cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
How do ponds on UBC’s campus play a role in the well-being of individuals?
Creators: name: Sano, Keita
name: Munwar, Lamisah
name: Niyaz, Morsal
name: Ke, Shi
Publisher: name: The University of British Columbia
Year: 2018

description: The purpose of this project is to provide the UBC SEEDS Sustainability Program and UBC Building Operations analysis on what role water features/ponds have on individuals at UBC. The ponds on campus need to be consistently maintained by the UBC Building Operations but are often costly, making it difficult to receive aid for its maintenance. In order to achieve a wider perspective on the issue, Biodiversity and Water Quality, were broken down into Green Coverage and Turbidity. Green coverage was chosen because it was found that this particular topic is a factor that the general public cares about in terms of assessing how much they care about ponds (Ngiam 2017). Turbidity was chosen as it is a component of water quality that fit best to our project, as it is something that can be noticed by the general public and will contribute in the overall assessment of the value of a pond. From 46 participants, the importance of water clarity was indicated to be 74% important. Almost 70% of survey participants responded the they enjoy ponds with more greenery and the exposure to green space was one of the top 4 reasons why people go to ponds. When asked how they felt around ponds at UBC: 96% chose relaxation, 91% chose enjoyment, 39% chose boredom and 17% chose disapproval (participants were able to choose one category or all that applied). This showed that more than 80% of the responses associated positive attributes towards ponds. The participants were also asked if they would favour the idea of having more ponds on campus. 43 of the participants did not hold a negative view. It is evident that people prefer to have more water features/ponds on campus or at least do not oppose greatly to the idea of it. This outcome is going to allow UBC Building Operations to determine how often specific ponds should undergo maintenance as well as if the cost of maintenance and repair are being put towards the appropriate ponds.
Brain network integration dynamics are associated with loss and recovery of consciousness induced by sevoflurane
Creators: name: Luppi, Andrea I.
name: Golkowski, Daniel
name: Ranft, Andreas
name: Ilg, Rüdiger
name: Jordan, Denis
name: Menon, David K.
name: Stamatakis, Emmanuel A.
Publisher: name: Wiley
Year: 2021
Subjects: Anaesthesia
Complexity
Consciousness
Dynamic functional connectivity
Integration - segregation
Sevoflurane
Small-world network

description: The dynamic interplay of integration and segregation in the brain is at the core of leading theoretical accounts of consciousness. The human brain dynamically alternates between a sub‐state where integration predominates, and a predominantly segregated sub‐state, with different roles in supporting cognition and behaviour. Here, we combine graph theory and dynamic functional connectivity to compare resting‐state functional MRI data from healthy volunteers before, during, and after loss of responsiveness induced with different concentrations of the inhalational anaesthetic, sevoflurane. We show that dynamic states characterised by high brain integration are especially vulnerable to general anaesthesia, exhibiting attenuated complexity and diminished small‐world character. Crucially, these effects are reversed upon recovery, demonstrating their association with consciousness. Higher doses of sevoflurane (3% vol and burst‐suppression) also compromise the temporal balance of integration and segregation in the human brain. Additionally, we demonstrate that reduced anticorrelations between the brain's default mode and executive control networks dynamically reconfigure depending on the brain's state of integration or segregation. Taken together, our results demonstrate that the integrated sub‐state of brain connectivity is especially vulnerable to anaesthesia, in terms of both its complexity and information capacity, whose breakdown represents a generalisable biomarker of loss of consciousness and its recovery.
MUMTOZ MUSIQIY NАMUNАLАR OʻQUVСHILАRNI ESTETIK TАRBIYАLАSHNING MUHIM OMILI SIFАTIDА
Creators: name: Kenjаyev, Bobir
Publisher: name: Zenodo
Year: 2024

description: Ushbu mаqolаdа mumtoz musiqiy nаmunаlаr vositаsidа oʻquvсhilаrni estetik tаrbiyаlаshning oʻzigа xos xususiyаtlаri, oʻquvсhilаrdа nаfosаt tаrbiyаsini shаkllаntirishdа mumtoz musiqа аsаrlаrining oʻrni vа аhаmiyаti hаqidа fikr yuritilgаn. Shuningdek mаqolаdа milliy mumtoz musiqа аsаrlаri vositаsidа oʻquvсhilаrdа estetik tаrbiyа tushunсhаlаrini tаrkib toptirish аlohidа аhаmiyаtgа egа boʻlib, uni rivojlаntirish uсhun mumtoz musiqа аsаrlаrini tа’lim jаrаyonidа tizimli tаrzdа tаqdim etish hаmdа oʻquvсhilаr ongigа сhuqur singdirib borish zаrurligi tа’kidlаngаn.
Supplementary analyses; Mathematica code; Mathematica code in Computable Document Format from Unbalanced selection: the challenge of maintaining a social polymorphism when a supergene is selfish
Creators: name: Tafreshi, Alireza G.
name: Otto, Sarah P.
name: Chapuisat, Michel
Publisher: name: The Royal Society
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: 60408 Genomics
subject: 10202 Biological Mathematics
subject: FOS: Mathematics

description: Numerical searches and local stability analyses;Mathematica file with all main analyses
Sample size does matter: scaling up analysis in Galaxy with metagenomics
Creators: name: Blankenberg, Daniel
name: Carnahan-Craig, Sarah
Publisher: name: F1000Research
Year: 2016

description: Metagenomics provides an exciting opportunity to begin to explore large-scale multiple sample analysis with Galaxy. As part of an obesity study, we have obtained over 400 buccal and stool samples from mother-child pairs. These samples have been subjected to 16S RNA extraction and sequencing on a MiSeq instrument. While sequencing 400 samples is no small feat, once generated, the data analysis reveals itself as crippling bottleneck.

Galaxy provides researchers with a vast quantity of tools and methods to analyze a wide-array of data, and makes connecting any number of tools together easy via Workflows. Although running a workflow individually over a handful of samples is approachable, how does one deal with 10, 20, or even 100 samples without becoming frustrated, introducing errors, breaking their mouse, or falling back to writing an API script? While Dataset Collection functionality provides a significant portion of a solution to this problem, there are still major hurdles that need to be overcome before Galaxy is usable for large multiple sample analysis.

Here we describe a generalizable metagenomic pipeline as implemented within Galaxy that is able to handle the simultaneous analysis of over 5,000 Human Microbiome Project samples. In addition to integrating a number of third-party algorithms and toolsets, some requiring the creation of upstream fixes and enhancements, we have developed new tools and approaches for dealing with large collections of data. Furthermore, we discuss the problems encountered using Galaxy at a large-scale, what has been done to overcome these issues, as well as initial results.
FROGS: Find Rapidly OTU with Galaxy Solution
Creators: name: Escudie, Frederic
name: Auer, Lucas
name: Bernard, Maria
name: Cauquil, Laurent
name: Vidal, Katia
name: Maman, Sarah
name: Mariadassou, Mahendra
name: Guillermina Hernandez-Raquet
name: Pascal, Geraldine
Publisher: name: F1000Research
Year: 2016

description: High-throughput sequencing of 16S/18S/23S RNA amplicons has opened new horizons in the study of microbe communities. With the sequencing at great depth the current processing pipelines struggle to run rapidly and the most effective solutions are often designed for specialists. These tools are designed to give both the abundance table of operational taxonomic units (OTUs) and their taxonomic affiliation. In this context we developed the pipeline FROGS: « Find Rapidly OTU with Galaxy Solution ». Developed for biologists on the Galaxy platform.

A preprocessing tool merges paired sequences into contigs with flash, cleans the data with cutadapt, deletes the chimeras with VSEARCH combined with a cross-validation method and dereplicates sequences with a home-made python script. The clusterisation tool runs with SWARM that uses a local clustering threshold, not a global clustering threshold like other software do. The affiliation tool returns taxonomic affiliation for each OTU using both RDPClassifier and NCBIBlast+ on different databases (Silva, Greengenes). And finally, the post processing tool allows users to process this table with the user-specified filters and provides statistical results and numerous graphical illustrations of these data.

FROGS has been developed to be very fast even on large amounts of 454/HiSeq/MiSeq data in using cutting-edge tools and an optimized design, also it is portable on all Galaxy platforms. FROGS was tested on numerous simulated datasets. The tool has been extremely rapid, robust and highly sensitive for the OTU detection with very few false positives compared to other pipelines widely used by the community.
Ktoolu and idFusion – Galaxy Solutions for plant immunity and pathogen informatics
Creators: name: Schudoma, Christian
name: Gupta, Yogesh
name: Pirasteh  Pahlavan
name: Jouet, Agathe
name: MacLean, Dan
name: Krasileva, Ksenia
Publisher: name: F1000Research
Year: 2016

description: Background
The analysis of plant immunity and plant-pathogen interactions are major topics in plant disease research.

Plant immunity is conferred by so-called nucleotide-binding leucine-rich repeat (NLR) proteins. A specific group of these proteins is fused to additional (integrated) domains that can recognise pathogen effector molecules. In a recent study, 41 plant genomes were computationally screened for such NLR-ID proteins.

Analysis of the interactions between plant-pathogens and their host can provide insight into both the pathogen’s effector proteins, i.e. its attack mechanisms, and the plant’s defense mechanisms. These interactions can be investigated by tailored metagenomics approaches.

Results
We present Galaxy tools/pipelines for screening of plant NLR-ID proteins (idFusion) and for complementing metagenomics analysis of plant-pathogen interactions (Ktoolu – Kraken tools and utilities). idFusion is a Galaxy implementation of the NLR-ID screening pipeline described in (Sarris et al, BMC Biology 2016). Ktoolu is a collection of tools and their Galaxy wrappers that allow to dissect sequencing datasets using the taxonomy information assigned by the Kraken metagenomics classifier as well as to visualise the results utilising the Krona tools.
GSuite HyperBrowser: Integrative genomic analyses across cells and epigenetic factors using Galaxy
Creators: name: Simovski, Boris
name: Gundersen, Sveinung
name: Vodák, Daniel
name: Abdulrahman  Azab
name: Domanska, Diana
name: Hovig, Eivind
name: Sandve, Geir Kjetil
Publisher: name: F1000Research
Year: 2016

description: Genomic investigations increasingly involve multiple genome-scale datasets (genomic tracks) representing diverse cell types and epigenetic factors. This raises the need for software tools that allow efficient management and appropriate statistical analysis of such data collections. The dataset lists in Galaxy represents a major advancement in this direction, allowing efficient management and per-dataset analysis of large numbers of datasets within a web-based system. A natural next step is to consider integrative analyses of collections of datasets. An example is to comparatively assess the co-occurrence of a dataset of disease-associated SNPs against a large number of datasets representing chromatin accessibility in diverse cell types. In addition to managing a large number of datasets (of chromatin accessibility), such an analysis requires efficient means of locating and compiling a collection of relevant datasets, as well as the provision of appropriate statistical measures.

We have developed GSuite Tools, a Galaxy-based analysis framework that offers a broad range of novel tools for managing and performing statistical analysis on collections of datasets (genomic tracks). The tools operate on GSuite files – an alternative to the standard Galaxy dataset lists that provides additional robustness and flexibility as needed for this range of tools. A prototype of GSuite Tools was presented at GCC2015. After a year of further focused work, GSuite Tools now has much broader capabilities, is based on a deeper statistical treatment of the problems, and is ready for practical use by the community. It is publicly available at: http://hyperbrowser.uio.no/gsuite
The Galaxy workflow for epigenetic profiling of progressing melanoma
Creators: name: Murat, Katarzyna
name: Poterlowicz, Krzysztof
Publisher: name: F1000Research
Year: 2016

description: Recent studies have found that distinct poor-prognosis tumours lack genetic alterations but are epigenetically heterogeneous, pointing to the important role that multi-domain epigenetic regulation in cancer progression. Researchers studying epigenetic regulation generated a vast amount of high-throughput sequencing data for processes such as DNA methylation, histone modifications and chromatin remodelers activity and transcriptomic profiling of non-coding DNA.

Although galaxy offers range of standalone tools that allow to investigate next generation sequencing data (i.e. Bismark, MACS, SICER, edgeR ), there is a lack of multi-layers epigenetic workflows characterizing tumor progression regulation.

Here we extend use of these software to investigate epigenetic profiling of the progressive melanoma which recognized early is almost always curable. Otherwise it spreads very quickly to other parts of the body making it one of the most deadliest cancer.

By integrating DNA methylation profiles, ChIP-Seq profiles for H3K27me3, H3K4me3, MITF and BRG1 for normal melanocytes and different stages of melanoma we were able to identify novel epigenetic switches responsible for metastatic progression of this tumor. Results and experiences using this framework demonstrate the potential for Galaxy to be a bioinformatics solution for multi-omics cancer biomarker discovery tool.
Hardwood Genomics Database (HGD): a web portal and database resource for hardwood tree genomic and genetic research
Creators: name: Chen, Ming
name: Henry, Nathan
name: Carlson, John
name: Staton, Margaret
Publisher: name: F1000Research
Year: 2016

description: The Hardwood Genomics Database (HGD, www.hardwoodgenomics.org) serves forest tree scientists by providing online access to hardwood tree genomic and genetic data. HGD currently houses data for economically and phylogenetically important hardwood species including assembled reference genomes, transcriptomes, and genetic mapping information. The results of bioinformatic analysis including functional annotation of genes, ontology assignment, analysis of gene expression patterns across RNASeq libraries and simple sequence repeat (SSR) identification are available to enhance the utility of the information. The web site provides access to online tools for mining and visualization of these data sets, including BLAST for comparing sequences, Jbrowse1 for browsing genomes, Apollo2 for community annotation and SyMAP3 for comparative genomics. However, these tools are limited in scope. To maximize the ability for users of community databases to harness this information and perform their own custom analysis, we are collaborating with other genome databases to build an interface to the Galaxy data analysis platform4. Users will be able to select and transfer data from the HGD to a Galaxy instance or run a pre-designed Galaxy workflow on selected datasets.
Engaging biologists with big data using interactive genome annotation
Creators: name: Marenco, Rémi
name: Leung, Wilson
name: Elgin, Sarah
name: Goecks, Jeremy
Publisher: name: F1000Research
Year: 2016

description: We are developing a customized version of Galaxy called G-OnRamp that will enable biologists to annotate the functional elements of eukaryotic genomes using large genomic datasets, a task that can also serve as an introduction to other “big data” biomedical analyses. Genome annotation—identifying functionally active regions within a genome—requires the use of diverse datasets and tools, including sequence similarity to known genes, gene prediction models, and high-throughput genomic data. To construct this interactive Web-based environment for genome annotation, we are building on two successful efforts, the Genomics Education Partnership (GEP) and Galaxy.

GEP (http://gep.wustl.edu) is a consortium of over 100 colleges/universities that provides classroom undergraduate research experiences in genomics for students at all levels. Students perform primary research on selected regions of Drosophila genomes using genomic databases (e.g., FlyBase) and bioinformatics tools (e.g., BLAST) while learning about gene structure, evolution, programming, and other topics. GEP faculty are now interested in annotating other eukaryotic genomes, reflecting their diverse research interests.

G-OnRamp will extend Galaxy by providing (a) analysis pipelines for functional genomic data (e.g., ChIP-Seq, RNA-Seq); (b) interactive visual analytics to annotate a genome (e.g., create UCSC Assembly Hubs); and (c) capacity for collaborative genome annotation. The GEP will serve as a key use case to validate and refine G-OnRamp, ensuring that it satisfies real educational needs. In this poster and demonstration, we will describe G-OnRamp’s vision and showcase its current features. G-OnRamp is available under the Academic Free License, and the software will be available via https://github.com/goeckslab
MYcrobiota: An open-source, user-friendly Galaxy application for microbiota determination and dynamic reporting from 16S sequences
Creators: name: Hiltemann, Saskia
name: S.A. Boers
name: A Kriesels
name: P.J. Van Der Spek
name: R Jansen
name: J.P. Hays
name: A.P. Stubbs
Publisher: name: F1000Research
Year: 2016

description: Microbiota profiling methods are greatly enhancing our insights into the microbial diversity and taxonomy of many different types of environments and ecosystems. These techniques are provided by an extensive array of sophisticated software such as Mothur and QIIME. Whilst many of these applications have graphical user interface (GUI), providing access to these technologies for the research or clinical scientist remains complex.

We have developed a Galaxy workflow for the analysis of metagenomics data using the Mothur suite of tools, incorporating Phinch and Krona for visualisation. We demonstrate our work using a previously published 16S rRNA gene dataset.
Incentivising a Shoreline Climate Change Adaptation Program
Creators: name: Dave, Kanchi
name: Jia, Elaine
name: Shao, Richard
name: Sun, Aini
Publisher: name: The University of British Columbia
Year: 2018

description: Green Shores for Homes (GSH) is a program under the Stewardship Center for BC (SCBC), with a goal is to persuade the maximum number of shoreline property owners to choose a soft shore1 approach instead. To achieve this, they want to find out what incentives are the most appealing to homeowners in order to best incentivize the program. The objective of this study is to identify incentives which will convince homeowners, in the pilot community, Powell River, to opt for Green Shores over conventional shores.
Supplementary document for Variable Optical True Time Delay Line Breaking Bandwidth-Delay Constraints - 6177465.pdf
Creators: name: Petrini, Matteo
name: Seyedinnavadeh, Seyedmohammad
name: Grimaldi, Vittorio
name: Milanizadeh, Maziyar
name: Zanetto, Francesco
name: Ferrari, Giorgio
name: Morichetti, Francesco
name: Melloni, Andrea
Publisher: name: Optica Publishing Group
Year: 2025
Subjects: Uncategorized

description: Supplementary Document
A Comprehensive Review On: A Vitiligo and its Cure from Nature
Creators: name: Patil HR*
name: Jain AS
name: Patil DR
name: Shaikh AZ
name: Shaikh SR
name: Dr. Pawar SP
Publisher: name: Zenodo
Year: 2024

description: Abstract

Vitiligo is a long lasting skin condition characterized by patches of the skin losing their pigment. The patches of skin affected become white and typically have sharp margins. The hair from the skin might also become white. The inside of the nose and mouth might also be concerned. The rate of colour loss from skin condition is unpredictable. Vitiligo happens when the cells that produce melanin stop or die functioning. Vitiligo affects the individual of all skin sorts; butit may be more noticeable in people with darker skin. Risk factors include a family history of the condition or other autoimmune diseases. In this review we focus on how plant based herbal products help in curing vitiligo.

Keywords: Vitiligo, Melanocyte, Repigmentation, Herbs, Herbal Medicine, Remedies, Treatments.
Games Operational Hazard Analysis and Recontextualisation of Hi-Impact Planet Amusement Park and Resort
Creators: name: Omoyi, C.O., Agbonko, E.B., Ana, R.R., & Omotehinse, S.A
Publisher: name: Nigerian Journal of Engineering Science Research (NIJESR).
Year: 2024

description: Health and safety are a major concern in developing countries like Nigeria. In the hospitality industry, recreational parks pose a whole lot of risks to all. The rides and games in amusement parks are becoming sophisticated day by day, thereby creating atmospheres where accidents and injuries are becoming rampant.  Hence a high degree of safety is essential for all and more reason why this research was set up. In this study, the safety measures of an amusement park, Hi-Impact Planet Amusement Park and Resort were evaluated with the aim of providing risk mitigation best practices in amusement parks. In this analysis, firstly a survey was conducted to assess current health and safety activities via the use of survey questionnaires. Then, operational hazard analysis document was proposed to identify likely hazards and proffer mitigating steps. A standard hazard policy was also formulated. Finally, some recommendations were postulated to improve and enhance existing legal framework.
"It matters very much whether you care that they live or die" : British Columbia Newspaper Responses to Jewish Persecution in Europe, 1933-1939
Creators: name: Lucky, Nathan
Publisher: name: The University of British Columbia
Year: 2019

description: This paper examines British Columbia press responses to Jewish persecution in Nazi Germany and Eastern Europe from 1933 to 1939. Using the Vancouver Jewish community paper as its focus, the study juxtaposes its responses with three non-Jewish papers. Vancouver Jews responded to the persecution of their coreligionists in Germany and Europe by countering neutral and skeptical reporting in the mainstream papers with explicit reporting of persecution. They tried to catalyze divided Jewish communities toward a common effort to help European Jews through fundraising efforts and lobbied for Canada to allow Jewish refugees. By 1938, they adapted to appeal to mainstream Canadian views by calling for “refugees” and “immigrants” to enter the country. They dispelled myths circulated in the non-Jewish papers about refugees and worked to change minds and gather support to convince Canada to open its doors. Finally, they emphasized that the threat of fascism was a crisis of civilization.
Cycle City : Investigating why UBC bikes
Creators: name: Chiong, Russell
name: Molina, Maria Alejandra
name: Liao, Sunny
name: Wang, Angelina
Publisher: name: The University of British Columbia
Year: 2019

description: Vancouver has seen a surge in bicycle ridership under the Vision Vancouver Party-led municipal government over the past decade. Working towards the ideas of sustainability and livability in our urban environment, Vancouver has approved multiple cycling infrastructure projects throughout the city. These projects, however, have often met criticism from the communities they were intended to serve. Recent examples including the Kitsilano Beach Park bike path (in development since 2013), where a February 2018 proposal to pave over green space is being met with fierce opposition from community members, who disapprove of the proposed location of the path, highlight the need for more community involvement throughout the process of adding to the city’s cycling infrastructure. While the total number of trips made around the city by bicycle has maintained a pattern of increase over the past decade, due in part to city initiatives promoting biking through the development of new infrastructure and amenities for cyclists, the proportion of all trips in Vancouver made by bike has actually plateaued in the past 2-3 years. At just 7%, biking is still overshadowed by other modes of transportation such as driving, and even walking. This slowing of progress regarding biking has occurred despite the completion of several projects across the city, including the Arbutus Greenway (opened in 2017). Possibly caused by inconsistencies between the wants and needs of the communities and the cycling infrastructure aimed to serve them, this warrants the question that this study seeks to answer, being: • Why is it that people bike into and around UBC? This project focuses on UBC as a pilot community for a survey aiming to investigate the factors affecting people’s decisions to bike. By using a smaller subset of the population in this preliminary survey, this project is able, in addition to finding the root causes keeping people from biking, providing some context for the recent plateau in ridership proportions in Vancouver, to act as a testing ground for questions and provide the groundwork for future studies concentrating on specific factors regarding biking.
Network analysis reveals a dominant role of protein-level regulation in coordinating gene functions
Creators: name: Wang, Jing
name: Zihao Ma
name: Carr, Steven
name: Mertins, Phillip
name: Zhang, Hui
name: Zhang, Zhen
name: Chan, Daniel
name: Ellis, Matthew
name: Townsend, Reid
name: Smith, Richard
name: McDermott, Jason
name: Chen, Xian
name: Paulovich, Amanda
name: Boja, Emily
name: Mesri, Mehdi
name: Kinsinger, Christopher
name: Rodriguez, Henry
name: Rodland, Karin
name: Leibler, Daniel
name: Zhang, Bing
Publisher: name: F1000Research
Year: 2016

description: Coordinated gene expression is central to cellular functions. Gene expression is regulated at both the transcript and protein levels, but the relative contributions of these two levels of regulation in coordinating gene functions have been largely unknown. Here, we address this fundamental question by constructing and analyzing mRNA and protein co-expression networks for three cancer types with matched mRNA and protein profiling data from The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC). Our analyses revealed a marked difference in wiring between the mRNA and protein co-expression networks. Whereas protein co-expression was driven primarily by functional similarity between co-expressed genes, mRNA co-expression was driven by both co-function and chromosomal co-localization of the genes. Functionally coherent mRNA modules were more likely to have their edges preserved in corresponding protein networks than functionally incoherent mRNA modules. Proteomics data strengthened the link between gene expression and function for at least 75% of Gene Ontology (GO) biological processes and 90% of KEGG pathways. Based on the three protein co-expression networks, we also developed a web tool gene2net (http://cptac.gene2net.org) that can reveal novel gene-function relationships. Our results indicate a dominant role of protein-level regulation in coordinating gene functions and emphasize the need to integrate proteomics into gene function and human disease studies.
Network analysis reveals a dominant role of protein-level regulation in coordinating gene functions
Creators: name: Wang, Jing
name: Zhang, Bing
Publisher: name: F1000Research
Year: 2016

description: Coordinated gene expression is central to cellular functions. Gene expression is regulated at both the transcript and protein levels, but the relative contributions of these two levels of regulation in coordinating gene functions have been largely unknown. Here, we address this fundamental question by constructing and analyzing mRNA and protein co-expression networks for three cancer types with matched mRNA and protein profiling data from The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC). Our analyses revealed a marked difference in wiring between the mRNA and protein co-expression networks. Whereas protein co-expression was driven primarily by functional similarity between co-expressed genes, mRNA co-expression was driven by both co-function and chromosomal co-localization of the genes. Functionally coherent mRNA modules were more likely to have their edges preserved in corresponding protein networks than functionally incoherent mRNA modules. Proteomics data strengthened the link between gene expression and function for at least 75% of Gene Ontology (GO) biological processes and 90% of KEGG pathways. Based on the three protein co-expression networks, we also developed a web tool gene2net (http://cptac.gene2net.org) that can reveal novel gene-function relationships. Our results indicate a dominant role of protein-level regulation in coordinating gene functions and emphasize the need to integrate proteomics into gene function and human disease studies.
Interaction analysis of vancomycin-resistome from RNA-seq data using Galaxy and functional examination of sRNA241 in S. aureus
Creators: name: Devika Subramanian
name: Natarajan, Jeyakumar
Publisher: name: F1000Research
Year: 2016

description: The widespread emergence of antibiotic-resistant Staphylococcus aureus is a major bottleneck in the development of novel treatments as the mechanisms triggering this phenomenon is largely unknown. The role of small-RNAs in regulating bacterial response to environmental stresses including antibiotic exposures is now recognized. However, the functions of a majority of them are still unknown. Here, a collection of RNA-seq expression profiles were analyzed to reconstruct a model of vancomycin-resistome interactions which was then used to predict the functions of sRNA241, a small-noncoding RNA which was consistently downregulated upon antibiotic exposures. The state-of-the-art tools Bowtie, Stringtie (ran from galaxy webserver) and Ballgown were used to align, assemble and identify the differentially expressed mRNAs that could be responsible for the development of resistance mechanisms. Based on this, an mRNA repertoire encompassing the major resistome components were identified and used to reconstruct a vancomycin-resistome network with 308 nodes and 2477 interactions. Clustering and enrichment analyses of the network indicate that a variety of gene clusters representing various metabolic pathways and defense mechanisms mediate the resistance to vancomycin. Subsequently, the resistome network was used to examine the functions of sRNA241. Predicted targets of the sRNA were refined by opposite expression pairing and a functional subnetwork of the resistome consisting of the specific sRNA-mRNA interactions were identified. Enrichment analysis of the subnetwork indicates the regulation of different metabolic pathways including quinone/menaquinone biosynthetic pathways by sRNA241. Thus the resistome network model is a good platform to expand the knowledge on cellular interactions behind antibiotic resistance.
D4.2: Establishment of PRACE Advanced Training Centres
Creators: name: Louhivuori, Martii
name: Manninen, Pekka
name: Wong, Simon
Publisher: name: Zenodo
Year: 2012
Subjects: Deliverable
HPC
Research infrastructure

description: This document describes the first steps carried out to establish hubs for high-performance computing training and education: PRACE Advanced Training Centres (PATC). The first six PATCs became operational early 2012, with the mission to serve as European hubs of advanced, world-class training and education for researchers and students in computational sciences, providing and coordinating knowledge transfer activities needed to achieve best utilisation of the PRACE research infrastructure by the community.
 In this deliverable, we document the process employed in the selection of the first six hosting sites, present those sites and discuss various practical matters, such as efforts coordination, finances and curriculum building, related to the operation of the PATC network. Finally, some future plans for the PATC concept and operation are discussed. These plans include a PATC focused on industrial R&D as well as roadmap for PATCs after the end of the PRACE project series. The role and responsibilities of the AISBL regarding the PATCs need still to be defined in the future.
The TRUElncRNA workflow: a Galaxy based workflow for identification of novel long non-coding RNAs.
Creators: name: Heydarian, Mohammad
name: Cutler, Jevon
name: Sauria, Mike
name: Taylor, James
name: Sollner-Webb, Barbara
name: Reddy, Karen
Publisher: name: F1000Research
Year: 2016

description: Long non-coding RNAs (lncRNAs) are a class of RNA that lack protein coding potential and exhibit features similar to protein coding RNAs, in that they are transcribed by RNA polymerase II, are 5' capped, and spliced in most cases. LncRNAs are expressed at levels lower than protein coding RNAs and exhibit tissue/cell type restricted expression. To identify lncRNAs in early B cell development in mouse, we performed RNA-sequencing on two developmentally arrested models of early hematopoiesis, a multi-potent progenitor (MPP) with the capacity to differentiate towards monocyte/lymphocyte lineages and a lineage committed pro-B (pro-B) cell system. Using the Tuxedo RNA-seq analysis suite with a de novo transcriptome reconstruction approach, we identified ~ 45,000 transcripts deemed to be long non-coding RNAs. To prioritize high confidence lncRNAs, we developed a Galaxy based workflow for discovery of novel and known high confidence lncRNAs that we call the 'TRUElncRNA workflow'. This workflow requires standard output file formats from the Tuxedo suite, as well as widely available reference data from the UCSC table browser, and returns high confidence novel and known lncRNAs. Using the TRUElncRNA workflow, we identified ~ 200 novel and ~2,300 known high confidence lncRNAs expressed in early B cell development. These high confidence lncRNAs demonstrate low coding potential relative to protein coding RNAs by PhyloCSF scoring. The identified high confidence lncRNAs exhibit chromatin profiles similar to annotated protein coding genes and show tissue restricted expression patterns across a comprehensive array of mouse tissues. Lastly, these lncRNAs also tend to reside in topological domains with genes of relevance to early hematopoiesis and in some cases interact with promoters of relevant genes across hundreds of kilobases.
ПОНЯТИЕ И СУЩНОСТЬ СТРАТЕГИЧЕСКОГО ПАРТНЁРСТВА В МЕЖДУНАРОДНОМ ПРАВЕ
Creators: name: Ирисметов, Хусан
Publisher: name: Zenodo
Year: 2025

description: Настоящая статья посвящена всестороннему исследованию понятия и сущности стратегического партнёрства в международном праве. В условиях трансформации глобального миропорядка, усиления взаимозависимости государств и усложнения архитектуры международных отношений стратегическое партнёрство приобретает всё большее значение как форма устойчивого, институционализированного и направленного на долгосрочную перспективу взаимодействия субъектов международного права. В рамках исследования проводится анализ понятийно-категориального аппарата, а также эволюции подходов к определению стратегического партнёрства в теории международного права и в международной практике.
Supplementary figures from Association mapping of colour variations in a butterfly provides evidences that a supergene locks together a cluster of adaptive loci
Creators: name: Jay, Paul
name: Leroy, Manon
name: Le Poul, Yann
name: Whibley, Annabel
name: Arias, Monica
name: Chouteau, Mathieu
name: Joron, Mathieu
Publisher: name: The Royal Society
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Ecology
subject: 60408 Genomics

description: Figure S1-22
D8.1.4: Plan for Community Code Refactoring
Creators: name: Gheller, Claudio
name: Sawyer, Will
Publisher: name: Zenodo
Year: 2012
Subjects: Deliverable
HPC
Research infrastructure
Scientific applications
Libraries
Performance modelling

description: In this deliverable we present the scientific codes performance modelling carried out during the first six months of work package 8 of PRACE-2IP. For each code selected in the domains of Astrophysics, Material Science, Climate and Particle Physics, we provide a short summary of the algorithms to be the subject of refactoring. A detailed description of the proposed work and its motivations are reported, for most cases motivated through a performance modelling analysis. Each code is supplied with a standard test suite, which allows the verification of quality and correctness of the re-implemented software. A detailed workplan for the implementation phase (M7-20) is presented for each application, specifying the timeline and the milestones for its refactoring, and clearly stating the main objectives of the development work.
 In the deliverable we also introduce a fifth scientific community, Engineering, which has recently joined the work package. At the time of the submission of the current document, this community has identified the relevant applications and specified the main targets for code refactoring. The performance analysis and modelling will be added as soon as data and results are available.
title: Dringlicher denn je: Was ist Antisemitismus?
Creators: name: Lindner, Urs
Publisher: name: DuEPublico: Duisburg-Essen Publications online, University of Duisburg-Essen, Germany
Year: 2024
Subjects: subject: 900

description: Rezensionsessay zu: Peter Ullrich, Sina Arnold, Anna Daniliina, Klaus Holz, Uffa Jensen, Ingolf Seidel, Jan Weyand (Hg.): Was ist Antisemitismus? Begriffe und Definitionen von Judenfeindschaft, Wallstein: Göttingen 2024, 315 Seiten The article reviews the volume “Was ist Antisemitismus? Begriffe und Definitionen von Judenfeindschaft” edited by Peter Ullrich, Sina Arnold, Anna Danilina, Klaus Holz, Uffa Jensen, Ingolf Seidel and Jan Weyand (Göttingen 2024). The book is lauded for its innovativeness and comprehensiveness: This is the first German volume on the epistemology and politics of defining antisemitism. It covers basic concepts, topics and approaches in the conceptualisation of anti-Jewish enmity followed by an in-depth theorisation by one of the editors. Although the volume by and large has a clear inclination towards the Jerusalem Declaration on Antisemitism, it also highlights the blind spots of this definition. Its sole weakness is an entry on “postcolonial antisemitism”, where typically German prejudices about postcolonialism are reproduced.
description: Sozial.Geschichte Online: Zeitschrift für historische Analyse des 20. und 21. Jahrhunderts, vol. 2024, no. 37, p. 159
Jumping across gene-disease contexts using compressive data fusion
Creators: name: Zitnik, Marinka
name: Blaz Zupan
Publisher: name: F1000Research
Year: 2016

description: We can now consider interactions between various biomedical objects, such as genes, chemicals, molecular signatures, diseases, pathways and environments. Often, any pair of objects—-like, a gene and a disease—-can be related in multiple different ways, for example, directly via gene-disease associations or indirectly via functional annotations, chemicals and pathways. Different ways of relating these objects carry different meanings and imply different similarities. However, present methods often disregard these semantics, which prevents them to fully exploit their potentials.

Our goal is to answer association queries on complex data systems and explicitly distinguish between diverse data semantics. For example, given a few diseases, infer the most significant size-k gene module. Or, given a list of genes, propose a group of k other genes that, taken together, will give the highest significance for a particular disease under an appropriate null hypothesis. Or, given a few pathways, find which k chemicals have collectively the largest impact on these pathways. To achieve this level of versatility we build on compressive data fusion to derive all possible semantics and formulate a submodular optimization program with theoretical guarantees about the detection quality.

In gene-disease association prediction and disease module detection studies on 310 complex diseases we show the new approach compares favorably to approaches that conflate data semantics. Importantly, we find that different semantics vary in their ability to make accurate predictions and that the utility of semantics depends on disease category. Overall, compressive data fusion provides a powerful mechanism for inference across gene-disease contexts.
title: Ideologische Leinwand? Die Präsentation jüdischer Erfahrung mit dem Nationalsozialismus im DEFA-Spielfilm
Creators: name: Hanloser, Gerhard
Publisher: name: DuEPublico: Duisburg-Essen Publications online, University of Duisburg-Essen, Germany
Year: 2024
Subjects: subject: 900

description: Lisa Schoß, Von verschiedenen Standpunkten. Die Darstellung jüdischer Erfahrung im Film der DDR, Bertz + Fischer: Berlin 2023. 656 Seiten This review essay on the presentation of Jewishness, antisemitism and the Holocaust in DEFA films examines the results of a monograph by Lisa Schoß. By discussing a selection of well-known and rather unknown GDR films on the subject, the author concludes that antisemitism, the persecution of Jews in the Third Reich and Jewish ways of life and existence were portrayed and honoured in a remarkable way in various DEFA films. Some negative portrayals and interpretations as well as Schoß’ storytelling are criticised.
description: Sozial.Geschichte Online: Zeitschrift für historische Analyse des 20. und 21. Jahrhunderts, vol. 2024, no. 37, p. 173
D3.2.1: Dissemination Package for Stakeholder
Creators: name: Jakobsson, Anni
name: Leiponen, Tiina
Publisher: name: Zenodo
Year: 2012
Subjects: Deliverable
HPC
Research infrastructure
Dissemination

description: This document describes the design, implementation, contents, and the upgrade process of the PRACE Dissemination Package.
 The Dissemination Package is a central element in all PRACE dissemination activities. It consists of the web presence and the Dissemination Media Package for Stakeholders, which includes PR material e.g. flyers, general brochure, posters, give-aways, and templates for communication.
 The Dissemination Package for Stakeholders itself is the actual deliverable D3.2.1 (PR material available). This document accompanies the deliverable and describes the design, implementation, contents and update process of the dissemination material. The Dissemination Package for Stakeholders can be found in digital format on the project intranet (BSCW). The deliverable should be accompanied with the Dissemination Package for Stakeholders.
Learning context-specific nested effects models from gene knockdown data
Creators: name: Sverchkov, Yuriy
name: Gasch, Audrey
name: Craven, Mark
Publisher: name: F1000Research
Year: 2016

description: Recent advances in systems biology have made clear the importance of network models for capturing knowledge about complex relationships in gene regulation, metabolism, and cellular signaling. A common approach to uncovering biological networks involves performing perturbations on elements of the network, such as gene knockdown experiments, and measuring how the perturbation affects some reporter of the process under study. We develop context-specific nested effects models (CSNEMs), an approach to inferring such networks that generalizes nested effects models (NEMs). In an NEM, a network of manipulated genes is constructed based on the effects on downstream transcript abundances, as measured by, e.g., microarray. NEMs assume that a single network structure applies across all data; however, there is evidence some biological processes do not necessarily follow this constraint. This led us to develop a representation and a learning method for CSNEMs, in which an interaction between two genes may be present in the network in one context but absent in another, to reflect the biological phenomenon that some sets of molecules might only be available in some pools in the cell. We hope that this type of model will aid in furthering general systems biology knowledge and help effectively apply this knowledge by more faithfully matching the biological process under study.
Final design of citizen surveys on individuals' perceptions and acceptance of SIE and EU energy transitions
Creators: name: Guetlein, Marie-Charlotte
name: Schleich, Joachim
name: Dütschke, Elisabeth
Publisher: name: Zenodo
Year: 2020

description: Deliverable D5.1 includes a description of the experimental methodology to be used and of the items to be included in the framework survey based on insights from WPs 1-4 and 6. While the general structure of the survey has been finalised, the experiments and framework survey items will continue to be updated based on general feedback and further insights from all project partners, notably from the case studies in WP3. The survey elements presented henceforward are thus subject to change. Prior to fielding the survey, pre-tests will be conducted - to be launched by the end of month 19 (MS9). Information from these pre-tests will be used to further refine the questionnaire. Also, constraints on survey length and the budget may require the questionnaire to be shortened.
title: Rassismus und Hegemonie. Die lange Normalisierung der extremen Rechten in Frankreich
Creators: name: Lindner, Kolja
Publisher: name: DuEPublico: Duisburg-Essen Publications online, University of Duisburg-Essen, Germany
Year: 2024
Subjects: subject: 900

description: Rezensionsessay zu Félicien Faury, Des électeurs ordinaires. Enquête sur la normalisation de l’extrême droite, Éditions du Seuil: Paris 2024, 238 Seiten France’s political landscape is characterised by a constant electoral rise of the far right. This shift has often been attributed to increased unemployment. In his much-discussed book “Des électeurs ordinaires”, sociologist Félicien Faury dives into the social representations of right-wing voters and observes that things are much more complicated: race is the modality in which a comprehensive crisis of capitalist society is lived. Hence the importance of antiracism in struggles against the far right, a conclusion that also speaks to the current German situation.
description: Sozial.Geschichte Online: Zeitschrift für historische Analyse des 20. und 21. Jahrhunderts, vol. 2024, no. 37, p. 199