Pennkenny0019
The data produced by long-read third-generation sequencers have unique characteristics compared to short-read sequencing data, often requiring tailored analysis tools for tasks ranging from quality control to downstream processing. The rapid growth in software that addresses these challenges for different genomics applications is difficult to keep track of, which makes it hard for users to choose the most appropriate tool for their analysis goal and for developers to identify areas of need and existing solutions to benchmark against.
We describe the implementation of long-read-tools.org, an open-source database that organizes the rapidly expanding collection of long-read data analysis tools and allows its exploration through interactive browsing and filtering. The current database release contains 478 tools across 32 categories. Most tools are developed in Python, and the most frequent analysis tasks include base calling, de novo assembly, error correction, quality checking/filtering, and isoform detection, while long-read single-cell data analysis and transcriptomics are areas with the fewest tools available.
Continued growth in the application of long-read sequencing in genomics research positions the long-read-tools.org database as an essential resource that allows researchers to keep abreast of both established and emerging software to help guide the selection of the most relevant tool for their analysis needs.
Continued growth in the application of long-read sequencing in genomics research positions the long-read-tools.org database as an essential resource that allows researchers to keep abreast of both established and emerging software to help guide the selection of the most relevant tool for their analysis needs.
SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.
The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines.
Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https//www.htslib.org.
1 million times via Bioconda. The source code and documentation are available from https//www.htslib.org.
The case-fatality rate of dengue in travelers is low. Secondary dengue virus (DENV) infections are considered a risk factor for fatal outcome in endemic populations; however, the impact of secondary infections on mortality in travelers has not been studied systematically. We performed a descriptive analysis of case reports of dengue fatalities in travelers.
We searched Medline for clinical case reports, using the free terms and MeSH headings 'Dengue' OR 'Severe Dengue' AND 'Travel-Related Illness' OR 'travel' AND 'Mortality' OR 'Fatal Outcome'. We analyzed case reports of fatal dengue in returning travelers published from 1995 to 2020, with the objective to detail risk factors for dengue mortality in this population. We verified the authors' classifications of primary or secondary dengue infections; infections were considered as primary by absence of anti-DENV immunoglobulin (Ig)G or by IgM-to-IgG ratios greater than or equal to 1.8 in the first 7 days post symptom onset.
We identified nine detailed repavelers are primary infections. Contrary to prevailing conceptions, we found that fatal outcomes of dengue in travelers from non-endemic countries were reported mainly with primary DENV infections. We alert health care providers that primary DENV infections are not always harmless and that in adult travelers from non-endemic countries, primary infections may contribute more to dengue-related mortality than secondary infections.The Asian longhorned tick, Haemaphysalis longicornis Neumann (Acari Ixodidae), was recently introduced into the United States and is now established in at least 15 states. Considering its ability for parthenogenetic propagation and propensity for creating high-density populations, there is concern that this tick may become involved in transmission cycles of endemic tick-borne human pathogens. Human granulocytic anaplasmosis (HGA) caused by Anaplasma phagocytophilum is one of the more common tick-borne diseases in the United States, especially in the northeastern and midwestern states. There is considerable geographical overlap between HGA cases and the currently known distribution of H. longicornis, which creates a potential for this tick to encounter A. phagocytophilum while feeding on naturally infected vertebrate hosts. Therefore, we evaluated the ability of H. longicornis to acquire and transmit the agent of HGA under laboratory conditions and compared it to the vector competence of I. scapularis. Haemaphysalis longicornis nymphs acquired the pathogen with the bloodmeal while feeding on infected domestic goats, but transstadial transmission was inefficient and PCR-positive adult ticks were unable to transmit the pathogen to naïve goats. Results of this study indicate that the Asian longhorned tick is not likely to play a significant role in the epidemiology of HGA in the United States.While trapping methods for Drosophila suzukii Matsumura (Diptera Drosophilidae) have typically relied on fermentation volatiles alone or in association with a visual stimulus, the relative contribution of visual and olfactory stimuli to the food- and host-seeking behavior of D. suzukii is poorly understood. This study quantified the type of response exhibited by male and female D. suzukii to color and the effects that volatiles (fermentation, fresh fruit, and leaf) exert on the outcome. Seven-, four- and two-choice assays were used to quantify interactions between visual and olfactory cues. When no volatiles were present in a seven-choice assay, D. suzukii preferred red, black, and green pigments. Black and red were preferred when yeast odors were present, and black alone was the most attractive color when blueberry odor was present. A strawberry leaf terpenoid, β-cyclocitral, seemed to have overridden the flies' response to color. In four-choice assays, blueberry odor was more likely to interact synergistically with color than yeast or β-cyclocitral. This study demonstrates that D. suzukii modulates the response to multimodal sensory modalities (vision and olfaction) depending, to some extent, on the type of olfactory stimuli. Our findings also provide insight into the relative importance of vision as a function of odor quality in this invasive species.
Concurrent use of tobacco cigarettes and e-cigarettes ("dual use") is common among tobacco users. Little is known about differences in demographics and toxicant exposure among subsets of dual users.
We analyzed data from adult dual users (current every/some day users of tobacco cigarettes and e-cigarettes, n = 792) included in the PATH Study Wave 1 (2013-2014) and provided urine samples. Samples were analyzed for biomarkers of exposure to nicotine and selected toxicants (tobacco-specific nitrosamine NNK [NNAL], lead, cadmium, naphthalene [2-naphthol], pyrene [1-hydroxypyrene], acrylonitrile [CYMA], acrolein [CEMA], and acrylamide [AAMA]). Subsets of dual users were compared on demographic, behavioral, and biomarker measures to exclusive cigarette smokers (n = 2411) and exclusive e-cigarette users (n = 247).
Most dual users were predominant cigarette smokers (70%), followed by daily dual users (13%), non-daily concurrent dual users (10%), and predominant vapers (7%). Dual users who smoked daily showed sitoxicant exposure.Information about invasive species needs to be spread rapidly across a wide geographic area following an invasion. However, in-person events can be time-consuming and costly for the participants, organizers, and presenters. Online programming like webinars can bridge this gap, but there is limited published data on how best to run these programs. We report on a 10-yr webinar program, Emerald Ash Borer University, and offer suggestions for improving their effectiveness as a communication tool. Webinar participants viewed the webinars positively and undertook recommended management actions. In addition, most of our survey respondents extended the reach of this program by widely sharing the information from the webinars. Posting the webinars on popular streaming platforms greatly extended their reach long after the live viewing event. Despite their longevity, viewers of recorded videos watched them differently than those viewing live events. We suggest modifying the format of future webinar presentations to accommodate these differences to improve information transfer.This study assessed the protective effects of paeoniflorin against preeclampsia-related endothelial damage (ED). Human umbilical vein endothelial cells (HUVECs) isolated from healthy puerperae were identified by immunofluorescence assay. After paeoniflorin treatment, HUVECs were induced by soluble fms-like tyrosine kinase 1 (sFlt-1) and soluble endoglin (sEng) to establish ED. Acetylcholine Chloride price Cell viability, migration, invasion, tube formation, and apoptosis were assessed by (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) tetrazolium MTT assay, Scratch assay, Transwell assay, tube formation assay, and flow cytometry. VEGFA expression in HUVECs was analyzed by Western blot. HUVECs were successfully isolated and identified as Von Willebrand factor (vWF) positive. Individual treatment or cotreatment of sFlt-1 and sEng inhibited migration, invasion and tube formation, enhanced apoptosis, and decreased VEGFA expression in HUVECs. link2 Paeoniflorin pretreatment partially reversed the effects delivered by cotreatment of sFlt-1 and sEng in HUVECs. Paeoniflorin alleviated preeclampsia-related ED caused by overexpression of sFlt-1 and sEng by upregulating VEGFA.Interleukin-6 (IL-6) binds to the IL-6 receptor (IL-6R) subunit, related to autoimmune diseases and cytokine storm in COVID-19. In this study, we performed systematic evolution of ligands by exponential enrichment and identified a novel RNA aptamer. This RNA aptamer not only bound to IL-6R with a dissociation constant of 200 n m, but also inhibited the interaction of IL-6R with IL-6.The overactivation of macrophages causes chronic inflammatory diseases. Short-chain fatty acids (SCFAs), potential drugs for clinical treatment, are modulators of macrophage inflammatory reaction. Therefore, the modulation of macrophage-mediated cell activity is expected to become a new therapeutic strategy for inflammatory diseases caused by Mycoplasma pneumoniae. In this study, 2 kinds of SCFAs (propionate and butyrate) were found to have anti-inflammatory effects in M. link3 pneumoniae-stimulated THP-1 cells inflammatory. They inhibited the expressions of IL-4, IL-6, ROS, and NLRP3 inflammasome, while enhancing the expressions of IL-10 and IFN-γ. Our study revealed these 2 agents to repress transcriptional activities of NF-κB, which are important modulators of inflammation. Meanwhile, SCFAs can significantly enhance the autophagy induced by M. pneumoniae. Considering that SCFAs have few side effects, they might be the promising adjuvant therapy for the prevention and/or treatment of various inflammatory diseases.
