Project description:MotivationFunctional genomics research has expanded enormously in the last decade thanks to the cost reduction in high-throughput technologies and the development of computational tools that generate, standardize and share information on gene and protein function such as the Gene Ontology (GO). Nevertheless, many biologists, especially working with non-model organisms, still suffer from non-existing or low-coverage functional annotation, or simply struggle retrieving, summarizing and querying these data.ResultsThe Blast2GO Functional Annotation Repository (B2G-FAR) is a bioinformatics resource envisaged to provide functional information for otherwise uncharacterized sequence data and offers data mining tools to analyze a larger repertoire of species than currently available. This new annotation resource has been created by applying the Blast2GO functional annotation engine in a strongly high-throughput manner to the entire space of public available sequences. The resulting repository contains GO term predictions for over 13.2 million non-redundant protein sequences based on BLAST search alignments from the SIMAP database. We generated GO annotation for approximately 150 000 different taxa making available 2000 species with the highest coverage through B2G-FAR. A second section within B2G-FAR holds functional annotations for 17 non-model organism Affymetrix GeneChips.ConclusionsB2G-FAR provides easy access to exhaustive functional annotation for 2000 species offering a good balance between quality and quantity, thereby supporting functional genomics research especially in the case of non-model organisms.AvailabilityThe annotation resource is available at http://www.b2gfar.org.
Project description:Crohn's disease is a chronic gastrointestinal inflammatory disorder, characterized by episodes of relapsing and remitting flares. As the disease mechanism becomes better elucidated, there is a significant increase in the number of available biologic therapies. This article summarizes and synthesizes current Food and Drug Administration-approved biological therapy for Crohn's disease and examines the positioning of medical therapy as emerging biologics break onto the market.
Project description:Delayed immune-mediated adverse drug reactions (IM-ADRs) are defined as reactions occurring more than 6 hours after dosing. They include heterogeneous clinical phenotypes that are typically T-cell-mediated reactions with distinct mechanisms across a wide spectrum of severity from benign exanthems through to life-threatening cutaneous or organ-specific diseases. For mild reactions such as benign exanthem, considerations for delabeling are similar to immediate reactions and may include a graded or single-dose drug challenge with or without preceding skin or patch testing. Evaluation of challenging cases such as the patient who is on multiple drugs at the time a severe delayed IM-ADR occurs should prioritize clinical ascertainment of the most likely phenotype and implicated drug(s). Although not widely available and validated, procedures such as patch testing, delayed intradermal skin testing, and laboratory-based functional drug assays or genetic (human leukocyte antigen) testing may provide valuable information to further help risk stratify patients and identify the likely implicated and/or cross-reactive drug(s). The decision to use a drug challenge as a diagnostic or delabeling tool in a patient with a severe delayed IM-ADR should weigh the risk-benefit ratio, balancing the severity and priority for the treatment of the underlying, and the availability of alternative efficacious and safe treatments.
Project description:The genus Azospirillum comprises plant-growth-promoting bacteria (PGPB), which have been broadly studied. The benefits to plants by inoculation with Azospirillum have been primarily attributed to its capacity to fix atmospheric nitrogen, but also to its capacity to synthesize phytohormones, in particular indole-3-acetic acid. Recently, an increasing number of studies has attributed an important role of Azospirillum in conferring to plants tolerance of abiotic and biotic stresses, which may be mediated by phytohormones acting as signaling molecules. Tolerance of biotic stresses is controlled by mechanisms of induced systemic resistance, mediated by increased levels of phytohormones in the jasmonic acid/ethylene pathway, independent of salicylic acid (SA), whereas in the systemic acquired resistance-a mechanism previously studied with phytopathogens-it is controlled by intermediate levels of SA. Both mechanisms are related to the NPR1 protein, acting as a co-activator in the induction of defense genes. Azospirillum can also promote plant growth by mechanisms of tolerance of abiotic stresses, named as induced systemic tolerance, mediated by antioxidants, osmotic adjustment, production of phytohormones, and defense strategies such as the expression of pathogenesis-related genes. The study of the mechanisms triggered by Azospirillum in plants can help in the search for more-sustainable agricultural practices and possibly reveal the use of PGPB as a major strategy to mitigate the effects of biotic and abiotic stresses on agricultural productivity.
Project description:BackgroundMexican state governments' actions are essential to control the COVID-19 pandemic within the country. However, the type, rigor and pace of implementation of public policies have varied considerably between states. Little is known about the subnational (state) variation policy response to the COVID-19 pandemic in Mexico.Material and methodsWe collected daily information on public policies designed to inform the public, as well as to promote distancing, and mask use. The policies analyzed were: School Closure, Workplace Closure, Cancellation of Public Events, Restrictions on Gatherings, Stay at Home Order, Public Transit Suspensions, Information Campaigns, Internal Travel Controls, International Travel Controls, Use of Face Masks We use these data to create a composite index to evaluate the adoption of these policies in the 32 states. We then assess the timeliness and rigor of the policies across the country, from the date of the first case, February 27, 2020.ResultsThe national average in the index during the 143 days of the pandemic was 41.1 out of a possible 100 points on our index. Nuevo León achieved the highest performance (50.4); San Luis Potosí the lowest (34.1). The differential between the highest versus the lowest performance was 47.4%.ConclusionsThe study identifies variability and heterogeneity in how and when Mexican states implemented policies to contain COVID-19. We demonstrate the absence of a uniform national response and widely varying stringency of state responses. We also show how these responses are not based on testing and do not reflect the local burden of disease. National health system stewardship and a coordinated, timely, rigorous response to the pandemic did not occur in Mexico but is desirable to contain COVID-19.
Project description:It is important to predict the neurological prognoses of in-hospital cardiac arrest (IHCA) patients immediately after recovery of spontaneous circulation (ROSC) to make further critical management. The aim of this study was to confirm the usefulness of the Cardiac Arrest Survival Post-Resuscitation In-hospital (CASPRI) and Good Outcome Following Attempted Resuscitation (GO-FAR) scores for predicting the IHCA immediately after the ROSC. This is a retrospective analysis of patient data from a tertiary general hospital located in South Korea. A total of 488 adult patients who had IHCA and achieved sustained ROSC from September 2016 to August 2021 were analyzed to compare effectiveness of the CASPRI and GO-FAR scores related to neurologic prognosis. The primary outcome was Cerebral Performance Category (CPC) score at discharge, defined as a CPC score of 1 or 2. The secondary outcomes were survival-to-discharge and normal neurological status or minimal neurological damage at discharge. Of the 488 included patients, 85 (20.8%) were discharged with good prognoses (CPC score of 1 or 2). The area under the receiver operating characteristic curve of CASPRI score for the prediction of a good neurological outcome was 0.75 (95% CI 0.69-0.81), whereas that of GO-FAR score was 0.67 (95% CI 0.60-0.73). The results of this study show that these scoring systems can be used for timely and satisfactory prediction of the neurological prognoses of IHCA patients after ROSC.
Project description:Behavioural flexibility is considered a key factor in the ability to adapt to changing environments. A traditional way of characterizing behavioural flexibility is to determine whether individuals invent solutions to novel problems, termed innovativeness. Great-tailed grackles are behaviourally flexible in that they can change their preferences when a task changes using existing behaviours; however, it is unknown how far they will go to invent solutions to novel problems. To begin to answer this question, I gave grackles two novel tests that a variety of other species can perform: stick tool use and string pulling. No grackle used a stick to access out-of-reach food, even after seeing a human demonstrate the solution. No grackle spontaneously pulled a vertically oriented string, but one did pull a horizontally oriented string twice. Additionally, a third novel test was previously conducted on these individuals and it was found that no grackle spontaneously dropped stones down a platform apparatus to release food, but six out of eight did become proficient after training. These results support the idea that behavioural flexibility is a multi-faceted trait because grackles are flexible, but not particularly innovative. This contradicts the idea that behavioural flexibility and innovativeness are interchangeable terms.
Project description:BackgroundNetwork meta-analysis may require substantially more resources than does a standard systematic review. One frequently asked question is "how far should I extend the network and which treatments should I include?"ObjectiveTo explore the increase in precision from including additional evidence.MethodsWe assessed the benefit of extending treatment networks in terms of precision of effect estimates and examined how this depends on network structure and relative strength of additional evidence. We introduced a "star"-shaped network. Network complexity is increased by adding more evidence connecting treatments under five evidence scenarios. We also examined the impact of heterogeneity and absence of evidence facilitating a "first-order" indirect comparison.ResultsIn all scenarios, extending the network increased the precision of the A versus B treatment effect. Under a fixed-effect model, the increase in precision was modest when the existing direct A versus B evidence was already strong and was substantial when the direct evidence was weak. Under a random-effects model, the gain in precision was lower when heterogeneity was high. When evidence is available for all "first-order" indirect comparisons, including second-order evidence has limited benefit for the precision of the A versus B estimate. This is interpreted as a "ceiling effect."ConclusionsIncluding additional evidence increases the precision of a "focal" treatment comparison of interest. Once the comparison of interest is connected to all others via "first-order" indirect evidence, there is no additional benefit in including higher order comparisons. This conclusion is generalizable to any number of treatment comparisons, which would then all be considered "focal." The increase in precision is modest when direct evidence is already strong, or there is a high degree of heterogeneity.