bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implementing an open source spatio-temporal search platform for Spatial Data Infrastructures
Authors: Corti Paolo , Lewis Benjamin G , Kralidis Tom , Mwenda Jude 
Published: January 2018

A Spatial Data Infrastructure (SDI) is a framework of geospatial data, metadata, users and tools intended to provide an efficient and flexible way to use spatial information. One of the key software components of an SDI is the catalogue service which is needed to discover, query, and manage the metadata. Catalogue services in an SDI are typically based on the Open Geospatial Consortium (OGC) Catalogue Service for the Web (CSW) standard which defines common interfaces for accessing the metadata information.
A search engine is a software system capable of supporting fast and reliable search, which may use “any means necessary” to get users to the resources they need quickly and efficiently. These techniques may include features such as full text search, natural language processing, weighted results, fuzzy tolerance results, faceting, hit highlighting, recommendations, feedback mechanisms based on log mining, usage statistic gathering, and many others. In this paper we will be focusing on improving geospatial search with a search engine platform that uses Lucene, a Java-based search library, at its core.
In work funded by the National Endowment for the Humanities, the Centre for Geographic Analysis (CGA) at Harvard University is in the process of re-engineering the search component of its public domain SDI (WorldMap http://worldmap.harvard.edu ) which is based on the GeoNode platform. In the process the CGA has developed Harvard Hypermap (HHypermap), a map services registry and search platform independent from WorldMap.
The goal of HHypermap is to provide a framework for building and maintaining a comprehensive registry of web map services, and because such a registry is expected to be large, the system supports the development of clients with modern search capabilities such as spatial and temporal faceting and instant previews via an open API. Behind the scenes HHypermap scalably harvests OGC and Esri service metadata from distributed servers, organizes that information, and pushes it to a search engine. The system monitors services for reliability and uses that to improve search. End users will be able to search the SDI metadata using standard interfaces provided by the internal CSW catalogue, and will benefit from the enhanced search possibilities provided by an advanced search engine. HHypermap is built on an open source software source stack.
A workflow to integrate pre-processing, analysis and comparison of MALDI-ToF mass spectra in GeenaR
Authors: Del Prete Eugenio , Facchiano Angelo , Profumo Aldo , Angelini Claudia , Romano Paolo 
Published: January 2018

Many large-scale proteomics studies have been performed in the last years, and this field of investigation is expanding up. If the analysis of any single spectrum can be performed by tools already made available along with the mass spectrometry (MS) instrumentation, comparison of spectra on a large scale represents a complex aspect of the analysis and interpretation of the study. Recently, we developed Geena 2, a tool for the automation of different steps in the MALDI/ToF MS data analysis. Integration of further tools can be performed, in order to improve some aspects of the whole workflow: the input of more data formats, the implementation of new algorithms for data cleaning, the graphical visualization and the reporting of the results, the use of advanced statistics for the comparison of mass spectra. For this motivations, we are now developing GeenaR, a new robust web tool for pre-processing, analysing, visualizing and comparing a set of MALDI-ToF mass spectra. The aim of this work is the presentation of on-going developments. The first results will be presented at the conference. GeenaR is being written in PHP, Perl (from Geena 2) and R languages. The R packages used are MALDIquant and MALDIquantForeign for mass spectra pre-processing and analysis, OrgMassSpecR for mass spectra comparison, dendextend and pvclust for clustering, and sda and crossval for variable selection. The system is being implemented in a LAMP (Linux, Apache, MySQL, PHP) environment. Proper interfaces between PHP on one side and perl and R on the other are then implemented. The aim of GeenaR is to provide to the users a wider range of statistical methods and graphical results, without making it more difficult to use for researchers with little expertise in programming. In order to achieve this goal, we have taken advantage of the availability of several packages, written in R language, for mass spectrometry statistical that are going to be integrated in the system. The complete pipeline of GeenaR includes some features already available in Geena 2 plus others under development thanks to the integration of the R environment. In fact, an original set of heuristic algorithms is already available in Geena 2. In particular, they are the identification of isotopic peaks by taking into account molecular weight of signals and the related trend of abundances; the normalization on the basis of a reference standard molecule; the peak selection by means of a threshold line, built by linearly interpolating values provided for given m/z values; the alignment, by selecting the nearest peaks, within a limited m/z difference, in the different mass spectra. By means of some R packages, GeenaR adds new statistical methods which are highly relevant for mass spectra analysis.
(Abstract truncated at 3,000 characters - the full version is available in the pdf file)
Cloud Computing in Bioinformatics: current solutions and challenges
Authors: Calabrese Barbara , Cannataro Mario 
Published: January 2018

Abstract truncated at 3,000 characters - the full version is available in the pdf file
MOTIVATIONS The availability of high-throughput technologies and the application of genomics and pharmacogenomics studies of large populations, are producing an increasing amount of experimental and clinical data, as well as specialized databases spread over the Internet. The storage, preprocessing and analysis of experimental data is becoming the main bottleneck of the analysis pipeline. Managing omics data requires both space for data storing as well as services for data preprocessing, analysis, and sharing. The resulting scenario comprises a set of bioinformatics tools, often implemented as web services, for the management and analysis of data stored in geographically distributed biological databases [1]. Cloud computing may play an important role in many phases of the bioinformatics analysis pipeline, from data management and processing, to data integration and analysis, including data exploration and visualization because it offers massive scalable computing and storage, data sharing, on-demand anytime and anywhere access to resources and applications, thus it may represent the key technology for facing those issues [2]. METHODS This work reviews main academic and industrial cloud-based bioinformatics solutions developed in the recent years; moreover, it underlines main issues and problems related to the use of such platforms for the storage and analysis of patients’ data. Specifically, the analysed solutions regard: - Data as a Service (DaaS): it provides data storage in a dynamic virtual space hosted by the cloud and allows to have updated data that are accessible from a wide range of connected devices on the web. - Software as a Service (SaaS): several cloud-based tools to execute different bioinformatics tasks, e.g. mapping applications, sequences alignment, gene expression analysis have been proposed and made available. - Platform as a Service (PaaS): unlike SaaS solutions, PaaS solutions allow users to customize the deployment of bioinformatics applications as well as to retain complete control over their instances and associated data. - Infrastructure as a Service (IaaS): this service model is offered in a computing infrastructure that includes servers (typically virtualized) with specific computational capability and/or storage. The user controls all the deployed storage resources, operating systems and bioinformatics applications. For each analysed solution, main technical characteristics as well as security and privacy issues arising when storing and analysing patients data, are reported. RESULTS The application of cloud computing in bioinformatics regards the efficient storage, retrieval and integration of experimental data and their efficient and high-throughput preprocessing and analysis.
Analysis of the interactions of a novel cephalosporin derivative with its potential targets penicillin-binding proteins from different sources using a covalent docking approac
Authors: Verdino Anna , De Rosa Margherita , Soriente Annunziata , Marabotti Anna 
Published: January 2018

Motivation. Cephalosporins are a class of beta-lactam antibiotics widely used in clinics for their antibacterial activity. Their mode of action, common to other beta lactam antibiotics such as penicillins, is the impairment of the synthesis of the peptidoglycan forming the bacterial cell wall. This polymer, essential for bacterium survival, is made by aminosugars connected by glycosidic bonds to form linear chains, and by short peptides forming cross-links between the linear chains. The enzymes catalyzing the creation of these cross-links are transpeptidases, also called penicillin binding proteins (PBPs) for their ability to interact with penicillins and other beta lactam antibiotics. These molecules mimic the D-Ala-D-Ala terminus of the peptides, therefore they competitively inactivate the PBPs by binding covalently to the Ser residue responsible for the catalysis and stopping the transpeptidation. This results in cell lysis and bacterial death. One of the main problems to face when using cephalosporins is the development of several mechanisms of resistance, either for the reduced affinity of PBPs to the beta lactams, or for the selection of new beta-lactam-insensitive PBPs, or for the production of beta lactamases, enzymes able to hydrolyze the beta lactam ring, thus deactivating the antibiotics. Additionally, most cephalosporins have a limited spectrum of action, against only Gram+ or Gram- bacteria. Therefore, during the time, many new beta lactam antibiotics have been synthesized with the aim of broadening the spectrum of action and/or overcoming the resistance. The prototype of a new group of cephalosporins is AMA-10, in which another beta lactam ring bound to a short alkyl chain has been linked to the aminocephalosporanic ring by means of an amidic bond. In order to develop other molecules, however, it is essential to understand how they interact with their target. Therefore, to apply a rational approach for the design of new derivatives, we have performed a computational study by simulating the binding of AMA-10 to selected PBPs of different species, whose crystallographic structures were available, using a particular approach, covalent docking, able to take into account the covalent bond formed between the antibiotic and the enzyme.
Methods. The structures of PBP3 and PBP4 from both Gram+ (S. aureus, B. subtilis) and Gram- (E. coli, P. aeruginosae) organisms were downloaded from Protein Data Bank (PDB) database, as well as the structures of beta-lactamase from S. aureus and from E. coli. The representative structures were selected on the basis of their quality. Then, covalent docking was made by using a modified version of the program AutoDock 4.2, using the flexible side chain method [Bianco et al, 2016]. [Abstract truncated at 3,000 characters - the full version is available in the pdf file].
MetaCRAST: Reference-guided extraction of CRISPR spacers from unassembled metagenomes
Authors: Moller Abraham G , Liang Chun 
Published: January 2018

Summary: Clustered regularly interspaced palindromic repeat (CRISPR) systems are prokaryotic adaptive immune systems against viral infection. CRISPR spacer sequences can provide valuable ecological insights by linking environmental viruses to microbial hosts. Despite this importance, metagenomic CRISPR detection remains a major challenge. Here we present a reference-guided CRISPR spacer detection tool (Metagenomic CRISPR Reference-Aided Search Tool - MetaCRAST) that constrains searches based on user-specified direct repeats (DRs). These DRs could be expected from assembly or taxonomic profiles of metagenomes. Our evaluation shows MetaCRAST improves CRISPR spacer detection in real metagenomes compared to de novo CRISPR detection methods. Simulations show it performs better than de novo tools for Illumina metagenomes.
Availability and implementation: MetaCRAST is implemented in Perl and takes metagenomic sequence reads and direct repeat queries (FASTA) as input. It is freely available for download at https://github.com/molleraj/MetaCRAST.
MetaCRAST: Reference-guided extraction of CRISPR spacers from unassembled metagenomes
Authors: Moller Abraham G , Liang Chun 
Published: January 2018

Summary: Clustered regularly interspaced palindromic repeat (CRISPR) systems are prokaryotic adaptive immune systems against viral infection. CRISPR spacer sequences can provide valuable ecological insights by linking environmental viruses to microbial hosts. Despite this importance, metagenomic CRISPR detection remains a major challenge. Here we present a reference-guided CRISPR spacer detection tool (Metagenomic CRISPR Reference-Aided Search Tool - MetaCRAST) that constrains searches based on user-specified direct repeats (DRs). These DRs could be expected from assembly or taxonomic profiles of metagenomes. Our evaluation shows MetaCRAST improves CRISPR spacer detection in real metagenomes compared to de novo CRISPR detection methods. Simulations show it performs better than de novo tools for Illumina metagenomes.
Availability and implementation: MetaCRAST is implemented in Perl and takes metagenomic sequence reads and direct repeat queries (FASTA) as input. It is freely available for download at https://github.com/molleraj/MetaCRAST.[p]
Angiosperm Phylogeny Poster – Flowering Plant Systematics
Authors: Cole Theodor C. H. , Hilger Hartmut H 
Published: January 2018

The "Angiosperm Phylogeny Poster – Flowering Plant Systematics" is an educational tool presenting an overview of the evolutionary relationships among flowering plants according to APG IV and APweb as of 2016. The phylogenetic tree depicts the 64 orders and the majority of the 416 families, listing the main apomorphies and plesiomorphies as well as diagnostic and nondiagnostic anatomical, morphological, and phytochemical features for orders and higher levels within the tree. The intuitive color-coding facilitates memorization and teaching.
Translations of the poster by internationally renown botanists are now available in more than a dozen world languages. Hyperlinks to APweb (Peter F. Stevens, Missouri Botanical Garden) are provided for the orders and higher ranks.
This is one in a series of three educational posters on the phylogeny of land plants: Poster 1: "Angiosperms", Poster 2: "Tracheophytes: Lycophytes, Ferns, Gymnosperms", Poster 3: "Bryophytes: Liverworts, Mosses, Hornworts".
Randomised Badger Culling Trial: Impact, based on more extensive data
Authors: Hendy David 
Published: January 2018

In 2007 the Independent Scientific Group (ISG) reported to the UK government the impact on bovine tuberculosis (TB) in cattle of the Randomised Badger Culling Trial (RBCT). Badgers were culled between 1998 and 2005 across 100 km2 (nominal) zones in the West of England. The results were based on a model of New Herd Incidence (NHI). It was concluded that reactive culling generated overall detrimental effects, while proactive culling achieved very modest overall benefits at the cost of elevated incidence in surrounding areas.
This work looks at more extensive RBCT data to examine if these findings hold true. Instead of presenting the results of a model, this work directly illustrates the data. The Animal and Plant Health Agency supplied this data in March 2016. Such data covers a greater number of years (1986 to 2012) and includes the prevalence of herd restrictions as well as herd incidence.
Whilst the proactive culls substantially and sustainably reduced cattle TB in treated areas, such culls did not significantly increase TB in the surrounding areas. NHIs between 2006 and 2012 dropped by 28%, 1% and 18% in the treated, outer 2km ring, and combined areas respectively. Based on the number of NHIs prevented since 1998 in the combined area, a break-even cost to complete a badger removal exercise was calculated to be £8,693 per km2. This figure may be under-estimated because it takes no account of any NHIs prevented after 2012.
The more limited reactive culls had no impact on both the treated area and outer 2km ring. Proactive culling only reduced confirmed TB with no significant impact on unconfirmed TB.
Conclusions in the RBCT Final Report, which were based on the results of a model of time-shifted early data, poorly reflect the overall greater benefits seen in this more extensive data. Badger culling is highly contentious in the UK and many press reports adversely report the effectiveness of badger culling in general and the culls which started in 2013 in particular. The RBCT conclusions are often cited to add credence to these press reports. After the first year of substantial culling in the RBCT, this work found that 9 years of data were needed to clearly see the full extent by which TB dropped when plotted against calendar year. This delay should be reflected on when accounting for the circumstances and assessing impact of the 2013 culls.
This work was restricted to looking at data showing total TB breakdowns over all zones. Further work to examine breakdowns by zone or groups of zones may reveal more.
Randomised Badger Culling Trial: Impact, based on more extensive data
Authors: Hendy David 
Published: January 2018

In 2007 the Independent Scientific Group (ISG) reported to the UK government the impact on bovine tuberculosis (TB) in cattle of the Randomised Badger Culling Trial (RBCT). Badgers were culled between 1998 and 2005 across 100 km2 (nominal) zones in the West of England. The results were based on a model of confirmed New Herd Incidence (NHI). It was concluded that reactive culling generated overall detrimental effects, while proactive culling achieved very modest overall benefits at the cost of elevated incidence in surrounding areas.
This work looks at more extensive RBCT data to examine if these findings hold true. Instead of presenting the results of a model, this work directly illustrates the data. The Animal and Plant Health Agency supplied this data in March 2016. Such data covers a greater number of years (1986 to 2012) and includes the prevalence of herd restrictions as well as herd incidence.
Whilst the proactive culls substantially reduced confirmed NHI in treated areas, such culls did not significantly increase NHI in the surrounding outer ring. In fact, between 1998 and 2012 these NHI slightly reduced in the outer ring . Between 2006 and 2012 they dropped by 28%, 1% and 18% in the treated, outer 2km ring, and combined areas respectively. Based on the total number of confirmed NHIs prevented between 1998 and 2012, a break-even cost to complete a badger removal exercise was calculated to be £8,693 per km2 with benefits continuing in 2012.
Proactive culling only reduced confirmed NHIs with no significant impact on unconfirmed NHIs. The more limited reactive culls had no impact on both the treated area and the outer 2km ring.
Conclusions in the RBCT Final Report, which were based on the results of a model of time-shifted early data, poorly reflect the overall greater benefits seen in this more extensive data. Badger culling is highly contentious in the UK and many press reports adversely report the effectiveness of badger culling in general and the culls which started in 2013 in particular. The RBCT conclusions are often cited to add credence to these press reports. After the first year of substantial culling in the RBCT, this work found that 9 years of data were needed to clearly see the full extent by which TB dropped when plotted against calendar year. This delay should be reflected on when accounting for the circumstances and assessing impact of the 2013 culls.
This work was restricted to looking at data showing total TB breakdowns over all zones. Further work to examine breakdowns by zone or groups of zones may reveal more.
Meiotic shugoshins differ from mitotic ones by arginine-reach C-terminal motif in yeast, plant, animals, and human
Authors: Grishaeva Tatiana M , Kulichenko Darya , Bogdanov Yuri F 
Published: January 2018

Background. Shugoshins (SGOs) are proteins that protect cohesins located at the centromeres of sister chromatids from their early cleavage during mitosis and meiosis in plants, fungi, and animals. Their function is to prevent premature sister-chromatid disjunction and segregation. Meiotic SGOs prevent segregation of sister chromatids in meiosis I, thus permitting homologous chromosomes to segregate and reduce chromosome number to haploid set. The study focused on the structural differences among shugoshins acting during mitosis and meiosis that cause differences in chromosome behavior in these two types of cell division in different organisms.
Methods. A bioinformatics analysis of protein domains, conserved amino acid motifs, and physicochemical properties of 32 proteins from 25 species of plants, fungi, and animals was performed.
Results. We identified a C-terminal arginine-reach amino acid motif that is highly evolutionarily conserved among the shugoshins protecting centromere cohesion of sister chromatids in meiotic anaphase I, but not among mitotic shugoshins. The motif looks like “arginine comb” capable of interaction by hydrogen bonds with guanine bases in the small groove of DNA helix. Shugoshins in different eukaryotic kingdoms differ also in the sets and location of amino acid motifs and the number of α-helical regions in the protein molecule.
Discussion. Meiosis-specific arginine-reach motif may be responsible for formation of SGO-DNA nucleoprotein complex, thus protecting meiotic shugoshins from degradation during meiotic metaphase I and anaphase I, while mitotic SGOs have a motif with less number of arginine residues. This structural difference between meiotic and mitotic shugoshins, probably, could be a key molecular element of the prolonged shugoshin resistance to degradation during meiotic metaphase I and anaphase I and be one of the molecular elements causing the difference in chromosome behavior in meiosis and mitosis. The finding of differences in SGO structure in plant, fungi and animals supports idea of independent evolution of meiosis in different lineages of multicellular organisms.