Immunoinformatic Approach for Rational Identification of Immunogenic Peptides Against Host Entry and/or Exit Mpox Proteins and Potential Multiepitope Vaccine Construction.

COVID-19 has intensified humanity's concern about the emergence of new pandemics. Since 2018, epidemic outbreaks of the mpox virus have become worrisome. In June 2022, the World Health Organization declared the disease a global health emergency, with 14 500 cases reported by the Centers for Disease Control and Prevention in 60 countries. Therefore, the development of a vaccine based on the current virus genome is paramount in combating new cases. In view of this, we hypothesized the obtainment of rational immunogenic peptides predicted from proteins responsible for entry of the mpox virus into the host (A17L, A26L/A30L, A33R, H2R, L1R), exit (A27L, A35R, A36R, C19L), and both (B5R). To achieve this, we aligned the genome sequencing data of mpox virus isolated from an infected individual in the United States in June 2022 (ON674051.1) with the reference genome dated 2001 (NC_003310.1) for conservation analysis. The Immune Epitope Database server was used for the identification and characterization of the epitopes of each protein related to major histocompatibility complex I or II interaction and recognition by B-cell receptors, resulting in 138 epitopes for A17L, 233 for A28L, 48 for A33R, 77 for H2R, 77 for L1R, 270 for A27L, 72 for A35R, A36R, 148 for C19L, and 276 for B5R. These epitopes were tested in silico for antigenicity, physicochemical properties, and allergenicity, resulting in 51, 40, 10, 34, 38, 57, 25, 7, 47, and 53 epitopes, respectively. Additionally, to select an epitope with the highest promiscuity of binding to major histocompatibility complexes and B-cell receptor simultaneously, all epitopes of each protein were aligned, and the most repetitive and antigenic regions were identified. By classifying the results, we obtained 23 epitopes from the entry proteins, 16 from the exit proteins, and 7 from both. Subsequently, 1 epitope from each protein was selected, and all 3 were fused to construct a chimeric protein that has potential as a multiepitope vaccine. The constructed vaccine was then analyzed for its physicochemical, antigenic, and allergenic properties. Protein modeling, molecular dynamics, and molecular docking were performed on Toll-like receptors 2, 4, and 8, followed by in silico immune simulation of the vaccine. Finally, the results indicate an effective, stable, and safe vaccine that can be further tested, especially in vitro and in vivo, to validate the findings demonstrated in silico.

Applying the bioisosterism strategy to obtain lead compounds against SARS-CoV-2 cysteine proteases: An in-silico approach.

SARS-CoV-2 cysteine proteases are essential nonstructural proteins due to their role in the formation of the virus multiple enzyme replication-transcription complex. As a result, those functional proteins are extremely relevant targets in the development of a new drug candidate to fight COVID-19. Based on this fact and guided by the bioisosterism strategy, the present work has selected 126 out of 1050 ligands from DrugBank website. Subsequently, 831 chemical analogs containing bioisosteres, some of which became structurally simplified, were created using the MB-Isoster software, and molecular docking simulations were performed using AutoDock Vina. Finally, a study of physicochemical properties, along with pharmacokinetic profiles, was carried out through SwissADME and ADMETlab 2.0 platforms. The promising results obtained with the molecules encoded as DB00549_BI_005, DB04868_BI_003, DB11984_BI_002, DB12364_BI_006 and DB12805_BI_004 must be confirmed by molecular dynamics studies, followed by in vitro and in vivo empirical tests that ratify the advocated in-silico results.

Neuroradiological features of patients with bilateral macronodular adrenocortical disease and meningiomas associated or not with genetic variants of ARMC5- a case series.

INTRODUCTION: Meningiomas are the most common primary brain and central nervous system tumors, accounting for approximately 40% of these tumors. The most important exams for the radiological study of meningiomas are computed tomography (CT) and magnetic resonance imaging (MRI). We aimed to analyze the radiological features of patients with meningioma related to the simultaneous presence of bilateral macronodular adrenocortical disease (BMAD), with or without pathogenic variants of ARMC5. METHODS: This study included 10 patients who were diagnosed with BMAD. All of them had a radiological diagnosis of expansive brain lesions suggestive of meningioma. All patients underwent brain MRI and a neuroradiolgist analyzed the following parameters: number, site and size of lesions; presence of calcification, edema and bone involvement. RESULTS AND DISCUSSION: Eight patients presented with germline variants of ARMC5; the other 2, did not. The most significant result was the incidence of multiple meningiomas, which was 50% in BMAD patients, whereas the average incidence described thus far is lower than 10%. Considering location, the 22 tumors in the BMAD patients were 5 convexity tumors (22.7%), and 17 skull base tumors (77.2%), the opposite proportion of patients without BMAD. A total of 40.9% of the tumors had calcification, 9% had cerebral edema and 40.9% had bone invasion due to hyperostosis. The literature describes meningioma calcification in 25% of patients, bone invasion by tumor hyperostosis in 20%, and cerebral edema in approximately 60%. CONCLUSION: Relevant results were found considering the rate of multiple meningiomas and tumor location. This finding reinforces the need for further research into the neurological effects caused by genetic variants of ARMC5 in patients with BMAD.

Use of High-Resolution Geospatial and Genomic Data to Characterize Recent Tuberculosis Transmission, Botswana.

Combining genomic and geospatial data can be useful for understanding Mycobacterium tuberculosis transmission in high-burden tuberculosis (TB) settings. We performed whole-genome sequencing on M. tuberculosis DNA extracted from sputum cultures from a population-based TB study conducted in Gaborone, Botswana, during 2012-2016. We determined spatial distribution of cases on the basis of shared genotypes among isolates. We considered clusters of isolates with ≤5 single-nucleotide polymorphisms identified by whole-genome sequencing to indicate recent transmission and clusters of ≥10 persons to be outbreaks. We obtained both molecular and geospatial data for 946/1,449 (65%) participants with culture-confirmed TB; 62 persons belonged to 5 outbreaks of 10-19 persons each. We detected geospatial clustering in just 2 of those 5 outbreaks, suggesting heterogeneous spatial patterns. Our findings indicate that targeted interventions applied in smaller geographic areas of high-burden TB identified using integrated genomic and geospatial data might help interrupt TB transmission during outbreaks.

Disseminated Mucor indicus infection in a marmoset (Callithrix sp.).

Mucormycosis is rarely described in Platyrrhines. Herein, we describe the pathologic and molecular features of a gastric and hepatic infection by Mucor indicus in a marmoset (Callithrix sp.).

Progress and promise of alternative animal and non-animal methods in biomedical research.

Cell culture and invertebrate animal models reflect a significant evolution in scientific research by providing reliable evidence on the physiopathology of diseases, screening for new drugs, and toxicological tests while reducing the need for mammals. In this review, we discuss the progress and promise of alternative animal and non-animal methods in biomedical research, with a special focus on drug toxicity.

A comparative analysis of clinical, functional and radiographic outcomes of patients with and without fusion between the first and second metatarsals after the lapidus procedure.

BACKGROUND: The aim of this study was to compare the clinical, functional and radiographic outcomes in patients who underwent the original Lapidus procedure (OLP) with fusion and undesired non-fusion between the first (M1) and second (M2) metatarsals. METHODS: A retrospective and comparative analysis of 29 patients (38 feet) who underwent the OLP was performed. They were divided in two groups: (1) 23 feet in which fusion occurred and (2) 15 with undesired non-fusion. Clinical and functional data were assessed with the VAS for pain, AOFAS, LEFS and SF-12. SF-12 comprises physical and mental health scales (PCS-12 and MCS-12). Radiographic parameters assessed were bony and soft tissue forefoot widths (BSFW), intermetatarsal-angle (IMA) and HV-angle (HVA). RESULTS: Separately, the groups presented significant improvements in all questionnaires (p < 0.001), except on MCS-12 (fusion p = 0.08 and non-fusion p = 0.27). When comparing both groups, patients with fusion had higher AOFAS scores (p < 0.05). Both groups presented the same improvements on BSFW, IMA and HVA (p = 0.09, p = 0.16, p = 0.52 and p = 0.63). CONCLUSION: Excellent results were observed, even when without fusion between M1 and M2. Patients who evolved with fusion between the M1 and M2 showed greater improvements in the AOFAS score. LEVEL OF EVIDENCE: III, retrospective comparative study.

Co-production of Classes A and B Carbapenemases BKC-1 and VIM-2 in a Clinical Pseudomonas Putida Group Isolate from Brazil.

Emergence of resistance to classical antimicrobial agents is a public health issue, especially in countries with high antimicrobial consumption rates. Carbapenems have been employed as first-choice option for empirical treatment complicated infections. However, in the last decades, frequency of carbapenemase-producing Gram-negative bacteria has rising, demanding the use of alternative antimicrobial agents. By sequencing the entire genomes with short and long reads technologies, we report the isolation and genomic characterization of a carbapenem-resistant Pseudomonas clinical isolate. The identification based on average nucleotide identity indicates a putative new species into the Pseudomonas putida Group, which carries both the blaBKC-1 and blaVIM-2 carbapenemase genes. The blaBKC-1 was found to be on a transferable IncQ plasmid backbone, whereas blaVIM-2 was found in a new integron, In2126 (intl1∆-blaVIM-2-aacA7-blaVIM-2∆-aacA27-3'CS), described in this study. Our findings indicate that co-occurrence of classes A and B carbapenemase enzymes underscores the evolving emergence of more complex antimicrobial resistance in opportunistic pathogens.

Differential Yellow Fever Susceptibility in New World Nonhuman Primates, Comparison with Humans, and Implications for Surveillance.

A major outbreak of yellow fever (YF) occurred in Brazil during 2016-2018. Epizootics in New World nonhuman primates are sentinel events for YF virus circulation. However, genus-specific susceptibilities and suitability for YF surveillance remain poorly understood. We obtained and compared epidemiologic, histopathologic, immunohistochemical, and molecular results from 93 human and 1,752 primate cases submitted during the recent YF outbreak in Brazil (2017), with the support of the Brazilian National YF Surveillance Program. We detected heterogeneous YF-associated profiles among the various genera of primates we analyzed. Alouatta primates were the most reliable sentinel; Sapajus and Callicebus primates had higher viral loads but lower proportional mortality rates. Callithrix primates were the least sensitive, showing lower viral loads, lower proportional mortality rates, and no demonstrable YF virus antigen or extensive lesions in liver, despite detectable viral RNA. These differences in susceptibility, viral load, and mortality rates should be considered in strategic surveillance of epizootics and control measures for YF.

Effects of gonadotropin inducible ovarian transcription factor 1 in the paraventricular nucleus on fluid intake after dehydration of ovariectomized female rats.

NEW FINDINGS: What is the central question of this study? Giot1, the gene for gonadotropin inducible ovarian transcription factor 1 (GIOT1), is upregulated in osmotically challenged rats: does Giot1 gene expression in the paraventricular nucleus have a role in controlling fluid intake following dehydration and what is the role of ovarian hormones in the modulation of GIOT1 actions? What is the main finding and its importance? GIOT1 acts to regulate water and salt intake as well as hormone secretion after dehydration. The identification of genes that participate in the hormone and behavioural responses involved with hydromineral homeostasis is essential for future exploration of novel drug targets for the treatment of metabolic disease. ABSTRACT: In order to maintain body fluid balance after dehydration, hypothalamic neurons of the paraventricular nucleus (PVN) are activated to promote secretion of vasopressin (AVP) and oxytocin (OXT) from the neurohypophysis, and to modulate the behavioural allostatic responses of thirst and salt appetite. Gonadotropin inducible transcription factor (GIOT1) is a Krüppel-type zinc finger protein induced by gonadotropins and oestradiol (E2). This transcription factor is expressed in the hypothalamus, specifically in the PVN where expression of Giot1 mRNA increases following hydromineral challenges such as water deprivation or salt loading, although its physiological role is not clear. We hypothesize that GIOT1 has a central role in the integrated homeostatic and allostatic responses to disturbances in hydromineral balance, especially in the presence of female gonadal hormones. Female rats with intact ovaries or ovariectomized rats were subjected to specific microinjection of a lentiviral vector mediating Giot1 knockdown in the PVN. Three weeks after injection, rats were subjected to 48 h water deprivation, and thereafter water and salt intake were evaluated. Giot1 knockdown in PVN reduced water and saline intake as well as AVP and OXT secretion. Furthermore, Giot1 knockdown had profound effects on gene expression in the PVN, reducing the abundance of transcripts encoded by the Avp, Oxt, Nr4a1 and Crh genes. In conclusion, the present study shows for the first time that GIOT1 in the PVN regulates both transcription and fluid intake, although any connection to ovarian hormones remains to be established.

Concurrent yellow fever and pulmonary aspergillosis due to Aspergillus fumigatus in a free-ranging howler monkey (Alouatta sp).

Herein, we describe a unique case of concomitant angioinvasive pulmonary aspergillosis due to Aspergillus fumigatus and yellow fever in a free-ranging howler monkey (Alouatta sp). Lung samples were negative for influenza viruses A and B.

Phosphatidylcholine PC ae C44:6 in cerebrospinal fluid is a sensitive biomarker for bacterial meningitis.

BACKGROUND: The timely diagnosis of bacterial meningitis is of utmost importance due to the need to institute antibiotic treatment as early as possible. Moreover, the differentiation from other causes of meningitis/encephalitis is critical because of differences in management such as the need for antiviral or immunosuppressive treatments. Considering our previously reported association between free membrane phospholipids in cerebrospinal fluid (CSF) and CNS involvement in neuroinfections we evaluated phosphatidylcholine PC ae C44:6, an integral constituent of cell membranes, as diagnostic biomarker for bacterial meningitis. METHODS: We used tandem mass spectrometry to measure concentrations of PC ae C44:6 in cell-free CSF samples (n = 221) from patients with acute bacterial meningitis, neuroborreliosis, viral meningitis/encephalitis (herpes simplex virus, varicella zoster virus, enteroviruses), autoimmune neuroinflammation (anti-NMDA-receptor autoimmune encephalitis, multiple sclerosis), facial nerve and segmental herpes zoster (shingles), and noninflammatory CNS disorders (Bell's palsy, Tourette syndrome, normal pressure hydrocephalus). RESULTS: PC ae C44:6 concentrations were significantly higher in bacterial meningitis than in all other diagnostic groups, and were higher in patients with a classic bacterial meningitis pathogen (e.g. Streptococcus pneumoniae, Neisseria meningitidis, Staphylococcus aureus) than in those with less virulent or opportunistic pathogens as causative agents (P = 0.026). PC ae C44:6 concentrations were only moderately associated with CSF cell count (Spearman's ρ = 0.45; P = 0.009), indicating that they do not merely reflect neuroinflammation. In receiver operating characteristic curve analysis, PC ae C44:6 equaled CSF cell count in the ability to distinguish bacterial meningitis from viral meningitis/encephalitis and autoimmune CNS disorders (AUC 0.93 both), but had higher sensitivity (91% vs. 41%) and negative predictive value (98% vs. 89%). A diagnostic algorithm comprising cell count, lactate and PC ae C44:6 had a sensitivity of 97% (specificity 87%) and negative predictive value of 99% (positive predictive value 61%) and correctly diagnosed three of four bacterial meningitis samples that were misclassified by cell count and lactate due to low values not suggestive of bacterial meningitis. CONCLUSIONS: Increased CSF PC ae C44:6 concentrations in bacterial meningitis likely reflect ongoing CNS cell membrane stress or damage and have potential as additional, sensitive biomarker to diagnose bacterial meningitis in patients with less pronounced neuroinflammation.

WavePacket: A Matlab package for numerical quantum dynamics. III. Quantum-classical simulations and surface hopping trajectories.

WavePacket is an open-source program package for numerical simulations in quantum dynamics. Building on the previous Part I (Schmidt and Lorenz, Comput. Phys. Commun. 2017, 213, 223] and Part II (Schmidt and Hartmann, Comput. Phys. Commun. 2018, 228, 229] which dealt with quantum dynamics of closed and open systems, respectively, the present Part III adds fully classical and mixed quantum-classical propagation techniques to WavePacket. There classical phase-space densities are sampled by trajectories which follow (diabatic or adiabatic) potential energy surfaces. In the vicinity of (genuine or avoided) intersections of those surfaces, trajectories may switch between them. To model these transitions, two classes of stochastic algorithms have been implemented: (1) Tully's fewest switches surface hopping and (2) Landau-Zener-based single switch surface hopping. The latter one offers the advantage of being based on adiabatic energy gaps only, thus not requiring nonadiabatic coupling information any more. The present work describes the MATLAB version of WavePacket 6.1.0, which is essentially an object-oriented rewrite of previous versions, allowing to perform fully classical, quantum-classical and quantum-mechanical simulations on an equal footing, that is, for the same physical system described by the same WavePacket input. The software package is hosted and further developed at the Sourceforge platform, where also extensive Wiki-documentation as well as numerous worked-out demonstration examples with animated graphics are available. © 2019 Wiley Periodicals, Inc.

Decreased plasma phospholipid concentrations and increased acid sphingomyelinase activity are accurate biomarkers for community-acquired pneumonia.

BACKGROUND: There continues to be a great need for better biomarkers and host-directed treatment targets for community-acquired pneumonia (CAP). Alterations in phospholipid metabolism may constitute a source of small molecule biomarkers for acute infections including CAP. Evidence from animal models of pulmonary infections and sepsis suggests that inhibiting acid sphingomyelinase (which releases ceramides from sphingomyelins) may reduce end-organ damage. METHODS: We measured concentrations of 105 phospholipids, 40 acylcarnitines, and 4 ceramides, as well as acid sphingomyelinase activity, in plasma from patients with CAP (n = 29, sampled on admission and 4 subsequent time points), chronic obstructive pulmonary disease exacerbation with infection (COPD, n = 13) as a clinically important disease control, and 33 age- and sex-matched controls. RESULTS: Phospholipid concentrations were greatly decreased in CAP and normalized along clinical improvement. Greatest changes were seen in phosphatidylcholines, followed by lysophosphatidylcholines, sphingomyelins and ceramides (three of which were upregulated), and were least in acylcarnitines. Changes in COPD were less pronounced, but also differed qualitatively, e.g. by increases in selected sphingomyelins. We identified highly accurate biomarkers for CAP (AUC ≤ 0.97) and COPD (AUC ≤ 0.93) vs. Controls, and moderately accurate biomarkers for CAP vs. COPD (AUC ≤ 0.83), all of which were phospholipids. Phosphatidylcholines, lysophosphatidylcholines, and sphingomyelins were also markedly decreased in S. aureus-infected human A549 and differentiated THP1 cells. Correlations with C-reactive protein and procalcitonin were predominantly negative but only of mild-to-moderate extent, suggesting that these markers reflect more than merely inflammation. Consistent with the increased ceramide concentrations, increased acid sphingomyelinase activity accurately distinguished CAP (fold change = 2.8, AUC = 0.94) and COPD (1.75, 0.88) from Controls and normalized with clinical resolution. CONCLUSIONS: The results underscore the high potential of plasma phospholipids as biomarkers for CAP, begin to reveal differences in lipid dysregulation between CAP and infection-associated COPD exacerbation, and suggest that the decreases in plasma concentrations are at least partially determined by changes in host target cells. Furthermore, they provide validation in clinical blood samples of acid sphingomyelinase as a potential treatment target to improve clinical outcome of CAP.

Nonlinear refractive index of electric field aligned gold nanorods suspended in index matching oil measured with a Hartmann-Shack wavefront aberrometer.

The capability to dynamically control the nonlinear refractive index of plasmonic suspensions may enable innovative nonlinear sensing and signaling nanotechnologies. Here, we experimentally determine the effective nonlinear refractive index for gold nanorods suspended in an index matching oil aligned using electric fields, demonstrating an approach to modulate the nonlinear optical properties of the suspension. The nonlinear optical experiments were carried out using a Hartmann-Shack wavefront aberrometer in a collimated beam configuration with a high repetition rate femtosecond laser. The suspensions were probed at 800 nm, overlapping with the long-axis absorption peak of the nanorods. We find that the effective nonlinear refractive index of the gold nanorods suspension depends linearly on the orientational order parameter, S, which can be understood by a thermally induced nonlinear response. We also show the magnitude of the nonlinear response can be varied by ∼ 60%.

Microscopic Aspects of Silicon-Mediated Rice Resistance to Leaf Scald.

This study investigated the effect of silicon (Si) on the potentiation of rice resistance against leaf scald at the microscopic level. Rice plants ('Primavera') were grown in a nutrient solution containing 0 (-Si) or 2 mM (+Si) Si. The foliar Si concentration of the +Si plants (3.6 dag/kg) increased in comparison with the -Si plants (0.3 dag/kg). An X-ray microanalysis revealed that the leaf tissue of +Si plants infected with Microdochium oryzae had higher peaks and deposition of insoluble Si than that of -Si plants. The high foliar Si concentration for the +Si plants reduced the expansion of leaf scald lesions. Scanning electron microscopy revealed that fungal hyphae and appressorium-like structures of M. oryzae were more abundant in the leaf surface of -Si plants relative to +Si plants. At both histopathological and ultrastructural levels, fungal hyphae grew abundantly into the leaf tissue of -Si plants. By contrast, rice cell walls were rarely degraded and fungal hyphae were often surrounded by amorphous granular material in the leaf tissue of +Si plants. Conidiophores emerged from stomata 36 h after fungal penetration, and conidia were noticed inside the leaf tissue of the -Si plants in great abundance. The collective results of the present study showed a high concentration and deposition of Si and a considerable deposition of phenolic-like compounds in the leaf tissue of +Si plants. These results indicate that the potentiation of the phenylpropanoid pathway in these plants supplied with Si was favorable for the increase in rice resistance to leaf scald.

Resistance in mango against infection by Ceratocystis fimbriata.

This study was designed to characterize and describe host cell responses of stem tissue to mango wilt disease caused by the fungus Ceratocystis fimbriata in Brazil. Disease progress was followed, through time, in inoculated stems for two cultivars, 'Ubá' (field resistant) and 'Haden' (field susceptible). Stem sections from inoculated areas were examined using fluorescence light microscopy and transmission and scanning electron microscopy, coupled with energy-dispersive X-ray microanalysis. Tissues from Ubá colonized by C. fimbriata had stronger autofluorescence than those from Haden. The X-ray microanalysis revealed that the tissues of Ubá had higher levels of insoluble sulfur and calcium than those of Haden. Scanning electron microscopy revealed that fungal hyphae, chlamydospores (aleurioconidia), and perithecia-like structures of C. fimbriata were more abundant in Haden relative to Ubá. At the ultrastructural level, pathogen hyphae had grown into the degraded walls of parenchyma, fiber cells, and xylem vessels in the tissue of Haden. However, in Ubá, plant cell walls were rarely degraded and hyphae were often surrounded by dense, amorphous granular materials and hyphae appeared to have died. Taken together, the results of this study characterize the susceptible and resistant basal cell responses of mango stem tissue to infection by C. fimbriata.

FSSH-2: Fewest Switches Surface Hopping with Robust Switching Probability.

This study introduces the FSSH-2 scheme, a redefined and numerically stable adiabatic Fewest Switches Surface Hopping (FSSH) method for mixed quantum-classical dynamics. It reformulates the standard FSSH hopping probability without using nonadiabatic coupling vectors and allows for numerical time integration with larger step sizes. The advantages of FSSH-2 are demonstrated by numerical experiments for five different model systems in one and two spatial dimensions with up to three electronic states.

Earth observation data uncover green spaces' role in mental health.

The prevalence of mental health disorders, a key disability cause, is linked to demographic and socioeconomic factors. However, limited data exists on mental health and the urban environment. Urbanization exposes populations to environmental stressors, particularly affecting low-middle-income countries with complex urban arrangements. We used remote sensing and census data to investigate potential connections between environmental factors and mental health disorders. Land cover variables were assessed using the European Space Agency (ESA) global WorldCover product at 10 m resolution together with the database of mental health diagnosed cases (n = 5769) from the Brazilian Unified Health System's Department of Informatics (DATASUS) from every health facility of the city of Porto Alegre. The association of mental health data with land cover was established with machine learning algorithms and polynomial regression models. The results suggest that higher trees cover at neighborhood level was associated with better mental health index. A lower mental health index was also found to be associated with an higher Human Development Index. Our results highlight the potential of greenness in the city environment to achieve substantially better mental health outcomes.