Exploring functional conservation in silico: a new machine learning approach to RNA-editing.

Around 50 years ago, molecular biology opened the path to understand changes in forms, adaptations, complexity, or the basis of human diseases through myriads of reports on gene birth, gene duplication, gene expression regulation, and splicing regulation, among other relevant mechanisms behind gene function. Here, with the advent of big data and artificial intelligence (AI), we focus on an elusive and intriguing mechanism of gene function regulation, RNA editing, in which a single nucleotide from an RNA molecule is changed, with a remarkable impact in the increase of the complexity of the transcriptome and proteome. We present a new generation approach to assess the functional conservation of the RNA-editing targeting mechanism using two AI learning algorithms, random forest (RF) and bidirectional long short-term memory (biLSTM) neural networks with an attention layer. These algorithms, combined with RNA-editing data coming from databases and variant calling from same-individual RNA and DNA-seq experiments from different species, allowed us to predict RNA-editing events using both primary sequence and secondary structure. Then, we devised a method for assessing conservation or divergence in the molecular mechanisms of editing completely in silico: the cross-testing analysis. This novel method not only helps to understand the conservation of the editing mechanism through evolution but could set the basis for achieving a better understanding of the adenosine-targeting mechanism in other fields.

Amphioxus functional genomics and the origins of vertebrate gene regulation.

Vertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that have been sculpted by two whole-genome duplications. Here we sequence the genome of the Mediterranean amphioxus (Branchiostoma lanceolatum) and characterize DNA methylation, chromatin accessibility, histone modifications and transcriptomes across multiple developmental stages and adult tissues to investigate the evolution of the regulation of the chordate genome. Comparisons with vertebrates identify an intermediate stage in the evolution of differentially methylated enhancers, and a high conservation of gene expression and its cis-regulatory logic between amphioxus and vertebrates that occurs maximally at an earlier mid-embryonic phylotypic period. We analyse regulatory evolution after whole-genome duplications, and find that-in vertebrates-over 80% of broadly expressed gene families with multiple paralogues derived from whole-genome duplications have members that restricted their ancestral expression, and underwent specialization rather than subfunctionalization. Counter-intuitively, paralogues that restricted their expression increased the complexity of their regulatory landscapes. These data pave the way for a better understanding of the regulatory principles that underlie key vertebrate innovations.

Medical staff dose estimation during pediatric cardiac interventional procedures.

The purpose of this study is to evaluate the occupational doses (eye lens, extremities and whole body) in paediatric cardiac interventional and diagnostic catheterization procedures performed in a paediatric reference hospital located in Recife, Pernambuco. For eye lens dosimetry, the results show that the left eye receives a higher dose than the right eye, and there is a small difference between the doses received during diagnostic (D) and therapeutic (T) procedures. The extrapolated annual values for the most exposed eye are close to the annual limit. For doses to the hands, it was observed that in a significant number of procedures (37 out of 45 therapeutic procedures, or 82%) at least one hand of the physician was exposed to the primary beam. During diagnostic procedures, the physician's hand was in the radiation field in 11 of the 17 catheterization procedures (65%). This resulted in a 10-fold increase in dose to the hands. The results underscore the need for optimization of radiation safety and continued efforts to engage staff in a radiation safety culture.

Planarian cell number depends on blitzschnell, a novel gene family that balances cell proliferation and cell death.

Control of cell number is crucial to define body size during animal development and to restrict tumoral transformation. The cell number is determined by the balance between cell proliferation and cell death. Although many genes are known to regulate those processes, the molecular mechanisms underlying the relationship between cell number and body size remain poorly understood. This relationship can be better understood by studying planarians, flatworms that continuously change their body size according to nutrient availability. We identified a novel gene family, blitzschnell (bls), that consists of de novo and taxonomically restricted genes that control cell proliferation:cell death ratio. Their silencing promotes faster regeneration and increases cell number during homeostasis. Importantly, this increase in cell number leads to an increase in body size only in a nutrient-rich environment; in starved planarians, silencing results in a decrease in cell size and cell accumulation that ultimately produces overgrowths. bls expression is downregulated after feeding and is related to activity of the insulin/Akt/mTOR network, suggesting that the bls family evolved in planarians as an additional mechanism for restricting cell number in nutrient-fluctuating environments.

Deficiency of the ywhaz gene, involved in neurodevelopmental disorders, alters brain activity and behaviour in zebrafish.

Genetic variants in YWHAZ contribute to psychiatric disorders such as autism spectrum disorder and schizophrenia, and have been related to an impaired neurodevelopment in humans and mice. Here, we have used zebrafish to investigate the mechanisms by which YWHAZ contributes to neurodevelopmental disorders. We observed that ywhaz expression was pan-neuronal during developmental stages and restricted to Purkinje cells in the adult cerebellum, cells that are described to be reduced in number and size in autistic patients. We then performed whole-brain imaging in wild-type and ywhaz CRISPR/Cas9 knockout (KO) larvae and found altered neuronal activity and connectivity in the hindbrain. Adult ywhaz KO fish display decreased levels of monoamines in the hindbrain and freeze when exposed to novel stimuli, a phenotype that can be reversed with drugs that target monoamine neurotransmission. These findings suggest an important role for ywhaz in establishing neuronal connectivity during development and modulating both neurotransmission and behaviour in adults.

CERKL, a retinal dystrophy gene, regulates mitochondrial function and dynamics in the mammalian retina.

The retina is a highly active metabolic organ that displays a particular vulnerability to genetic and environmental factors causing stress and homeostatic imbalance. Mitochondria constitute a bioenergetic hub that coordinates stress response and cellular homeostasis, therefore structural and functional regulation of the mitochondrial dynamic network is essential for the mammalian retina. CERKL (ceramide kinase like) is a retinal degeneration gene whose mutations cause Retinitis Pigmentosa in humans, a visual disorder characterized by photoreceptors neurodegeneration and progressive vision loss. CERKL produces multiple isoforms with a dynamic subcellular localization. Here we show that a pool of CERKL isoforms localizes at mitochondria in mouse retinal ganglion cells. The depletion of CERKL levels in CerklKD/KO(knockdown/knockout) mouse retinas cause increase of autophagy, mitochondrial fragmentation, alteration of mitochondrial distribution, and dysfunction of mitochondrial-dependent bioenergetics and metabolism. Our results support CERKL as a regulator of autophagy and mitochondrial biology in the mammalian retina.

Kinetics of Torque Teno virus DNA in stools may predict occurrence of acute intestinal graft versus host disease early after allogeneic hematopoietic stem cell transplantation.

Torque Teno virus (TTV) DNA load in blood may act as a marker of immune competence after allogeneic hematopoietic stem cell transplant recipients (allo-HSCT). Conflicting data have been reported as to the value of this biomarker for anticipating acute Graft versus host disease (aGvHD) occurrence. Here, we hypothesized that quantitation of TTV DNA load in stool specimens early after allo-HSCT could be used to identify patients at high risk of acute intestinal graft versus host disease (aIGvHD). In this prospective two-center study, we recruited a total of 83 nonconsecutive adult patients undergoing allo-HSCT. The study period comprised the first 120 days after allo-HSCT. TTV DNA was quantitated in paired stool samples collected at a median of 2 days prior to cell infusion and at a median of 14 days after allo-HSCT by real-time PCR. Thirty-seven patients developed aGVHD, of whom 25 had aIGVHD (diagnosed at a median of 42 days after allo-HSCT). Median TTV DNA load values in posttransplant stools specimens were comparable (P = .34) in patients with or without subsequent aIGvHD; nevertheless, a falling trajectory (decrease in TTV DNA load >0.5 log10 copies/0.1 g) in paired pretransplant and posttransplant specimens was independently associated with the occurrence of aIGvHD (OR, 5.2; 95% CI, 1.3-21.3; P = .02). Notably, displaying a rising trajectory had a negative predictive value of 87.5% for aIGvHD. In summary, in this hypothesis-generating study, we suggest that the decrease in TTV DNA load from baseline in stool specimens may identify patients at risk of aIGVHD.

Mutation of amphioxus Pdx and Cdx demonstrates conserved roles for ParaHox genes in gut, anus and tail patterning.

BACKGROUND: The homeobox genes Pdx and Cdx are widespread across the animal kingdom and part of the small ParaHox gene cluster. Gene expression patterns suggest ancient roles for Pdx and Cdx in patterning the through-gut of bilaterian animals although functional data are available for few lineages. To examine evolutionary conservation of Pdx and Cdx gene functions, we focus on amphioxus, small marine animals that occupy a pivotal position in chordate evolution and in which ParaHox gene clustering was first reported. RESULTS: Using transcription activator-like effector nucleases (TALENs), we engineer frameshift mutations in the Pdx and Cdx genes of the amphioxus Branchiostoma floridae and establish mutant lines. Homozygous Pdx mutants have a defect in amphioxus endoderm, manifest as loss of a midgut region expressing endogenous GFP. The anus fails to open in homozygous Cdx mutants, which also have defects in posterior body extension and epidermal tail fin development. Treatment with an inverse agonist of retinoic acid (RA) signalling partially rescues the axial and tail fin phenotypes indicating they are caused by increased RA signalling. Gene expression analyses and luciferase assays suggest that posterior RA levels are kept low in wild type animals by a likely direct transcriptional regulation of a Cyp26 gene by Cdx. Transcriptome analysis reveals extensive gene expression changes in mutants, with a disproportionate effect of Pdx and Cdx on gut-enriched genes and a colinear-like effect of Cdx on Hox genes. CONCLUSIONS: These data reveal that amphioxus Pdx and Cdx have roles in specifying middle and posterior cell fates in the endoderm of the gut, roles that likely date to the origin of Bilateria. This conclusion is consistent with these two ParaHox genes playing a role in the origin of the bilaterian through-gut with a distinct anus, morphological innovations that contributed to ecological change in the Cambrian. In addition, we find that amphioxus Cdx promotes body axis extension through a molecular mechanism conserved with vertebrates. The axial extension role for Cdx dates back at least to the origin of Chordata and may have facilitated the evolution of the post-anal tail and active locomotion in chordates.

Sclerosing angiomatoid nodular transformation of the spleen. A case report.

A 57 year old woman presenting with heartburn and a one month history of epigastric abdominal pain and left hypochondrium pain. After conducting an ultrasound scan and a CT scan, a low attenuation lesion in the spleen was found, and the definitive diagnosis was sclerosing angiomatoid nodular transformation of the spleen (STANT) which was based on a splenectomy and a pathologic study. SANT is a benign rare vascular disease consisting of proliferation of angiomatoid/vascular nodules which predominantly affects women aged 27 to 68. It is usually detected as a coincidental finding in asymptomatic patients. The presumptive diagnosis is established by imaging tests, especially CT and MR; and the final diagnosis is as well established on the basis of pathology after a splenectomy.

Biplane interventional pediatric system with cone-beam CT: dose and image quality characterization for the default protocols.

The aim of this study was to assess image quality and radiation dose of a biplane angiographic system with cone-beam CT (CBCT) capability tuned for pediatric cardiac procedures. The results of this study can be used to explore dose reduction techniques. For pulsed fluoroscopy and cine modes, polymethyl methacrylate phantoms of various thicknesses and a Leeds TOR 18-FG test object were employed. Various fields of view (FOV) were selected. For CBCT, the study employed head and body dose phantoms, Catphan 504, and an anthropomorphic cardiology phantom. The study also compared two 3D rotational angiography protocols. The entrance surface air kerma per frame increases by a factor of 3-12 when comparing cine and fluoroscopy frames. The biggest difference in the signal-to- noise ratio between fluoroscopy and cine modes occurs at FOV 32 cm because fluoroscopy is acquired at a 1440 × 1440 pixel matrix size and in unbinned mode, whereas cine is acquired at 720 × 720 pixels and in binned mode. The high-contrast spatial resolution of cine is better than that of fluoroscopy, except for FOV 32 cm, because fluoroscopy mode with 32 cm FOV is unbinned. Acquiring CBCT series with a 16 cm head phantom using the standard dose protocol results in a threefold dose increase compared with the low-dose protocol. Although the amount of noise present in the images acquired with the low-dose protocol is much higher than that obtained with the standard mode, the images present better spatial resolution. A 1 mm diameter rod with 250 Hounsfield units can be distinguished in reconstructed images with an 8 mm slice width. Pediatric-specific protocols provide lower doses while maintaining sufficient image quality. The system offers a novel 3D imaging mode. The acquisition of CBCT images results in increased doses administered to the patients, but also provides further diagnostic information contained in the volumetric images. The assessed CBCT protocols provide images that are noisy, but with very good spatial resolution.

Regional Workshop on Optimization of Protection in Pediatric Interventional Radiology in Latin American and Caribbean Countries.

ABSTRACT: The purpose of this article is to describe the activities developed within the framework "Regional Workshop on Optimization of Protection in Pediatric Interventional Radiology in Latin American and Caribbean countries," developed between October 16th and 19th of the year 2023 in the city of San José, Costa Rica. The workshop was carried out as part of a joint work between the Pan American Health Organization (PAHO) and the World Health Organization (WHO), in cooperation with the International Atomic Energy Agency (IAEA). The main objective of the regional workshop was to gather the experiences and future work planning among participants in the Optimization of Protection in Pediatric Interventional Radiology in Latin America and the Caribbean (OPRIPALC) program. It involved professionals from 14 centers across 11 countries in the region, along with 4 experts from PAHO/WHO/IAEA. The work modalities during the workshop consisted of keynote presentations, individual presentations, group work, and general discussions. An online survey was carried out after the workshop, with the objective of knowing the opinion of the event participants and determining the impact and projection of the OPRIPALC program. During the workshop the centers had to present their experiences: the use of the DOLQA dose management system was presented and work was done on the consensus document on good practices. The activities, topics and organization of the workshop were valued positively by the participants. There is unanimity among the centers that the OPRIPALC program has had a positive impact and they wish to continue actively participating in the next biennium.

Influence of the antiscatter grid on dose and image quality in pediatric interventional cardiology X-ray systems.

OBJECTIVE: To present a methodology and experimental results to assess the influence, in terms of dose and image quality, of the antiscatter grid (AG) in a pediatric cardiology X-ray system. METHOD: Entrance surface air kerma and image quality, using a test object and different added thicknesses of polymethyl methacrylate (PMMA), for three different acquisition protocols, were measured with and without the AG, for fluoroscopy and cine modes. The image quality parameters, signal-to-noise ratio (SNR), high-contrast spatial resolution (HCSR) and two figures of merit (FOM) were evaluated. RESULTS: The average bucky factor values measured during this experiment were 1.99, 2.49, 2.85, and 3.30, respectively for 4, 8, 12, and 16 cm of PMMA. SNR variations do not appear to be relevant when removing the AG. However, the use of AG improves HCSR significantly. Imaging the test object with 4 cm of PMMA seems appropriate without the AG, but for 8 cm (equivalent to chest thicknesses of 12 cm) and greater thicknesses, a good image quality would require the use of AG. CONCLUSIONS: The AG should not be used for neonates and very young children with chest thicknesses equal to or less than 6 cm and weight less that 6 kg.

New Optimization Strategies on Radiation Protection in Fluoroscopy-Guided Interventional Procedures in Pediatrics.

The term fluoroscopically guided interventional procedure describes a clinical practice in medicine, where fluoroscopic systems are used to conduct diagnostic procedures or provide image guidance for therapeutic interventional procedures performed via percutaneous or other access routes [...].

Diagnostic Reference Levels in Interventional Pediatric Cardiology: Two-Year Experience in a Tertiary Referral Hospital in Latin America.

The goal of the present study was to propose the first local diagnostic reference levels (DRLs) for interventional pediatric cardiology procedures in a large hospital in Colombia. The data collection period was from April 2020 to July 2022. The local DRLs were calculated as the 3rd quartile of patient-dose distributions for the kerma-area product (Pka) values. The sample of collected clinical procedures (255) was divided into diagnostic and therapeutic procedures and grouped into five weight and five age bands. The Pka differences found between diagnostic and therapeutic procedures were statistically significant in all weight and age bands, except for the 1-5-year age group. The local DRLs for weight bands were 3.82 Gy·cm2 (<5 kg), 7.39 Gy·cm2 (5-<15 kg), 19.72 Gy·cm2 (15-<30 kg), 28.99 Gy·cm2 (30-<50 kg), and 81.71 Gy·cm2 (50-<80 kg), respectively. For age bands, the DRLs were 3.97 Gy·cm2 (<1 y), 9.94 Gy·cm2 (1-<5 y), 20.82 Gy·cm2 (5-<10 y), 58.00 Gy·cm2 (10-<16 y), and 31.56 Gy·cm2 (<16 y), respectively. In conclusion, when comparing our results with other existing DRL values, we found that they are similar to other centers and thus there is scope to continue optimizing the radiation dose values. This will contribute to establishing national DRLs for Colombia in the near future.

Local Diagnostic Reference Levels for Pediatric Interventional Cardiology Procedures in Argentina.

The aim of this work was to propose a preliminary local diagnostic reference levels (DRL) for pediatric interventional cardiology (PIC) procedures in Argentina, for different ranges of age and weight. This work has been conducted in the framework of the "Optimization of Protection in Pediatric Interventional Radiology in Latin America and the Caribbean" (OPRIPALC) program coordinated by the World Health Organization and the Pan American Health Organization in cooperation with the International Atomic Energy Agency to ensuring that radiation exposures of pediatric patients are the minimum necessary during fluoroscopy-guided interventional procedures. The local DRL values presented in this paper by weight group and age group were 7.1 Gy·cm2 (<5 kg), 10.7 Gy·cm2 (5-15 kg), 18.0 Gy·cm2 (15-30 kg), 15.9 Gy·cm2 (30-50 kg), and 28.2 Gy·cm2 (50-80 kg) and 5.3 Gy·cm2 (<1), 11.2 Gy·cm2 (1 to 5<), 19.6 Gy·cm2 (5 to 10<), and 21.4 Gy·cm2 (10 to 16<), respectively. Our dose results are among the values found in other international studies; however, there is great potential for dose optimization.

Optimization of Radiation Protection in Pediatric Interventional Radiology in Latin America and the Caribbean: Development, Advancements, Challenges and Achievements of the OPRIPALC Program.

This article presents the development, advancements, challenges and achievements of the "Optimization of Protection in Pediatric Interventional Radiology in Latin America and the Caribbean" (OPRIPALC) program. This international initiative is led by the World Health Organization, the Pan American Health Organization and the International Atomic Energy Agency. The main objectives of OPRIPALC are to foster a culture of radiological protection in pediatric interventions, enhance these procedures' quality, and define optimization strategies such as the use of diagnostic reference levels (DRLs). Currently, 33 centers from 12 countries participate actively in the program. Significant progress has been made towards the proposed objectives, overcoming the challenges posed by the COVID-19 pandemic. Through many virtual meetings for coordination, planning, training and follow-up, a comprehensive set of DRLs for both diagnostic and therapeutic procedures, categorized by weight and age, have been established and are in use. A consensus document on good practices is in the final stage of development. The program's continuation into at least a second phase is essential to address pending issues, including the integration of automatic dose management systems, the levels of occupational radiation doses, their correlation with pediatric patient doses, and strategies to reduce them.

Exacerbated response to oxidative stress in the Retinitis Pigmentosa CerklKD/KO mouse model triggers retinal degeneration pathways upon acute light stress.

The retina is particularly vulnerable to genetic and environmental alterations that generate oxidative stress and cause cellular damage in photoreceptors and other retinal neurons, eventually leading to cell death. CERKL (CERamide Kinase-Like) mutations cause Retinitis Pigmentosa and Cone-Rod Dystrophy in humans, two disorders characterized by photoreceptor degeneration and progressive vision loss. CERKL is a resilience gene against oxidative stress, and its overexpression protects cells from oxidative stress-induced apoptosis. Besides, CERKL contributes to stress granule-formation and regulates mitochondrial dynamics in the retina. Using the CerklKD/KO albino mouse model, which recapitulates the human disease, we aimed to study the impact of Cerkl knockdown on stress response and activation of photoreceptor death mechanisms upon light/oxidative stress. After acute light injury, we assessed immediate or late retinal stress response, by combining both omic and non-omic approaches. Our results show that Cerkl knockdown increases ROS levels and causes a basal exacerbated stress state in the retina, through alterations in glutathione metabolism and stress granule production, overall compromising an adequate response to additional oxidative damage. As a consequence, several cell death mechanisms are triggered in CerklKD/KO retinas after acute light stress. Our studies indicate that Cerkl gene is a pivotal player in regulating light-challenged retinal homeostasis and shed light on how mutations in CERKL lead to blindness by dysregulation of the basal oxidative stress response in the retina.

Pilot program on patient dosimetry in pediatric interventional cardiology in Chile.

PURPOSE: The aim of this study was to present the results of a pilot program on patient dosimetry carried out in Chile during the last 5 yr, using a biplane x-ray angiography system settled for pediatrics. This research was conducted in Latin America under the auspices of the International Atomic Energy Agency (IAEA) supporting programs on radiological protection (RP) of patients. METHODS: Patient age, gender, weight, height, number of cine series, total number of cine frames, fluoroscopy time, and two dosimetric quantities [air kerma-area product (P(ka)) and cumulative dose (CD) at the patient entrance reference point] were recorded for each procedure. RESULTS: The study includes 544 patients grouped into four age groups. The distributions by age group were 150 for <1 yr; 203 for 1 to <5 yr; 97 for 5 to <10 yr; and 94 for 10 to <16 yr. Median values of P(ka) and CD for the four age groups were 0.94, 1.46, 2.13, and 5.03 Gy cm(2) and 23.9, 26.8, 33.5, and 51.6 mGy, respectively. No significant statistical differences were found between diagnostic and therapeutic procedures. A moderate correlation (r = 0.64) was seen between P(ka) and patient weight. CONCLUSIONS: The dose values reported in this paper were lower than those published in the previous work for the same age groups as a result of the optimization actions carried out by cardiologists and medical physicists with the support of the IAEA. Methodology and results will be used as a starting point for a wider survey in Chile and Latin America with the goal to obtain regional diagnostic reference levels as recently recommended by the International Commission on Radiological Protection for interventional procedures.

Influence of image metrics when assessing image quality from a test object in cardiac X-ray systems: Part II.

The images generated in modern IC laboratories are created with high-quality standard (1,024×1,024 pixels and 10-12 bits/pixel) enabling cardiologists to perform interventions in the best conditions. But these images are in most of the cases archived in a basic quality standard (512×512 pixels and 8 bits/pixel). The purpose of this work is to complete the research developed in a previous paper and analyze the influence of the matrix size and the bit depth reduction on the image quality acquired on a polymethylmethacrylate (PMMA) phantom with a test object. The variation in contrast-to-noise ratio (CNR) and high contrast spatial resolution (HCSR) were investigated when the matrix size and the bit depth were independently modified for different phantom thicknesses. These two image quality parameters did not suffer noticeable alterations under bits depth reduction from 10 to 8 bits. Such a result seems to imply that bits depth reduction could be used to reduce file sizes with a suitable algorithm and without losing perceptible image quality information. But when the matrix size was reduced from 1,024×1,024 to 512×512 pixels, a reduction from 17% to 25% in HCSR was noticed when changing phantom thickness, and an increase of 27% in CNR was observed. These findings should be taken into account and it would be wise to conduct further investigations in the field of clinical images.

Influence of image metrics when assessing image quality from a test object in cardiac X-ray systems.

Modern fluoroscopic systems used for invasive cardiology typically acquire digital images in a 1,024 × 1,024 × 12 bits. These images are maintained in the original format while they remain on the imaging system itself. However, images are usually stored using a reduced 512 × 512 × 8-bits format. This paper presents a method for digital analysis of test objects images. The results obtained using image-intensifier and flat-detector systems are given for the original and reduced matrices. Images were acquired using a test object (TO) and a range of polymethyl methacrylate (PMMA) thicknesses from 4 to 28 cm. Adult patient protocols were evaluated for 16-28 cm of PMMA using the image-intensifier system. Pediatric protocols were evaluated for 4-16 cm of PMMA using the flat-detector system. The TO contains disks of various thicknesses to evaluate low contrast sensitivity and a bar pattern to evaluate high-contrast spatial resolution (HCSR). All available fluoroscopic and cine modes were evaluated. Entrance surface air kerma was also measured. Signal-to-noise ratio (SNR) was evaluated using regions of interest (ROI). HCSR was evaluated by comparing the statistical analysis of a ROI placed over the image of the bar pattern against a reference ROI. For both systems, an improvement of approximately 20% was observed for the SNR on the reduced matrices. However, the HCSR parameter was substantially lower in the reduced metrics. Cardiologists should consider the clinical influence of reduced spatial resolution when using the archived images.