Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator

BACKGROUND: Computational methods for problem solving need to interleave information access and algorithm execution in a problem-specific workflow. The structures of these workflows are defined by a scaffold of syntactic, semantic and algebraic objects capable of representing them. Despite the proliferation of GUIs (Graphic User Interfaces) in bioinformatics, only some of them provide workflow capabilities; surprisingly, no meta-analysis of workflow operators and components in bioinformatics has been reported. RESULTS: We present a set of syntactic components and algebraic operators capable of representing analytical workflows in bioinformatics. Iteration, recursion, the use of conditional statements, and management of suspend/resume tasks have traditionally been implemented on an ad hoc basis and hard-coded; by having these operators properly defined it is possible to use and parameterize them as generic re-usable components. To illustrate how these operations can be orchestrated, we present GPIPE, a prototype graphic pipeline generator for PISE that allows the definition of a pipeline, parameterization of its component methods, and storage of metadata in XML formats. This implementation goes beyond the macro capacities currently in PISE. As the entire analysis protocol is defined in XML, a complete bioinformatic experiment (linked sets of methods, parameters and results) can be reproduced or shared among users. Availability: (interactive), (download). CONCLUSION: From our meta-analysis we have identified syntactic structures and algebraic operators common to many workflows in bioinformatics. The workflow components and algebraic operators can be assimilated into re-usable software components. GPIPE, a prototype implementation of this framework, provides a GUI builder to facilitate the generation of workflows and integration of heterogeneous analytical tools

In the pursuit of a semantic similarity metric based on UMLS annotations for articles in PubMed Central

Motivation Although full-text articles are provided by the publishers in electronic formats, it remains a challenge to find related work beyond the title and abstract context. Identifying related articles based on their abstract is indeed a good starting point; this process is straightforward and does not consume as many resources as full-text based similarity would require. However, further analyses may require in-depth understanding of the full content. Two articles with highly related abstracts can be substantially different regarding the full content. How similarity differs when considering title-and-abstract versus full-text and which semantic similarity metric provides better results when dealing with full-text articles are the main issues addressed in this manuscript. Methods We have benchmarked three similarity metrics – BM25, PMRA, and Cosine, in order to determine which one performs best when using concept-based annotations on full-text documents. We also evaluated variations in similarity values based on title-and-abstract against those relying on full-text. Our test dataset comprises the Genomics track article collection from the 2005 Text Retrieval Conference. Initially, we used an entity recognition software to semantically annotate titles and abstracts as well as full-text with concepts defined in the Unified Medical Language System (UMLS®). For each article, we created a document profile, i.e., a set of identified concepts, term frequency, and inverse document frequency; we then applied various similarity metrics to those document profiles. We considered correlation, precision, recall, and F1 in order to determine which similarity metric performs best with concept-based annotations. For those full-text articles available in PubMed Central Open Access (PMC-OA), we also performed dispersion analyses in order to understand how similarity varies when considering full-text articles. Results We have found that the PubMed Related Articles similarity metric is the most suitable for full-text articles annotated with UMLS concepts. For similarity values above 0.8, all metrics exhibited an F1 around 0.2 and a recall around 0.1; BM25 showed the highest precision close to 1; in all cases the concept-based metrics performed better than the word-stem-based one. Our experiments show that similarity values vary when considering only title-and-abstract versus full-text similarity. Therefore, analyses based on full-text become useful when a given research requires going beyond title and abstract, particularly regarding connectivity across articles. Availability Visualization available at ljgarcia.github.io/semsim.benchmark/, data available at http://dx.doi.org/10.5281/zenodo.13323.The authors acknowledge the support from the members of Temporal Knowledge Bases Group at Universitat Jaume I. Funding: LJGC and AGC are both self-funded, RB is funded by the “Ministerio de Economía y Competitividad” with contract number TIN2011-24147

Hierarchical Catalysts Prepared by Interzeolite Transformation

Interzeolite transformation has been used to produce a novel family of hierarchical catalysts featuring excellent textural properties, strong acidity, and superior catalytic performance for the Friedel–Crafts alkylation of indole with benzhydrol, the Claisen–Schmidt condensation of benzaldehyde and hydroxyacetophenone, and the cracking of polystyrene. Intermediate solids of the FAU interzeolite transformation into BEA display both increased accessibility─due to the development of mesoporosity─and strong acidity─caused by the presence of ultrasmall crystals or zeolitic fragments in their structure. The use of surfactants allows for the development of the hierarchical catalysts with very narrow pore size distribution. The properties of interzeolite transformation intermediates (ITIs) can be fine-tuned simply by stopping the interconversion at different times.The authors thank the European Commission for funding through the H2020-MSCA-RISE-2019 program (Ref. ZEOBIOCHEM-872102) and the Spanish MINECO and AEI/FEDER, UE, through Project Ref. RTI2018-099504-B-C21. N.L. also acknowledges the University of Alicante support (UATALENTO17-05). M.J.M. thanks the Generalitat Valenciana for a PhD fellowship (GRISOLIAP/2020/165). Carlos A. Trujillo and Nelcari T. Ramírez M. express their gratitude to the Universidad Nacional de Colombia for providing physical and technical resources for this research also to Minciencias and Ecopetrol in the frame of Contract 0402-2013

c-Fos induces chondrogenic tumor formation in immortalized human mesenchymal progenitor cells

Mesenchymal progenitor cells (MPCs) have been hypothesized as cells of origin for sarcomas, and c-Fos transcription factor has been showed to act as an oncogene in bone tumors. In this study, we show c-Fos is present in most sarcomas with chondral phenotype, while multiple other genes are related to c-Fos expression pattern. To further define the role of c-Fos in sarcomagenesis, we expressed it in primary human MPCs (hMPCs), immortalized hMPCs and transformed murine MPCs (mMPCs). In immortalized hMPCs, c-Fos expression generated morphological changes, reduced mobility capacity and impaired adipogenic- and osteogenic-differentiation potentials. Remarkably, immortalized hMPCs or mMPCs expressing c-Fos generated tumors harboring a chondrogenic phenotype and morphology. Thus, here we show that c-Fos protein has a key role in sarcomas and that c-Fos expression in immortalized MPCs yields cell transformation and chondrogenic tumor formation.This work was supported by grants from the Fondo de Investigaciones Sanitarias (FIS: PI11/00377 to J.G.-C.; and RTICC: RD12/0036/0027 to J.G-C, RD12/0036/0020 to S.M.) and the Madrid Regional Government (CellCAM; P2010/BMD-2420 to J.G.-C) in Spain. A.A. was supported by Juan de la Cierva program of the Spanish Plan Nacional (MINECO) and Sara Borrell program of the ISCIII/FEDER. A.Al. was supported by the “Miguel Servet” program of the ISCIII/FEDER. We gratefully acknowledge support from Asociación Pablo Ugarte (CIF G86121019) and AFANION (CIF G02223733). The experiments were approved by the appropriate committees.S

Diseño del plan de auditoría interna para la panadería artesanal don Josué con el fin de implementar el plan HACCP- norma ISO 2200:2018

Bajo el grado de cumplimiento y el avance en el sistema HACCP en conjunto con la ISO 22000:2018 la panificadora artesanal Don Josué, se realizó e implemento un plan de verificación, refuerzo y auditoria al sistema HACCP, por lo que se realiza un plan de auditoria con el fin de analizar la criticidad de aspectos que interfieran en la calidad e inocuidad de manera directa con la etapa de proceso o productos.Under the degree of compliance and progress under the HACCP system in conjunction with ISO 22000:2018, the artisan bakery Don Josue, carried out and implemented a verification, reinforcement and audit plan to the HACCP system. An audit plan is carried out in order to highlight the criticality of aspects that interfere with quality and safety directly with the process or products stage

An atlas of spider development at single-cell resolution provides new insights into arthropod embryogenesis

Spiders are a diverse order of chelicerates that diverged from other arthropods over 500 million years ago. Research on spider embryogenesis, particularly studies using the common house spider Parasteatoda tepidariorum, has made important contributions to understanding the evolution of animal development, including axis formation, segmentation, and patterning. However, we lack knowledge about the cells that build spider embryos, their gene expression profiles and fate. Single-cell transcriptomic analyses have been revolutionary in describing these complex landscapes of cellular genetics in a range of animals. Therefore, we carried out single-cell RNA sequencing of P. tepidariorum embryos at stages 7, 8 and 9, which encompass the establishment and patterning of the body plan, and initial differentiation of many tissues and organs. We identified 20 cell clusters, from 18.5 k cells, which were marked by many developmental toolkit genes, as well as a plethora of genes not previously investigated. We found differences in the cell cycle transcriptional signatures, suggestive of different proliferation dynamics, which related to distinctions between endodermal and some mesodermal clusters, compared with ectodermal clusters. We identified many Hox genes as markers of cell clusters, and Hox gene ohnologs were often present in different clusters. This provided additional evidence of sub- and/or neo-functionalisation of these important developmental genes after the whole genome duplication in an arachnopulmonate ancestor (spiders, scorpions, and related orders). We also examined the spatial expression of marker genes for each cluster to generate a comprehensive cell atlas of these embryonic stages. This revealed new insights into the cellular basis and genetic regulation of head patterning, hematopoiesis, limb development, gut development, and posterior segmentation. This atlas will serve as a platform for future analysis of spider cell specification and fate, and studying the evolution of these processes among animals at cellular resolution

An atlas of spider development at single-cell resolution provides new insights into arthropod embryogenesis

Spiders are a diverse order of chelicerates that diverged from other arthropods over 500 million years ago. Research on spider embryogenesis, particularly studies using the common house spider Parasteatoda tepidariorum, has made important contributions to understanding the evolution of animal development, including axis formation, segmentation, and patterning. However, we lack knowledge about the cells that build spider embryos, their gene expression profiles and fate. Single-cell transcriptomic analyses have been revolutionary in describing these complex landscapes of cellular genetics in a range of animals. Therefore, we carried out single-cell RNA sequencing of P. tepidariorum embryos at stages 7, 8 and 9, which encompass the establishment and patterning of the body plan, and initial differentiation of many tissues and organs. We identified 20 cell clusters, from 18.5 k cells, which were marked by many developmental toolkit genes, as well as a plethora of genes not previously investigated. We found differences in the cell cycle transcriptional signatures, suggestive of different proliferation dynamics, which related to distinctions between endodermal and some mesodermal clusters, compared with ectodermal clusters. We identified many Hox genes as markers of cell clusters, and Hox gene ohnologs were often present in different clusters. This provided additional evidence of sub- and/or neo-functionalisation of these important developmental genes after the whole genome duplication in an arachnopulmonate ancestor (spiders, scorpions, and related orders). We also examined the spatial expression of marker genes for each cluster to generate a comprehensive cell atlas of these embryonic stages. This revealed new insights into the cellular basis and genetic regulation of head patterning, hematopoiesis, limb development, gut development, and posterior segmentation. This atlas will serve as a platform for future analysis of spider cell specification and fate, and studying the evolution of these processes among animals at cellular resolution

Massive stars in extremely metal-poor galaxies: a window into the past

Cosmic history has witnessed the lives and deaths of multiple generations of massive stars, all of them invigorating their host galaxies with ionizing photons, kinetic energy, fresh material, and stellar-mass black holes. Ubiquitous engines as they are, astrophysics needs a good understanding of their formation, evolution, properties and yields throughout the history of the Universe, and with decreasing metal content mimicking the environment at the earliest epochs. Ultimately, a physical model that could be extrapolated to zero metallicity would enable tackling long-standing questions such as “What did the first, very massive stars of the Universe look like?” or “What was their role in the re-ionization of the Universe?” Yet, most of our knowledge of metal-poor massive stars is drawn from one single point in metallicity. Massive stars in the Small Magellanic Cloud (SMC, ∼1/5Z⊙ ) currently serve as templates for low-metallicity objects in the early Universe, even though significant differences with respect to massive stars with poorer metal content have been reported. This White Paper summarizes the current knowledge on extremely (sub-SMC) metal poor massive stars, highlighting the most outstanding open questions and the need to supersede the SMC as standard. A new paradigm can be built from nearby extremely metal-poor galaxies that make a new metallicity ladder, but massive stars in these galaxies are out of reach to current observational facilities. Such a task would require an L-size mission, consisting of a 10m-class space telescope operating in the optical and the ultraviolet ranges. Alternatively, we propose that ESA unites efforts with NASA to make the LUVOIR mission concept a reality, thus continuing the successful partnership that made the Hubble Space Telescope one of the greatest observatories of all time

Energy Estimation of Cosmic Rays with the Engineering Radio Array of the Pierre Auger Observatory

The Auger Engineering Radio Array (AERA) is part of the Pierre Auger Observatory and is used to detect the radio emission of cosmic-ray air showers. These observations are compared to the data of the surface detector stations of the Observatory, which provide well-calibrated information on the cosmic-ray energies and arrival directions. The response of the radio stations in the 30 to 80 MHz regime has been thoroughly calibrated to enable the reconstruction of the incoming electric field. For the latter, the energy deposit per area is determined from the radio pulses at each observer position and is interpolated using a two-dimensional function that takes into account signal asymmetries due to interference between the geomagnetic and charge-excess emission components. The spatial integral over the signal distribution gives a direct measurement of the energy transferred from the primary cosmic ray into radio emission in the AERA frequency range. We measure 15.8 MeV of radiation energy for a 1 EeV air shower arriving perpendicularly to the geomagnetic field. This radiation energy -- corrected for geometrical effects -- is used as a cosmic-ray energy estimator. Performing an absolute energy calibration against the surface-detector information, we observe that this radio-energy estimator scales quadratically with the cosmic-ray energy as expected for coherent emission. We find an energy resolution of the radio reconstruction of 22% for the data set and 17% for a high-quality subset containing only events with at least five radio stations with signal.Comment: Replaced with published version. Added journal reference and DO