1,180 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
A 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
African voices from the ground : motives, benefits and managing risk of migration towards Europe
No full textFriedrich-Ebert-Stiftung (FES), Institute for Peace and Security Studies (IPSS) ; [Author: Amr Abdalla, Ph.D.
Identification and specificity validation of unique and antimicrobial resistance genes to trace suspected pathogenic AMR bacteria and to monitor the development of AMR in non-AMR strains in the environment and clinical settings
No full textThe detection of developing antimicrobial resistance (AMR) has become a global issue. The detection of developing antimicrobial resistance has become a global issue. The growing number of AMR bacteria poses a new threat to public health. Therefore, a less laborious and quick confirmatory test becomes important for further investigations into developing AMR in the environment and in clinical settings. This study aims to present a comprehensive analysis and validation of unique and antimicrobial-resistant strains from the WHO priority list of antimicrobial-resistant bacteria and previously reported AMR strains such as Acinetobacter baumannii, Aeromonas spp., Anaeromonas frigoriresistens, Anaeromonas gelatinfytica, Bacillus spp., Campylobacter jejuni subsp. jejuni, Enterococcus faecalis, Escherichia coli, Haemophilus influenzae, Helicobacter pylori, Klebsiella pneumonia subsp. pneumoniae, Pseudomonas aeruginosa, Salmonella enterica subsp. enterica serovar Typhimurium, Thermanaeromonas toyohensis, and Vibrio proteolyticus. Using in-house designed gene-specific primers, 18 different antibiotic resistance genes (algJ, alpB, AQU-1, CEPH-A3, ciaB, CMY-1-MOX-7, CMY-1-MOX-9, CMY-1/MOX, cphA2, cphA5, cphA7, ebpA, ECP_4655, fliC, OXA-51, RfbU, ThiU2, and tolB) from 46 strains were selected and validated. Hence, this study provides insight into the identification of strain-specific, unique antimicrobial resistance genes. Targeted amplification and verification using selected unique marker genes have been reported. Thus, the present detection and validation use a robust method for the entire experiment. Results also highlight the presence of another set of 18 antibiotic-resistant and unique genes (Aqu1, cphA2, cphA3, cphA5, cphA7, cmy1/mox7, cmy1/mox9, asaI, ascV, asoB, oxa-12, acr-2, pepA, uo65, pliI, dr0274, tapY2, and cpeT). Of these sets of genes, 15 were found to be suitable for the detection of pathogenic strains belonging to the genera Aeromonas, Pseudomonas, Helicobacter, Campylobacter, Enterococcus, Klebsiella, Acinetobacter, Salmonella, Haemophilus, and Bacillus. Thus, we have detected and verified sets of unique and antimicrobial resistance genes in bacteria on the WHO Priority List and from published reports on AMR bacteria. This study offers advantages for confirming antimicrobial resistance in all suspected AMR bacteria and monitoring the development of AMR in non-AMR bacteria, in the environment, and in clinical settings. © 2023 The Author(s)Deemed to be University; King Saud University, KSUUniversidad Autónoma de Chil
Synthesis and Characterization of Nano-Tungsten Oxide Precipitated onto Natural Inorganic Clay for Humidity-Sensing Applications
No full textA wet chemical method was used to obtain tungsten oxide nanoparticles from tungsten tetrachloride and natural microfibrous inorganic clay (sepiolite) as a starting material. Precipitation of tungsten oxide species onto sepiolite under basic conditions and subsequent thermal treatment was investigated, prompted by the abundance of sepiolite in nature and the useful environmental applications that could be attained. Laser granulometry, X-ray diffraction, field emission scanning electron microscopy (FE-SEM), energy dispersive X-ray spectroscopy (EDX), and high-resolution transmission electron microscopy (HR-TEM) techniques were used to study the particle-size distribution, the morphology, and the composition of the prepared sample. Our findings show the presence of tungsten oxide nanoparticles, which are less than 50 nm, on the needles of the modified sepiolite
Spatio-Temporal Scanning and Statistical Test of the Accelerating Moment Release (AMR) Model Using Australian Earthquake Data
No full textThe Accelerating Moment Release (AMR) preceding earthquakes with magnitude above 5 in Australia that occurred during the last 20 years was analyzed to test the Critical Point Hypothesis. Twelve earthquakes in the catalog were chosen based on a criterion for the number of nearby events. Results show that seven sequences with numerous events recorded leading up to the main earthquake exhibited accelerating moment release. Two occurred near in time and space to other earthquakes preceded by AM R. The remaining three sequences had very few events in the catalog so the lack of AMR detected in the analysis may be related to catalog incompleteness. Spatio-temporal scanning of AMR parameters shows that 80% of the areas in which AMR occurred experienced large events. In areas of similar background seismicity with no large events, 10 out of 12 cases exhibit no AMR, and two others are false alarms where AMR was observed but no large event followed. The relationship between AMR and Load-Unload Response Ratio (LURR) was studied. Both methods predict similar critical region sizes, however, the critical point time using AMR is slightly earlier than the time of the critical point LURR anomaly
sj-docx-1-jcn-10.1177_08830738221078683 - Supplemental material for Clinicoradiologic Correlation in 22 Egyptian Children With Megalencephalic Leukoencephalopathy With Subcortical Cysts
No full textSupplemental material, sj-docx-1-jcn-10.1177_08830738221078683 for Clinicoradiologic Correlation in 22 Egyptian Children With Megalencephalic Leukoencephalopathy With Subcortical Cysts by Abdelrahim A. Sadek, Mohammed A. Aladawy, Tarek M. M. Mansour, Mohamed F. Ibrahim, Montaser M. Mohamed, Eman F. Gad, Amr A. Othman, Hosny A. Ahmed, Abdin K. Kasim, Wael M. Wagdy, Mohamed H. T. Hasan and Elsayed Abdelkreem in Journal of Child Neurology</p
sj-docx-2-jcn-10.1177_08830738221078683 - Supplemental material for Clinicoradiologic Correlation in 22 Egyptian Children With Megalencephalic Leukoencephalopathy With Subcortical Cysts
No full textSupplemental material, sj-docx-2-jcn-10.1177_08830738221078683 for Clinicoradiologic Correlation in 22 Egyptian Children With Megalencephalic Leukoencephalopathy With Subcortical Cysts by Abdelrahim A. Sadek, Mohammed A. Aladawy, Tarek M. M. Mansour, Mohamed F. Ibrahim, Montaser M. Mohamed, Eman F. Gad, Amr A. Othman, Hosny A. Ahmed, Abdin K. Kasim, Wael M. Wagdy, Mohamed H. T. Hasan and Elsayed Abdelkreem in Journal of Child Neurology</p
Euchondrus adwani Eike Neubert & Zuhair Amr 2016, n. sp.
No full textEuchondrus adwani n. sp. (Figure 1) Material: Holotype NMBE 539263; paratype NMBE 539264 /1. Type locality: Syria, surrounding of the monastery of Deir Moussa, 34.0219°N 36.8423°E, 1300 m a.s.l., 11.iii. 2010, leg. Adwan Shehab. *Corresponding author. Email: [email protected] © 2016 Taylor & Francis Measurements (holotype): Height = 11.04 mm; diameter = 4.13 mm; peristome height = 4.03 mm; peristome diameter = 2.97 mm; number of whorls = 8. Diagnosis. Euchondrus adwani n. sp. differs from the widespread E. septemdentatus by its conical shell (broadly oval in E. septemdentatus), its flat suture and teleoconch whorls (suture deeper, whorls much more rounded in E. septemdentatus), the heavy palatal labial callus (weaker in E. septemdentatus), the bar-like subangularis (weaker in E. septemdentatus), and the keeled last whorl (rounded in E. septemdentatus). Description: Shell solid, dextral, cylindrical, upper part cylindro-conical in outline; shell pale brownish to horny yellow coloured; 8 rather flat-sided teleoconch whorls, suture flat with a distinct white sutural thread; teleoconch smooth, glossy, last whorl with fine, straight and irregularly spaced striae; aperture subtriangular, peristome strongly thickened by a labial callus, moderately reflected, with a rich dentition (description clockwise): palatum with a small suturalis followed by a conical palatalis superior and a broad infrapalatalis with the latter two denticles placed on a thick callus; columellar side with a basalis and a straight columellaris; parietum with a strong and long parietalis, bordered by a small spiralis, subangularis large, bar-like, left side of the parietum with another small denticle at the attachment site of the peristome; last teleoconch whorl dorsally compressed forming a distinct blunt ridge (arrows); umbilicus slit-like open, periomphalum large, dish-like. Remarks: This species shows some superficial similarities with E. desertorum Rochanaburananda in Forcart, 1981 (Figure 2), which is endemic to the Negev Desert (Heller, 2009). Both species have a straight conical shell, but E. desertorum is considerably larger than E. adwani n. sp. and its aperture is rounded and not subtriangular. It also differs in the formation of the dentition: in E. desertorum, the infrapalatalis is bifid (simple in E. adwani), the spiralis is large and connected to the parietalis (small and disconnected in E. adwani), and the subangularis is weaker (very strong in E. adwani). The last whorl of E. adwani displays a distinct keel with an enlarged periomphalum, while in E. desertorum the dorsum is rounded, and the periomphalum is much smaller. Etymology: This species is named in honour of Dr. Adwan Shawabi, who was a keen collector of molluscs from Syria, and a personal friend, and who was killed in February 2015 in the Syrian civil war (Amr, 2015).Published as part of Eike Neubert & Zuhair Amr, 2016, On a new species of Euchondrus Boettger, 1883 from Syria (Pulmonata: Enidae), pp. 58-60 in Zoology in the Middle East 62 on pages 58-60, DOI: 10.1080/09397140.2015.1132564, http://zenodo.org/record/88703
Analisis tujuan amr berkaitan makanan halal dalam surah al-Baqarah: Analysis of the purpose of amr in the context of halal food in surah al-Baqarah
No full textDo all the verses of amr have haqīqī and majāzī meanings? This study discusses the purpose of amr in surah al-Baqarah. The objective of this study is to identify the form and purpose of amr in the context of halal food in surah al-Baqarah. This is a qualitative study that uses Kuckartz (2014) text analysis techniques based on sentences and uses interpretations carried out by past and modern scholars. The author uses the ‘Abbās Theory (1997). The findings of the study found five verses about halal food in surah al-Baqarah which uses fi‘l amr. There are three purposes of amr which are wajib, ibāḥat and al-qudrat. The purpose of amr that is regularly used is ibāḥat five times, followed by wajib four times, and al-qudrat only once. In conclusion, it clearly shows that the verses of amr in the context of halal food possess the meaning of haqīqī and majāzī in surah al-Baqarah
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