Deepvirusclassifier: a deep learning tool for classifying SARS-CoV-2 based on viral subtypes within the coronaviridae family.

PURPOSE: In this study, we present DeepVirusClassifier, a tool capable of accurately classifying Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) viral sequences among other subtypes of the coronaviridae family. This classification is achieved through a deep neural network model that relies on convolutional neural networks (CNNs). Since viruses within the same family share similar genetic and structural characteristics, the classification process becomes more challenging, necessitating more robust models. With the rapid evolution of viral genomes and the increasing need for timely classification, we aimed to provide a robust and efficient tool that could increase the accuracy of viral identification and classification processes. Contribute to advancing research in viral genomics and assist in surveilling emerging viral strains. METHODS: Based on a one-dimensional deep CNN, the proposed tool is capable of training and testing on the Coronaviridae family, including SARS-CoV-2. Our model's performance was assessed using various metrics, including F1-score and AUROC. Additionally, artificial mutation tests were conducted to evaluate the model's generalization ability across sequence variations. We also used the BLAST algorithm and conducted comprehensive processing time analyses for comparison. RESULTS: DeepVirusClassifier demonstrated exceptional performance across several evaluation metrics in the training and testing phases. Indicating its robust learning capacity. Notably, during testing on more than 10,000 viral sequences, the model exhibited a more than 99% sensitivity for sequences with fewer than 2000 mutations. The tool achieves superior accuracy and significantly reduced processing times compared to the Basic Local Alignment Search Tool algorithm. Furthermore, the results appear more reliable than the work discussed in the text, indicating that the tool has great potential to revolutionize viral genomic research. CONCLUSION: DeepVirusClassifier is a powerful tool for accurately classifying viral sequences, specifically focusing on SARS-CoV-2 and other subtypes within the Coronaviridae family. The superiority of our model becomes evident through rigorous evaluation and comparison with existing methods. Introducing artificial mutations into the sequences demonstrates the tool's ability to identify variations and significantly contributes to viral classification and genomic research. As viral surveillance becomes increasingly critical, our model holds promise in aiding rapid and accurate identification of emerging viral strains.

Compensatory strategy use in diverse older adults with subjective cognitive complaints.

OBJECTIVES: The current study aimed to evaluate the relationship between subjective cognitive complaints (SCC) and compensatory strategy (CS) use in a diverse sample of non-Latinx White (NLW), Black, and Latinx American older adults. METHOD: 807 older adults (Mage = 65.38, 62.7% female) were recruited through Amazon's Mechanical Turk (MTurk) and Qualtrics Panel to complete questionnaires on SCC and CS use. Kruskall-Wallis tests were used to evaluate differences in SCC across groups given non-normal distributions. Analysis of variance (ANOVA) was used to evaluate group differences in CS use. The PROCESS macro for SPSS was used to examine whether demographic factors moderated the relationship between SCC and CS use. RESULTS: NLWs reported higher levels of SCC and greater overall use of CS in comparison to Latinx and Black individuals. Several demographic and psychosocial factors including age, ethno-racial group, education, and anxiety level were found to be associated with CS use. Education was found to moderate the association between SCC and CS use. CONCLUSION: Inconsistent with prior studies, our study found that NLWs reported the highest levels of SCC. CS were used across all racial/ethnic groups, but the frequency of CS use may be impacted by education level. While all education groups increased their CS in response to higher levels of SCC, this increase was more substantial for those with lower levels of education. Future work should consider individuals' cultural and educational background when examining SCC and/or developing CS-based intervention for the aging population.

Inaugural editorial for Journal of Counseling Psychology.

The Journal of Counseling Psychology serves as the premier journal for critical and rigorous research within the field and beyond. In their inaugural editorial for Journa, Liu is joined by their associated editors and inaugural JCP fellows who have agreed to share authorship and their positionalities. In considering the Journal of Counseling Psychology for research, the editors encourage authors to reflect on these positionalities and how they might integrate their own into their publications. The editorial provides direction and some suggestions on submitted articles and research directions for JCP in the following areas: positionality and critical reflexivity; theoretical and conceptual advancement and clarity; body ideas, frameworks, and conceptualization; data clarity; and cultural validity of research instruments. The editors look forward to working with their communities as they transform their scholarship. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Modeling Lysosomal Storage Disorders in an Innovative Way: Establishment and Characterization of Stem Cell Lines from Human Exfoliated Deciduous Teeth of Mucopolysaccharidosis Type II Patients.

Among the many lysosomal storage disorders (LSDs) that would benefit from the establishment of novel cell models, either patient-derived or genetically engineered, is mucopolysaccharidosis type II (MPS II). Here, we present our results on the establishment and characterization of two MPS II patient-derived stem cell line(s) from deciduous baby teeth. To the best of our knowledge, this is the first time a stem cell population has been isolated from LSD patient samples obtained from the dental pulp. Taking into account our results on the molecular and biochemical characterization of those cells and the fact that they exhibit visible and measurable disease phenotypes, we consider these cells may qualify as a valuable disease model, which may be useful for both pathophysiological assessments and in vitro screenings. Ultimately, we believe that patient-derived dental pulp stem cells (DPSCs), particularly those isolated from human exfoliated deciduous teeth (SHEDs), may represent a feasible alternative to induced pluripotent stem cells (iPSCs) in many labs with standard cell culture conditions and limited (human and economic) resources.

Development of Engineered-U1 snRNA Therapies: Current Status.

Splicing of pre-mRNA is a crucial regulatory stage in the pathway of gene expression. The majority of human genes that encode proteins undergo alternative pre-mRNA splicing and mutations that affect splicing are more prevalent than previously thought. Targeting aberrant RNA(s) may thus provide an opportunity to correct faulty splicing and potentially treat numerous genetic disorders. To that purpose, the use of engineered U1 snRNA (either modified U1 snRNAs or exon-specific U1s-ExSpeU1s) has been applied as a potentially therapeutic strategy to correct splicing mutations, particularly those affecting the 5' splice-site (5'ss). Here we review and summarize a vast panoply of studies that used either modified U1 snRNAs or ExSpeU1s to mediate gene therapeutic correction of splicing defects underlying a considerable number of genetic diseases. We also focus on the pre-clinical validation of these therapeutic approaches both in vitro and in vivo, and summarize the main obstacles that need to be overcome to allow for their successful translation to clinic practice in the future.

Spatial analysis of socio-economic factors and their relationship with the cases of COVID-19 in Pernambuco, Brazil.

OBJECTIVES: To analyse the spatial distribution of rates of COVID-19 cases and its association with socio-economic conditions in the state of Pernambuco, Brazil. METHODS: Autocorrelation (Moran index) and spatial association (Geographically weighted regression) models were used to explain the interrelationships between municipalities and the possible effects of socio-economic factors on rates. RESULTS: Two isolated clusters were revealed in the inner part of the state in sparsely inhabited municipalities. The spatial model (Geographically Weighted Regression) was able to explain 50% of the variations in COVID-19 cases. The variables proportion of people with low income, percentage of rented homes, percentage of families in social programs, Gini index and running water had the greatest explanatory power for the increase in infection by COVID-19. CONCLUSIONS: Our results provide important information on socio-economic factors related to the spread of COVID-19 and can serve as a basis for decision-making in similar circumstances.

Convolutional Neural Network Applied to SARS-CoV-2 Sequence Classification.

COVID-19, the illness caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus belonging to the Coronaviridade family, a single-strand positive-sense RNA genome, has been spreading around the world and has been declared a pandemic by the World Health Organization. On 17 January 2022, there were more than 329 million cases, with more than 5.5 million deaths. Although COVID-19 has a low mortality rate, its high capacities for contamination, spread, and mutation worry the authorities, especially after the emergence of the Omicron variant, which has a high transmission capacity and can more easily contaminate even vaccinated people. Such outbreaks require elucidation of the taxonomic classification and origin of the virus (SARS-CoV-2) from the genomic sequence for strategic planning, containment, and treatment of the disease. Thus, this work proposes a high-accuracy technique to classify viruses and other organisms from a genome sequence using a deep learning convolutional neural network (CNN). Unlike the other literature, the proposed approach does not limit the length of the genome sequence. The results show that the novel proposal accurately distinguishes SARS-CoV-2 from the sequences of other viruses. The results were obtained from 1557 instances of SARS-CoV-2 from the National Center for Biotechnology Information (NCBI) and 14,684 different viruses from the Virus-Host DB. As a CNN has several changeable parameters, the tests were performed with forty-eight different architectures; the best of these had an accuracy of 91.94 ± 2.62% in classifying viruses into their realms correctly, in addition to 100% accuracy in classifying SARS-CoV-2 into its respective realm, Riboviria. For the subsequent classifications (family, genera, and subgenus), this accuracy increased, which shows that the proposed architecture may be viable in the classification of the virus that causes COVID-19.

Racial/ethnic differences in pediatric asthma management: the importance of asthma knowledge, symptom assessment, and family-provider collaboration.

BACKGROUND: Asthma disproportionately impacts youth from marginalized minority backgrounds. Aspects of core asthma management (asthma management and medication beliefs) were examined among a cohort of diverse families. METHODS: Caregiver-youth dyads (N = 92; Mage= 13.8 years; non-Hispanic/Latinx White (NLW) = 40%; Black/African-American = 25%; Hispanic/Latinx= 35%) completed a medication beliefs questionnaire (Medication Necessity, Medication Concerns) and a semi-structured interview (Family Asthma Management System Scale (FAMSS)). FAMSS subscales (Asthma Knowledge, Symptom Assessment, Family Response to Symptoms, Child Response to Symptoms, Environmental Control, Medication Adherence, Family-Provider Collaboration, and Balanced Integration) were used for analyses. RESULTS: More Hispanic/Latinx families were at or below the poverty line (75%) relative to NLW (22%) and Black/African-American (39%) families (p < 0.001). Adherence (p < 0.01), Knowledge (p < 0.001), and Symptom Assessment (p < 0.01) were higher for NLW relative to Black/African-American families. Collaboration was higher among NLW (p = 0.01) and Hispanic/Latinx families (p = 0.05). Effect sizes were moderate (η2= 0.10-0.12). Parental race/ethnicity moderated the relationship between adherence and parental perceived medication concern and necessity for NLW and Hispanic/Latinx families. As medication concerns increased, medication adherence decreased, however, only for NLW and Hispanic/Latinx families. CONCLUSIONS: In this sample, racial/ethnic differences emerged for elements of asthma management. Interview-based ratings of asthma management among Black/African-American families depicted lower asthma knowledge, lower levels of family-provider collaboration, and lower medication adherence. The relationship between medication concerns and adherence appeared to differ by ethnic group. Future research is needed to elucidate cultural factors that influence family-provider relationships and health-related behaviors, like medication use/adherence.

An Overview of Health Disparities in Asthma.

Asthma is a heterogeneous disease characterized by inflammation in the respiratory airways which manifests clinically with wheezing, cough, and episodic periods of chest tightness; if left untreated it can lead to permanent obstruction or death. In the US, asthma affects all ages and genders, and individuals from racial and ethnic minority groups are disproportionately burdened by this disease. The financial cost of asthma exceeds $81 billion every year and despite all the resources invested, asthma is responsible for over 3,500 deaths annually in the nation. In this overview, we highlight important factors associated with health disparities in asthma. While they are complex and overlap, we group these factors in five domains: biological, behavioral, socio-cultural, built environment, and health systems. We review the biological domain in detail, which traditionally has been best studied. We also acknowledge that implicit and explicit racism is an important contributor to asthma disparities and responsible for many of the socio-environmental factors that worsen outcomes in this disease.

Lysosomal Storage Disease-Associated Neuropathy: Targeting Stable Nucleic Acid Lipid Particle (SNALP)-Formulated siRNAs to the Brain as a Therapeutic Approach.

More than two thirds of Lysosomal Storage Diseases (LSDs) present central nervous system involvement. Nevertheless, only one of the currently approved therapies has an impact on neuropathology. Therefore, alternative approaches are under development, either addressing the underlying enzymatic defect or its downstream consequences. Also under study is the possibility to block substrate accumulation upstream, by promoting a decrease of its synthesis. This concept is known as substrate reduction therapy and may be triggered by several molecules, such as small interfering RNAs (siRNAs). siRNAs promote RNA interference, a naturally occurring sequence-specific post-transcriptional gene-silencing mechanism, and may target virtually any gene of interest, inhibiting its expression. Still, naked siRNAs have limited cellular uptake, low biological stability, and unfavorable pharmacokinetics. Thus, their translation into clinics requires proper delivery methods. One promising platform is a special class of liposomes called stable nucleic acid lipid particles (SNALPs), which are characterized by high cargo encapsulation efficiency and may be engineered to promote targeted delivery to specific receptors. Here, we review the concept of SNALPs, presenting a series of examples on their efficacy as siRNA nanodelivery systems. By doing so, we hope to unveil the therapeutic potential of these nanosystems for targeted brain delivery of siRNAs in LSDs.

Assessing Lysosomal Disorders in the NGS Era: Identification of Novel Rare Variants.

Lysosomal storage diseases (LSDs) are a heterogeneous group of genetic disorders with variable degrees of severity and a broad phenotypic spectrum, which may overlap with a number of other conditions. While individually rare, as a group LSDs affect a significant number of patients, placing an important burden on affected individuals and their families but also on national health care systems worldwide. Here, we present our results on the use of an in-house customized next-generation sequencing (NGS) panel of genes related to lysosome function as a first-line molecular test for the diagnosis of LSDs. Ultimately, our goal is to provide a fast and effective tool to screen for virtually all LSDs in a single run, thus contributing to decrease the diagnostic odyssey, accelerating the time to diagnosis. Our study enrolled a group of 23 patients with variable degrees of clinical and/or biochemical suspicion of LSD. Briefly, NGS analysis data workflow, followed by segregation analysis allowed the characterization of approximately 41% of the analyzed patients and the identification of 10 different pathogenic variants, underlying nine LSDs. Importantly, four of those variants were novel, and, when applicable, their effect over protein structure was evaluated through in silico analysis. One of the novel pathogenic variants was identified in the GM2A gene, which is associated with an ultra-rare (or misdiagnosed) LSD, the AB variant of GM2 Gangliosidosis. Overall, this case series highlights not only the major advantages of NGS-based diagnostic approaches but also, to some extent, its limitations ultimately promoting a reflection on the role of targeted panels as a primary tool for the prompt characterization of LSD patients.

RNA Therapeutics: How Far Have We Gone?

In recent years, the RNA molecule became one of the most promising targets for therapeutic intervention. Currently, a large number of RNA-based therapeutics are being investigated both at the basic research level and in late-stage clinical trials. Some of them are even already approved for treatment. RNA-based approaches can act at pre-mRNA level (by splicing modulation/correction using antisense oligonucleotides or U1snRNA vectors), at mRNA level (inhibiting gene expression by siRNAs and antisense oligonucleotides) or at DNA level (by editing mutated sequences through the use of CRISPR/Cas). Other RNA approaches include the delivery of in vitro transcribed (IVT) mRNA or the use of oligonucleotides aptamers. Here we review these approaches and their translation into clinics trying to give a brief overview also on the difficulties to its application as well as the research that is being done to overcome them.

Coutinho et al. Less Is More: Substrate Reduction Therapy for Lysosomal Storage Disorders. Int. J. Mol. Sci. 2016, 17, 1065.

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Temper Loss and Persistent Irritability in Preschoolers: Implications for Diagnosing Disruptive Mood Dysregulation Disorder in Early Childhood.

Disruptive Mood Dysregulation Disorder (DMDD) is a new and controversial child psychiatric disorder characterized by persistent irritability and frequent temper loss. Among the controversies surrounding DMDD is whether the age of onset criterion-that DMDD may not be diagnosed before age 6 years-is justified. This study examined DMDD symptoms and associated patterns of psychiatric comorbidity, behavioral, and family functioning in a sample of 139 preschoolers (ages 4-0 to 5-11 years) admitted to an early childhood psychiatric day treatment program. DMDD symptoms were common in this acute clinical sample, with 63 children (45.3 %) presenting with frequent temper outbursts and chronic irritability. As compared to children who did not present with DMDD symptoms, these children demonstrated more aggression and emotional reactivity and lower receptive language skills, with high rates of comorbidity with the disruptive behavior disorders. Findings contribute to an emerging literature on preschool DMDD, with implications for early childhood psychiatric assessment and clinical interventions.

From rare to common and back again: 60years of lysosomal dysfunction.

Sixty years after its discovery, the lysosome is no longer considered as cell's waste bin but as an organelle playing a central role in cell metabolism. Besides its well known association with lysosomal storage disorders (mostly rare and life-threatening diseases), recent data have shown that the lysosome is also a player in some of the most common conditions of our time; and, perhaps even most important, it is not only a target for orphan drugs (rare disease therapeutic approaches) but also a putative target to treat patients suffering from common complex diseases worldwide. Here we review the striking associations linking rare lysosomal storage disorders such as the well-known Gaucher disease, or even the recently discovered, extremely rare Neuronal Ceroid Lipofuscinosis-11 and some of the most frequent, multifaceted and complex disorders of modern society such as cancer, Parkinson's disease and frontotemporal lobar degeneration.

Less Is More: Substrate Reduction Therapy for Lysosomal Storage Disorders.

Lysosomal storage diseases (LSDs) are a group of rare, life-threatening genetic disorders, usually caused by a dysfunction in one of the many enzymes responsible for intralysosomal digestion. Even though no cure is available for any LSD, a few treatment strategies do exist. Traditionally, efforts have been mainly targeting the functional loss of the enzyme, by injection of a recombinant formulation, in a process called enzyme replacement therapy (ERT), with no impact on neuropathology. This ineffectiveness, together with its high cost and lifelong dependence is amongst the main reasons why additional therapeutic approaches are being (and have to be) investigated: chaperone therapy; gene enhancement; gene therapy; and, alternatively, substrate reduction therapy (SRT), whose aim is to prevent storage not by correcting the original enzymatic defect but, instead, by decreasing the levels of biosynthesis of the accumulating substrate(s). Here we review the concept of substrate reduction, highlighting the major breakthroughs in the field and discussing the future of SRT, not only as a monotherapy but also, especially, as complementary approach for LSDs.

Mucolipidosis II-related mutations inhibit the exit from the endoplasmic reticulum and proteolytic cleavage of GlcNAc-1-phosphotransferase precursor protein (GNPTAB).

Mucolipidosis (ML) II and MLIII alpha/beta are two pediatric lysosomal storage disorders caused by mutations in the GNPTAB gene, which encodes an α/ß-subunit precursor protein of GlcNAc-1-phosphotransferase. Considerable variations in the onset and severity of the clinical phenotype in these diseases are observed. We report here on expression studies of two missense mutations c.242G>T (p.Trp81Leu) and c.2956C>T (p.Arg986Cys) and two frameshift mutations c.3503_3504delTC (p.Leu1168GlnfsX5) and c.3145insC (p.Gly1049ArgfsX16) present in severely affected MLII patients, as well as two missense mutations c.1196C>T (p.Ser399Phe) and c.3707A>T (p.Lys1236Met) reported in more mild affected individuals. We generated a novel α-subunit-specific monoclonal antibody, allowing the analysis of the expression, subcellular localization, and proteolytic activation of wild-type and mutant α/ß-subunit precursor proteins by Western blotting and immunofluorescence microscopy. In general, we found that both missense and frameshift mutations that are associated with a severe clinical phenotype cause retention of the encoded protein in the endoplasmic reticulum and failure to cleave the α/ß-subunit precursor protein are associated with a severe clinical phenotype with the exception of p.Ser399Phe found in MLIII alpha/beta. Our data provide new insights into structural requirements for localization and activity of GlcNAc-1-phosphotransferase that may help to explain the clinical phenotype of MLII patients.

Diagnostic and prognostic contribution of DPD scintigraphy in transthyretin V30M cardiac amyloidosis.

BACKGROUND: Early diagnosis and prognostic stratification of cardiac transthyretin amyloidosis are crucial. Although 99mTc 3,3-diphosphono-1,2-propanedicarboxylic acid (DPD) scintigraphy is the preferred method for the non-invasive diagnosis, its accuracy appears to be limited in transthyretin amyloidosis protein (ATTR) V30M mutation. Furthermore, its prognostic value in this mutation is unknown. This study investigated the diagnostic value of DPD scintigraphy to detect ATTR cardiomyopathy in V30M mutation and explored its prognostic value regarding mortality. METHODS: A total of 288 ATTR V30M mutation carriers (median age: 46 years; 49% males) without myocardial thickening (defined as septal thickness ≥13mm) attributable to other causes and who underwent DPD scintigraphy were enrolled. ATTR cardiomyopathy was defined by septal thickness ≥13mm and at least one of the criteria: late heart-to-mediastinum (H/M) 123I-metaiodobenzylguanidine (MIBG) uptake ratio <1.60; electrical heart disease or biopsy-documented amyloidosis. RESULTS: ATTR cardiomyopathy was identified in 41 (14.2%) patients and cardiac DPD uptake in 34 (11.8%). During a mean follow-up of 33.6 ± 1.2 months, 16 patients died (5.6%). Mortality was 14 times higher in patients with ATTR cardiomyopathy, 13 times higher in those with DPD uptake and 10 times higher in those with late H/M MIBG <1.60. The combined assessment of septal thickness and cardiac DPD uptake improved risk stratification: patients without septal thickening and without DPD retention had an excellent prognosis while those who presented either or both of them had a significantly worse prognosis, with 5-year mortality rates ranging from 39.9 to 53.3%. CONCLUSIONS: DPD scintigraphy is useful for prognostic stratification of ATTR V30M mutation carriers. Patients without septal thickening and no DPD uptake present the best prognosis compared to those with any signs of cardiac involvement.

Hypophosphatemia as a possible biomarker for epileptic seizures at the emergency department.

INTRODUCTION: Hypophosphatemia seems to be temporally associated with seizures, despite not being considered a trigger. We aimed to evaluate hypophosphatemia as a biomarker for seizures. METHODS: Retrospective study, including all consecutive patients admitted at our central hospital's emergency department from 01/01-31/03/2021, screened as "altered consciousness/syncope" or "seizures", with available phosphate levels. RESULTS: 277 patients included, mostly male (61.7%), mean age 64.3 years. Final diagnosis was "seizure" in 34.7% and "other diagnosis" in 65.3%. Patients with seizures were younger (p<0.001), had more frequent epilepsy (p<0.001) and alcoholism (p=0.01). Patients with other diagnosis had more often renal failure (p<0.001) and statin (p=0.02) or diuretic (p=0.003) therapy. Time to blood collection (from the event and from admission) was similar between groups. Patients with seizures had lower mean phosphate levels and more frequent hypophosphatemia (<2.4mg/dL) (p<0.001). Mean CK levels were similar in both groups (p=0.25). HyperCK (>200U/L) was more frequent in the seizure group (p=0.04). Odds ratio (OR) of hypophosphatemia for seizures was 4.330 (CI 95% 2.170-8.640, p<0.001), persisting after correction for confounders. OR of hyperCK was 1.890 (CI 95% 1.060-3.371, p=0.03), losing significance when adjusted. Sensitivity was low for both. Hypophosphatemia was more specific (91.2% vs 79.9%). CONCLUSIONS: Our findings support hypophosphatemia as a seizure biomarker. More studies are needed.

MicroRNA Profile, Putative Diagnostic Biomarkers and RNA-Based Therapies in the Inherited Lipid Storage Disease Niemann-Pick Type C.

Lipids are essential for cellular function and are tightly controlled at the transcriptional and post-transcriptional levels. Dysregulation of these pathways is associated with vascular diseases, diabetes, cancer, and several inherited metabolic disorders. MicroRNAs (miRNAs), in particular, are a family of post-transcriptional gene repressors associated with the regulation of many genes that encode proteins involved in multiple lipid metabolism pathways, thereby influencing their homeostasis. Thus, this class of non-coding RNAs (ncRNAs) has emerged as a promising therapeutic target for the treatment of lipid-related metabolic alterations. Most of these miRNAs act at an intracellular level, but in the past few years, a role for miRNAs as intercellular signaling molecules has also been uncovered since they can be transported in bodily fluids and used as potential biomarkers of lipid metabolic alterations. In this review, we point out the current knowledge on the miRNA signature in a lysosomal storage disorder associated with lipid dysfunction, Niemann-Pick type C, and discuss the potential use of miRNAs as biomarkers and therapeutic targets for RNA-based therapies.