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.

Evaluation of Anxiety and Vital Signs in Adults Undergoing Different Dental Procedures: A Prospective Study

The aim of this study was to evaluate the vital signs related with different dental treatments, and correlate with demographic data and participants' anxiety level. This is a prospective clinical study with 60 participants, divided into 3 groups of dental procedures: (1) restorative treatment, (2) extractions and biopsies, and (3) gingival treatment. A level of anxiety questionnaire before dental procedure proposed by Corah's Dental Anxiety Scale was collected. Respiratory rate, systolic and diastolic pressure, temperature and oxygenation were measured before, during and after the procedures. 31 (51.7 %) women and 29 (48.3 %) men were included, with mean age of 41.75 years old. Most participants (50 %) were classified as very little anxious. Diastolic pressure before the procedure was higher for slightly anxious patients when compar ed with very little anxious patients (p=0.028). Systolic pressure before, during and after the procedure was higher for participan ts above 40 years old (p=0,001). Heart rate (p=0,050) and temperature (p=0,041) was higher before the restorative treatment. Anxiety can promote changes in vital signs in the dental environment. Vital signs, sex, age and level of anxiety do influence the blood pressure at different clinical moments. Dental procedures have association with variations in temperature, heart and respiratory rate.

El objetivo de este estudio fue evaluar los signos vitales relacionados con diferentes tratamientos dentales y correlacionarlos con datos demográficos y el nivel de ansiedad de los participantes. Este es un estudio clínico prospectivo con 60 participantes, divididos en 3 grupos de procedimientos dentales: (1) tratamiento restaurador, (2) extracciones y biopsias, y (3) tratamiento gingival. Se recogió un cuestionario de nivel de ansiedad antes del procedimiento odontológico propuesto por la Escala de Ansiedad Dental de Corah. Se midieron la frecuencia respiratoria, la presión sistólica y diastólica, la temperatura y la oxigenación antes, durante y después de los procedimientos. Se incluyeron 31 (51,7 %) mujeres y 29 (48,3 %) hombres, con edad media de 41,75 años. La mayoría de los participantes (50 %) fueron clasificados como muy poco ansiosos. La presión diastólica antes del procedimiento fue mayor en los pacientes ligeramente ansiosos en comparación con los pacientes muy poco ansiosos(p=0,028). La presión sistólica antes, durante y después del procedimiento fue mayor para los participantes mayores de 40 años (p=0,001). La frecuencia cardíaca (p=0,050) y la temperatura (p=0,041) fueron mayores antes del tratamiento restaurativo. La ansiedad puede promover cambios en los signos vitales en el entorno dental. Los signos vitales, el sexo, la edad y el nivel de ansiedad sí influyen en la presión arterial en los diferentes momentos clínicos. Los procedimientos dentales tienen asociación con variaciones de temperatura, frecuencia cardíaca y respiratoria.

Primary Hepatic EBV-DLBCL Lymphoma in the Setting of COVID-19 Infection.

This case study describes an instance of primary hepatic diffuse large B cell lymphoma (DLBCL) in a patient who had prolonged coronavirus disease 2019 (COVID-19). DLBCL rarely presents as a primary hepatic mass. The 53-year-old man sought emergency care because of fatigue and weight loss. Diagnostic tests showed mildly elevated liver enzymes and imaging pointed to several low-density liver lesions. A liver biopsy paired with immunohistochemical testing verified the DLBCL diagnosis. Notably, the patient had COVID-19 4 months before the liver-related symptoms. The link between COVID-19 and the emergence of solid tumor cancers is unclear, but this case underscores its potential significance and the need for further research. This report stresses the importance of recognizing and documenting instances where COVID-19 might influence the onset of solid tumor cancers, including primary hepatic DLBCL.

New proposal of viral genome representation applied in the classification of SARS-CoV-2 with deep learning.

BACKGROUND: In December 2019, the first case of COVID-19 was described in Wuhan, China, and by July 2022, there were already 540 million confirmed cases. Due to the rapid spread of the virus, the scientific community has made efforts to develop techniques for the viral classification of SARS-CoV-2. RESULTS: In this context, we developed a new proposal for gene sequence representation with Genomic Signal Processing techniques for the work presented in this paper. First, we applied the mapping approach to samples of six viral species of the Coronaviridae family, which belongs SARS-CoV-2 Virus. We then used the sequence downsized obtained by the method proposed in a deep learning architecture for viral classification, achieving an accuracy of 98.35%, 99.08%, and 99.69% for the 64, 128, and 256 sizes of the viral signatures, respectively, and obtaining 99.95% precision for the vectors with size 256. CONCLUSIONS: The classification results obtained, in comparison to the results produced using other state-of-the-art representation techniques, demonstrate that the proposed mapping can provide a satisfactory performance result with low computational memory and processing time costs.

Evaluating a Living Donor With Rheumatoid Arthritis for a Recipient With End-Stage Renal Disease From Antineutrophil Cytoplasmic Antibodies Associated Vasculitis.

A 60-year-old Caucasian female with sero-positive rheumatoid arthritis (RA) was evaluated as a potential kidney donor for her brother-in-law with end-stage kidney disease (ESKD) secondary to c-antineutrophil cytoplasmic antibody (c-ANCA) associated vasculitis (AAV) and membranous nephropathy (MN). With little to no data supporting or contradicting this unique scenario, in addition to the varying viewpoints expressed by the different specialists, our multidisciplinary transplant committee encountered a difficult decision of whether to approve a candidate with RA for a living kidney donation or not. As a result, we carried out a careful literature review addressing aspects of recipients' outcomes following kidney transplants from a living donor with RA, especially when the recipient has AAV, living donor's short- and long-term outcomes post kidney donation, renal disease in AAV and RA, and maintenance of disease remission.

An auspicious triumph of recovery from dialysis-requiring acute kidney injury in COVID-19 in a patient with chronic kidney disease, α-1 antitrypsin deficiency, and liver transplant: A case report.

We report a unique case of an immunosuppressed 67-year-old female with homozygous Z-allele mutation A1AT deficiency and liver transplant with baseline chronic kidney disease (CKD) stage IIIa with creatinine of 1 mg/dL and glomerular filtration rate (GFR) of 49 mL/min/1.73m2 ~ 6 months before the presentation. She presented with COVID-19 mediated hypoxic respiratory failure complicated by AKI requiring provisional renal replacement therapy with recovery of kidney function with a new baseline of creatinine of 1.6 - 1.8 mg/dL with GFR of 31 mL/min/1.73m2.

Post-operative intensive care unit admission after elective non-cardiac surgery: A single-center analysis of the NSQIP database.

BACKGROUND: Admission to the intensive care unit (ICU) after surgery can be associated with significant morbidity and mortality. This observational cohort study aims to identify perioperative factors associated with post-operative ICU admission in patients undergoing elective non-cardiac surgery. METHODS: Data from the ACS NSQIP® database at a tertiary care academic medical center were analyzed from January 2011 to September 2016. Univariable and multivariable logistic regression of patient and surgery-specific characteristics was performed to assess association with post-operative ICU admission. The Current Procedural Terminology (CPT) and International Classification of Diseases (ICD-9) billing codes, as well as associated outcomes, were reviewed. RESULTS: Of 5254 database patient records, 1150 met our inclusion criteria. Elevated body mass index (BMI), longer procedure duration and a diagnosis of disseminated cancer were associated with post-operative ICU admission. Prostatectomy and morbid obesity were the most common CPT and ICD-9 codes identified. Patients who were admitted to the ICU after surgery had a longer hospital length of stay (LOS), had a higher frequency of readmission, re-operation, and in-hospital mortality. CONCLUSION: Admission to the ICU after elective non-cardiac surgery is common. Our analysis of the ACS NSQIP® database identified elevated BMI, longer duration of surgery and disseminated cancer as predictors of post-operative ICU admissions in patients undergoing elective non-cardiac surgery.

Novel Association of Juvenile Polyposis Syndrome With Atrial Septal Aneurysm and Patent Foramen Ovale: A Case Report.

Juvenile polyposis syndrome is an autosomal-dominant disorder characterized by the presence of hundreds of gastrointestinal polyps. The genes most commonly found are BMPR1A and SMAD4. The latter has been linked to vascular malformations and hereditary hemorrhagic telangiectasias. We present the case of a young woman diagnosed with juvenile polyposis syndrome and SMAD-4 mutation, who developed embolic strokes from an atrial septal aneurysm and patent foramen ovale. This case highlights the propensity of patients with juvenile polyposis syndrome and SMAD-4 mutations to develop atrial septal aneurysm and patent foramen ovale, and warrants appropriate cardiac workup in at-risk individuals.

Future of circulating tumor cells in the melanoma clinical and research laboratory settings.

Circulating tumor cells (CTC) have become a field of interest for oncologists based on the premise that they constitute the underpinning for metastatic dissemination. The lethal nature of cancer is no longer attributed to solid tumor formation, but rather to the process of metastasis; shifting the focus of current studies towards the isolation and identification of metastatic progenitors, such as CTCs. CTCs originate from primary tumor masses that undergo morphologic and genetic alterations, which involve the release of mesenchymal-like cancer cells into the bloodstream, capable of invading nearby tissues for secondary tumor development. Cancerous cells contained in the primary tumor mass acquire the motile mesenchymal phenotype as a result of the Epithelial-to-Mesenchymal Transition, where substantial variations in protein expression and signaling pathways take place. CTCs that migrate from the primary tumor, intravasate into the systemic vasculature, are transported through the bloodstream, and invade tissues and organs suitable for secondary tumor development. While only a limited number of CTCs are viable in the bloodstream, their ability to elude the immune system, evade apoptosis and successfully metastasize at secondary tumor sites, makes CTCs promising candidates for unraveling the triggers that initiates the metastatic process. In this article, these subjects are explored in greater depth to elucidate the potential use of CTCs in the detection, disease staging and management of metastatic melanoma.

Causal attribution to cervical cáncer / Atribución causal del cáncer cervical

This study aimed to examine the causal attribution for cervical cancer for women with and without the disease. Seventy-eight (78) users from the public healthcare system participated, which were divided into: a clinical group (CG) of women with cervical cancer and a non-clinical group (NCG) of women without cervical cancer. A Form covering sociodemographic and clinical data was utilized along with the Portuguese version of the Illness Perception Questionnaire for ill patients and healthy people. The responses were grouped into six categories: 1) Psychological attributions; 2) Behavioral risk factors; 3) Biological factors; 4) Bad luck; 5) Lack of resources; 6) Chemical agents. The CG attributed more emotional causes to the Cervical Cancer while the NCG more causes associated with behavioral risk factors. These results suggest that women with cancer may blame themselves for the illness. Distorted beliefs about the etiology of cervical cancer can harm preventative conduct and self-care practices

El estudio buscó examinar la atribución de causas del cáncer cervical de mujeres con y sin la enfermedad. Participaron setenta y ocho (78) usuarias del sistema público de salud, que fueron divididas en: grupo clínico (GC) de mujeres con cáncer cervical, y grupo no-clínico (GNC) de mujeres sin cáncer cervical. Fue utilizado un cuestionario de datos sociodemográficos y clínicos y la versión en portugués del Illness Perception Questionnaire para pacientes enfermos y personas sanas. Las respuestas fueron agrupadas en seis categorías: 1) Atribuciones psicológicas; 2) Factores de riscos comportamentales; 3) Factores biológicos; 4) Mala suerte; 5) Falta de recursos; 6) Agentes químicos. El GC atribuyó más causas emocionales al cáncer cervical, mientras el GNC atribuyó más causas asociadas a factores de risco comportamentales. Los resultados sugieren que mujeres con cáncer pueden culparse a sí mismas por la enfermedad. Creencias equivocadas sobre la etiología del cáncer cervical pueden perjudicar conductas de prevención y prácticas de autocuidado

Functional expression and activity of the recombinant antifungal defensin PvD1r from Phaseolus vulgaris L. (common bean) seeds.

BACKGROUND: Defensins are basic, cysteine-rich antimicrobial peptides that are important components of plant defense against pathogens. Previously, we isolated a defensin, PvD1, from Phaseolus vulgaris L. (common bean) seeds. RESULTS: The aim of this study was to overexpress PvD1 in a prokaryotic system, verify the biologic function of recombinant PvD1 (PvD1r) by comparing the antimicrobial activity of PvD1r to that of the natural defensin, PvD1, and use a mutant Candida albicans strain that lacks the gene for sphingolipid biosynthesis to unravel the target site of the PvD1r in C. albicans cells. The cDNA encoding PvD1, which was previously obtained, was cloned into the pET-32 EK/LIC vector, and the resulting construct was used to transform bacterial cells (Rosetta Gami 2 (DE3) pLysS) leading to recombinant protein expression. After expression had been induced, PvD1r was purified, cleaved with enterokinase and repurified by chromatographic steps. N-terminal amino acid sequencing showed that the overall process of the recombinant production of PvD1r, including cleavage with the enterokinase, was successful. Additionally, modeling revealed that PvD1r had a structure that was similar to the defensin isolated from plants. Purified PvD1 and PvD1r possessed inhibitory activity against the growth of the wild-type pathogenic yeast strain C. albicans. Both defensins, however, did not present inhibitory activity against the mutant strain of C. albicans. Antifungal assays with the wild-type C. albicans strains showed morphological changes upon observation by light microscopy following growth assays. PvD1r was coupled to FITC, and the subsequent treatment of wild type C. albicans with DAPI revealed that the labeled peptide was intracellularly localized. In the mutant strain, no intracellular labeling was detected. CONCLUSION: Our results indicate that PvD1r retains full biological activity after recombinant production, enterokinase cleavage and purification. Additionally, our results from the antimicrobial assay, the microscopic analysis and the PvD1r-FITC labeling assays corroborate each other and lead us to suggest that the target of PvD1 in C. albicans cells is the sphingolipid glucosylceramide.