Abstract
The Clusters of Orthologous Genes (COG) database, also referred to as the Clusters of Orthologous Groups of proteins, was created in 1997 and went through several rounds of updates, most ...recently, in 2014. The current update, available at https://www.ncbi.nlm.nih.gov/research/COG, substantially expands the scope of the database to include complete genomes of 1187 bacteria and 122 archaea, typically, with a single genome per genus. In addition, the current version of the COGs includes the following new features: (i) the recently deprecated NCBI’s gene index (gi) numbers for the encoded proteins are replaced with stable RefSeq or GenBank\ENA\DDBJ coding sequence (CDS) accession numbers; (ii) COG annotations are updated for >200 newly characterized protein families with corresponding references and PDB links, where available; (iii) lists of COGs grouped by pathways and functional systems are added; (iv) 266 new COGs for proteins involved in CRISPR-Cas immunity, sporulation in Firmicutes and photosynthesis in cyanobacteria are included; and (v) the database is made available as a web page, in addition to FTP. The current release includes 4877 COGs. Future plans include further expansion of the COG collection by adding archaeal COGs (arCOGs), splitting the COGs containing multiple paralogs, and continued refinement of COG annotations.
The quantification of RNA sequencing (RNA-seq) abundance using a normalization method that calculates transcripts per million (TPM) is a key step to compare multiple samples from different ...experiments. TPMCalculator is a one-step software to process RNA-seq alignments in BAM format and reports TPM values, raw read counts and feature lengths for genes, transcripts, exons and introns. The program describes the genomic features through a model generated from the gene transfer format file used during alignments reporting of the TPM values and the raw read counts for each feature. In this paper, we show the correlation for 1256 samples from the TCGA-BRCA project between TPM and FPKM reported by TPMCalculator and RSeQC. We also show the correlation for raw read counts reported by TPMCalculator, HTSeq and featureCounts.
TPMCalculator is freely available at https://github.com/ncbi/TPMCalculator. It is implemented in C++14 and supported on Mac OS X, Linux and MS Windows.
Supplementary data are available at Bioinformatics online.
ABSTRACT Soils can act as carbon sinks mitigating global warming. This generates interest in determining how agricultural practices affect the stock of soil organic carbon (SOC). Fertilization ...increases SOC stocks and its impacts have been calculated at a global level. The aim of this study was to determine if fertilization leads to carbon sequestration in the Pampas of Argentina. A meta-analysis of local studies was performed to determine how fertilization impacts SOC stocks in agricultural soils. Forty studies were compiled presenting data from 27 experiments from which 109 comparisons of SOC stocks between fertilized and unfertilized treatments were extracted. Fertilization caused a significant increase of ca. 3% in the topsoil (0-20 cm) SOC stock. When nutrients application rate could be accurately defined (n= 71), the average increase in SOC stock was ca. 1 t ha-1. Increments were much smaller in comparison with those reported in literature and the carbon footprint of applied nutrients (2.31 t Ceq. ha-1). Even if increments in SOC stock in the subsoil were similar to those measured in the topsoil, greenhouse gas emission from fertilizer application would not be offset by the carbon sequestered in the soil. Fertilization has a low impact on SOC stocks and does not compensate greenhouse gases emissions in the Pampas. Rates of SOC increments resulting from fertilization identified in other regions of the world should not be applied in this region.
Biomedical researchers use alignments produced by BLAST (Basic Local Alignment Search Tool) to categorize their query sequences. Producing such alignments is an essential bioinformatics task that is ...well suited for the cloud. The cloud can perform many calculations quickly as well as store and access large volumes of data. Bioinformaticians can also use it to collaborate with other researchers, sharing their results, datasets and even their pipelines on a common platform.
We present ElasticBLAST, a cloud native application to perform BLAST alignments in the cloud. ElasticBLAST can handle anywhere from a few to many thousands of queries and run the searches on thousands of virtual CPUs (if desired), deleting resources when it is done. It uses cloud native tools for orchestration and can request discounted instances, lowering cloud costs for users. It is supported on Amazon Web Services and Google Cloud Platform. It can search BLAST databases that are user provided or from the National Center for Biotechnology Information.
We show that ElasticBLAST is a useful application that can efficiently perform BLAST searches for the user in the cloud, demonstrating that with two examples. At the same time, it hides much of the complexity of working in the cloud, lowering the threshold to move work to the cloud.
BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs ...of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters).
The software is freely available at github.com/BioContainers/.
yperez@ebi.ac.uk.
Literature search is a routine practice for scientific studies as new discoveries build on knowledge from the past. Current tools (e.g. PubMed, PubMed Central), however, generally require significant ...effort in query formulation and optimization (especially in searching the full-length articles) and do not allow direct retrieval of specific statements, which is key for tasks such as comparing/validating new findings with previous knowledge and performing evidence attribution in biocuration. Thus, we introduce LitSense, which is the first web-based system that specializes in sentence retrieval for biomedical literature. LitSense provides unified access to PubMed and PMC content with over a half-billion sentences in total. Given a query, LitSense returns best-matching sentences using both a traditional term-weighting approach that up-weights sentences that contain more of the rare terms in the user query as well as a novel neural embedding approach that enables the retrieval of semantically relevant results without explicit keyword match. LitSense provides a user-friendly interface that assists its users to quickly browse the returned sentences in context and/or further filter search results by section or publication date. LitSense also employs PubTator to highlight biomedical entities (e.g. gene/proteins) in the sentences for better result visualization. LitSense is freely available at https://www.ncbi.nlm.nih.gov/research/litsense.
It has been suggested that financial literacy plays a crucial role in the understanding of the overall performance of small and medium-sized enterprises (SMEs). Nonetheless, its impact remains ...underexplored, and the few existing findings are fragmented. This study conducts a systematic literature review focused on the antecedents and consequences of financial literacy in SMEs. The findings show that some educational, cultural, and specific contextual factors are antecedents of financial literacy; in turn, financial literacy influences the financial attitudes, financial behaviors, organizational capabilities, and performance of SMEs. Further research should analyze the uncovered lines of study suggested in our research agenda to consolidate the conceptualization of financial literacy in the context of SMEs, overcome the limitations of the current methodology, extend the current evidence about the antecedents and consequences of financial literacy in SMEs and analyze these relationships from behavioral economics and decision-making perspectives.
A fast pathway for fear in human amygdala Méndez-Bértolo, Constantino; Moratti, Stephan; Toledano, Rafael ...
Nature neuroscience,
08/2016, Letnik:
19, Številka:
8
Journal Article
Recenzirano
A fast, subcortical pathway to the amygdala is thought to have evolved to enable rapid detection of threat. This pathway's existence is fundamental for understanding nonconscious emotional responses, ...but has been challenged as a result of a lack of evidence for short-latency fear-related responses in primate amygdala, including humans. We recorded human intracranial electrophysiological data and found fast amygdala responses, beginning 74-ms post-stimulus onset, to fearful, but not neutral or happy, facial expressions. These responses had considerably shorter latency than fear responses that we observed in visual cortex. Notably, fast amygdala responses were limited to low spatial frequency components of fearful faces, as predicted by magnocellular inputs to amygdala. Furthermore, fast amygdala responses were not evoked by photographs of arousing scenes, which is indicative of selective early reactivity to socially relevant visual information conveyed by fearful faces. These data therefore support the existence of a phylogenetically old subcortical pathway providing fast, but coarse, threat-related signals to human amygdala.
Sometimes technology and development of society run slightly different roads. This situation is now happening in the case of hydrogen as an energy carrier in the automotive world. In the article ...presented here, the authors propose a change in the structure of the power plant of Battery Electric Vehicles (BEV). The objective is that these vehicles can be presently used until the development of an electric and/or hydrogen recharge/refuel network allows being useful with the current status. In this paper a new concept of Extended Range Electric Vehicle (EREV) based in a Fuel Cell Electric Vehicle (FCEV) set model is presented. A study is then developed in order to determine the working conditions that will lead to better efficiency and performance, referring to capacity of both energy sources: electricity stored in a Lithium-Ion battery and hydrogen gas in high pressure tanks. The possibilities here shown open the door to strategic advantages and innovation for car designers in the future.
•The authors propose a change in the structure of the power plant of Battery Electric Vehicles (BEV) including a range extender system based in a Fuel Cell.•The objective is that these vehicles can be presently used until the deployment of a full electric and/or hydrogen recharge network is fulfilled.•The results presented show a powertrain concept that could avoid the commercialization problem associated to Battery Electric Vehicles and Fuel Cell Vehicles.•The sizing of the components and the drivetrain architecture and control is explained. The system is capable of handling real world situations within the limits of design requirements and will improve the current BEV and FCEV architectures, allowing longer trips and easy refuelling at the same time.
Searching for generic behaviors has been one of the driving forces leading to a deep understanding and classification of diverse phenomena. Usually a starting point is the development of a ...phenomenology based on observations. Such is the case for power law distributions encountered in a wealth of situations coming from physics, geophysics, biology, lexicography as well as social and financial networks. This finding is however restricted to a range of values outside of which finite size corrections are often invoked. Here we uncover a universal behavior of the way in which elements of a system are distributed according to their rank with respect to a given property, valid for the full range of values, regardless of whether or not a power law has previously been suggested. We propose a two parameter functional form for these rank-ordered distributions that gives excellent fits to an impressive amount of very diverse phenomena, coming from the arts, social and natural sciences. It is a discrete version of a generalized beta distribution, given by f(r) = A(N+1-r)(b)/r(a), where r is the rank, N its maximum value, A the normalization constant and (a, b) two fitting exponents. Prompted by our genetic sequence observations we present a growth probabilistic model incorporating mutation-duplication features that generates data complying with this distribution. The competition between permanence and change appears to be a relevant, though not necessary feature. Additionally, our observations mainly of social phenomena suggest that a multifactorial quality resulting from the convergence of several heterogeneous underlying processes is an important feature. We also explore the significance of the distribution parameters and their classifying potential. The ubiquity of our findings suggests that there must be a fundamental underlying explanation, most probably of a statistical nature, such as an appropriate central limit theorem formulation.
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