues/organs more robustly and rigorously by extending the tau score algorithm. INTRODUCTION: Tissue-specific genes are a class of genes whose functions and expressions are preferred in one or several tissues restrictedly. Identification of tissue-specific genes is essential for discovering multi-cellular biological processes such as tissue-specific molecular regulations, tissue development, physiology, and the pathogenesis of tissue-associated diseases. MATERIALS AND METHODS: Gene expression data derived from five large RNA sequencing (RNA-seq) projects, spanning 96 different human tissues, were retrieved from ArrayExpress and ExpressionAtlas. The first step is categorizing genes using significant filters and tau score as a specificity index. After calculating tau for each gene in all datasets separately, statistical distance from the maximum expression level was estimated using a new meaningful procedure. Specific expression of a gene in one or several tissues was calculated after the integration of tau and statistical distance estimation, which is called as extended tau approach. Obtained tissue-specific genes for 96 different human tissues were functionally annotated, and some comparisons were carried out to show the effectiveness of the extended tau method. RESULTS AND DISCUSSION: Categorization of genes based on expression level and identification of tissue-specific genes for a large number of tissues/organs were executed. Genes were successfully assigned to multiple tissues by generating the extended tau approach as opposed to the original tau score, which can assign tissue specificity to single tissue only.

HVIOnet: A deep learning based hybrid visual-inertial odometry approach for unmanned aerial system position estimation.

Sensor fusion is used to solve the localization problem in autonomous mobile robotics applications by integrating complementary data acquired from various sensors. In this study, we adopt Visual-Inertial Odometry (VIO), a low-cost sensor fusion method that integrates inertial data with images using a Deep Learning (DL) framework to predict the position of an Unmanned Aerial System (UAS). The developed system has three steps. The first step extracts features from images acquired from a platform camera and uses a Convolutional Neural Network (CNN) to project them to a visual feature manifold. Next, temporal features are extracted from the Inertial Measurement Unit (IMU) data on the platform using a Bidirectional Long Short Term Memory (BiLSTM) network and are projected to an inertial feature manifold. The final step estimates the UAS position by fusing the visual and inertial feature manifolds via a BiLSTM-based architecture. The proposed approach is tested with the public EuRoC (European Robotics Challenge) dataset and simulation environment data generated within the Robot Operating System (ROS). The result of the EuRoC dataset shows that the proposed approach achieves successful position estimations comparable to previous popular VIO methods. In addition, as a result of the experiment with the simulation dataset, the UAS position is successfully estimated with 0.167 Mean Square Error (RMSE). The obtained results prove that the proposed deep architecture is useful for UAS position estimation.

Ab interno 180-degree trabeculectomy with a dual blade in a patient with refractory primary congenital glaucoma.

A 13-year-old female patient with refractory primary congenital glaucoma (PCG) in the right eye who had a history of multiple glaucoma operations underwent ab interno 180-degree trabeculectomy with the Kahook Dual Blade (KDB) targeting the nasal and inferior angles. On postoperative day 1, the intraocular pressure (IOP) of the right eye reduced from 43 to 15 mmHg while on medical therapy. The patient maintained this IOP level throughout the 6-month follow-up. Ab interno KDB trabeculectomy targeting both nasal and inferior angles may be an effective and safe procedure for the treatment of PCG even in eyes with a history of previously failed glaucoma procedures.

Optical Coherence Tomography Angiography in Patients with Cone Dystrophy.

PURPOSE: This study aimed to evaluate macular perfusion using optical coherence tomography angiography (OCTA) in patients with cone dystrophy and to determine the associations between the quantitative data of OCTA and functional parameters. METHODS: The data of 36 eyes of 18 patients with cone dystrophy and 38 eyes of 19 healthy controls were analyzed. The superficial and deep capillary plexus (SCP and DCP) vessel densities (VD) of the macula, the foveal avascular zone (FAZ) and choriocapillary flow density values were obtained using OCTA. The associations between visual acuity (VA) and full-field electroretinography (ffERG) and the quantitative data of OCTA, and the associations between OCTA and ffERG were analyzed. RESULTS: : VD was significantly lower in all areas except the foveal area in SCP in the cone dystrophy group compared to the control group. VA was found to be associated with the VDs of the SCP and DCP except for that of the foveal SCP. VA was also associated with dark-adapted, light-adapted wave amplitudes. CONCLUSION: OCTA quantitatively showed that macular perfusion was decreased in cone dystrophy compared to the healthy controls. In addition, there was an association between VA and ffERG parameters and quantitative data of OCTA.

Effect of SARS-CoV-2 infection on host competing endogenous RNA and miRNA network.

Competing endogenous RNAs (ceRNA) play a crucial role in cell functions. Computational methods that provide large-scale analysis of the interactions between miRNAs and their competitive targets can contribute to the understanding of ceRNA regulations and critical regulatory functions. Recent reports showed that viral RNAs can compete with host RNAs against host miRNAs. Regarding SARS-CoV-2 RNA, no comprehensive study had been reported about its competition with cellular ceRNAs. In this study, for the first time, we used the ceRNAnetsim package to assess ceRNA network effects per individual cell and competitive behavior of SARS-CoV-2 RNA in the infected cells using single-cell sequencing data. Our computations identified 195 genes and 29 miRNAs which vary in competitive behavior specifically in presence of SARS-CoV-2 RNA. We also investigated 18 genes that are affected by genes that lost perturbation ability in presence of SARS-CoV-2 RNA in the human miRNA:ceRNA network. These transcripts have associations with COVID-19-related symptoms as well as many dysfunctions such as metabolic diseases, carcinomas, heart failure. Our results showed that the effects of the SARS-CoV-2 genome on host ceRNA interactions and consequent dysfunctions can be explained by competition among various miRNA targets. Our perturbation ability perspective has the potential to reveal yet to be discovered SARS-CoV-2 induced effects invisible to conventional approaches.

Evaluation of the functionality of EUROP carcass classification system in thin-tailed and fat-tailed lambs.

Aim of study was to investigate the relationship of EUROP carcass fatness and conformation classes with carcass and meat quality characteristics in thin-tailed (Kivircik) and a fat-tailed (Kangal Akkaraman) lambs. A total of 96 lamb carcasses (48 Kivircik and 48 Kangal Akkaraman breed) were examined. Distribution of carcasses in conformation and fatness classes were more limited in Kangal Akkaraman carcasses. More accurate predictions were obtained in Kivircik lambs compared to Kangal Akkaraman lambs in terms of backfat thickness, kidney knob and channel fat percentage, longissimus thoracis muscle area, weights of high-value carcass joints, weights of tissues in the hind limb and muscle/bone ratio. EUROP classification system was not appropriate for predicting meat quality in thin-tailed and fat-tailed lambs. The combination of EUROP fatness and conformation classes with cold carcass weight can be used to predict weights of high-value carcass joints and weights of hind limb tissues.

A Case of Multiple Optic Disc Pits: 21-Year Follow-up

Optic disc pits (ODP) are an uncommon congenital abnormality. Patients remain asymptomatic unless they develop maculopathy. The use of optic coherence tomography has critical benefits in the follow-up of patients who are at the amblyogenic age. The aim of this study is to present a case of double ODP in the right eye and single ODP in the left eye in a partially accommodative esotropia patient followed for 21 years. To our knowledge, multiple ODP has never been described in a patient with partially accommodative esotropia.

Network based multifactorial modelling of miRNA-target interactions.

Competing endogenous RNA (ceRNA) regulations and crosstalk between various types of non-coding RNA in humans is an important and under-explored subject. Several studies have pointed out that an alteration in miRNA:target interaction can result in unexpected changes due to indirect and complex interactions. In this article, we defined a new network-based model that incorporates miRNA:ceRNA interactions with expression values. Our approach calculates network-wide effects of perturbations in the expression level of one or more nodes in the presence or absence of miRNA interaction factors such as seed type, binding energy. We carried out the analysis of large-scale miRNA:target networks from breast cancer patients. Highly perturbing genes identified by our approach coincide with breast cancer-associated genes and miRNAs. Our network-based approach takes the sponge effect into account and helps to unveil the crosstalk between nodes in miRNA:target network. The model has potential to reveal unforeseen regulations that are only evident in the network context. Our tool is scalable and can be plugged in with emerging miRNA effectors such as circRNAs, lncRNAs, and available as R package ceRNAnetsim: https://www.bioconductor.org/packages/release/bioc/html/ceRNAnetsim.html.

An Alternative Approach for External Drainage of Suprachoroidal Hemorrhage: Active Aspiration with Butterfly Needle.

Purpose: To describe a novel surgical technique for external drainage of choroidal detachment/suprachoroidal hemorrhage with a butterfly needle.Materials and Methods: This is a retrospective case series on six eyes with serous and/or hemorrhagic choroidal detachments due to previous intraocular surgery or perforating ocular trauma that underwent active external suprachoroidal fluid drainage procedure with butterfly needle. The primary outcome measures were perioperative controlled fluid discharge and presence of choroidal detachment at 1 week, 1 month, and 6 months postoperatively. Secondary outcome measures were postoperative visual acuity and intraocular pressure.Results: During drainage, controlled hemorrhage discharge was observed. Drainage resolved hemorrhagic choroidal detachments at 1 week postoperatively. Intraocular pressure significantly increased, and visual acuity improved in all eyes. No complications were noted.Conclusion: Management of hemorrhagic choroidal detachment is challenging, and external drainage can be complicated. Active aspiration of hemorrhagic material with a butterfly needle may help early resolution.

Comparative study of retinal nerve fibre layer thickness and retinal peripapillary capillary plexus microvascular vessel density: structure-function relationship analysis in glaucoma.

BACKGROUND: To investigate whether the retinal peripapillary capillary plexus vessel density (RPCP VD) or the retinal nerve fibre layer thickness (RNFLT) is better in showing the structure-function relationship in glaucoma. METHODS: Sixty-seven patients with primary open-angle glaucoma (POAG) in one eye and no visual field loss in fellow eye were included in this study. The scans of RPCP VD and RNFLT, and the standard automated perimetry data [including mean deviation (MD), pattern standard deviation (PSD), sector-based pattern deviation (PD) values] were analysed and compared. RESULTS: The global RNFLT was associated with MD (P = 0.035). RNFLTs of the superotemporal, superonasal, inferotemporal and inferonasal quadrants were associated with the corresponding PD (P = 0.004, <0.001, 0.002 and 0.012). The global RPCP VD was found to be associated with MD and PSD (P = 0.030 and 0.049, respectively). RPCP VD of the superotemporal quadrant was associated with PD of the corresponding quadrant, as well as with PSD (P = 0.003 and 0.043, respectively). Remaining RPCP VD values were only associated with the PD values of the corresponding quadrants (P < 0.05). The associations of the RPCP VD with PD were stronger than those of the RNFLT with PD [RPCP VD vs RNFLT: R2 = 0.624 vs 0.558 (P < 0.001 for both) for the superotemporal, 0.649 vs 0.552 for the superonasal (P < 0.001 for both), 0.598 vs 0.427 for the inferotemporal (P < 0.001 for both), 0.581 vs 0.408 for the inferonasal (P < 0.001 for both), 0.594 vs 0.068 (P < 0.001 vs 0.098) for the temporal, and 0.338 vs 0.195 (P < 0.001 vs 0.004) for the nasal quadrants]. CONCLUSION: In conclusion, the VD of RPCP was more informative in terms of the structure-function relationship in POAG. Future prospective follow-up studies with larger sample sizes are required to confirm the findings.

The agreement between optical coherence tomography angiography and non-mydriatic retinal camera in estimating the optic nerve head parameters and relations with the peripapillary vessel density in primary open-angle glaucoma.

BACKGROUND/OBJECTIVES: To investigate the agreement between optical coherence tomography angiography (OCT-A) and non-mydriatic retinal camera (NMRC) in estimating the optic nerve head (ONH) parameters and evaluate the associations between peripapillary vessel density (VD) with ONH parameters assessed by both devices. METHODS: The OCT-A and NMRC images of 262 participants (138 eyes were diagnosed with POAG, 63 were glaucoma suspect, and 61 were healthy subjects) were screened retrospectively. The vertical cup-to-disc ratio (VCDR), cup-to-disc area ratio (CDAR), rim area (RA), disc area (DA), and cup volume (CV) were recorded using both devices. Peripapillary VD data were also recorded using OCT-A. The intraclass correlation coefficient (ICC) and Bland-Altman plots were obtained to investigate the agreement between the devices. Age- and intraocular pressure (IOP)-corrected associations between the VD and ONH parameters measured by the two devices were analyzed using linear regression models. RESULTS: ICC revealed excellent agreement for VCDR and CDAR, but poor agreement for RA, DA, and CV (ICC = 0.801, 0.793, 0.445, 0.298, and 0.527, respectively). The Bland-Altman plots showed poor agreement for VCDR and CDAR with a large span of limits of agreement (0.500 and 0.528, respectively) and significant proportional biases (P < 0.05). VD was found to be strongly associated with the VCDR and CDAR measurements of both devices (P < 0.001), but the associations were stronger for the measurements of NMRC. CONCLUSIONS: The disagreement between the devices should be considered in clinical practice. The associations between the VD and ONH parameters proved once again the importance of the ONH parameters in terms of the management of glaucoma patients.

A Wearable Augmented Reality Navigation System for Surgical Telementoring Based on Microsoft HoloLens.

This paper reports a new type of augmented reality (AR) system that integrates a Microsoft HoloLens device with a three-dimensional (3D) point tracking module for medical training and telementored surgery. In this system, a stereo camera is used to track the 3D position of a scalpel and transfer its coordinates wirelessly to a HoloLens device. In the scenario of surgical training, a virtual surgical scene with pre-recorded surgical annotations is superimposed with the actual surgical scene so that the surgical trainee is able to operate following virtual instructions. In the scenario of telementored surgery, the virtual surgical scene is co-registered with the actual surgical scene so that the virtual scalpel remotely mentored by an experienced surgeon provides the AR guidance for the inexperienced on-site operator. The performance characteristics of the proposed AR telementoring system are verified by benchtop experiments. The clinical applicability of the proposed system in telementored skin grafting surgery and fasciotomy is validated in a New Zealand rabbit model. Our benchtop and in vivo experiments demonstrate the potential to improve surgical performance and reduce healthcare disparities in remote areas with limited resources.