Summary Background Bacterial meningitis continues to be a substantial cause of morbidity and mortality, but the epidemiological trends after adjunctive dexamethasone recommendations are unknown in ...the USA. We aimed to describe the changing patterns among the most common bacterial causes in the USA after conjugate vaccination and to assess the association between adjunctive dexamethasone and mortality. Methods For this population-based observational study, we searched information available from hospital discharges about incidence and inpatient mortality for the most important causes of community and nosocomial bacterial meningitis based on International Classification of Diseases coding across all hospitals in the USA between 1997 and 2010 with the HealthCare Cost Utilization Project (HCUP) network database. We calculated incidences according to US Census Bureau data and used a negative binomial regression model to evaluate the significance of changes over time. We assessed mortality from pneumococcus for three periods 1997–2001 (baseline), 2002–04 (transition years), and 2005–08 (after corticosteroid recommendations were available). Findings Streptococcus pneumoniae incidence fell from 0·8 per 100 000 people in 1997, to 0·3 per 100 000 people by the end of 2010 (RR 0·3737, 95% CI 0·1825–0·7656). Mortality from pneumococcal meningitis decreased between 2005 (0·049 per 100 000 people) and 2008 (0·024 per 100 000 people) compared with between 2002 (0·073 per 100 000 people) and 2004 (0·063 per 100 000 people; RR 0·5720, 95% CI 0·4303–0·7582). The incidence of Neisseria meningitidis infection decreased from 0·721 per 100 000 people in 1997, to 0·123 per 100 000 people in 2010 (RR 0·1386, 95% CI 0·048–0·4284), which has placed this pathogen close to common bacterial causes of nosocomial meningitis such as staphylococcus and Gram-negative bacteria and to Haemophilus influenzae. Interpretation S pneumoniae continues to be the leading identifiable cause of bacterial meningitis in the USA, but with a significant decrease in incidence and mortality associated with the introduction of conjugated vaccines and a mortality decrease that is associated with the introduction of recommendations for use of adjunctive dexamethasone for pneumococcal meningitis. Funding National Center for Research Resources.
Since 2009 the EMBL-EBI provides free and unrestricted access to several bioinformatics tools via the user's browser as well as programmatically via Web Services APIs. Programmatic access to these ...tools, which is fundamental to bioinformatics, is increasingly important as more high-throughput data is generated, e.g. from proteomics and metagenomic experiments. Access is available using both the SOAP and RESTful approaches and their usage is reviewed regularly in order to ensure that the best, supported tools are available to all users. We present here an update describing the latest enhancement to the Job Dispatcher APIs as well as the governance under it.
Frontotemporal dementia (FTD), the second most common form of dementia in people under 65 years of age, is characterized by progressive atrophy of the frontal and/or temporal lobes. FTD overlaps ...extensively with the motor neuron disease amyotrophic lateral sclerosis (ALS), especially at the genetic level. Both FTD and ALS can be caused by many mutations in the same set of genes; the most prevalent of these mutations is a GGGGCC repeat expansion in the first intron of C9ORF72. As shown by recent intensive studies, some key cellular pathways are dysregulated in the ALS‐FTD spectrum disorder, including autophagy, nucleocytoplasmic transport, DNA damage repair, pre‐mRNA splicing, stress granule dynamics, and others. These exciting advances reveal the complexity of the pathogenic mechanisms of FTD and ALS and suggest promising molecular targets for future therapeutic interventions in these devastating disorders.
A review of the key cellular pathways affected in ALS and FTD neurodegenerative diseases highlights the complexity of the underlying pathogenic mechanisms and the potential for identifying future therapeutic targets.
Abstract
The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI’s data resources and core bioinformatics analytical tools. EBI Search ...(https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. Here, we describe recent improvements to these services and updates made to accommodate the increasing data requirements during the COVID-19 pandemic.
Graphical Abstract
Graphical Abstract
Overview of the tools and data resources provided by EBI Search and Job Dispatcher services accessible via their webpage and programmatic interfaces.
Since 2009 the EMBL-EBI Job Dispatcher framework has provided free access to a range of mainstream sequence analysis applications. These include sequence similarity search services ...(https://www.ebi.ac.uk/Tools/sss/) such as BLAST, FASTA and PSI-Search, multiple sequence alignment tools (https://www.ebi.ac.uk/Tools/msa/) such as Clustal Omega, MAFFT and T-Coffee, and other sequence analysis tools (https://www.ebi.ac.uk/Tools/pfa/) such as InterProScan. Through these services users can search mainstream sequence databases such as ENA, UniProt and Ensembl Genomes, utilising a uniform web interface or systematically through Web Services interfaces (https://www.ebi.ac.uk/Tools/webservices/) using common programming languages, and obtain enriched results with novel visualisations. Integration with EBI Search (https://www.ebi.ac.uk/ebisearch/) and the dbfetch retrieval service (https://www.ebi.ac.uk/Tools/dbfetch/) further expands the usefulness of the framework. New tools and updates such as NCBI BLAST+, InterProScan 5 and PfamScan, new categories such as RNA analysis tools (https://www.ebi.ac.uk/Tools/rna/), new databases such as ENA non-coding, WormBase ParaSite, Pfam and Rfam, and new workflow methods, together with the retirement of depreciated services, ensure that the framework remains relevant to today's biological community.
The EMBL-EBI provides free access to popular bioinformatics sequence analysis applications as well as to a full-featured text search engine with powerful cross-referencing and data retrieval ...capabilities. Access to these services is provided via user-friendly web interfaces and via established RESTful and SOAP Web Services APIs (https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/EMBL-EBI+Web+Services+APIs+-+Data+Retrieval). Both systems have been developed with the same core principles that allow them to integrate an ever-increasing volume of biological data, making them an integral part of many popular data resources provided at the EMBL-EBI. Here, we describe the latest improvements made to the frameworks which enhance the interconnectivity between public EMBL-EBI resources and ultimately enhance biological data discoverability, accessibility, interoperability and reusability.
Analysis Tool Web Services from the EMBL-EBI McWilliam, Hamish; Li, Weizhong; Uludag, Mahmut ...
Nucleic acids research,
07/2013, Volume:
41, Issue:
Web Server issue
Journal Article
Peer reviewed
Open access
Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across ...the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services (http://www.ebi.ac.uk/Tools/webservices/) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods.
Ageing, dental caries and periodontal diseases López, Rodrigo; Smith, Patricio C; Göstemeyer, Gerd ...
Journal of clinical periodontology,
March 2017, 2017-Mar, 2017-03-00, 20170301, Volume:
44, Issue:
S18
Journal Article
Peer reviewed
Open access
Aim
To review the burden of caries and periodontitis in the elderly, changes with age that can explain this burden, and the vulnerability to disease of elderly populations.
Methods
An assessment of ...surveys in two populations was conducted. Indicators for caries were identified by updating a systematic review. Secular trends for smoking and type 2 diabetes were discussed.
Results
Changes in the susceptibility to periodontitis with age may be explained by exposure to pro‐inflammatory conditions and changes in the healing capacity of cells and tissues. Due to accumulated periodontal destruction, the number of surfaces at risk for caries increases. The sequels of restorative treatment contribute to an increased susceptibility for caries development. Population‐based surveys in the United States and Germany demonstrate a high caries experience among elderly people. A comparison of surveys demonstrates a relative improvement of periodontal health among elderly during the last few decades. Nevertheless, prevalence estimates for periodontitis remain high. Risk indicators for root caries include caries experience, the number of surfaces at risk and poor oral hygiene. Secular trends of main risk factors for periodontitis and their likely influence on the future periodontitis burden in the elderly are discussed.
Conclusion
Caries and periodontitis burden in the elderly remain high.
Abstract
This article examines three novels that use fiction to revise the figure of the Argentine author Leopoldo Lugones: Ricardo Piglia’s
Respiración artificial
(1980), C. E. Feiling’s
Un poeta ...nacional
(1993), and César Aira’s
Lugones
(2020). These three novels present different portrayals of Lugones, which also mirror their opposing views of the Argentine literary tradition. Piglia, Feiling, and Aira look back at the so-called national poet when self-fashioning themselves as writers and outlining a literary project in a (post)dictatorial scenario. In a cultural field marked by the effects of state terror and neoliberal reform policies, these fictional renderings of Lugones become a means of reflecting on the political past and the future of literature. Ultimately, I argue that
Respiración artificial
,
Un poeta nacional
, and
Lugones
devise a figure of the Argentine author decoupled from the mission of consolidating a national identity that Lugones epitomized for nearly half a century.
Resumen
Este artículo estudia tres novelas que utilizan la ficción para revisitar la vida y obra del autor argentino Leopoldo Lugones:
Respiración artificial
(1980), de Ricardo Piglia,
Un poeta nacional
(1993), de C. E. Feiling, y
Lugones
(2020), de César Aira. Estas tres novelas presentan retratos divergentes de Lugones, que a su vez reflejan sus miradas opuestas sobre la tradición literaria argentina. Piglia, Feiling y Aira repiensan retrospectivamente la figura del “poeta nacional” al momento de diseñar sus propias estampas autorales y proyectos literarios en un contexto (post)dictatorial. En un campo cultural marcado por los efectos del terrorismo de estado y las reformas neoliberales, estos retratos ficcionales de Lugones son un medio para reflexionar sobre el pasado de la política y el futuro de la literatura. En última instancia,
Respiración artificial
,
Un poeta nacional
y
Lugones
imaginan un paradigma del autor argentino por fuera de la misión de consolidar una identidad nacional, misión que el espectro de Lugones epitomizó durante casi medio siglo.
The notion of periodontal disease being the major cause of tooth loss among adults was rooted in the focal infection paradigm that dominated the first half of the 20th century. This paradigm was ...established largely by personal opinions, and it was not until the development of periodontal indices in the mid‐1950s that periodontal epidemiology gained momentum. Unfortunately, the indices used suffered from a number of flaws, whereby the interpretation of the research results took the form of circular reasoning. It was under this paradigm that therapeutic and preventive intervention for periodontal diseases became entirely devoted to oral hygiene, as poor oral hygiene and older age were understood to explain nearly all the variation in disease occurrence. In the early 1980s, studies appeared that contradicted the concepts of poor oral hygiene as the inevitable trigger of periodontitis and of linear and ubiquitous periodontitis progression, whereby periodontal epidemiology was led into a relatively short‐lived high‐risk era. At this time, it became evident that old scourges continue to haunt periodontology: the inability to agree in operational clinical criteria for a periodontitis diagnosis and the inability to devise both a meaningful and a useful classification of periodontal diseases based on nominalist principles. The meager outcome of the high‐risk era led researchers to resurrect the focal infection paradigm, which is now dressed up as periodontal medicine. Unfortunately, these developments have left the core of periodontology somewhat disheveled and deserted.
PDF
