66 research outputs found
Multiple narratives of il/legality and im/morality: The case of small-scale hashish harvesting in Kyrgyzstan
No full textThe aim of this study is to contribute to the current literature concerning the social acceptance of illegal practices. Using legal pluralism as a general framework of analysis, this study discusses the relationship between state law and alternative perspectives concerning its legitimacy. It presents the experience of people involved in hashish harvesting in one of the regions of Kyrgyzstan, how the state defines it as an ‘illegal practice’ and how the local population subsequently invokes normative systems based on local spiritual knowledge and the local moral economy of hashish production. It argues that acceptance of hashish harvesting as a legitimate means of support is not a straightforward process. Despite the predominant legitimating narrative of hashish harvesting, it enters into a conversation with state defined notions of ‘illegality’ and is also shaped by the customary understanding of the spiritual power of cannabis plants that requires caution when making hashish.© 2019, The Author(s). This is an author produced version of a paper published in THEORETICAL CRIMINOLOGY uploaded in accordance with the publisher’s self- archiving policy. The final published version (version of record) is available online at the link. Some minor differences between this version and the final published version may remain. We suggest you refer to the final published version should you wish to cite from it
The Reveries of Orientalism and the realities of fiction: an analysis of the short story “The Hashish Man” by Lord Dunsany: An analysis of the short story “The Hashish Man” by Lord Dunsany
No full textLord Dunsany, pseudônimo de Edward John Moreton Drax Plunkett, é ainda um obscuro autor de literatura de fantasia que, no entanto, é reconhecido como influência decisiva na obra de outros escritores modernos de gêneros como o fantástico, a ficção científica e o horror cósmico. A partir da análise do conto intitulado “The Hashish Man”, investigamos como Lord Dunsany apresenta inflexões originais e novas angulações no tocante às temáticas e imagens orientalistas comuns em sua época. Para isso, exploramos primeiramente como as narrativas novecentistas que tematizam ou versam sobre a toxicomania, sobretudo o ópio e o haxixe, revelam uma faceta das ansiedades imperiais e suas tensões políticas, culturais e econômicas. Em seguida, buscamos uma formulação do modo como o autor, mediante recursos como a metatextualidade e a metaficção (recursos não tão habituais em sua tradição e época), desarticula ou desloca alguns dos tropos e lugares-comuns do Orientalismo, conduzindo sua narrativa não só para um horror cósmico avant la lettre, mas também para um questionamento da própria natureza do real e da literatura.Lord Dunsany (pseudonym of Edward John Moreton Drax Plunkett) is still a relatively obscure author of fantasy literature. Nonetheless, he is recognized as a decisive influence on the work of other modern writers in literary genres such as the fantastic, science fiction, and cosmic horror. Through analysing his short story "The Hashish Man," we examine how Lord Dunsany introduces original nuances and new angles regarding the Orientalist themes and imagery common in his time. To accomplish this, we first explore how the 19th-century narratives that thematize or address drug addiction, particularly opium and hashish, reveal a certain feature of imperial anxieties and their political, cultural, and economic tensions. Then we proceed to formulate how the author, through techniques such as metatextuality and metafiction (which were not so common in his tradition and historical period), disarticulates or displaces some of the tropes and clichés of Orientalism, leading his narrative not only towards a cosmic horror avant la lettre but also towards a questioning of the very nature of reality and literature
Code for: Semantic prioritization of novel causative genomic variants
No full textAbstract: Discriminating the causative disease variant(s) for individuals with inherited or de novo mutations present one of the main challenges faced by the clinical genetics community today. Computational approaches for variant prioritization include machine learning methods utilizing a large number of features, including molecular information, interaction networks, or phenotypes. Here, we demonstrate the PhenomeNET Variant Predictor (PVP) system that exploits semantic technologies and automated reasoning over genotype-phenotype relations to filter and prioritize variants in whole exome and whole genome sequencing datasets. We demonstrate the performance of PVP in identifying causative variants on a large number of synthetic whole-exome and whole-genome sequences, covering a wide range of diseases and syndromes. In a retrospective study, we further illustrate the application of PVP for the interpretation of whole-exome sequencing data in patients suffering from congenital hypothyroidism. We find that PVP accurately identifies causative variants in whole exome and whole genome sequencing datasets and provides a powerful resource for the discovery of causal variants.
PhenomeNet Variant Predictor (PVP) - User Guide
A phenotype-based tool to annotate and prioritize disease variants in WES and WGS data
This user guide have been tested on Ubuntu version 16.04.
For details regarding model training and evaluation, please refer to dev/ directory above.
Hardware requirements
At least 32 GB RAM.
At least 1TB free disk space to process and accommodate the necessary databases for annotation
Software requirements (for native installation)
Any Unix-based operating system
Java 8
Python 2.7 (as a system default version) and install the dependencies (for Python 2.7) with:
pip install -r requirements.txt
Run python 2 for the script test.py (available above) to test the installation of the python dependencies. If the script fails, please try again to install the required dependencies ( using "pip2" instead of "pip", checking for permissions, or try the docker image instead).
Native Installation
Download the distribution file phenomenet-vp-2.1.zip
Download the data files phenomenet-vp-2.1-data.zip
Extract the distribution files phenomenet-vp-2.1.zip
Extract the data files data.tar.gz inside the directory phenomenet-vp-2.1
cd phenomenet-vp-2.1
Run the command: bin/phenomenet-vp to display help and parameters.
Database requirements
Download CADD database file.
Download and run the script generate.sh (Requires TABIX).
Copy the generated files cadd.txt.gz and cadd.txt.gz.tbi to directory phenomenet-vp-1.0/data/db.
Download DANN database file and its indexed file to directory phenomenet-vp-1.0/data/db.
Rename the DANN files as dann.txt.gz and dann.txt.gz.tbi respectively.
Docker Container
Install Docker
Download the data files phenomenet-vp-2.1-data.zip and database requirements
Build phenomenet-vp docker image:
docker build -t phenomenet-vp .
Run phenomenet
docker run -v $(pwd)/data:/data phenomenet-vp -f data/Miller.vcf -o OMIM:263750
Parameters
--file, -f
Path to VCF file
--outfile, -of
Path to results file
--inh, -i
Mode of inheritance
Default: unknown
--json, -j
Path to PhenoTips JSON file containing phenotypes
--omim, -o
OMIM ID
--phenotypes, -p
List of phenotype ids separated by commas
--human, -h
Propagate human disease phenotypes to genes only
Default: false
--sp, -s
Propagate mouse and fish disease phenotypes to genes only
Default: false
--digenic, -d
Rank digenic combinations
Default: false
--trigenic, -t
Rank trigenic combinations
Default: false
--combination, -c
Maximum Number of variant combinations to prioritize (for digenic and
trigenic cases only)
Default: 1000
--ngenes, -n
Number of genes in oligogenic combinations (more than three)
Default: 4
--oligogenic, -og
Rank oligogenic combinations
Default: false
--python, -y
Path to Python executable (ex. /usr/bin/python)
Default: python
Usage:
To run the tool, the user needs to provide a VCF file along with either an OMIM ID of the disease or a list of phenotypes (HPO or MPO terms).
a) Prioritize disease-causing variants using an OMIM ID:
bin/phenomenet-vp -f data/Miller.vcf -o OMIM:263750
b) Prioritize digenic disease-causing variants using an OMIM ID, and gene-to-phenotype datta from human studies only:
bin/phenomenet-vp -f data/Miller.vcf -o OMIM:263750 --human --digenic
c) Prioritize disease-causing variants using a set of phenotypes, and recessive inheritance mode
bin/phenomenet-vp -f data/Miller.vcf -p HP:0000007,HP:0000028,HP:0000054,HP:0000077,HP:0000175 -i recessive
The result file will be at the directory containg the input file. The output file has the same name as input file with .res extension. For digenic, trigenic or oligogenic prioritization, the result file will have .digenic, .trigenic, or .oligogenic extension repectivly.
Analysis of Rare Variants:
In order to effectively analysis rare variants, it is strongly recommended to filter the input VCF files by MAF prior to running phenomenet-vp on it. To do so, follow the instructions below:
a) Install VCFtools.
b) Run the following command using VCFtools on your input VCF file to filter out variants with MAF > 1%:
vcftools --vcf input_file.vcf --recode --max-maf 0.01 --out filtered
c) Run PVP on the output file filtered.recode.vcf generated from the command above.
PVP 1.0
The original random-forest-based PVP tool is available to download here along with its required data files here. The prepared set of exomes and genomes used for the analysis and results are provided here.
DeepPVP
The updated neural-network model, DeepPVP is available to download here along with its required data files here. The prepared set of exomes used for the analysis and comparative results are provided here. The comparison with PVP is based on PVP-1.1 available here along with its required data files here.
OligoPVP
OligoPVP is provided as part of DeepPVP tool using the parameters --digenic, --trigenicm and --oligogenic for ranking candidate disease-causing variant pairs and triples. Our prepared set of synthetic genomes digenic combinations are available here using data from the DIgenic diseases DAtabase (DIDA). The comparison results with other methods are also provided. Results were obtained using DeepPVP v2.0.
People
PVP is jointly developed by researchers at the University of Birmingham (Prof George Gkoutos and his team), University of Cambridge (Dr Paul Schofield and his team), and King Abdullah University of Science and Technology (Prof Vladimir Bajic, Robert Hoehndorf, and teams).
Publications
[1] Boudellioua I, Mahamad Razali RB, Kulmanov M, Hashish Y, Bajic VB, Goncalves-Serra E, Schoenmakers N, Gkoutos GV., Schofield PN., and Hoehndorf R. (2017) Semantic prioritization of novel causative genomic variants. PLOS Computational Biology. https://doi.org/10.1371/journal.pcbi.1005500
[2] Boudellioua I, Kulmanov M, Schofield PN., Gkoutos GV., and Hoehndorf R . (2018) OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants. Scientific Reports. https://doi.org/10.1038/s41598-018-32876-3
[3] Boudellioua I, Kulmanov M, Schofield PN., Gkoutos GV., and Hoehndorf R . (2019) DeepPVP: phenotype-based prioritization of causative variants using deep learning. BMC Bioinformatics. https://doi.org/10.1186/s12859-019-2633-8
License
Copyright (c) 2016-2018, King Abdullah University of Science and Technology
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
3. All advertising materials mentioning features or use of this software
must display the following acknowledgment:
This product includes software developed by the King Abdullah University
of Science and Technology.
4. Neither the name of the King Abdullah University of Science and Technology
nor the names of its contributors may be used to endorse or promote products
derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY
''AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY
BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.NS was funded by Wellcome Trust (Grant 100585/Z/12/Z) and the National Institute for Health Research Cambridge Biomedical Research Centre. IB, RBMR, MK, YH, VBB, RH were funded by the King Abdullah University of Science and Technology. GVG acknowledges funding from the National Science Foundation (NSF grant number: IOS-1340112) and the European Commission H2020 (Grant Agreement No. 731075)
Machining of aluminium based Metal Matrix Composite (MMC)
No full textThe machining of aluminium 2618 particulate reinforced Metal Matrix Composite
(MMC) with 18 vol. % silicon carbide (SiC) using cemented carbide cutting tools
has been undertaken. Two grades of cemented carbide inserts, uncoated K68 grade
and coated KC910 grade (coated with TiC and A1203) having negative and positive
rake angles (with and without chip breaker) have been used to machine this material
in order to understand the machining process, tool failure modes and wear
mechanisms. Turning tests in the speed range 15 - 10 m/min have been carried out at
0.2,0.4 and 0.6 mm/rev feed rates and 2 mm and 4 mm depths of cut.
Both cemented carbide tools have been shown to be capable of machining the MMC
and give reasonable tool lives. Low speed and high feed rate are found to be a good
combination in order to machine this material effectively. Coated KC910 grade
inserts with negative rake angle gave the best performance. The use of a chip breaker
has no significant effect on the machining process of the NMC because the material
is one which inherently short chips due to ductility limitations caused by the
particles.
Tool failure mode studies showed that the tools failed by flank wear. Tool wear
mechanism analysis indicated that abrasion wear was the tool life controlling factor
under all cutting conditions. The tool wear is related to the direct contact between
the abrasive hard SiC particles and the cutting edge and their relative motion to the
rake and clearance face. Hence, the hardness of the SiC particles is a dominant factor
for the tool wear. Two separatem odels of abrasio. n haye.b een suggested.B uilt-up
edge (BUE) which has a distinct shape was more pro i1ounced at lower cutting
speeds, high feed rates and greater depth of cut. The presence of BUE has been
found to increase tool life and reduce tool wear but at the expense of surface finish.
The increase in tool life or reduction in tool wear is likely due to the protective layer
that the BUE formed on the tool surface preventing a direct contact between the tool
and chip. Linear regression analysis showed that the value of Taylor exponent n is
high (0.8-1.0) compared to the values of n (0.2-0.3) obtained when machining steel.
This indicates that the tool life is less sensitive to cutting speed for MMC than it is
for steel
Event-Triggered Control for Vehicle Platooning: Application to heterogeneous platoons
No full textThis thesis covers the implementation of Event-Triggering Control (ETC) on Cooperative Adaptive Cruise Control (CACC). CACC has the potential to increase road capacity, by having safe vehicle following with small intervehicle distance (less than 1 second), to increase traffic flow by eliminating shockwave effects, such that string-stable behavior is achieved, and it increases vehicle safety and driving comfort. CACC uses Vehicle-To-Vehicle (V2V) or Vehicle-To-Infrastructure (V2I) communication. However, excessive use of this wireless communication may result in reliability issues of the communication network. By means of Event-Triggered Control, this issue can be tackled by establishing communication only when it is necessary, while guaranteeing desired closed-loop performance. In this thesis, an event-triggered controller for heterogeneous vehicle platooning is designed, which is decentralized, guarantees vehicle-following with small intervehicle distances, is robust against time-varying delays, and guarantees a positive minimum inter-event time. The algorithm is backed up by simulations, and it shows that communication is significantly reduced while maintaining desired closed-loop performance, when compared to periodic communication.Mechanical Engineering | Systems and Contro
Data warehousing quality
No full textThis thesis was scanned from the print manuscript for digital preservation and is copyright the author.
Researchers can access this thesis by asking their local university, institution or public library to
make a request on their behalf. Monash staff and postgraduate students can use the link in the References field
Pour une histoire du cannabis
No full textWhat is known about the history of hashish in France or, more precisely, the history of the relationship between cannabis and the inhabitants of France? Which aspects of these relationships deserve more detailed investigation by historians? Which periods have been most extensively studied and which periods have been neglected? To answer these questions, this article is essentially based on the author’s contribution to Cannabis et adolescence. Les liaisons dangereuses. Before the 19th century, although lndian hemp was not completely unknown in France, it was very poorly known and essentially described in travellers’ tales. For example, no trace was found in the medical literature before the book by Aubert-Roche, De la peste et du typhus en Orient published in 1840. Five years later, the publication of Du haschisch et de l’aliénation mentale by Moreau de Tours raised a certain amount of interest in the medical world. This “alienist”, working at Bicêtre and then at Salpêtrière hospitals, played a major role in the introduction of cannabis in France. The history of this substance therefore begins in the middle of the 19th century. The author distinguishes three levels of analysis, which, although related to each other, possess a certain degree of independence. The author examines the place of hashish in scientific and more particularly medical thought and practice and then examines the place of hashish in literary and artistic representations. Finally, the sociological aspects of hashish consumption are studied. These three aspects obviously do not exhaust the subject. For example, cannabis in relation to the law and public policies constitutes another especially heuristic aspect
PathoPhenoDB, linking human pathogens to their phenotypes in support of infectious disease research
No full textUnderstanding the relationship between the pathophysiology of infectious disease, the biology of the causative agent and the development of therapeutic and diagnostic approaches is dependent on the synthesis of a wide range of types of information. Provision of a comprehensive and integrated disease phenotype knowledgebase has the potential to provide novel and orthogonal sources of information for the understanding of infectious agent pathogenesis, and support for research on disease mechanisms. We have developed PathoPhenoDB, a database containing pathogen-to-phenotype associations. PathoPhenoDB relies on manual curation of pathogen-disease relations, on ontology-based text mining as well as manual curation to associate host disease phenotypes with infectious agents. Using Semantic Web technologies, PathoPhenoDB also links to knowledge about drug resistance mechanisms and drugs used in the treatment of infectious diseases. PathoPhenoDB is accessible at http://patho.phenomebrowser.net/, and the data are freely available through a public SPARQL endpoint.This work was supported by funding from King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) under Award No. URF/1/3454-01-01, URF/1/3790-01-01, and FCC/1/1976-08-01
PathoPhenoDB: linking human pathogens to their disease phenotypes in support of infectious disease research
No full textUnderstanding the relationship between the pathophysiology of infectious disease, the biology of the causative agent and the development of therapeutic and diagnostic approaches is dependent on the synthesis of a wide range of types of information. Provision of a comprehensive and integrated disease phenotype knowledgebase has the potential to provide novel and orthogonal sources of information for the understanding of infectious agent pathogenesis, and support for research on disease mechanisms. We have developed PathoPhenoDB, a database containing pathogen-to-phenotype associations. PathoPhenoDB relies on manual curation of pathogen-disease relations, on ontology-based text mining as well as manual curation to associate phenotypes with infectious disease. Using Semantic Web technologies, PathoPhenoDB also links to knowledge about drug resistance mechanisms and drugs used in the treatment of infectious diseases. PathoPhenoDB is accessible at http://patho.phenomebrowser.net/, and the data is freely available through a public SPARQL endpoint.This work was supported by funding from King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) under Award No. URF/1/3454-01-01 and FCC/1/1976-08-01
- …
