68 research outputs found
RegEl Database: text-mined regulatory elements from the literature and their associations to genes and disease
No full text@article{garda2022regel,
title={RegEl corpus: identifying DNA regulatory elements in the scientific literature},
author={Garda, Samuele and Lenihan-Geels, Freyda and Proft, Sebastian and Hochmuth, Stefanie and Sch{\"u}lke, Markus and Seelow, Dominik and Leser, Ulf},
journal={Database},
volume={2022},
year={2022},
publisher={Oxford Academic}
}
# RegEl PubMed Database
This database contains the annotations generated by running [HunFlair](https://github.com/flairNLP/flair/blob/master/resources/docs/HUNFLAIR.md) models trained on the [RegEl corpus](https://zenodo.org/record/5776679) over >20M PubMed abstracts.
By pairing these annotations with the one provided by PubTator this generates a large text mining database of regulatory elements associated with genes (normalized to NCBI Gene ids) and disease (normalized to either MeSH or OMIM).
The tables composing the database are:
* abstracts.db:
- pmid = PubMed ID of the given abstracts
- sid = sentence ID of the given abstracts (from 0 to # of sentences)
- text = text of the given sentence
* gene.db and disease.db:
- pmid = PubMed ID of the given abstracts
- sid = sentence ID of the given abstracts (from 0 to # of sentences)
- etype = entity type (enhancer, promoter, TFBS)
- ann_text = mention of the regulatory element as found in the abstract
- start = position (# character) in which the mention begins
- end = position (# characters) in which the mention ends
- score = model's confidence
- cui = gene or disease identifier
- cui_symbol = official symbol of cui (if available
Three-dimensional modelling of masonry using the partition of unity method
No full textThis paper uses the Generalized Finite Element method for the introduction of the cohesive joint behaviour to model masonry. Cracked joints are modelled as displacement discontinuities and are introduced in the finite element model by additional degrees of freedom. These degrees of freedom are activated when the stress state in the joint reaches a critical level. The joint behaviour is governed by a rigid plasticity model.Structural EngineeringCivil Engineering and Geoscience
A smooth yield surface based on interpolation of Bézier curves for masonry modelling
No full textA smooth yield surface for the modelling of masonry on mesoscopic scale is presented, using interpolation by second order Bzier curves. The cracked joints are modelled as displacement discontinuities using the partition of unity property of finite element shape functions.Structural EngineeringCivil Engineering and Geoscience
Rushlight: 2019 Spring
No full textCamera flash while caught mid-chew / Christina Smith -- The Moon is a Black Woman (Acrylic Paint) / Angel Bird -- Girl Seeking God / Petra -- The Frozen Leaf /Christopher Stack -- Fern Fantasy (Photography) / Lily Fiore -- rose-colored sky / Sydney Evans -- Pitchforks /Shannon Connolly -- Untitled (Photography) / Maia Hay -- Intentionally Random (Ink) / Bailey DeBiase -- Untitled / Faheem Dyer -- Temptress (Pen and Photoshop) / Gracie Vicente -- serve god, love me, and mend / Mazie Starratt -- Wilted / Emily Gray -- A Love Poem / Anonymous -- Salvation in a Highway Motel (Photography) / Caroline Chaffiotte -- A Poet’s Sunrise /Christopher Stack -- The Stories of Strangers / Gracie Vicente -- Traveling Monster (Pen and Marker) / Timothy McCormack -- hot takes from the Target changing room / Christina Smith -- A Grievance from One Burdened by the Knowledge of an Ever Present Sense of Oblivion / Caroline Chaffiotte -- The Anatomy Lesson / Hannah McIssac -- Tchaikovsky (Photography) / Nadia Joan -- I wandered lonely as a fish / Rebecca Spadacenta -- Rule: Night Bed Start Prowl Floor / Caroline Fournier Dyhrberg -- epiphany at noon (Watercolor and Pen) / Emily Gray -- to the person looking at the same painting that i am right now / Mazie Starratt -- Canty Bay (Photography) / Maia Hay -- Continental Drift / Eliza Browning -- The Matador’s Lament / Eli Teitelman -- Nautilus (Pen and Ink) / Min Bae -- Seagrass / Eric R. Pfeiffer -- Essential Foundations / Shannon Connolly -- King’s Sunset / Sierra Proft -- Cloud Creator / Jessica Heberlein -- a poem for the mist and my morning tea / Emily Gray -- Lost in Thought? (Relief Printmaking) / Bhavika Dugar -- The Streets of Quebec / Gracie Vicente -- Sana, Sana, Culito de Rana... / Tessa Demko -- Almost Like Home (Ink) / Bailey DeBaise -- field notes / Sydney EvansWheaton College (Norton, MA) student literary magazine.camera flash while caught mid-chewThe Moon is a Black Woman (Acrylic Paint)Girl Seeking GodThe Frozen LeafFern Fantasy (Photograph)rose-colored skyPitchforksUntitled (photograph)Intentionally Random (Ink)UntitledTemptress (Pen and Photoshop)serve god, love me, and mendWiltedA Love PoemSalvation in a Highway Motel (Photography)A Poet's SunriseThe Stories of StrangersTraveling Monster (Pen and Marker)hot takes from the Target changing roomA Grievance from One Burdened by the Knowledge of an Ever Present Sense of OblivonThe Anatomy LessonTchaikovsky (Photograph)I wandered lonely as a fishRule: Night Bed Start Prowl Floorepiphany at noon (Watercolor and Pen)to the person looking at the same painting i am right nowCanty Bay (Photograph)Continental DriftThe Matador's LamentNautilus (Pen and Ink)SeagrassEssential FoundationsKing's SecretCloud Creatora poem for the mist and my morning teaLost in Thought? (Relief Printmaking)The Streets of QuebecSana, Sana, Culito de Rana...Almost Like Home (Ink)field note
Modelling crack initiation and propagation in masonry using the partition of unity method
No full textA mesoscopic masonry model is presented using the partition of unity finite element method. Joints are only explicitly introduced when a critical stress state is exceeded, resulting in a computationally more efficient procedure when compared to models in which all joints are a priori active. The performance of the presented model is demonstrated by several numerical examples.Structural EngineeringCivil Engineering and Geoscience
The PKC, HOG and Ca2+ signalling pathways co-ordinately regulate chitin synthesis in Candida albicans
No full textOpen Access via PMC2649417Peer reviewe
Combined experimental-computational study to discrete fracture of brittle materials
No full textIn this paper, a combined experimental-computational study of a double-edge notched specimen subjected to tensile loading is presented. In the experimental part, the loaddeformation response and the displacement field around the crack tip are recorded. An Electronic Speckle Pattern Interferometer (ESPI) is used to obtain the local displacement field. The experimental results are used to validate a numerical model for the description of fracture using finite elements. The numerical model uses displacement discontinuities to model cracks. The discontinuities are able to pass through finite elements. At the discontinuity, a plasticity-based and a combined damage-plasticity cohesive zone model are used, while the continuum remains elastic. Both local and global results from the numerical simulations are compared with experimental data.Civil Engineering and Geoscience
Molecular characterization of Streptococcus Pyogenes group A isolates from a tertiary hospital in Lebanon
No full textStreptococcus pyogenes [Group A Streptococcus (GAS)] is one of the most important human pathogens, responsible for numerous diseases with diverse clinical manifestations. As the epidemiology of GAS infections evolves, a rapid and reliable characterization of the isolates remains essential for epidemiological analysis and infection control. This study investigated the epidemiological patterns and genetic characteristics of 150 GAS isolates from a tertiary hospital in Lebanon by emm typing, superantigens (SAgs) detection, PFGE and antibiotic profiling. The results revealed 41 distinct emm types, the most prevalent of which were emm89 (16 percent), emm12 (10 percent), emm2 (9percent) and emm1 (8 percent). Testing for the presence of superantigens showed that speB (87 percent), ssa (36 percent) and speG (30 percent) were predominant. PFGE detected 39 pulsotypes when a similarity cut-off value of 80percent was implemented. Antibiotic-susceptibility testing against seven different classes of antibiotics showed that 9percent of the isolates were resistant to clindamycin, 23percent were resistant to erythromycin and 4percent showed the macrolide-lincosamide- streptogramin B (MLSB) phenotype. The emergence of tetracycline-resistant strains (37 percent) was high when compared with previous reports from Lebanon. This study provided comprehensive evidence of the epidemiology of GAS in Lebanon, highlighting the association between emm types and toxin genes, and providing valuable information about the origin and dissemination of this pathogen. © 2014 The Authors.Ardanuy C, 2010, J ANTIMICROB CHEMOTH, V65, P634, DOI 10.1093-jac-dkq006; Bahnan W, 2011, J MED MICROBIOL, V60, P98, DOI 10.1099-jmm.0.023317-0; Beall B, 2000, MICROBIOL-UK, V146, P1195; Chatellier S, 2000, INFECT IMMUN, V68, P3523, DOI 10.1128-IAI.68.6.3523-3534.2000; Chiou CS, 2004, J CLIN MICROBIOL, V42, P3998, DOI 10.1128-JCM.42.9.3998-4006.2004; Ciftci E., 2003, J ANKARA MED SCH, V25, P15; CLSI, 2011, M100S20 CLSI; Cole JN, 2011, NAT REV MICROBIOL, V9, P724, DOI 10.1038-nrmicro2648; Commons R, 2008, J MED MICROBIOL, V57, P1238, DOI 10.1099-jmm.0.2008-001156-0; Creti R, 2007, J CLIN MICROBIOL, V45, P2249, DOI 10.1128-JCM.00513-07; Gracia M, 2009, DIAGN MICR INFEC DIS, V64, P52, DOI 10.1016-j.diagmicrobio.2008.12.018; Imohl M, 2010, FEMS IMMUNOL MED MIC, V58, P389, DOI 10.1111-j.1574-695X.2010.00652.x; Jasir A, 2001, J CLIN MICROBIOL, V39, P586, DOI 10.1128-JCM.39.2.586-590.2001; Kidd TJ, 2011, J CLIN MICROBIOL, V49, P263, DOI 10.1128-JCM.01421-10; Luca-Harari B, 2008, J CLIN MICROBIOL, V46, P79, DOI 10.1128-JCM.01626-07; Luca-Harari B, 2009, J CLIN MICROBIOL, V47, P1155, DOI 10.1128-JCM.02155-08; Ma Y, 2009, EPIDEMIOL INFECT, V137, P1414, DOI 10.1017-S0950268809002118; McMillan DJ, 2013, CLIN MICROBIOL INFEC, V19, pE222, DOI 10.1111-1469-0691.12134; Meisal R, 2010, J CLIN MICROBIOL, V48, P842, DOI 10.1128-JCM.01312-09; Mihaila-Amrouche L, 2004, J CLIN MICROBIOL, V42, P3844, DOI 10.1128-JCM.42.8.3844-3846.2004; Mitchell DT, 2000, J MOL EVOL, V51, P520; MUSSER JM, 1991, P NATL ACAD SCI USA, V88, P2668, DOI 10.1073-pnas.88.7.2668; Mzoughi R, 2004, East Mediterr Health J, V10, P488; Ndiaye A. G., 2009, Microbiology Insights, V2, P25; Nielsen HUK, 2004, MICROB DRUG RESIST, V10, P231, DOI 10.1089-mdr.2004.10.231; Nir-Paz R, 2010, EPIDEMIOL INFECT, V138, P53, DOI 10.1017-S0950268809002805; Proft T, 1999, J EXP MED, V189, P89, DOI 10.1084-jem.189.1.89; Proft T, 2001, J IMMUNOL, V166, P6711; Proft T, 2003, INFECT IMMUN, V71, P1361, DOI 10.1128-IAI.71.3.1361-1369.2003; Rantala S, 2012, EUR J CLIN MICROBIOL, V31, P859, DOI 10.1007-s10096-011-1385-9; Rivera A, 2006, J MED MICROBIOL, V55, P1115, DOI 10.1099-jmm.0.46481-0; Smeesters PR, 2009, EXPERT REV VACCINES, V8, P1705, DOI [10.1586-erv.09.133, 10.1586-ERV.09.133]; Smoot LM, 2002, INFECT IMMUN, V70, P7095, DOI 10.1128-IAI.70.12.7095-7104.2002; Steer AC, 2009, LANCET INFECT DIS, V9, P611, DOI 10.1016-S1473-3099(09)70178-1; Villasenor-Sierra A, 2012, INT J INFECT DIS, V16, pE178, DOI 10.1016-j.ijid.2011.11.0050
PRAVO AUTORA NA REVIZIJU UGOVORNE ODREDBE O IZNOSU AUTORSKOG HONORARA
No full textThe right to revise contractual provisions concerning author’s fee exists in instances of „obvious disproportion“ between the stipulated amount of author’s fee and the income/proft which is made based on exploitation of the author’s work in question. Additionally, in some European countries this right is also applicable in cases when the amount of author’s fee has not been agreed upon initially. The party entitled to exercise this right is solely the author, as a contracting party with a weaker negotiating position compared to user of author’s work. By exercising this right, author’s participation in distribution of income/proft arising from economic exploitation of the author’s work becomes more just.U radu se razmatra iz ugla srpskog i uporednog prava revizija odredbe autorskog ugovora o iznosu autorskog honorara u slučajevima povećanja prihoda, odnosno dobiti ostvarene ekonomskim iskorišćavanjem autorskog dela, kao i u slučajevima kada iznos autorskog honorara prvobitno nije ugovoren. Ovo pravo autora, nastalo po uzoru na nemačko pravo, štiti načelo jednaskosti vrednosti uzajamnih prestacija i ravnopravnost volja ugovornih strana. Njegov značaj i neophodnost ogleda se u zaštiti autora, kao strane koja je u ekonomski slabijem položaju u odnosu na korisnika autorskog dela.
U prvom delu rada određuje se sadržina autorskog ugovora u pogledu iznosa autorskog honorara, kao njegovog tržišnog elementa i ispituje se da li on predstavlja bitan ili prirodni element autorskog ugovora. Kao posledica toga razmatra se i pravo autora da zahteva reviziju autorskog ugovora u slučajevima kada iznos autorskog honorara nije prvobitno ugovoren. Naročita pažnja posvećuje se konceptima određivanja iznosa autorskog honorara u nacionalnim pravima. U seldećem delu se precizira pravna prirodna autorskog ugovora i defniše „očigledna“ nesrazmera koja se smatra relevantnom za reviziju autorskog ugovora, a koja postoji između prihoda, odnosno dobiti, ostvarene plaćanjem tržišne cene autorskog dela, sa jedne strane i autorskog honorara koji je iz nje fnansiran, sa druge strane. Nakon toga, govori se o shvatanju revizije ovakve ugovorne odredbe iz razloga pravičnosti
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