Development of an amplicon-based sequencing approach in response to the global emergence of mpox

The 2022 multicountry mpox outbreak concurrent with the ongoing Coronavirus Disease 2019 (COVID-19) pandemic further highlighted the need for genomic surveillance and rapid pathogen whole-genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox infections, these methods are resource intensive and require samples with high viral DNA concentrations. Given the atypical clinical presentation of cases associated with the outbreak and uncertainty regarding viral load across both the course of infection and anatomical body sites, there was an urgent need for a more sensitive and broadly applicable sequencing approach. Highly multiplexed amplicon-based sequencing (PrimalSeq) was initially developed for sequencing of Zika virus, and later adapted as the main sequencing approach for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Here, we used PrimalScheme to develop a primer scheme for human monkeypox virus that can be used with many sequencing and bioinformatics pipelines implemented in public health laboratories during the COVID-19 pandemic. We sequenced clinical specimens that tested presumptively positive for human monkeypox virus with amplicon-based and metagenomic sequencing approaches. We found notably higher genome coverage across the virus genome, with minimal amplicon drop-outs, in using the amplicon-based sequencing approach, particularly in higher PCR cycle threshold (Ct) (lower DNA titer) samples. Further testing demonstrated that Ct value correlated with the number of sequencing reads and influenced the percent genome coverage. To maximize genome coverage when resources are limited, we recommend selecting samples with a PCR Ct below 31 Ct and generating 1 million sequencing reads per sample. To support national and international public health genomic surveillance efforts, we sent out primer pool aliquots to 10 laboratories across the United States, United Kingdom, Brazil, and Portugal. These public health laboratories successfully implemented the human monkeypox virus primer scheme in various amplicon sequencing workflows and with different sample types across a range of Ct values. Thus, we show that amplicon-based sequencing can provide a rapidly deployable, cost-effective, and flexible approach to pathogen whole-genome sequencing in response to newly emerging pathogens. Importantly, through the implementation of our primer scheme into existing SARS-CoV-2 workflows and across a range of sample types and sequencing platforms, we further demonstrate the potential of this approach for rapid outbreak response.This publication was made possible by CTSA Grant Number UL1 TR001863 from the National Center for Advancing Translational Science (NCATS), a component of the National Institutes of Health (NIH) awarded to CBFV. INSA was partially funded by the HERA project (Grant/ 2021/PHF/23776) supported by the European Commission through the European Centre for Disease Control (to VB).info:eu-repo/semantics/publishedVersio

UM Translog: A Planning Domain for the Development and Benchmarking of Planning Systems

The last twenty years of AI planning research has discovered a wide variety of planning techniques such as state-space search, hierarchical planning, case-based planning and reactive planning. These techniques have been implemented in numerous planning systems (e.g., [12,8,9,10,11]). Initially, a number of simple toy domains have been devised to assist in the analysis and evaluation of planning systems and techniques. The most well know examples are ﲂlocks World and ﲔowers of Hanoi . As planning systems grow in sophistication and capabilities, however, there is a clear need for planning benchmarks with matching complexity to evaluate those new features and capabilities. UM Translog is a planning domain designed specifically for this purpose.UM Translog was inspired by the CMU Transport Logistics domain developed by Manuela Veloso. UM Translog is an order of magnitude larger in size (41 actions versus 6), number of features and types interactions. It provides a rich set of entities, attributes, actions and conditions, which can be used to specify rather complex planning problems with a variety of plan interactions. The detailed set of operators provides long plans (40 steps) with many possible solutions to the same problem, and thus this domain can also be used to evaluate the solution quality of planning systems. The UM Translog domain has been used with the UMCP, UM Nonlin, and CaPER planning systems thus far

Possible role of Helicobacter pylori in the etiopathogenesis of chronic otitis media

WOS: 000233259100007PubMed ID: 16272928Objective: To investigate a possible contribution from Helicobacter pylori to the etiopathogenesis of chronic otitis media. Study Design: Prospective clinical trial. Methods: Tympanomastoidectomy, radical mastoidectomy, and modified radical mastoidectomy procedures were performed according to the pathology of ear disease. Biopsy specimens were taken from middle ear, mastoid antrum, and tympanic orifice of eustachian tube. Helicobacter pylori DNA was extracted from these biopsy specimens by using nested polymerase chain reaction. Results: Helicobacter pylori DNA was detected in 3 (7.9%) of 38 chronic otitis media patients. Conclusion: Even though it is possible to detect Helicobacter pylori in middle ear cleft in chronic otitis media, its role in the etiopathogenesis of the issue is controversial

Polyostotic fibrous dysplasia with craniofacial localization presenting with frontal lobe compression in a 14-year-old girl

We describe a rare case of polyostotic fibrous dysplasia with craniofacial localization associated with involvement of the spine and extremities. A 14-year-old girl presented with progressive headache, left frontal swelling, exophthalmos of the left eye, deformity and palpable mass in the left frontal area. Cranial computerized tomography revealed extensive involvement of all cranial bones except right frontal and right parietal bones. Most of the facial bones were invaded. Especially, there was the involvement of ethmoidal air sinuses and frontal sinus also. Computerized tomography showed left frontal lobe compression. In addition, the spine and bones of the extremities were involved in the patient. Craniofacial approach was planned. Cranial surgery was performed by an extradural frontal approach. Firstly, the frontal cyst was excised. For left frontal lobe decompression, we removed successfully all the abnormal bones causing mass effect and frontal deformity. Secondly, facial surgery was performed with external approach. An attempt to remove all of the involved bone is necessary, as the lesion may recur and grow if a portion of dysplastic bone is left in place. However, the present case suggests that removal of all the involved bones in the polyostotic fibrous dysplasia may be possible in spite of extensive involvement. In this situation, it may be removal of only abnormal bones responsible for compression of affected neural elements is indicated

Effects of lisinopril on NMDA receptor subunits 2A and 2B levels in the hippocampus of rats with l-NAME-induced hypertension

PubMed: 22943192Hypertension is major risk factor leading to cerebrovascular pathologies. N-methyl d-aspartate receptors (NMDARs) and renin-angiotensin system are involved in neuronal plasticity, as well as cognitive functions in the hippocampus. In this study, we examined the effects of lisinopril, an ACE inhibitor, on the levels of hippocampal NMDAR subunits; NR2A and NR2B in l-NAME (N?-nitro-l-arginine Methyl Ester)-induced hypertensive rats. In addition, malondialdehyde (MDA) levels were measured as a marker for lipid peroxidation. Compared with the control group, the MDA level was significantly increased after 8 weeks in the l-NAME-treated group. Rats treated with lisinopril and l-NAME plus lisinopril were found to have significantly decreased hippocampal MDA levels. Regarding the hippocampal concentrations of NR2A and NR2B, there were no statistically significant differences between groups. We demonstrated that lisinopril treatment has no direct regulatory effect on the levels of NR2A and NR2B in the rat hippocampus. Our results showed that Lisinopril could act as an antioxidant agent against hypertension-induced oxidative stress in rat hippocampus. The findings support that the use of lisinopril may offer a good alternative in the treatment of hypertension by reducing not only blood pressure but also prevent hypertensive complications in the brain. © 2012 Informa Healthcare USA, Inc

Are there Correleations among histologic radiologic and cytopathologic findings in non-allergic Chronic rinosinusitis without nasal polyposis

Purpose: To investigate any correlations among cytopathologic, radiologic, and historic findings in non-allergic chronic rhinosinusitis without nasal polyposis. Materials and Methods: This prospective study was done on 40 adult patients who had undergone functional endoscopic sinus surgery due to chronic rhinosinusitis. Symptom, nasal smear, paranasal computed tomography, as well as histopathologic findings of uncinate process, anterior ethmoid cells, and ethmoidal infundibulum were scored. Correlations were analysed among symptom, radiologic, and cytopathologic scores. Results: While the symptom scores of patients with chronic rhinosinusitis were positively correlated with only nasal smear scores, it was not correlated with computed tomography and histopathologic scores. On the other hand, radiologic scores were correlated with tissue eosinophils scores of uncinate process, anterior ethmoidal cells, and ethmoidal infundibulum Conclusions: The correlation of symptom score to nasal smear score in chronic sinusitis may be an evidence for the positive relationship symptoms and acute inflammation. The correlation of radiologic score to eosinophilia scores of uncinate process, anterior ethmoidal cells, and infundibulum may signify the importance of tissue eosinophils in chronic sinusitis. Keywords: Rhinosinusitits, nasal polyposis, non-allergic rhinosinusitis. Nigerian Journal of Otorhinolaryngology Vol. 3 (2) 2006: pp. 45-5

Detection of cholesteatoma: High-resolution DWI using RS-EPI and parallel imaging at 3 tesla

The purpose of this study is to evaluate the impact of RS-EPI-DWI in the detection of cholesteatoma and to compare with single-shot echo-planar DWI (SS-EPI-DWI). Diffusion-weighted and apparent diffusion-coefficient (ADC) images were obtained using RS-EPI and SS-EPI techniques in 30 patients. Presence of cholesteatoma (3 point scale), amount of artefacts (4 point scale), visibility (4 point scale), and ADC values of the lesions were assessed. The results of both techniques were compared with each other and gold-standard (GS) test results. Lesion visibility and presence of artefact scores of RS-EPI-DWI group were significantly different from those of the SS-EPI group. RS-EPI-DWI images had fewer artefacts and higher visibility scores. The sensitivity, specificity, negative/positive-predictive, and overall-agreement values of RS-EPI-DWI technique were 100%, 78%, 100%, 74%, and 87%; respectively. These values for SS-EPI-DWI technique were 91%, 60%, 88%, 67%, and 75%; respectively. Also, these values were higher on axial plane than coronal plane images for ADC measurements. Based on gold-standard test findings, agreement values were good (κ = 0.74) for RS-EPI-DWI and moderate for SS-EP-DWI (κ = 0.50) techniques (P < 0.001 for both). The RS-EPI-DWI technique allows a higher spatial-resolution and this technique is less susceptible to artefacts when compared with SS-EPI technique. © 2017 Elsevier Masson SA