Search Results (16)

Introduction: This study aims to predict mortality using chest radiographs obtained on the first day of intensive care admission, thereby contributing to better planning of doctors’ treatment strategies and more efficient use of limited resources through early and accurate predictions. Methods: We retrospectively analyzed 510 ICU patients. After data augmentation, a total of 3019 chest radiographs were used for model training and validation, while an independent, non-augmented test set of 100 patients (100 images) was reserved for final evaluation. Seventy-four (74) radiomic features were extracted from the images and analyzed using machine learning algorithms. Model performances were evaluated using the area under the ROC curve (AUC), sensitivity, and specificity metrics. Results: A total of 3019 data samples were included in the study. Through feature selection methods, the initial 74 features were gradually reduced to 10. The Subspace KNN algorithm demonstrated the highest prediction accuracy, achieving AUC 0.88, sensitivity 0.80, and specificity 0.87. Conclusions: Machine learning algorithms such as Subspace KNN and features obtained from PAAC radiographs, such as GLCM Contrast, Kurtosis, Cobb angle, Haralick, Bilateral Infiltrates, Cardiomegaly, Skewness, Unilateral Effusion, Median Intensity, and Intensity Range, are promising tools for mortality prediction in patients hospitalized in the internal medicine intensive care unit. These tools can be integrated into clinical decision support systems to provide benefits in patient management. Full article

RNA G-quadruplexes (rG4s) in 5′-UTRs represent complex regulatory elements capable of both inhibiting and activating mRNA translation through diverse mechanisms in eukaryotes. This review analyzes the evolution of our understanding of 5′-UTR rG4-mediated translation regulation, from early discoveries of simple translation inhibitors to the current recognition of their multifaceted regulatory roles. We discuss canonical and non-canonical rG4 structures, their interactions with regulatory proteins, including helicases and FMRP, and their function in both cap-dependent and IRES-mediated translation. Special attention is given to the synergistic effects between rG4s and upstream open reading frames (uORFs), stress-responsive translation regulation, and their role in repeat-associated non-AUG (RAN) translation linked to neurodegenerative diseases. We critically evaluate methodological challenges in the field, including limitations of current detection methods, reporter system artifacts, and the necessity to verify rG4 presence in endogenous transcripts. Recent technological advances, including genome editing and high-throughput sequencing approaches, have revealed that rG4 effects are more complex and context-dependent than initially thought. This review highlights the importance of developing more robust methodologies for studying rG4s at endogenous levels and carefully reevaluating previously identified targets, while emphasizing their potential as therapeutic targets in various diseases. Full article

Parkinson’s Disease (PD) is a progressive neurodegenerative disorder affecting millions worldwide. Early detection is crucial for improving patient outcomes. Spiral drawing analysis has emerged as a non-invasive tool to detect early motor impairments associated with PD. This study examines the performance of hybrid deep learning and machine learning models in detecting PD using spiral drawings, with a focus on the impact of data augmentation techniques. We compare the accuracy of Vision Transformer (ViT) with K-Nearest Neighbors (KNN), Convolutional Neural Networks (CNN) with Support Vector Machines (SVM), and Residual Neural Networks (ResNet-50) with Logistic Regression, evaluating their performance on both augmented and non-augmented data. Our findings reveal that ViT with KNN, initially achieving 96.77% accuracy on unaugmented data, experienced a notable decline across all augmentation techniques, suggesting it relies heavily on global patterns in spiral drawings. In contrast, ResNet-50 with Logistic Regression showed consistent improvement with data augmentation, reaching 93.55% accuracy when rotation and flipping techniques were applied. These results highlight that hybrid models respond differently to augmentation, and careful selection of augmentation strategies is necessary for optimizing model performance. Our study provides important insights into the development of reliable diagnostic tools for early PD detection, emphasizing the need for appropriate augmentation techniques in medical image analysis. Full article

Objectives: The purpose of this study was to develop a deep learning algorithm capable of diagnosing radicular cysts in the lower jaw on panoramic radiographs. Materials and Methods: In this study, we conducted a comprehensive analysis of 138 radicular cysts and 100 normal panoramic radiographs collected from 2013 to 2023 at Clinical Hospital Dubrava. The images were annotated by a team comprising a radiologist and a maxillofacial surgeon, utilizing the GNU Image Manipulation Program. Furthermore, the dataset was enriched through the application of various augmentation techniques to improve its robustness. The evaluation of the algorithm’s performance and a deep dive into its mechanics were achieved using performance metrics and EigenCAM maps. Results: In the task of diagnosing radicular cysts, the initial algorithm performance—without the use of augmentation techniques—yielded the following scores: precision at 85.8%, recall at 66.7%, mean average precision (mAP)@50 threshold at 70.9%, and mAP@50-95 thresholds at 60.2%. The introduction of image augmentation techniques led to the precision of 74%, recall of 77.8%, mAP@50 threshold to 89.6%, and mAP@50-95 thresholds of 71.7, respectively. Also, the precision and recall were transformed into F1 scores to provide a balanced evaluation of model performance. The weighted function of these metrics determined the overall efficacy of our models. In our evaluation, non-augmented data achieved F1 scores of 0.750, while augmented data achieved slightly higher scores of 0.758. Conclusion: Our study underscores the pivotal role that deep learning is poised to play in the future of oral and maxillofacial radiology. Furthermore, the algorithm developed through this research demonstrates a capability to diagnose radicular cysts accurately, heralding a significant advancement in the field. Full article

The dicistrovirus intergenic (IGR) IRES uses the most streamlined translation initiation mechanism: the IRES recruits ribosomes directly without using protein factors and initiates translation from a non-AUG codon. Several subtypes of dicistroviruses IRES have been identified; typically, the IRESs adopt two -to three overlapping pseudoknots with key stem-loop and unpaired regions that interact with specific domains of the ribosomal 40S and 60S subunits to direct translation. We previously predicted an atypical IGR IRES structure and a potential -1 programmed frameshift (-1 FS) signal within the genome of the whitefly Bemisia-associated dicistrovirus 2 (BaDV-2). Here, using bicistronic reporters, we demonstrate that the predicted BaDV-2 -1 FS signal can drive -1 frameshifting in vitro via a slippery sequence and a downstream stem-loop structure that would direct the translation of the viral RNA-dependent RNA polymerase. Moreover, the predicted BaDV-2 IGR can support IRES translation in vitro but does so through a mechanism that is not typical of known factorless dicistrovirus IGR IRES mechanisms. Using deletion and mutational analyses, the BaDV-2 IGR IRES is mapped within a 140-nucleotide element and initiates translation from an AUG codon. Moreover, the IRES does not bind directly to purified ribosomes and is sensitive to eIF2 and eIF4A inhibitors NSC1198983 and hippuristanol, respectively, indicating an IRES-mediated factor-dependent mechanism. Biophysical characterization suggests the BaDV-2 IGR IRES contains several stem-loops; however, mutational analysis suggests a model whereby the IRES is unstructured or adopts distinct conformations for translation initiation. In summary, we have provided evidence of the first -1 FS frameshifting signal and a novel factor-dependent IRES mechanism in this dicistrovirus family, thus highlighting the diversity of viral RNA-structure strategies to direct viral protein synthesis. Full article

Non-canonical translation mechanisms have been described for many viral RNAs. In the case of several plant viruses, their protein synthesis is controlled by RNA elements in their genomic 3′-ends that are able to enhance cap-independent translation (3′-CITE). The proposed general mechanism of 3′-CITEs includes their binding to eukaryotic translation initiation factors (eIFs) that reach the 5′-end and AUG start codon through 5′-3′-UTR-interactions. It was previously shown that cucurbit aphid-borne yellows virus (CABYV) has a 3′-CITE, which varies in sequence and structure depending on the phylogenetic group to which the isolate belongs, possibly as a result of adaptation to the different geographical regions. In this work, the cap-independent translation mechanisms of two CABYV 3′-CITEs belonging to the Mediterranean (CMTE) and Asian (CXTE) groups, respectively, were studied. In vivo cap-independent translation assays show that these 3′-CITEs require the presence of the CABYV short genomic 5′-UTR with at least 40% adenines in cis and an accessible 5′-end for its activity. Additionally, they suggest that the eIF4E-independent CABYV 3′-CITE activities may not require either eIF4A or the eIF4F complex, but may depend on eIF4G and PABP. By pulling down host proteins using RNA baits containing both 5′- and 3′-CABYV-UTRs, 80 RNA binding proteins were identified. These interacted preferentially with either CMTE, CXTE, or both. One of these proteins, specifically interacting with the RNA containing CMTE, was HSP70.2. Preliminary results suggested that HSP70.2 may be involved in CMTE- but not CXTE-mediated cap-independent translation activity. Full article

The premutation of the fragile X messenger ribonucleoprotein 1 (FMR1) gene is characterized by an expansion of the CGG trinucleotide repeats (55 to 200 CGGs) in the 5’ untranslated region and increased levels of FMR1 mRNA. Molecular mechanisms leading to fragile X-premutation-associated conditions (FXPAC) include cotranscriptional R-loop formations, FMR1 mRNA toxicity through both RNA gelation into nuclear foci and sequestration of various CGG-repeat-binding proteins, and the repeat-associated non-AUG (RAN)-initiated translation of potentially toxic proteins. Such molecular mechanisms contribute to subsequent consequences, including mitochondrial dysfunction and neuronal death. Clinically, premutation carriers may exhibit a wide range of symptoms and phenotypes. Any of the problems associated with the premutation can appropriately be called FXPAC. Fragile X-associated tremor/ataxia syndrome (FXTAS), fragile X-associated primary ovarian insufficiency (FXPOI), and fragile X-associated neuropsychiatric disorders (FXAND) can fall under FXPAC. Understanding the molecular and clinical aspects of the premutation of the FMR1 gene is crucial for the accurate diagnosis, genetic counseling, and appropriate management of affected individuals and families. This paper summarizes all the known problems associated with the premutation and documents the presentations and discussions that occurred at the International Premutation Conference, which took place in New Zealand in 2023. Full article

Objectives: to evaluate whether hospitalist co-management would lead to improved outcomes and value in patients undergoing urethroplasty (UPL) with a single surgeon for urethral stricture disease (USD). Material: A co-management model with hospitalists was introduced in August 2019 for all patients undergoing UPL for USD with a single surgeon in a United States teaching center. The hospitalist worked closely with the urologic surgeon and the support staff. The hospitalist managed post-operative concerns, such as pain and comorbidities, as well as conducted rounds with the urological team for disposition planning and addressing interdisciplinary needs. Retrospective analysis compared a 42-month period before initiation of co-management (Jan 2016–July 2019) with a 32-month period after initiation (Aug 2019–March 2022). Outcomes assessed were recurrence of stricture, complications, length of stay, readmission, and emergency room visits. Results: A total of 135 patients (71 surgeon-managed, 64 co-managed) underwent urethroplasty from January 2016 to March 2022. Hospitalist co-management did not affect complications, length of stay, readmission, and emergency room visits. Accounting for confounding variables using multivariable analysis, no factors were independently associated with recurrence. There were no demographic, comorbidity, or American Society of Anesthesiologists (ASA) score differences between the two groups. Conclusions: This study suggests that hospitalist care for patients undergoing urethroplasty may be non-inferior to surgeon care, based on similar outcomes between the two groups. There were no significant differences in the total length of stay or blood pressure readings, and the complication rates and hospital readmission rates were also similar. Full article

Viruses are obligate parasites that only undergo genomic replication in their host organisms. ORF3a, a newly identified non-AUG-initiated ORF encoded by members of the genus Polerovirus, is required for long-distance movement in plants. However, its interactions with host proteins still remain unclear. Here, we used Brassica yellows virus (BrYV)-P3a as bait to screen a plant split-ubiquitin-based membrane yeast two-hybrid (MYTH) cDNA library to explain the functional role of P3a in viral infections. In total, 138 genes with annotations were obtained. Bioinformatics analyses revealed that the genes from carbon fixation in photosynthetic, photosynthesis pathways, and MAPK signaling were affected. Furthermore, Arabidopsis thaliana purine permease 14 (AtPUP14), glucosinolate transporter 1 (AtGTR1), and nitrate transporter 1.7 (AtNRT1.7) were verified to interact with P3a in vivo. P3a and these three interacting proteins mainly co-localized in the cytoplasm. Expression levels of AtPUP14, AtGTR1, and AtNRT1.7 were significantly reduced in response to BrYV during the late stages of viral infection. In addition, we characterized the roles of AtPUP14, AtGTR1, and AtNRT1.7 in BrYV infection in A. thaliana using T-DNA insertion mutants, and the pup14, gtr1, and nrt1.7 mutants influenced BrYV infection to different degrees. Full article

p53 is the most commonly mutated gene in human cancers. Two fundamental reasons for this are its long protein isoforms protect from cancer, while its shorter C-terminal isoforms can support cancer and metastasis. Previously, we have shown that the Δ160p53 protein isoform enhances survival and the invasive character of cancer cells. Here, we identified a translation initiation site nine codons downstream of codon 160—the known initiation codon for the translation of Δ160p53—that is recognized by the translation machinery. When translation failed to initiate from AUG160 due to mutation, it initiated from AUG169 instead, producing similar levels of a similar protein, Δ169p53, which promoted cell survival as efficiently as Δ160p53 following DNA damage. Interestingly, almost all mammalian species with an orthologue to human AUG160 also possess one for AUG169, while none of the non-mammalian species lacking AUG160 have AUG169, even if that region of the p53 gene is well conserved. In view of our findings, we do not believe that Δ169p53 acts as a different p53 protein isoform; instead, we propose that the double translation initiation site strengthens the translation of these products with a critical role in cell homeostasis. Future studies will help verify if this is a more general mechanism for the expression of essential proteins in mammals. Full article

Objectives: The present systematic review and meta-analysis aims to analyse the clinical performance of short compared to longer implants inserted in sites without the need for bone augmentation. Methods: The protocol of the present PRISMA-driven meta-analysis was registered on PROSPERO (CRD42021264781). Electronic and manual searches were performed up to January 2022. All Randomized Controlled Trials (RCTs) comparing short (≤6 mm) to longer (≥8.5 mm) implants placed in non-atrophic and non-augmented sites were included. The quality of the included studies was assessed using the Cochrane risk of bias tool for randomized clinical trials (RoB 2) and the quality of evidence was determined with the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) approach. A meta-analysis was performed on implant survival rate, marginal bone level change (MBLc), and technical and biological complications at the available follow-up time points. The power of the meta-analytic findings was determined by trial sequential analysis (TSA). Results: From 1485 initial records, 13 articles were finally included. No significant difference was found in the survival rate between short and long implant at any follow-up (moderate quality of evidence). Significantly more bone loss for long implants at 1 and 5 years from implant placement and more technical complications with short implants at 10 years were found. No other significant inter-group differences in terms of MBLc and biological complications were detected. Conclusions: Moderate evidence exists suggesting that short implants perform as well as longer ones in the rehabilitation of edentulous sites without the need for bone augmentation. Further long-term, well-designed RCTs, however, are still needed to provide specific evidence-based clinical recommendations for an extended use of short implants in non-atrophic sites. Full article

RNA toxicity contributes to diseases caused by anomalous nucleotide repeat expansions. Recent work demonstrated RNA-based toxicity from repeat-associated, non-AUG-initiated translation (RAN translation). RAN translation occurs around long nucleotide repeats that form hairpin loops, allowing for translation initiation in the absence of a start codon that results in potentially toxic, poly-amino acid repeat-containing proteins. Discovered in Spinocerebellar Ataxia Type (SCA) 8, RAN translation has been documented in several repeat-expansion diseases, including in the CAG repeat-dependent polyglutamine (polyQ) disorders. The ATXN3 gene, which causes SCA3, also known as Machado–Joseph Disease (MJD), contains a CAG repeat that is expanded in disease. ATXN3 mRNA possesses features linked to RAN translation. In this paper, we examined the potential contribution of RAN translation to SCA3/MJD in Drosophila by using isogenic lines that contain homomeric or interrupted CAG repeats. We did not observe unconventional translation in fly neurons or glia. However, our investigations indicate differential toxicity from ATXN3 protein-encoding mRNA that contains pure versus interrupted CAG repeats. Additional work suggests that this difference may be due in part to toxicity from homomeric CAG mRNA. We conclude that Drosophila is not suitable to model RAN translation for SCA3/MJD, but offers clues into the potential pathogenesis stemming from CAG repeat-containing mRNA in this disorder. Full article

ATP-binding cassette subfamily E member 1 (ABCE1) belongs to the ABC protein family of transporters; however, it does not behave as a drug transporter. Instead, ABCE1 actively participates in different stages of translation and is also associated with oncogenic functions. Ribosome profiling analysis in colorectal cancer cells has revealed a high ribosome occupancy in the human ABCE1 mRNA 5′-leader sequence, indicating the presence of translatable upstream open reading frames (uORFs). These cis-acting translational regulatory elements usually act as repressors of translation of the main coding sequence. In the present study, we dissect the regulatory function of the five AUG and five non-AUG uORFs identified in the human ABCE1 mRNA 5′-leader sequence. We show that the expression of the main coding sequence is tightly regulated by the ABCE1 AUG uORFs in colorectal cells. Our results are consistent with a model wherein uORF1 is efficiently translated, behaving as a barrier to downstream uORF translation. The few ribosomes that can bypass uORF1 (and/or uORF2) must probably initiate at the inhibitory uORF3 or uORF5 that efficiently repress translation of the main ORF. This inhibitory property is slightly overcome in conditions of endoplasmic reticulum stress. In addition, we observed that these potent translation-inhibitory AUG uORFs function equally in cancer and in non-tumorigenic colorectal cells, which is consistent with a lack of oncogenic function. In conclusion, we establish human ABCE1 as an additional example of uORF-mediated translational regulation and that this tight regulation contributes to control ABCE1 protein levels in different cell environments. Full article

Non-coding RNAs (ncRNAs) are essential players in many cellular processes, from normal development to oncogenic transformation. Initially, ncRNAs were defined as transcripts that lacked an open reading frame (ORF). However, multiple lines of evidence suggest that certain ncRNAs encode small peptides of less than 100 amino acids. The sequences encoding these peptides are known as small open reading frames (smORFs), many initiating with the traditional AUG start codon but terminating with atypical stop codons, suggesting a different biogenesis. The ncRNA-encoded peptides (ncPEPs) are gradually becoming appreciated as a new class of functional molecules that contribute to diverse cellular processes, and are deregulated in different diseases contributing to pathogenesis. As multiple publications have identified unique ncPEPs, we appreciated the need for assembling a new web resource that could gather information about these functional ncPEPs. We developed FuncPEP, a new database of functional ncRNA encoded peptides, containing all experimentally validated and functionally characterized ncPEPs. Currently, FuncPEP includes a comprehensive annotation of 112 functional ncPEPs and specific details regarding the ncRNA transcripts that encode these peptides. We believe that FuncPEP will serve as a platform for further deciphering the biologic significance and medical use of ncPEPs. The link for FuncPEP database can be found at the end of the Introduction Section. Full article

Initiation of protein synthesis in eukaryotes is a complex process requiring more than 12 different initiation factors, comprising over 30 polypeptide chains. The functions of many of these factors have been established in great detail; however, the precise role of some of them and their mechanism of action is still not well understood. Eukaryotic initiation factor 2A (eIF2A) is a single chain 65 kDa protein that was initially believed to serve as the functional homologue of prokaryotic IF2, since eIF2A and IF2 catalyze biochemically similar reactions, i.e., they stimulate initiator Met-tRNA_i binding to the small ribosomal subunit. However, subsequent identification of a heterotrimeric 126 kDa factor, eIF2 (α,β,γ) showed that this factor, and not eIF2A, was primarily responsible for the binding of Met-tRNA_i to 40S subunit in eukaryotes. It was found however, that eIF2A can promote recruitment of Met-tRNA_i to 40S/mRNA complexes under conditions of inhibition of eIF2 activity (eIF2α-phosphorylation), or its absence. eIF2A does not function in major steps in the initiation process, but is suggested to act at some minor/alternative initiation events such as re-initiation, internal initiation, or non-AUG initiation, important for translational control of specific mRNAs. This review summarizes our current understanding of the eIF2A structure and function. Full article