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Motivation: The speed and accuracy of deep learning-based structure prediction algorithms make it now possible to perform in silico "pull-downs" to identify protein-protein interactions on a proteome-wide scale. However, on such a large scale, existing scoring algorithms are often insufficient to discriminate biologically relevant interactions from false positives. Results: Here, we introduce AlphaCRV, a Python package that helps identify correct interactors in a one-against-many AlphaFold screen by clustering, ranking, and visualizing conserved binding topologies, based on protein sequence and fold. Availability and implementation: AlphaCRV is a Python package for Linux, freely available at https://github.com/strubelab/AlphaCRV.

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BACKGROUND: Early infantile epileptic encephalopathy 25 (EIEE25) is a distinct type of neonatal epileptic encephalopathy caused by autosomal recessive mutations in the SLC13A5 gene. SLC13A5 encodes a transmembrane sodium/citrate cotransporter required for regulating citrate entry into cells. METHODS: Four families with recessively inherited epileptic encephalopathy were sequenced by clinically accredited laboratories using commercially available epilepsy gene panels. Patients were examined by a neurologist and were clinically diagnosed with infantile epileptic encephalopathy. RESULTS: We present four families with global developmental delay, intellectual disability, and defective tooth development with four novel homozygous mutations in SLC13A5. The neurological examination showed spastic quadriplegia with increased deep tendon reflexes. Brain magnetic resonance imaging showed nonspecific signal abnormality of the bilateral hemispheric white matter. Despite similar clinical features, the conditions were based on different molecular mechanisms acting on SLC13A5 (abnormal splicing, large-scale deletions, and tandem-residue insertion). CONCLUSIONS: Our results extend the landscape of autosomal recessive inherited homozygous mutations in SLC13A5 that cause a distinctive syndrome of severe neonatal epileptic encephalopathy. Our observations confirm the homogeneity of epileptic encephalopathy and dental abnormalities as a distinct clinical marker for EIEE25 despite the heterogeneous functional and mutational background.

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The COVID-19 pandemic, caused by SARS-CoV-2, has emphasized the necessity for scalable diagnostic workflows using locally produced reagents and basic laboratory equipment with minimal dependence on global supply chains. We introduce an open-source automated platform for high-throughput RNA extraction and pathogen diagnosis, which uses reagents almost entirely produced in-house. This platform integrates our methods for self-manufacturing magnetic nanoparticles and qRT-PCR reagents-both of which have received regulatory approval for clinical use-with an in-house, open-source robotic extraction protocol. It also incorporates our "Nanopore Sequencing of Isothermal Rapid Viral Amplification for Near Real-time Analysis" (NIRVANA) technology, designed for tracking SARS-CoV-2 mutations and variants. The platform exhibits high reproducibility and consistency without cross-contamination, and its limit of detection, sensitivity, and specificity are comparable to commercial assays. Automated NIRVANA effectively identifies circulating SARS-CoV-2 variants. Our in-house, cost-effective reagents, automated diagnostic workflows, and portable genomic surveillance strategies provide a scalable and rapid solution for COVID-19 diagnosis and variant tracking, essential for current and future pandemic responses.

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Understanding how a gene variant affects protein function is important in life science, as it helps explain traits or dysfunctions in organisms. In a clinical setting, this understanding makes it possible to improve and personalize patient care. Bioinformatic tools often only assign a pathogenicity score, rather than providing information about the molecular basis for phenotypes. Experimental testing can furnish this information, but this is slow and costly and requires expertise and equipment not available in a clinical setting. Conversely, mapping a gene variant onto the three-dimensional (3D) protein structure provides a fast molecular assessment free of charge. Before 2021, this type of analysis was severely limited by the availability of experimentally determined 3D protein structures. Advances in artificial intelligence algorithms now allow confident prediction of protein structural features from sequence alone. The aim of the protocols presented here is to enable non-experts to use databases and online tools to investigate the molecular effect of a genetic variant. The Basic Protocol relies only on the online resources AlphaFold, Protein Structure Database, and UniProt. Alternate Protocols document the usage of the Protein Data Bank, SWISS-MODEL, ColabFold, and PyMOL for structure-based variant analysis. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: 3D Mapping based on UniProt and AlphaFold Alternate Protocol 1: Using experimental models from the PDB Alternate Protocol 2: Using information from homology modeling with SWISS-MODEL Alternate Protocol 3: Predicting 3D structures with ColabFold Alternate Protocol 4: Structure visualization and analysis with PyMOL.

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BACKGROUND: Phosphodiesterase 10A (PDE10A) controls body movements by regulating cyclic adenosine monophosphate signaling in the basal ganglia. Two classes of PDE10A variants are reported with distinctive genotype-phenotype correlation. The autosomal recessive mutations in the GAF-A and catalytic domains are associated with compromised membrane localization, and manifest with infantile onset chorea, developmental, and cognition delay with normal brain MRI. Conversely, autosomal dominant mutations in the GAF-B domain cause protein aggregates which results in childhood onset chorea in the context of normal cognition and development, with striatal lesions. METHODS: Phenotypic characteristics of affected individuals with PDE10A mutations belonging to a single family were recorded. In addition, Sanger sequencing and in silico analysis were used to identify the mutations. Homozygosity mapping was applied together with whole exome sequencing. RESULTS: Four individuals from a consanguineous family affected with PDE10A mutations were observed for up to 40 years. Although these individuals displayed a clinical phenotype attributed to the recessive GAF-A mutations, they revealed a bi-allelic GAF-B mutation (c.883G > A:p. D295 N; p.Asp295Asn) that was segregated with all affected individuals. In addition to chorea, we observed peculiar foot deformities and pronounced social phobia, with normal brain MRI. In silico structural analysis suggested that the GAF-B mutation blocked allosteric PDE10A activation. The resulting lack of PDE10A activity likely phenocopies GAF-A mutations, and this is achieved through a distinct mechanism. CONCLUSIONS: Collectively, our findings demonstrate the association of recessive and dominant phenotypes of known variants, and further expands the genotype-phenotype landscape of PDE10A-associated movement disorders.

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To prevent and control foodborne diseases, there is a fundamental need to identify the foods that are most likely to cause illness. The goal of this study was to rank 25 commonly consumed food products associated with Salmonella enterica contamination in the Central Region of Mexico. A multicriteria decision analysis (MCDA) framework was developed to obtain an S. enterica risk score for each food product based on four criteria: probability of exposure to S. enterica through domestic food consumption (Se); S. enterica growth potential during home storage (Sg); per capita consumption (Pcc); and food attribution of S. enterica outbreak (So). Risk scores were calculated by the equation Se*W1 +Sg*W2 +Pcc*W3 +So*W4 , where each criterion was assigned a normalized value (1-5) and the relative weights (W) were defined by 22 experts' opinion. Se had the largest effect on the risk score being the criterion with the highest weight (35%; IC95% 20%-60%), followed by So (24%; 5%-50%), Sg (23%; 10%-40%), and Pcc (18%; 10%-35%). The results identified chicken (4.4 ± 0.6), pork (4.2 ± 0.6), and beef (4.2 ± 0.5) as the highest risk foods, followed by seed fruits (3.6 ± 0.5), tropical fruits (3.4 ± 0.4), and dried fruits and nuts (3.4 ± 0.5), while the food products with the lowest risk were yogurt (2.1 ± 0.3), chorizo (2.1 ± 0.4), and cream (2.0 ± 0.3). Approaches with expert-based weighting and equal weighting showed good correlation (R2  = 0.96) and did not show significant differences among the ranking order in the top 20 tier. This study can help risk managers select interventions and develop targeted surveillance programs against S. enterica in high-risk food products.

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Chicken meat is often associated withSalmonella entericacontamination worldwide. This study proposes a risk assessment model for human salmonellosis linked to the domestic consumption of chicken meat in the central region of Mexico, incorporating genotypic and phenotypic data. SixS. entericagroups were used, considering the presence of specific virulence genes and multidrug resistance (MDR). Sixteen exposure scenarios were established considering retail point (RP1 = fresh market/butcher shop; RP2 = mini-super/supermarket), transportation, home storage, cooking, and cross-contamination. The model predicted a mean annual salmonellosis cases of 66,754 due to chicken consumption (CI95% 10775-231606). The mean probability of illness (Pill) among the exposure scenarios ranged from 2.5 × 10-9 to 3.7 × 10-6, 7.7 × 10-8 to 1.1 × 10-4, and 6.7 × 10-4 to 7.8 × 10-2 for low, moderate, and high virulence groups. Exposure scenarios with the highest Pill were not responsible for most cases due to their low frequency of occurrence. The high virulence/ MDR group was responsible for most cases (66.5 %), despite the low S. enterica prevalence (RP1 0.5 % and RP2 5.0 %). The years lost due to disability (YLD) value for MDR was 2.6 × higher than for non-MDR. Spearman rank showed that the inputs with higher influence on the variability of salmonellosis depended on the type of exposure scenario. For example, the cooking temperature and time had the most significant influence in the scenarios where S. enterica can survive after cooking. Including the microbial genotypic and phenotypic characteristics in risk assessment modeling highlights the importance of focusing on high-virulent and MDR strains, which are not the most frequent but represent the highest public health risk.

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In this paper we investigate the application of free space optical (FSO) communications, energy harvesting, and unmanned aerial vehicles (UAVs) as key technology enablers of a cost-efficient backhaul/fronthaul framework for 5G and beyond (5G+) networks. This novel approach is motivated by several facts. First, the UAVs, acting as relay nodes, represent an easy-to-deploy and adaptive network that can provide line-of-sight between the base stations and the gateways connected to the core network. Second, FSO communications offer high data rates between the UAVs and the network nodes, while avoiding any potential interference with the 5G radio access networks. Third, energy harvesting in the optical domain has the potential to extend the UAVs' battery life. Nevertheless, the presence of atmospheric turbulence, atmospheric attenuation, and pointing errors in the FSO links severely degrades their performance. For this reason an accurate yet tractable modelling framework is required to fully understand whether an UAV-FSO backhaul/fronthaul network with energy harvesting can be applied. To this end, we consider a composite channel attenuation model that includes the effect of turbulence fading, pointing errors, and atmospheric attenuation. Using this model, we derive analytical closed-form expressions of the average harvested energy as a function of the FSO link parameters. These expressions can be used to improve energy harvesting efficiency in FSO link design. We have applied our proposed expressions to evaluate the energy harvested in vertical FSO links for a variety of real scenarios under a modified on-off keying (OOK) scheme optimized for energy harvesting. From the simulations carried out in this paper, we demonstrate that significant values of harvested energy can be obtained. Such performance enhancement can complement the existing deployment charging stations.

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Whole exome sequencing has provided significant opportunities to discover novel candidate genes for intellectual disability and autism spectrum disorders. Variants in the spectrin genes SPTAN1, SPTBN1, SPTBN2, and SPTBN4 have been associated with neurological disorders; however, SPTBN5 gene-variants have not been associated with any human disorder. This is the first report that associates SPTBN5 gene variants (ENSG00000137877: c.266A>C; p.His89Pro, c.9784G>A; p.Glu3262Lys, c.933C>G; p.Tyr311Ter, and c.8809A>T; p.Asn2937Tyr) causing neurodevelopmental phenotypes in four different families. The SPTBN5-associated clinical traits in our patients include intellectual disability (mild to severe), aggressive tendencies, accompanied by variable features such as craniofacial and physical dysmorphisms, autistic behavior, and gastroesophageal reflux. We also provide a review of the existing literature related to other spectrin genes, which highlights clinical features partially overlapping with SPTBN5.

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BACKGROUND: Plasmodium simium, a malaria parasite of non-human primates (NHP), was recently shown to cause zoonotic infections in humans in Brazil. We sequenced the P. simium genome to investigate its evolutionary history and to identify any genetic adaptions that may underlie the ability of this parasite to switch between host species. RESULTS: Phylogenetic analyses based on whole genome sequences of P. simium from humans and NHPs reveals that P. simium is monophyletic within the broader diversity of South American Plasmodium vivax, suggesting P. simium first infected NHPs as a result of a host switch of P. vivax from humans. The P. simium isolates show the closest relationship to Mexican P. vivax isolates. Analysis of erythrocyte invasion genes reveals differences between P. vivax and P. simium, including large deletions in the Duffy-binding protein 1 (DBP1) and reticulocyte-binding protein 2a genes of P. simium. Analysis of P. simium isolated from NHPs and humans revealed a deletion of 38 amino acids in DBP1 present in all human-derived isolates, whereas NHP isolates were multi-allelic. CONCLUSIONS: Analysis of the P. simium genome confirmed a close phylogenetic relationship between P. simium and P. vivax, and suggests a very recent American origin for P. simium. The presence of the DBP1 deletion in all human-derived isolates tested suggests that this deletion, in combination with other genetic changes in P. simium, may facilitate the invasion of human red blood cells and may explain, at least in part, the basis of the recent zoonotic infections.

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PURPOSE: Pathogenic variants in SETD1B have been associated with a syndromic neurodevelopmental disorder including intellectual disability, language delay, and seizures. To date, clinical features have been described for 11 patients with (likely) pathogenic SETD1B sequence variants. This study aims to further delineate the spectrum of the SETD1B-related syndrome based on characterizing an expanded patient cohort. METHODS: We perform an in-depth clinical characterization of a cohort of 36 unpublished individuals with SETD1B sequence variants, describing their molecular and phenotypic spectrum. Selected variants were functionally tested using in vitro and genome-wide methylation assays. RESULTS: Our data present evidence for a loss-of-function mechanism of SETD1B variants, resulting in a core clinical phenotype of global developmental delay, language delay including regression, intellectual disability, autism and other behavioral issues, and variable epilepsy phenotypes. Developmental delay appeared to precede seizure onset, suggesting SETD1B dysfunction impacts physiological neurodevelopment even in the absence of epileptic activity. Males are significantly overrepresented and more severely affected, and we speculate that sex-linked traits could affect susceptibility to penetrance and the clinical spectrum of SETD1B variants. CONCLUSION: Insights from this extensive cohort will facilitate the counseling regarding the molecular and phenotypic landscape of newly diagnosed patients with the SETD1B-related syndrome.

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Background: Craniosynostosis (CS) is defined as pre-mature fusion of one or more of the cranial sutures. CS is classified surgically as either simple or complex based on the number of cranial sutures involved. CS can also be classified genetically as isolated CS or syndromic CS if the patient has extracranial deformities. Currently, the link between clinical and genetic patterns of CS in the Saudi population is poorly understood. Methodology: We conducted a retrospective cohort study among 28 CS patients, of which 24 were operated and four were not. Clinical and genetic data were collected between February 2015 and February 2019, from consenting patient's families. The electronic chart data were collected and analyzed including patient demographics, craniofacial features, other anomalies and dysmorphic features, operative data, intra cranial pressure (ICP), parent consanguinity and genetic testing results. Results: The most common deformity in our population was trigonocephaly. The most performed procedure was cranial vault reconstruction with fronto-orbital advancement, followed by posterior vault distraction osteogenesis and suturectomy with barrel staving. Genetics analysis revealed pathogenic mutations in FGFR2 (6 cases), TWIST1 (3 cases), ALPL (2 cases), and TCF12 (2 cases), and FREM1 (2 case). Conclusion: Compared to Western countries, our Saudi cohort displays significant differences in the prevalence of CS features, such as the types of sutures and prevalence of inherited CS. The genomic background allows our phenotype-genotype study to reclassify variants of unknown significance. Worldwide, the sagittal suture is the most commonly affected suture in simple CS, but in the Saudi population, the metopic suture fusion was most commonly seen in our clinic. Further studies are needed to investigate the characteristics of CS in our population in a multicenter setting.

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Gingival recession (GR) can cause aesthetic and functional problems. Using connective tissue graft (CTG) and coronally advanced flap (CAF) is considered the technique of choice for treating GR. Considering the morbidity resulting from taking CTG, different alternative biomaterials have been described, including plasma-rich fibrin (PRF) membrane. Studies in lower teeth are few because of the complexity of the factors that can influence obtaining less predictable outcomes. Objective. To compare between CAF + PRF and CAF + CTG in the treatment of lower teeth Miller I gingival recession. Methodology. Split-mouth included 26 isolated GR (13 in each side of the mouth). The left side was treated with CAF + PRF and the right side with CAF + CTG. Clinical variables, probing depth (PD), GR, keratinized tissue (KT), vestibular soft tissue thickness (VSTT), and teeth sensitivity (TS), were assessed at the baseline. GR, KT, VSTT, extraoral inflammation (EI), and patient discomfort (PaD) were assessed at 45 days. Results. Statistically greater VSTT at 45 days was obtained using CAF + CTG (p < 0.05). Less EI and PaD were obtained using CAF + PRF (p < 0.05). No change was observed in GR, KT, and TS values in the intergroup or intragroup comparisons. Conclusion. Even with the limitations of this study, using PRF and CTG in lower teeth demonstrated an improvement in terms of root coverage, although it was without a total percentage of coverage. Regarding the VSTT, better results were obtained using the CTG + CAF, suggesting eventually long-term stable clinical results. We suggest a combined technique for future investigations.