736 research outputs found
msberends/AMR: v0.6.0
No full text<p><strong>AMR 0.6.0</strong></p>
<p><strong>New website!</strong></p>
<p>We’ve got a new website: <a href="https://msberends.gitlab.io/AMR/">https://msberends.gitlab.io/AMR</a> (built with the great <a href="https://pkgdown.r-lib.org/"><code>pkgdown</code></a>)</p>
<ul>
<li>Contains the complete manual of this package and all of its functions with an explanation of their parameters</li>
<li>Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis, import data from WHONET or SPSS and many more.</li>
</ul>
<p>New</p>
<ul>
<li><strong>BREAKING</strong>: removed deprecated functions, parameters and references to ‘bactid’. Use <code><a href="https://msberends.gitlab.io/AMR/reference/as.mo.html">as.mo()</a></code> to identify an MO code.</li>
<li>Catalogue of Life as a new taxonomic source for data about microorganisms, which also contains all ITIS data we used previously. The <code>microorganisms</code> data set now contains:
<ul>
<li>All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria and Protozoa</li>
<li>All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales (covering at least like all species of <em>Aspergillus</em>, <em>Candida</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>)</li>
<li>All ~2,000 (sub)species from ~100 other relevant genera, from the kingdoms of Animalia and Plantae (like <em>Strongyloides</em> and <em>Taenia</em>)</li>
<li>All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed</li>
<li>
<p>The responsible author(s) and year of scientific publication</p>
This data is updated annually - check the included version with the new function <code><a href="https://msberends.gitlab.io/AMR/reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code>.</li>
<li>Due to this change, some <code>mo</code> codes changed (e.g. <em>Streptococcus</em> changed from <code>B_STRPTC</code> to <code>B_STRPT</code>). A translation table is used internally to support older microorganism IDs, so users will not notice this difference.</li>
<li>New function <code><a href="https://msberends.gitlab.io/AMR/reference/mo_property.html">mo_rank()</a></code> for the taxonomic rank (genus, species, infraspecies, etc.)</li>
<li>New function <code><a href="https://msberends.gitlab.io/AMR/reference/mo_property.html">mo_url()</a></code> to get the direct URL of a species from the Catalogue of Life</li>
</ul>
</li>
<li>Support for data from <a href="https://whonet.org/">WHONET</a> and <a href="https://ecdc.europa.eu/en/about-us/partnerships-and-networks/disease-and-laboratory-networks/ears-net">EARS-Net</a> (European Antimicrobial Resistance Surveillance Network):
<ul>
<li>Exported files from WHONET can be read and used in this package. For functions like <code><a href="https://msberends.gitlab.io/AMR/reference/first_isolate.html">first_isolate()</a></code> and <code><a href="https://msberends.gitlab.io/AMR/reference/eucast_rules.html">eucast_rules()</a></code>, all parameters will be filled in automatically.</li>
<li>This package now knows all antibiotic abbrevations by EARS-Net (which are also being used by WHONET) - the <code>antibiotics</code> data set now contains a column <code>ears_net</code>.</li>
<li>The function <code><a href="https://msberends.gitlab.io/AMR/reference/as.mo.html">as.mo()</a></code> now knows all WHONET species abbreviations too, because almost 2,000 microbial abbreviations were added to the <code>microorganisms.codes</code> data set.</li>
</ul>
</li>
<li>
<p>New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:</p>
<pre><code><a href="https://msberends.gitlab.io/AMR/reference/filter_ab_class.html">filter_aminoglycosides</a>()
<a href="https://msberends.gitlab.io/AMR/reference/filter_ab_class.html">filter_carbapenems</a>()
<a href="https://msberends.gitlab.io/AMR/reference/filter_ab_class.html">filter_cephalosporins</a>()
<a href="https://msberends.gitlab.io/AMR/reference/filter_ab_class.html">filter_1st_cephalosporins</a>()
<a href="https://msberends.gitlab.io/AMR/reference/filter_ab_class.html">filter_2nd_cephalosporins</a>()
<a href="https://msberends.gitlab.io/AMR/reference/filter_ab_class.html">filter_3rd_cephalosporins</a>()
<a href="https://msberends.gitlab.io/AMR/reference/filter_ab_class.html">filter_4th_cephalosporins</a>()
<a href="https://msberends.gitlab.io/AMR/reference/filter_ab_class.html">filter_fluoroquinolones</a>()
<a href="https://msberends.gitlab.io/AMR/reference/filter_ab_class.html">filter_glycopeptides</a>()
<a href="https://msberends.gitlab.io/AMR/reference/filter_ab_class.html">filter_macrolides</a>()
<a href="https://msberends.gitlab.io/AMR/reference/filter_ab_class.html">filter_tetracyclines</a>()</code></pre>
<p>The <code>antibiotics</code> data set will be searched, after which the input data will be checked for column names with a value in any abbreviations, codes or official names found in the <code>antibiotics</code> data set. For example:</p>
<pre><code>septic_patients %>% <a href="https://msberends.gitlab.io/AMR/reference/filter_ab_class.html">filter_glycopeptides</a>(result = "R")
# Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R
septic_patients %>% <a href="https://msberends.gitlab.io/AMR/reference/filter_ab_class.html">filter_glycopeptides</a>(result = "R", scope = "all")
# Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</code></pre>
</li>
<li>
<p>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions:</p>
<pre><code>ab_property -> <a href="https://msberends.gitlab.io/AMR/reference/atc_property.html">atc_property</a>()
ab_name -> <a href="https://msberends.gitlab.io/AMR/reference/atc_property.html">atc_name</a>()
ab_official -> <a href="https://msberends.gitlab.io/AMR/reference/atc_property.html">atc_official</a>()
ab_trivial_nl -> <a href="https://msberends.gitlab.io/AMR/reference/atc_property.html">atc_trivial_nl</a>()
ab_certe -> <a href="https://msberends.gitlab.io/AMR/reference/atc_property.html">atc_certe</a>()
ab_umcg -> <a href="https://msberends.gitlab.io/AMR/reference/atc_property.html">atc_umcg</a>()
ab_tradenames -> <a href="https://msberends.gitlab.io/AMR/reference/atc_property.html">atc_tradenames</a>()</code></pre>
These functions use <code><a href="https://msberends.gitlab.io/AMR/reference/as.atc.html">as.atc()</a></code> internally. The old <code>atc_property</code> has been renamed <code><a href="https://msberends.gitlab.io/AMR/reference/atc_online.html">atc_online_property()</a></code>. This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class <code>atc</code> or must be coerable to this class. Properties of these classes should start with the same class name, analogous to <code><a href="https://msberends.gitlab.io/AMR/reference/as.mo.html">as.mo()</a></code> and e.g. <code>mo_genus</code>.</li>
<li>New functions <code><a href="https://msberends.gitlab.io/AMR/reference/mo_source.html">set_mo_source()</a></code> and <code><a href="https://msberends.gitlab.io/AMR/reference/mo_source.html">get_mo_source()</a></code> to use your own predefined MO codes as input for <code><a href="https://msberends.gitlab.io/AMR/reference/as.mo.html">as.mo()</a></code> and consequently all <code>mo_*</code> functions</li>
<li>Support for the upcoming <a href="https://dplyr.tidyverse.org"><code>dplyr</code></a> version 0.8.0</li>
<li>New function <code><a href="https://msberends.gitlab.io/AMR/reference/guess_ab_col.html">guess_ab_col()</a></code> to find an antibiotic column in a table</li>
<li>New function <code><a href="https://msberends.gitlab.io/AMR/reference/as.mo.html">mo_failures()</a></code> to review values that could not be coerced to a valid MO code, using <code><a href="https://msberends.gitlab.io/AMR/reference/as.mo.html">as.mo()</a></code>. This latter function will now only show a maximum of 10 uncoerced values and will refer to <code><a href="https://msberends.gitlab.io/AMR/reference/as.mo.html">mo_failures()</a></code>.</li>
<li>New function <code><a href="https://msberends.gitlab.io/AMR/reference/as.mo.html">mo_uncertainties()</a></code> to review values that could be coerced to a valid MO code using <code><a href="https://msberends.gitlab.io/AMR/reference/as.mo.html">as.mo()</a></code>, but with uncertainty.</li>
<li>New function <code><a href="https://msberends.gitlab.io/AMR/reference/as.mo.html">mo_renamed()</a></code> to get a list of all returned values from <code><a href="https://msberends.gitlab.io/AMR/reference/as.mo.html">as.mo()</a></code> that have had taxonomic renaming</li>
<li>New function <code><a href="https://msberends.gitlab.io/AMR/reference/age.html">age()</a></code> to calculate the (patients) age in years</li>
<li>New function <code><a href="https://msberends.gitlab.io/AMR/reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</li>
<li>
<p>New function <code><a href="https://msberends.gitlab.io/AMR/reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="https://msberends.gitlab.io/AMR/reference/resistance_predict.html">resistance_predict()</a></code>:</p>
<pre><code>x <- <a href="https://msberends.gitlab.io/AMR/reference/resistance_predict.html">resistance_predict</a>(septic_patients, col_ab = "amox")
<a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a>(x)
<a href="https://msberends.gitlab.io/AMR/reference/resistance_predict.html">ggplot_rsi_predict</a>(x)</code></pre>
</li>
<li>
<p>Functions <code><a href="https://msberends.gitlab.io/AMR/reference/first_isolate.html">filter_first_isolate()</a></code> and <code><a href="https://msberends.gitlab.io/AMR/reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
<pre><code>septic_patients %>% <a href="https://msberends.gitlab.io/AMR/reference/first_isolate.html">filter_first_isolate</a>(...)
# or
<a href="https://msberends.gitlab.io/AMR/reference/first_isolate.html">filter_first_isolate</a>(septic_patients, ...)</code></pre>
<p>is equal to:</p>
<pre><code>septic_patients %>%
mutate(only_firsts = <a href="https://msberends.gitlab.io/AMR/reference/first_isolate.html">first_isolate</a>(septic_patients, ...)) %>%
<a href="https://www.rdocumentation.org/packages/stats/topics/filter">filter</a>(only_firsts == TRUE) %>%
select(-only_firsts)</code></pre>
</li>
<li>New function <code><a href="https://msberends.gitlab.io/AMR/reference/availability.html">availability()</a></code> to check the number of available (non-empty) results in a <code>data.frame</code></li>
<li>
<p>New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the <em>G</em>-test and more. These are also available (and even easier readable) on our website: <a href="https://msberends.gitlab.io/AMR">https://msberends.gitlab.io/AMR</a>.</p>
</li>
</ul>
<p>Changed</p>
<ul>
<li>Function <code><a href="https://msberends.gitlab.io/AMR/reference/eucast_rules.html">eucast_rules()</a></code>:
<ul>
<li>Updated EUCAST Clinical breakpoints to <a href="http://www.eucast.org/clinical_breakpoints/">version 9.0 of 1 January 2019</a>, the data set <code>septic_patients</code> now reflects these changes</li>
<li>Fixed a critical bug where some rules that depend on previous applied rules would not be applied adequately</li>
<li>Emphasised in manual that penicillin is meant as benzylpenicillin (ATC <a href="https://www.whocc.no/atc_ddd_index/?code=J01CE01">J01CE01</a>)</li>
<li>New info is returned when running this function, stating exactly what has been changed or added. Use <code><a href="https://msberends.gitlab.io/AMR/reference/eucast_rules.html">eucast_rules(..., verbose = TRUE)</a></code> to get a data set with all changed per bug and drug combination.</li>
</ul>
</li>
<li>Removed data sets <code>microorganisms.oldDT</code>, <code>microorganisms.prevDT</code>, <code>microorganisms.unprevDT</code> and <code>microorganismsDT</code> since they were no longer needed and only contained info already available in the <code>microorganisms</code> data set</li>
<li>Added 65 antibiotics to the <code>antibiotics</code> data set, from the <a href="http://ec.europa.eu/health/documents/community-register/html/atc.htm">Pharmaceuticals Community Register</a> of the European Commission</li>
<li>Removed columns <code>atc_group1_nl</code> and <code>atc_group2_nl</code> from the <code>antibiotics</code> data set</li>
<li>Functions <code><a href="https://msberends.gitlab.io/AMR/reference/AMR-deprecated.html">atc_ddd()</a></code> and <code><a href="https://msberends.gitlab.io/AMR/reference/AMR-deprecated.html">atc_groups()</a></code> have been renamed <code><a href="https://msberends.gitlab.io/AMR/reference/atc_online.html">atc_online_ddd()</a></code> and <code><a href="https://msberends.gitlab.io/AMR/reference/atc_online.html">atc_online_groups()</a></code>. The old functions are deprecated and will be removed in a future version.</li>
<li>Function <code><a href="https://msberends.gitlab.io/AMR/reference/AMR-deprecated.html">guess_mo()</a></code> is now deprecated in favour of <code><a href="https://msberends.gitlab.io/AMR/reference/as.mo.html">as.mo()</a></code> and will be removed in future versions</li>
<li>Function <code><a href="https://msberends.gitlab.io/AMR/reference/AMR-deprecated.html">guess_atc()</a></code> is now deprecated in favour of <code><a href="https://msberends.gitlab.io/AMR/reference/as.atc.html">as.atc()</a></code> and will be removed in future versions</li>
<li>Improvements for <code><a href="https://msberends.gitlab.io/AMR/reference/as.mo.html">as.mo()</a></code>:
<ul>
<li>
<p>Now handles incorrect spelling, like <code>i</code> instead of <code>y</code> and <code>f</code> instead of <code>ph</code>:</p>
<pre><code># mo_fullname() uses as.mo() internally
<a href="https://msberends.gitlab.io/AMR/reference/mo_property.html">mo_fullname</a>("Sthafilokockus aaureuz")
#> [1] "Staphylococcus aureus"
<a href="https://msberends.gitlab.io/AMR/reference/mo_property.html">mo_fullname</a>("S. klossi")
#> [1] "Staphylococcus kloosii"</code></pre>
</li>
<li>
<p>Uncertainty of the algorithm is now divided into four levels, 0 to 3, where the default <code>allow_uncertain = TRUE</code> is equal to uncertainty level 2. Run <code><a href="https://msberends.gitlab.io/AMR/reference/as.mo.html">?as.mo</a></code> for more info about these levels.</p>
<pre><code># equal:
<a href="https://msberends.gitlab.io/AMR/reference/as.mo.html">as.mo</a>(..., allow_uncertain = TRUE)
<a href="https://msberends.gitlab.io/AMR/reference/as.mo.html">as.mo</a>(..., allow_uncertain = 2)
# also equal:
<a href="https://msberends.gitlab.io/AMR/reference/as.mo.html">as.mo</a>(..., allow_uncertain = FALSE)
<a href="https://msberends.gitlab.io/AMR/reference/as.mo.html">as.mo</a>(..., allow_uncertain = 0)</code></pre>
Using <code><a href="https://msberends.gitlab.io/AMR/reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a></code> could lead to very unreliable results.</li>
<li>Implemented the latest publication of Becker <em>et al.</em> (2019), for categorising coagulase-negative <em>Staphylococci</em></li>
<li>All microbial IDs that found are now saved to a local file <code>~/.Rhistory_mo</code>. Use the new function <code><a href="https://msberends.gitlab.io/AMR/reference/as.mo.html">clean_mo_history()</a></code> to delete this file, which resets the algorithms.</li>
<li>
<p>Incoercible results will now be considered ‘unknown’, MO code <code>UNKNOWN</code>. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:</p>
<pre><code><a href="https://msberends.gitlab.io/AMR/reference/mo_property.html">mo_genus</a>("qwerty", language = "es")
# Warning:
# one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.
#> [1] "(género desconocido)"</code></pre>
</li>
<li>Fix for vector containing only empty values</li>
<li>Finds better results when input is in other languages</li>
<li>Better handling for subspecies</li>
<li>Better handling for <em>Salmonellae</em>, especially the ‘city like’ serovars like <em>Salmonella London</em></li>
<li>Understanding of highly virulent <em>E. coli</em> strains like EIEC, EPEC and STEC</li>
<li>There will be looked for uncertain results at default - these results will be returned with an informative warning</li>
<li>Manual (help page) now contains more info about the algorithms</li>
<li>Progress bar will be shown when it takes more than 3 seconds to get results</li>
<li>Support for formatted console text</li>
<li>Console will return the percentage of uncoercable input</li>
</ul>
</li>
<li>Function <code><a href="https://msberends.gitlab.io/AMR/reference/first_isolate.html">first_isolate()</a></code>:
<ul>
<li>Fixed a bug where distances between dates would not be calculated right - in the <code>septic_patients</code> data set this yielded a difference of 0.15% more isolates</li>
<li>Will now use a column named like “patid” for the patient ID (parameter <code>col_patientid</code>), when this parameter was left blank</li>
<li>Will now use a column named like “key(…)ab” or “key(…)antibiotics
Caratterizzazione funzionale dei mutanti di Rab7 responsabili della neuropatia Charcot-Marie-Tooth di tipo 2b
No full textDictyostelium discoideum as a model host for meningococcal pathogenesis
No full textBACKGROUND: The aim of the present study was to evaluate the possibility of studying meningococcal virulence in a new model organism, Dictyostelium discoideum, a haploid social soil amoeba that is an established host model for several human pathogens, leading to the discovery of novel virulence mechanisms. MATERIAL/METHODS: A number of virulent and hyper-virulent N. meningitidis strains, including isogenic encapsulated, unencapsulated, and lipooligosaccharide (LOS) outer core-defective derivatives, were used to test the ability of D. discoideum to internalize and grow in the presence of bacteria. Intracellular survival of the internalized bacteria was also monitored. RESULTS: Meningococci were internalized and killed by D. discoideum cells. The presence of a capsule did not affect the internalization, but, as in human cells, it increased the resistance of the internalized bacteria. Although both encapsulated and unencapsulated meningococci supported the growth and development of D. discoideum on an agar surface, in liquid medium the encapsulated strains were toxic to the slime mould cells. Toxicity inversely correlated with meningococcal survival in the assay medium that was not favorable to bacterial replication, suggesting that it may be due to some toxic compound released after bacterial autolysis. Intriguingly, unencapsulated isogenic strains efficiently supported Dictyostelium growth in suspension, opening the possibility that the toxicity may be associated with the capsular polysaccharide. CONCLUSIONS: These results suggest that several meningococcal virulence determinants, such as the capsular polysaccharide, may be remarkably effective also in Dictyostelium cells, stimulating the use of this model host to search for novel meningococcal virulence determinants
Functional characterization of Rab7 mutant proteins associated with Charcot-Marie-Tooth type 2B disease
No full text
Caratterizzazione funzionale dei mutanti della proteina Rab7 che causano la neuropatia Charco-Marie-Tooth di tipo 2b
No full textA generalized patch AMR platform that uses cell centered or cell vertex solvers
No full textA patch adaptive mesh refinement (AMR) platform is presented. Presently two Navier-Stokes solvers are available within this platform : a MUSCL and DG solver (FLUX AMR) and a multi-species MUSCL solver (MAJIC) for reacting flows. The first solver is based on cell centered approaches of finite volume type, the second solver is based on a cell vertex and a time splitting method. The modifications of AMR treatments, especially those concerning the interpolation at fine-coarse boundaries are detailed. This platform is first tested on the subsonic flow over a deep cavity and secondly on the interaction of a steady planar shock with a H2-air circular diffusion flame
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