756 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.
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
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
USLUB AL AMR DALAM SURAT YASIN
No full textThe Al-Qur\u27an employs language in a remarkably eloquent manner, carefully selecting appropriate words where each holds its own significance. Some scholars argue that the Qur\u27an possesses a profound balaghah value that is unparalleled. Thus, the purpose of this paper is to examine this linguistic style, particularly the language style of Amr, which encompasses both its essential (original) meaning and its figurative (majazi) meaning. Surah Yasin is classified as a Makkiyah Surah because it was revealed in the city of Mecca. This Surah encompasses admonitions from Allah SWT and His Messenger, instructions for worshipping Allah SWT, retribution for believers and disbelievers, manifestations of Allah SWT\u27s power, and warnings from the Prophet about Hell. It is named Yasin due to its opening with the letters Yaasiin. According to the interpretation provided by the Ministry of Religion, just as the meanings of the alphabet letters are present at the beginning of several Surahs in the Qur\u27an, so too does Yaasiin hold significance within the verses at the start of this Surah, indicating that significant matters will be discussed subsequently. Allah solemnly swears by the Qur\u27an that Muhammad SAW is truly His messenger sent to a people who had not previously received any messengers. Within this Surah, the author identifies approximately 11 instances of al-Amr forms, each with its intrinsic or figurative meaning. Consequently, the author is intrigued to conduct a deeper study, analyze, and map the occurrences of al-Amr in Yasin based on their respective parts and meanings. This written work adopts an analytical descriptive approach. Materials and research sources obtained through library research will be detailed, described, and analyzed, after which the findings will be presented in written form to provide a comprehensive depiction of the uslub al-Amr form in Surah Yasin.
Keywords: Style, al-amr, yasin.
 
AMR Sign - An Arthroscopic S-shaped Fold Signifying Adequate Medial Meniscus Repair
No full textIntroduction:
The preferred management of medial meniscus tears has notably moved from meniscectomies towards repair. With a higher volume of meniscal repairs being done all across the world with every passing day, the lack of an objective and definitive sign suggesting the adequacy of its repair is daunting. The purpose of our study was to introduce a unique and novel arthroscopic sign formed after adequate repair of the medial meniscus, the AMR (Adequacy of Medial meniscus Repair) sign. We hypothesised that it is not only the objective end point for repair, but can also form the indicator for excellent clinical, functional, and radiological outcome even in the long term.
Materials and methods:
This was a multicentric, prospective study initiated by the corresponding author, and the findings validated subsequently by the other authors. Overall, it included 804 patients of isolated medial meniscus tear operated with arthroscopic all-inside technique between January 2014 and December 2017. Patients were segregated into three groups based on whether an S-shaped curve in the free, inner edge of the medial meniscus sign was formed post-repair, lost after further tightening, or not formed upon subjective completion of repair. All the patients were followed-up and evaluated based of medial joint line tenderness, McMurray’s test for medial meniscus, IKDC score, WOMET score, and radiologically using an MRI at the terminal follow-up.
Results:
The mean terminal follow-up was 42.34±4.54 months. There was significant (p<0.01) improvement in all patients at the terminal follow-up post-surgery, irrespective of the group. The group in which AMR sign was formed and maintained showed a significantly better functional outcome on terminal follow-up as well as lower failure rates compared to the other two groups.
Conclusion:
AMR sign is an S-shaped fold at the inner, free edge of medial meniscus, formed after an adequate repair of isolated medial meniscus tear, as viewed on arthroscopy. It is an objective sign denoting regained integrity of the collagen architecture of the medial meniscus following repair. It is also a reliable indicator of excellent long term functional, clinical, and radiological outcome and also lower failure rates in patients after arthroscopic medial meniscus repair
Automatic AMR Generation for Simple Sentences Using Dependency Parser
No full textAbstractInformation retrieval is an important task in the field of natural language processing. Retrieving information requires a basic representation at the sentence level. Representation for sentences with same meaning should be same so that we can claim that the representation seems to be good enough to use in various natural language tasks. AMR is such a semantic representation aimed at large-scale human annotation inorder to built a giant semantic bank. In this paper, we present an automatic AMR tool for simple sentences with the help of dependency parser
Interviews with Muhammad Jamal Amr
No full textهذه المقابلة مع مؤلف أدب الأطفال و الشاعر الأردني محمد جمال عمرو يتحدث عن مجلة للأطفال صدرت في الأردن بعنوان ""أروى"". يسلط الضوء على المعايير الأساسية التي يجب إتباعها عند كتابة قصائد للأطفال ، علاوة على ذلك ، يروي بعض النماذج من قصائده. أجرى المقابلة حسن شمس الدين.In this interview, Jordanian author of children books Muhammad Jamal Amr speaks about ""Arwa"" magazine published in Jordan and highlights standards for writing children poems.. The interview was conducted by Hasan Shams al-Din
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