Search

Abstract Structure predictions have become invaluable tools, but viral proteins are absent from the EMBL/DeepMind AlphaFold database. Here, we provide proteome-wide structure predictions for all nine human herpesviruses and analyze them in depth with explicit scoring thresholds. By clustering these predictions into structural similarity groups, we identified new families, such as the HCMV UL112-113 cluster, which is conserved in alpha- and betaherpesviruses. A domain-level search found protein families consisting of subgroups with varying numbers of duplicated folds. Using large-scale structural similarity searches, we identified viral proteins with cellular folds, such as the HSV-1 US2 cluster possessing dihydrofolate reductase folds and the EBV BMRF2 cluster that might have emerged from cellular equilibrative nucleoside transporters. Our HerpesFolds database is available at https://www.herpesfolds.org/herpesfolds and displays all models and clusters through an interactive web interface. Here, we show that system-wide structure predictions can reveal homology between viral species and identify potential protein functions.

The impact of social media on teens' mental health and development raises the need for educational interventions that equip them with the knowledge and skills to cope with dangerous situations. In spite of the growing effort to expand social media literacy among youngsters, social media interventions still rely on conventional methods that tend to prioritize cognitive skills while overlooking important socio-emotional competencies. To bridge this gap and offer innovative solutions to social media education, this article presents the narrative scripts (NS) approach implemented in a learning technology environment that integrates pedagogical strategies of authentic learning, narratives, and scripted collaborative learning within a simulated educational social media platform. A longitudinal study with 370 high school students in urban schools in Barcelona (Spain) was designed to assess NS in an intervention to foster the development of social media self-protection skills. The findings demonstrated that NS supported the development of social media self-protection skills, while the students expressed positive perceptions of their overall learning experience. The intervention notably enhanced the socio-emotional competencies of responsible decision-making, self-awareness, and social awareness. This research makes a valuable contribution to the design and development of technology aimed at facilitating authentic learning experiences for social media education, with a specific focus on interventions targeting socio-emotional competencies.

IntroductionBuildings that constitute cultural heritage and that are the identity of a defined geographical area are increasingly being restored to offer the community historical places to enjoy. Often the restoration preserves the original structure and building materials, which are usually natural stones. In this study, a radioprotection protocol dedicated to this kind of built environment was proposed and validated.MethodsAfter identifying the two predominant types of building material stones (Rosso ammonitico and Pietra Serena), radiometric measurements for natural gamma-emitting radionuclides (Ra-226, Th-232, and K-40) and measurements of the emanation coefficient and calculation of the exhalation rate of radon gas were carried out.ResultsThe two types of stone have a content of natural radionuclides that do not exceed the levels recommended by the regulations. The difference between the two types of stone is of an order of magnitude indicating that the red ammonite has a greater radiological impact than the pietra serena.DiscussionThe results, in addition to ensuring the radioprotection of the population, highlighted the need to increase the number of this kind of investigations to implement scientific knowledge and serve the stakeholders involved.

BackgroundThere are increasing reports of the misuse of prescription psychostimulants for cognitive enhancement together with recreational cannabis. This raises a concern that chronic use of cannabis high in Δ9-THC may alter the sensitivity to amphetamines. In this exploratory study we hypothesized chronic exposure to Δ9-THC through vaporized cannabis would diminish the central nervous system (CNS) activity of Adderall.MethodsTo address this issue we exposed male and female mice to inhaled vaporized cannabis (10.3% Δ9-THC) or placebo for 30 min each day for ten consecutive days. After 24 h, mice were imaged fully awake for changes in BOLD signal following an IP injection of Adderall (60 µg) during the scanning session. After a 2-week washout, without any cannabis or placebo exposure, mice were again imaged and challenged with Adderall during the scanning session. The data were registered to a mouse 3D MRI atlas with 134 brain regions providing site-specific increases and decreases in global brain activity.ResultsMice exposed to cannabis when compared to placebo showed a decrease in brain activation to Adderall. The blunted Adderall response was characterized by a decrease in positive BOLD signal and increase in negative BOLD. The prefrontal cortex, accumbens, ventral pallidum, caudate/putamen, and thalamus were most affected. After a 2-week wash out there were no significant differences between the cannabis and placebo groups when challenged with Adderall.SummaryThis exploratory study shows that short, daily exposures to inhaled cannabis, something equivalent to recreational use, affects the sensitivity to the psychostimulant Adderall. The reduced Adderall effect on brain activity, particularly circuitry associated with dopaminergic signaling raises concerns about escalation in psychostimulant use.

Abstract WDR44 prevents ciliogenesis initiation by regulating RAB11-dependent vesicle trafficking. Here, we describe male patients with missense and nonsense variants within the WD40 repeats (WDR) of WDR44, an X-linked gene product, who display ciliopathy-related developmental phenotypes that we can model in zebrafish. The patient phenotypic spectrum includes developmental delay/intellectual disability, hypotonia, distinct craniofacial features and variable presence of brain, renal, cardiac and musculoskeletal abnormalities. We demonstrate that WDR44 variants associated with more severe disease impair ciliogenesis initiation and ciliary signaling. Because WDR44 negatively regulates ciliogenesis, it was surprising that pathogenic missense variants showed reduced abundance, which we link to misfolding of WDR autonomous repeats and degradation by the proteasome. We discover that disease severity correlates with increased RAB11 binding, which we propose drives ciliogenesis initiation dysregulation. Finally, we discover interdomain interactions between the WDR and NH2-terminal region that contains the RAB11 binding domain (RBD) and show patient variants disrupt this association. This study provides new insights into WDR44 WDR structure and characterizes a new syndrome that could result from impaired ciliogenesis.

The impact of common and rare variants in COVID-19 host genetics has been widely studied. In particular, in Fallerini et al. (Human genetics, 2022, 141, 147–173), common and rare variants were used to define an interpretable machine learning model for predicting COVID-19 severity. First, variants were converted into sets of Boolean features, depending on the absence or the presence of variants in each gene. An ensemble of LASSO logistic regression models was used to identify the most informative Boolean features with respect to the genetic bases of severity. After that, the Boolean features, selected by these logistic models, were combined into an Integrated PolyGenic Score (IPGS), which offers a very simple description of the contribution of host genetics in COVID-19 severity.. IPGS leads to an accuracy of 55%–60% on different cohorts, and, after a logistic regression with both IPGS and age as inputs, it leads to an accuracy of 75%. The goal of this paper is to improve the previous results, using not only the most informative Boolean features with respect to the genetic bases of severity but also the information on host organs involved in the disease. In this study, we generalize the IPGS adding a statistical weight for each organ, through the transformation of Boolean features into “Boolean quantum features,” inspired by quantum mechanics. The organ coefficients were set via the application of the genetic algorithm PyGAD, and, after that, we defined two new integrated polygenic scores (IPGSph1 and IPGSph2). By applying a logistic regression with both IPGS, (IPGSph2 (or indifferently IPGSph1) and age as inputs, we reached an accuracy of 84%–86%, thus improving the results previously shown in Fallerini et al. (Human genetics, 2022, 141, 147–173) by a factor of 10%.

Background: Erythrocyte Sedimentation Rate (ESR) is an easy test used to diagnose and monitor inflammatory and infectious diseases. The aim of this study was the evaluation of the performance of three ESR automated analyzers, VES-MATIC 5, CUBE 30 TOUCH, and MINI-CUBE, involving four Italian polyclinics in Rome, Siena, Como, and Arezzo, as well as inter-site variability assessment to detect possible device-dependent and operator-dependent influences. Methods: Accuracy analysis was carried out by analyzing the same samples with all three instruments and comparing them with the Westergren method. Precision was assessed with quality control material through intra-run and inter-run precision. Repeatability was estimated by reanalyzing fresh blood samples belonging to three ESR ranges (low, intermediate, and high) six times. Results: The results showed a strong correlation (Spearman coefficients R2) between the manual method and VES-MATIC 5 (0.978), CUBE 30 TOUCH (0.981), and MINI-CUBE (0.974). The accuracy of all clinics was excellent, with coefficients of variation (CVs) of less than 10% for all instruments. Repeatability confirmed an excellent level for all ESR ranges, with CVs below 10%. Conclusions: The study proved that all three automated instruments offer optimal performance for accuracy and precision and are suitable for both large and small facilities without influences of the laboratory environment.

Papillary thyroid cancer (PTC) is a common endocrine malignancy, and its incidence is reported to be constantly increasing. BRAF mutation is detected in approximately 44% of PTCs, and the most common BRAF mutation is thymine (T) to adenine (A) missense mutation in nucleotide 1796 (T1796A, V600E). Although BRAFV600E represents 95% of all BRAF mutations, uncommon BRAF mutations have been reported in thyroid carcinomas and represent an alternative mechanism of BRAF activation with unclear clinical significance. We report a novel non-V600E mutation (c.1799_1812delinsAT, p.V600_W604delinsD), identified preoperatively with next-generation sequencing (NGS) on the material obtained with fine-needle aspiration cytology (FNAC) performed on a thyroid nodule cytologically suspicious for malignancy in a 35-year-old male patient. The presence of this new variant of BRAF mutation was subsequently confirmed in the postoperative phase by direct Sanger sequencing. In conclusion, we report a new non-V600E variant previously undetected in papillary thyroid cancer. In addition, this case report shows that the NGS technique on cytological tissue allows to detect the presence of rare mutations, thus increasing the diagnostic specificity of molecular analysis.

The occurrence of an abdominal tumor invading the spinal canal and causing symptoms of epidural compression is rare in an infant, and exceptional at birth. Peripheral neuroblastic tumors are by far the most common cause. Emergency chemotherapy is commonly curative, though permanent sequelae are possible. Although other malignancies may be involved, no case of rhabdoid tumors at birth has been reported. We describe the case of a neonate who presented symptoms of spinal epidural compression at birth secondary to a rhabdoid tumor. As expected with this highly malignant tumor, the patient experienced a rapidly progressive clinical course and died within three months of diagnosis.

The Erythrocyte Sedimentation Rate (ESR) is a diagnostic estimator of systemic inflammation as a reflection of acute phase proteins circulating in the blood. The purpose of this manuscript is to evaluate the blood stability at room temperature (RT) and at 4 °C to avoid ESR diagnostic errors, as well as the accuracy of the VES-MATIC 5 analyzer. The ESR stability evaluation at RT for 24 h (4 h “T1”, 6 h “T2”, 8 h “T3”, 10 h “T4”, 24 h “T5”) and at 4 °C (24 h, 36 h, 48 h) was carried out using 635 total samples, starting with T0 (2 h of venipuncture). For method comparison, 164 patients were analyzed using VES-MATIC 5 and then the Westergren reference method. The sample at RT is established by a significant gradual decrease in correlation R = 0.99 (T0 vs. T1), R = 0.97 (T0 vs. T2), R = 0.92 (T0 vs. T3), R = 0.87 (T0 vs. T4), and R = 0.40 (T0 vs. T5). The stability at 4 °C after 24 h, 36 h, and 48 h showed a regression of R = 0.99, R = 0.97, and R = 0.95, respectively. Therefore, ESR measurements on RT samples beyond 6 h after collection cannot be carried out, but the ESR can be measured until 36 h for samples stored at 4 °C. Moreover, the VES-MATIC 5 accuracy performance compared to the Westergren method (R = 0.96) is confirmed.

Legius syndrome, commonly referred to as SPRED1‐related neurofibromatosis type 1‐like syndrome, is a rare autosomal dominant disorder characterized by café‐au‐lait macules, freckling, lipomas, macrocephaly, and heterogeneous neurodevelopmental manifestations, including a different degree of learning difficulties. Although a partial clinical overlap exists with neurofibromatosis type 1 (NF1), Legius syndrome is distinguished by its genetic etiology and the absence of neurofibromas, indicating an inherent lack of tumor risk. The SPRED1 gene encodes the Sprouty‐related protein with an EVH1 domain 1 (SPRED1), a negative regulator of the RAS‐MAPK signaling pathway with a crucial role in cellular growth and development. Despite various genetic variants and genomic deletions associated with Legius syndrome, the full genetic spectrum of this condition remains elusive. In this study, we investigated the underlying genetic etiology in a cohort of patients presenting with typical manifestations of Legius syndrome using a custom Next Generation Sequencing (NGS) panel and Multiplex Ligation‐Dependent Probe Amplification (MLPA) for NF1 and SPRED1. We identified 12 novel SPRED1 damaging variants segregating with the phenotype in all families. These rare variants affect conserved residues of the protein and are predicted damaging according to in silico tools. No clear genotype–phenotype correlations could be observed in the current cohort and previously reported patients, underscoring the heterogeneous genotype spectrum of this condition. Our findings expand the understanding of SPRED1 variants causing Legius syndrome and underscore the importance of comprehensively characterizing the genetic landscape of this disorder. Despite the absence of clear genotype–phenotype correlations, elucidating the genetic etiology of Legius syndrome is pertinent for facilitating accurate diagnosis, genetic counseling, and therapeutic interventions. [ABSTRACT FROM AUTHOR]

Structure predictions have become invaluable tools, but viral proteins are absent from the EMBL/DeepMind AlphaFold database. Here, we provide proteome-wide structure predictions for all nine human herpesviruses and analyze them in depth with explicit scoring thresholds. By clustering these predictions into structural similarity groups, we identified new families, such as the HCMV UL112-113 cluster, which is conserved in alpha- and betaherpesviruses. A domain-level search found protein families consisting of subgroups with varying numbers of duplicated folds. Using large-scale structural similarity searches, we identified viral proteins with cellular folds, such as the HSV-1 US2 cluster possessing dihydrofolate reductase folds and the EBV BMRF2 cluster that might have emerged from cellular equilibrative nucleoside transporters. Our HerpesFolds database is available at https://www.herpesfolds.org/herpesfolds and displays all models and clusters through an interactive web interface. Here, we show that system-wide structure predictions can reveal homology between viral species and identify potential protein functions. The nine human herpesviruses encode hundreds of genes, but the activity and function of many are unclear. Generating protein structure predictions of entire proteomes, the authors could infer the function of many so-far uncharacterized genes. [ABSTRACT FROM AUTHOR]

Introduction: Buildings that constitute cultural heritage and that are the identity of a defined geographical area are increasingly being restored to offer the community historical places to enjoy. Often the restoration preserves the original structure and building materials, which are usually natural stones. In this study, a radioprotection protocol dedicated to this kind of built environment was proposed and validated. Methods: After identifying the two predominant types of building material stones (Rosso ammonitico and Pietra Serena), radiometric measurements for natural gamma-emitting radionuclides (Ra-226, Th-232, and K-40) and measurements of the emanation coefficient and calculation of the exhalation rate of radon gas were carried out. Results: The two types of stone have a content of natural radionuclides that do not exceed the levels recommended by the regulations. The difference between the two types of stone is of an order of magnitude indicating that the red ammonite has a greater radiological impact than the pietra serena. Discussion: The results, in addition to ensuring the radioprotection of the population, highlighted the need to increase the number of this kind of investigations to implement scientific knowledge and serve the stakeholders involved. [ABSTRACT FROM AUTHOR]

Background: There are increasing reports of the misuse of prescription psychostimulants for cognitive enhancement together with recreational cannabis. This raises a concern that chronic use of cannabis high in Δ9-THC may alter the sensitivity to amphetamines. In this exploratory study we hypothesized chronic exposure to Δ9-THC through vaporized cannabis would diminish the central nervous system (CNS) activity of Adderall. Methods: To address this issue we exposed male and female mice to inhaled vaporized cannabis (10.3% Δ9-THC) or placebo for 30 min each day for ten consecutive days. After 24 h, mice were imaged fully awake for changes in BOLD signal following an IP injection of Adderall (60 µg) during the scanning session. After a 2-week washout, without any cannabis or placebo exposure, mice were again imaged and challenged with Adderall during the scanning session. The data were registered to a mouse 3D MRI atlas with 134 brain regions providing sitespecific increases and decreases in global brain activity. Results: Mice exposed to cannabis when compared to placebo showed a decrease in brain activation to Adderall. The blunted Adderall response was characterized by a decrease in positive BOLD signal and increase in negative BOLD. The prefrontal cortex, accumbens, ventral pallidum, caudate/putamen, and thalamus were most affected. After a 2-week wash out there were no significant differences between the cannabis and placebo groups when challenged with Adderall. Summary: This exploratory study shows that short, daily exposures to inhaled cannabis, something equivalent to recreational use, affects the sensitivity to the psychostimulant Adderall. The reduced Adderall effect on brain activity, particularly circuitry associated with dopaminergic signaling raises concerns about escalation in psychostimulant use. [ABSTRACT FROM AUTHOR]

Background: Erythrocyte Sedimentation Rate (ESR) is an easy test used to diagnose and monitor inflammatory and infectious diseases. The aim of this study was the evaluation of the performance of three ESR automated analyzers, VES-MATIC 5, CUBE 30 TOUCH, and MINI-CUBE, involving four Italian polyclinics in Rome, Siena, Como, and Arezzo, as well as inter-site variability assessment to detect possible device-dependent and operator-dependent influences. Methods: Accuracy analysis was carried out by analyzing the same samples with all three instruments and comparing them with the Westergren method. Precision was assessed with quality control material through intra-run and inter-run precision. Repeatability was estimated by reanalyzing fresh blood samples belonging to three ESR ranges (low, intermediate, and high) six times. Results: The results showed a strong correlation (Spearman coefficients R2) between the manual method and VES-MATIC 5 (0.978), CUBE 30 TOUCH (0.981), and MINI-CUBE (0.974). The accuracy of all clinics was excellent, with coefficients of variation (CVs) of less than 10% for all instruments. Repeatability confirmed an excellent level for all ESR ranges, with CVs below 10%. Conclusions: The study proved that all three automated instruments offer optimal performance for accuracy and precision and are suitable for both large and small facilities without influences of the laboratory environment. [ABSTRACT FROM AUTHOR]

Generative Artificial Intelligence (AI) is a rapidly expanding field that aims to develop machines capable of performing tasks that were previously considered unique to humans, such as learning, reasoning, problem-solving, and decision-making. The recent release of several tools based on AI (e.g. ChatGPT) has sparked debates on the potential of this technology and garnered widespread attention in the mainstream media.Using a socio-psychological approach, in three studies (total N = 410), we demonstrate that when faced with Generative AI’s ability to reproduce the complexity of human cognitive capabilities, participants reported significantly higher negative emotions than those in the control group. In turn, negative emotions elicited by a specific type of AI (e.g. generative AI) were associated to the perception of threat extended to AI technologies as a whole, understood as a threat to various aspects of human life, including jobs, resources, identity, uniqueness, and value.Our findings emphasise the importance of considering emotional and societal impacts when developing and deploying advanced AI technologies and implementing responsible guidelines to minimise adverse effects. As AI technology advances, addressing public concerns and regulating its usage is crucial for the benefit of society. To achieve this goal, collaboration between experts, policymakers, and the public is necessary. [ABSTRACT FROM AUTHOR]