bluuebunny/crossref_metadata_2025_split huggingface dataset:
Algorithms for the compression of genomic big data
Authors: Prezza Nicola , Policriti Alberto 
Published: January 2018

Motivations. Building the Burrows-Wheeler transform (BWT) and computing the Lempel-Ziv parsing (LZ77) of huge collections of genomes is becoming an important task in bioinformatic analyses as these datasets often need to be compressed and indexed prior to analysis. Given that the sizes of such datasets often exceed RAM capacity of common machines however, standard algorithms cannot be used to solve this problem as they require a working space at least linear in the input size. One way to solve this problem is to exploit the intrinsic compressibility of such datasets: two genomes from the same species share most of their information (often more than 99%), so families of genomes can be considerably compressed. A solution to the above problem could therefore be that of designing algorithms working in compressed working space, i.e. algorithms that stream the input from disk and require in RAM a space that is proportional to the size of the compressed text.
Methods. In this work we present algorithms and data structures to compress and index text in compressed working space. These results build upon compressed dynamic data structures, a sub-field of compressed data structures research that is lately receiving a lot of attention. We focus on two measures of compressibility: the empirical entropy H of the text and the number r of equal-letter runs in the BWT of the text. We show how to build the BWT and LZ77 using only O(Hn) and (rlog n) working space, n being the size of the collection. For the case of repetitive text collections (such as sets of genomes from the same species), this considerably improves the working space required by state-of-the art algorithms in the literature. The algorthms and data structures here discussed have all been implemented in a public C++ library, available at github.com/nicolaprezza/DYNAMIC. The library includes dynamic gap-encoded bitvectors, run-length encoded (RLE) strings, and RLE FM-indexes.
Results. We conclude with an overview of the experimental results that we obtained running our algorithms on highly repetitive genomic datasets. As expected, our solutions require only a small fraction of the working space used by solutions working in non-compressed space, making it feasible to compute BWT and LZ77 of huge collections of genomes even on desktop computers with small amounts of RAM available. As a downside of using complex dynamic data structures however, running times are still not practical so improvements such as parallelization may be needed in order to make these solutions fully practical.
A computational study to identify potential inhibitors for human chymase from natural and/or biogenic sources
Authors: Dubey Amit , Marabotti Anna , Ramteke Pramod W , Facchiano Angelo 
Published: January 2018

Motivation. The human chymase (EC 3.4.21.39) is a hydrolase abundant in secretory granules of mast cells, responsible for the synthesis of angiotensin II from its precursor. Moreover, it is also responsible for the conversion of transforming growth factor-β (TGF-β) and matrix metalloproteinase (MMP)-9 precursors to their active forms. Since a link between heart failure and chymase has been proved, specific chymase inhibitors are actively searched to develop new therapeutic treatments for cardiovascular diseases, considering also that chymase has no enzymatic activity in normal tissues. Therefore, specific chymase inhibitors may have no effects on any other target in healthy states. The use of natural products has been an integral part of the treatment of different diseases throughout the world since past centuries. Many plants with potential therapeutic activity were widely used as natural medicines with negligible undesired effects. Therefore, the search for new active compounds from natural sources is gaining interest in the scientific community, and the application of novel approaches to an old science could result in the discovery of valuable compounds useful to develop innovative drugs. We present here our search for novel inhibitors of chymase enzyme from natural sources or inspired by nature, using a computational approach that allowed us to screen databases of compounds and to predict which molecules can be able to bind to chymase with a good affinity and selectivity against other serine proteases. Methods. The crystal structure of human chymase complexed to a known inhibitor, available in the Protein Data Bank (PDB code 1T31), was selected for the development of ten structure-based pharmacophore models, using the protocol available in Discovery Studio. After a validation step, the best pharmacophore was used to screen a special subset of ZINC database (ZINC Biogenic compounds) containing more than 120,000 nature-inspired compounds. After identification of the best potential compounds matching the pharmacophore features, and further filtering strategies, few potential ZINC compounds were selected for further steps. In parallel, selected compounds from plants were identified as potential candidates, also on the basis of their correspondence to the pharmacophore features obtained in the previous step. The 3D structures of all these selected compounds, as well as those of the known co-crystallized chymase inhibitor and of other known inhibitors used as reference molecules, were retrieved from ZINC and/or PubChem databases and were docked in the active site of human chymase. Their predicted binding affinities and their interactions with the enzyme were then compared. Finally, all these molecules were docked into the active sites of other human serine proteases (kallikrein, elastase and tryptase), whose 3D structures were selected ...
Abstract truncated at 3,000 characters - the full version is available in the pdf file
Adulteration of herbal products: Bamboo tea authentication
Authors: Horn Thomas , Häser Annette 
Published: January 2018

Background. Names for ”substances” used in food products are rarely precise. The term bamboo (Bambusoideae, Poaceae) comprises over 1600 distinct species of which only few are well established sources for food products on the European market (i.e. bamboo sprouts).
Methods. We analysed bamboo species and tea products containing an exotic ingredient (bamboo leaves) using anatomical leaf characters and DNA sequence data. Our primary concern was to determine the taxonomic origin of bamboo leaves to establish a baseline for EU legislation, to introduce a simple PCR based test to distinguish bamboo from other Poaceae leaf components and to assess the diagnostic potential of DNA Barcoding markers to resolve taxonomic entities within the bamboo subfamily and tribes.
Results. Based on anatomical and DNA data we can pinpoint the taxonomic origin of genuine bamboo leaves used in commercial products to the genera Phyllostachys and Pseudosasa from the temperate ”woody” bamboo tribe (Arundinarieae). We detected adulteration by carnation in 4 of 8 tea products and, after adapting our objectives, could trace the taxonomic origin of the adulterant to Dianthus chinensis (Caryophyllaceae), a well known traditional Chinese medicine with counter indications for pregnant women.
Impact of the catchment land use on some factors of lakes trophic status: a GIS approach
Authors: Sługocki Łukasz , Czerniawski Robert 
Published: January 2018

Background. Artificial enrichment of lakes has posed serious management problems for water supply. In results many European lakes had already undergone significant eutrophication. It seems that a good tool to determine the influence of catchment use on the trophic changes in lakes is Geographic Information System (GIS) and its databases.
Methods. The study covered 31 stratified lakes located in northwestern Poland. These lakes were chosen on account of their considerable recreation value and economic importance. The parameters chosen as dependent variables were Secchi depth and electrical conductivity. Local catchments and network catchment of studied lakes as independent variables were prepared using QGIS Wien (2.8.7). The land use variables were prepared with Corine Land Cover, 2006 (CLC2006).
Results. According to Carlson index the studied lakes ranged from mesotrophic to eutrophic. Both dependent variables Secchi depth and conductivity values were significantly correlated with independent land use variables (P < 0.05).
Discussion. Our survey revealed that percentage use of the catchment (developed in the Geographic Information System) can be a useful tool in the assessment of the lakes risks. With the GIS tools we also confirmed a significant impact of land use on changes transparency and conductivity values in North West lakes in Poland.
An integrated multi-level comparison highlights common aspects and specific features between distantly-related species: Tomato and Grapevine
Authors: Ambrosino Luca , Bostan Hamed , Ruggieri Valentino , Chiusano Maria Luisa 
Published: January 2018

Motivation. Even after years from the first completion of genomes by sequencing, comparative genomics still remains a challenge, also enhanced by the availability of numerous draft genomes with still poor annotation quality. The detection of ortholog genes between different species is a key approach for comparative genomics. For example, ortholog gene detection may support investigations on mechanisms that shaped the organization of the genomes, highlighting on gain or loss of function and on gene annotation. On the other hand, the detection of paralog genes is fundamental for understanding the evolutionary mechanisms that drove gene function innovation and support gene families analyses. Here we report on the gene comparison between two distantly related plants, Solanum lycopersicum (Tomato) (The Tomato Genome Consortium 2012) and Vitis vinifera (Grapevine) (Jaillon et al. 2007), considered as economically important species from asterids and rosids clades, respectively. The strategy was accompanied by integration of multilevel analyses, from domain investigations to expression profiling, to get to the most reliable results and to offer powerful resources, in order to understand different useful aspects of plant evolution and physiology and to dissect traits and molecular aspects that could provide novel tools for agriculture applications and biotechnologies.
Methods. In order to predict best putative orthologs and paralogs between Tomato and Grapevine, and to overcome possible annotation issues, all-against-all sequence similarity searches between genes, mRNAs and proteins collections of both species were performed. A Bidirectional Best Hit approach was implemented to detect the best orthologs between the two species. Moreover we developed a dedicated algorithm in Python programming language able to define more extended alignments between mRNA sequences. NetworkX package (Hagberg et al. 2008) was used to define networks of paralogs and orthologs. Proteins domain prediction was carried out on the entire Tomato and Grapevine protein collection by using InterProScan program (Jones et al. 2014). The enzyme classification was obtained by sequence similarity searches between Tomato and Grapevine mRNA collections and the entire UniProt reviewed protein collection (UniProt consortium 2015). The metabolic pathways associated to the detected enzymes were identified exploiting the KEGG Database (Kanehisa and Goto 2000). Expression level of three developmental stages of Tomato (2 cm fruit, breaker and mature red) and the corresponding stages of Grapevine (post-setting, veraison, mature berry) was defined on the basis of the iTAG loci (Shearer et al. 2014) and v1 vitis loci, respectively. The expression was normalized by Reads Per Kilobases per Million (RPKM) for each tissue/stage.
Abstract truncated at 3,000 characters - the full version is available in the pdf file
BioPaxCOMP: an efficient system for integrating, compressing, and querying BioPAX
Authors: Agapito Giuseppe , Greco Andrea , Cannataro Mario 
Published: January 2018

Abstract truncated at 3,000 characters - the full version is available in the pdf file.
Biological networks and, in particular, biological pathways are composed of thousands of nodes and edges, posing several challenge regarding analysis and storage. The primary format used to represent pathways data is BioPAX (http://biopax.org.) BioPAX is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. BioPAX is an open and collaborative effort made by the community of researchers, software developers, and institutions and it specifically supports data exchange between pathway data groups. BioPAX is defined in OWL and is represented in the RDF/XML format. OWL (Web Ontology Language) is a W3C standard and is designed for use by applications that need to process the content of information instead of just presenting information to humans. RDF is a standard model for data interchange on the Web. Although OWL allows a standard representation of pathways, since it is based on XML, it is a verbose and redundant language, so the storage of pathways may be very huge, preventing an efficient transmission and sharing of this data. The typical size of a pathway is related to the organism, for example, the size of Homo Sapiens pathways (from Reactome database) is near to 200 MB on disk. Moreover, integrating pathways data coming from different data sources may require GBytes of space. A second problem with pathways is related to the possibility to integrate information coming from different data sources to have updated information in a centralized way. There exist several different databases for pathways data that emphasizes different aspect of the same pathway, thus, it could be useful to integrate and annotate together pathways coming from different databases to obtain a centralized and more informative pathway data. The principal obstacle for integrating, storing and exchanging such data is the extreme size growth when several pathways data are merged together, posing several challenges from the computational and archiving point of view. Pathways data can be easily classified as big data, because they meet all the 5V (Volume, Velocity, Variety, Veracity, Value) characteristics typical of Big Data, thus, the necessity to efficiently integrate and compress pathways data arises. The methodology for pathways data integration is based on the following steps: i) aggregation and validation locally of data coming from several pathway databases, ii) identification and normalization of compounds and reactions identifier and iii) integration. Integration occurs at the level of physical entities, such as proteins and small molecules. This is accomplished by linking interaction and pathway records together if they use the same physical entities (such as from UniProt for proteins) and by adding annotation data from UniProt or GeneOntology.
Why respiratory viruses or bacteria have the highest probability to be deposited in the respiratory tract in flu seasons
Authors: Ishmatov Aleksandr N 
Published: January 2018

Objective:
The main aspects of influenza transmission via fine and ultrafine bioaerosols were considered. Here, we aimed to estimate the impact of the different environment conditions on the processes of heat and mass transfer in the upper respiratory tract and its role in the deposition rate of the infectious bioaerosols in the lungs.
Background:
The latest researches show the infected people generate the fine and ultrafine infectious bioaerosols with submicron particles/droplets (size below 1 µm). The airborne transmission of these particles/droplets is effective. It is considered the deposition of submicron particles in the respiratory tract (RT) has very low probability. But most studies examined the deposition of the particles in the lungs under normal environmental conditions and did not paid attention to the different environmental factors.
Methods:
We review the problems of epidemiology of respiratory infections and aspects of airborne transmission/spread of infectious agents. We contrast these approaches with known data from next area: inhalation toxicology, respiratory drug delivery and physics of heat and mass transfer in the airways.
Results:
On the basis of these analyses, we propose the next main concepts:
1 Breathing cool air leads to the supersaturation of air in RT;
2 the air supersaturation leads to the intensive condensational growth(CG) of inhaled viruses or bacteria in RT;
3 CG leads to the intensive and dramatically growth of deposition rate of viruses or bacteria in RT.
We have shown:
a) Under normal conditions of inhaled air (T>20˚C; Relatively Humidity (RH)=60%) there is no transition in supersaturated condition in RT and CG is insignificant and probability of virus deposition on epithelium of RT is low – no more than 20%.
b) Breathing cool/cold air of T<+15˚C and RH of [30..60]% leads to the supersaturation in the airways and it can dramatically increase the deposition rate of inhaled bioaresols in the lungs (up to 97%).
c) With an increase in RH of inhaled air the supersaturation in RT occurs even at warm temperature of inhaled air (for inhaled air of T<20°C and RH>70% ; T<25°C and RH>90%). It also indicates the high deposition rate of bioaerosols in the lungs.
Conclusion:
Under specific environmental conditions (when flu seasons) the processes of supersaturation in the RT can be observed. These results indicate the high probability of virus deposition on epithelium of RT and correspond to influenza and seasonal respiratory infections in temperate and tropical climates.
We believe the effect of supersaturation in the lungs can be the key to understanding of ‘the age-old epidemiologic mystery of influenza seasonality in the different climatic conditions’.
Why respiratory viruses or bacteria have the highest probability to be deposited in the respiratory tract in flu seasons
Authors: Ishmatov Aleksandr N 
Published: January 2018

Objective:

In this study the main aspects of influenza transmission via fine and ultrafine bioaerosols were considered. Here, we aimed to estimate the impact of the different environment conditions on the deposition rate of the infectious bioaerosols in the respiratory tract.

Background:

The latest researches show the infected people generate the fine and ultrafine infectious bioaerosols with submicron particles/droplets (size below 1 µm). The airborne transmission of these particles/droplets in the environment is effective. It is considered the deposition of submicron particles in the respiratory tract (RT) has very low probability. But most studies examined the aerosol deposition in RT under normal environmental conditions and did not paid attention to the affecting the different environmental factors.

Methods:

We review the problems of epidemiology of respiratory infections and aspects of airborne transmission/spread of infectious agents. We contrast these approaches with known data from next areas: inhalation toxicology, respiratory drug delivery and physics of heat and mass transfer in the airways.

Results:

Based on the conducted analysis, we propose the next main concepts:
1 Breathing cool air leads to the supersaturation of air in RT;
2 the air supersaturation leads to the intensive condensational growth(CG) of inhaled viruses or bacteria in RT;
3 CG leads to the intensive and dramatically growth of deposition rate of viruses or bacteria in RT.
We have shown:
a) Under normal conditions of inhaled air (T>20˚C; Relatively Humidity, RH=60%) there is no transition in supersaturated condition in RT and CG is insignificant and probability of virus deposition on epithelium of RT is low – no more than 20%.
b) Breathing cool/cold air of T<+15˚C and RH of [30..60]% leads to the supersaturation in the airways and it can dramatically increase the deposition rate of inhaled bioaerosols in RT(up to 96%).
c) With an increase in RH of inhaled air the supersaturation in RT occurs even at warm temperature of inhaled air (for inhaled air of T<20°C and RH>70% ; T<25°C and RH>90%). Which also indicates the deposition rate of bioaerosols in RT under these conditions is high.

Conclusion:

Under specific environmental conditions (when flu seasons) the processes of supersaturation in the RT can be observed. These results indicate the high probability of virus deposition on epithelium of RT and correspond to influenza and seasonal respiratory infections in temperate and tropical climates.
We believe the effect of supersaturation in the airways can be the key to understanding of ‘the age-old epidemiologic mystery of influenza seasonality in the different climatic conditions’.
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 the most efficient and flexible way to use spatial information. One of the key software components of a SDI is the catalogue service, needed to discover, query and manage the metadata. Catalogue services in a SDI are typically based on the Open Geospatial Consortium (OGC) Catalogue Service for the Web (CSW) standard, that defines common interfaces to access the metadata information.
A search engine is a software system able to perform very fast and reliable search, with features such as full text search, natural language processing, weighted results, fuzzy tolerance results, faceting, hit highlighting and many others.
The Centre of Geographic Analysis (CGA) at Harvard University is trying to integrate within its public domain SDI (named WorldMap), the benefits of both worlds (OGC catalogues and search engines).
Harvard Hypermap (HHypermap) is a component that will be part of WorldMap, totally built on an open source stack, implementing an OGC catalogue, based on pycsw, to provide access to metadata in a standard way, and a search engine, based on Solr/Lucene, to provide the advanced search features typically found in search engines.