Get my pizza right: Repairing missing is-a relations in ALC ontologies (extended version)

With the increased use of ontologies in semantically-enabled applications, the issue of debugging defects in ontologies has become increasingly important. These defects can lead to wrong or incomplete results for the applications. Debugging consists of the phases of detection and repairing. In this paper we focus on the repairing phase of a particular kind of defects, i.e. the missing relations in the is-a hierarchy. Previous work has dealt with the case of taxonomies. In this work we extend the scope to deal with ALC ontologies that can be represented using acyclic terminologies. We present algorithms and discuss a system

Variation in assignment of the COPD patients into a GOLD group according to symptoms severity

Introduction: The Global Organization of Lung Disease (GOLD) classifies patients with chronic obstructive pulmonary disease (COPD) taking into account the symptoms. The modified Medical Research Council’s dyspnea scale (mMRC) and the COPD assessment test (CAT) are used to assess these symptoms. In this study, we analyze the concordance of GOLD classification using mMRC and CAT. Patients and Methods: This is an observational study of a cohort of 169 patients with COPD, who were classified following the GOLD 2017 recommendations, using both mMRC and CAT. A concordance analysis was applied, and a ROC curve was generated to identify the CAT score that best concorded with the mMRC scale. Results: The concordance for the GOLD groups classified by CAT and mMRC was moderate (kappa 0.492). For mMRC score of 1 and 2, a CAT score of =9 and =16 showed the maximum value of the Youden index, respectively. By reclassifying the patients with the new cut-off points obtained, the best concordance was obtained between the cut-off point for CAT of 16 and for mMRC of 2, followed by CAT of 9 and mMRC of 1. Conclusion: Because of the deficient concordance between CAT and mMRC, we propose the use of new cut-off points in future updates of the GOLD strategy

Variation in Assignment of the COPD Patients into a GOLD Group According to Symptoms Severity.

Introduction: The Global Organization of Lung Disease (GOLD) classifies patients with chronic obstructive pulmonary disease (COPD) taking into account the symptoms. The modified Medical Research Council’s dyspnea scale (mMRC) and the COPD assessment test (CAT) are used to assess these symptoms. In this study, we analyze the concordance of GOLD classification using mMRC and CAT. Patients and Methods: This is an observational study of a cohort of 169 patients with COPD, who were classified following the GOLD 2017 recommendations, using both mMRC and CAT. A concordance analysis was applied, and a ROC curve was generated to identify the CAT score that best concorded with the mMRC scale. Results: The concordance for the GOLD groups classified by CAT and mMRC was moderate (kappa 0.492). For mMRC score of 1 and 2, a CAT score of ≥9 and ≥16 showed the maximum value of the Youden index, respectively. By reclassifying the patients with the new cut-off points obtained, the best concordance was obtained between the cut-off point for CAT of 16 and for mMRC of 2, followed by CAT of 9 and mMRC of 1. Conclusion: Because of the deficient concordance between CAT and mMRC, we propose the use of new cut-off points in future updates of the GOLD strategy.post-print2909 K

The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis

Post-transcriptional mechanisms have the potential to influence complex changes in gene expression, yet their role in cell fate transitions remains largely unexplored. Here, we show that suppression of the RNA helicase DDX6 endows human and mouse primed embryonic stem cells (ESCs) with a differentiation-resistant, “hyper-pluripotent” state, which readily reprograms to a naive state resembling the preimplantation embryo. We further demonstrate that DDX6 plays a key role in adult progenitors where it controls the balance between self-renewal and differentiation in a context-dependent manner. Mechanistically, DDX6 mediates the translational suppression of target mRNAs in P-bodies. Upon loss of DDX6 activity, P-bodies dissolve and release mRNAs encoding fate-instructive transcription and chromatin factors that re-enter the ribosome pool. Increased translation of these targets impacts cell fate by rewiring the enhancer, heterochromatin, and DNA methylation landscapes of undifferentiated cell types. Collectively, our data establish a link between P-body homeostasis, chromatin organization, and stem cell potency

PÉRDIDAS DE CARBONO EN SUELOS DE LA LLANURA COSTERA DE NAYARIT, MÉXICO

Se analizaron las pérdidas de carbono orgánico en suelos a partir de 12 perfiles localizados en el delta del río San Pedro y distribuidos por nivel geomorfológico en la llanura costera del estado de Nayarit, México. El estudio se realizó comparando el contenido de carbono de los suelos con mayor conservación bajo bosque y cultivados. Los niveles considerados para este análisis fueron llanura alta, llanura media y sus depresiones, llanura baja y barras costeras. Las reservas de carbono (RCO) se determinaron teniendo en cuenta la densidad aparente (Da), el espesor de cada horizonte y el contenido de carbono. Los resultados se ponderaron para las profundidades 0-20, 0-50 y 0-100 cm. Las pérdidas de carbono identificadas fueron del 36 % para suelos Cambisoles de la llanura alta, 40 % para Feozem y Cambisoles de la llanura media, 60 % en suelos Feozem y Solonetz de las depresiones de la llanura media, 67 % para Cambisoles de la llanura baja y 90 % para Arenosoles de las barras costeras. Se demostró que la actividad agrícola intensiva y continuada, ha ocasionado pérdidas en el contenido de carbono; así mismo, la capa agrícola (20 cm) resulta la más afectada por esta actividad antropogénica

Maternal genetic inheritance of red pericarp in the grain of maize

The diversity of colors in the grain of corn is wide, from whites to blacks and including a continuum of various shades of yellows, pinks, reds, purples and blues. The most abundant commercial colors are yellow and white, however other colors have become more important because of the presence of pigments to which are attributed favorable effects as a food. The pigments are also considered natural barriers of the grain against the invasion of pests and diseases in the production fields. The colors of the grain of corn occur in three different parts of the seed: the cover of the grain or pericarp, derived from the maternal tissue, with a diploid genetic content; the endo-sperm, including the aleurone layers that are cells in the grain immediately below the pericarp with a chromosome content of 3n; and the embryo, with a genetic content of 2n. The red color considered in this study is present in the pericarp ignoring possible effects in other tissues of grain and other organs of the plant. In this study, we used materials with colorless or red pericarp, and white or yellow endosperm; with the purpose of describing the type of inheritance of this character in the grain of corn. The results indicated a maternal genetic inheritance with classical complete dominance of the red color of pericarp over the clear or transparent phenotype, where the red color of the grains on ear is determined by the genotype of the mother grain but not by the seed embryo genotypes, which is characterized by uniformity of grain color of the ear. This type of inheritance could be useful in the development of pigmented varieties of higher food quality for humans

Experimental study on the effect of adaptive flaps on the aerodynamics of an Ahmed body

We perform an experimental study on the turbulent flow around a square-back Ahmed body of height, h, at varying Re=u∞h/ν∈[0.5,1]×105, where u∞ is the free-stream velocity and ν is the incoming flow kinematic viscosity, under different yaw angles β=(0∘,-5∘,-10∘), to analyze the use of rear flexibly hinged parallel plates as a control strategy to reduce the drag in a self-adaptive manner under changing flow conditions. The model implements rear parallel rigid flaps of depth d=0.5h, which are mounted with torsional joints through embedded flexible foils of calibrated thickness. This holding system restricts the motion of the plates to a rotary displacement, θ. The fluid-structure dynamics is characterized by the reduced velocity, defined as U∗=u∞/fnh, where fn is the natural frequency of rotary oscillations of the hinged plates, measured in free-decay tests of flaps. In fact, we have explored the range of reduced velocity, U∗=[0,65], varying u∞ and consequently Re. We perform force and pressure measurements to quantify the variations of the drag and the base pressure coefficients while laser displacement sensors are used to obtain the angular flaps motion. Results show that the hinged plates decrease the drag coefficient of the original body by nearly 4.4% for flow conditions aligned with the body axis. Under cross-flow conditions, their efficiency is even larger, attaining relative reductions drag of nearly 9.1% at β=-10∘ (13.5% in comparison with a body with fixed rigid plates of the same depth). Such variations are shown to be associated with a passive reconfiguration process of rear flaps. Additionally, hinged flaps are shown to interact with the reflectional-symmetry-breaking (RSB) modes, typically present in the wake of three-dimensional bodies. At aligned conditions, the interaction with the RSB modes is characterized by two regimes, in such a way that the hinged flaps manage to partially stabilize the RSB modes, and consequently to inhibit the bistable behavior at low values of U∗ (in a similar manner to rigid flaps), while at high values of U∗, they respond dynamically to switches between the opposite wake deflections of the RSB modes, deviating themselves accordingly

Soil contamination in nearby natural areas mirrors that in urban greenspaces worldwide

Soil contamination is one of the main threats to ecosystem health and sustainability. Yet little is known about the extent to which soil contaminants differ between urban greenspaces and natural ecosystems. Here we show that urban greenspaces and adjacent natural areas (i.e., natural/semi-natural ecosystems) shared similar levels of multiple soil contaminants (metal(loid)s, pesticides, microplastics, and antibiotic resistance genes) across the globe. We reveal that human influence explained many forms of soil contamination worldwide. Socio-economic factors were integral to explaining the occurrence of soil contaminants worldwide. We further show that increased levels of multiple soil contaminants were linked with changes in microbial traits including genes associated with environmental stress resistance, nutrient cycling, and pathogenesis. Taken together, our work demonstrates that human-driven soil contamination in nearby natural areas mirrors that in urban greenspaces globally, and highlights that soil contaminants have the potential to cause dire consequences for ecosystem sustainability and human wellbeing

Bile microbiome signatures associated with pancreatic ductal adenocarcinoma compared to benign disease: a UK pilot study

Pancreatic ductal adenocarcinoma (PDAC) has a very poor survival. The intra-tumoural microbiome can influence pancreatic tumourigenesis and chemoresistance and, therefore, patient survival. The role played by bile microbiota in PDAC is unknown. We aimed to define bile microbiome signatures that can effectively distinguish malignant from benign tumours in patients presenting with obstructive jaundice caused by benign and malignant pancreaticobiliary disease. Prospective bile samples were obtained from 31 patients who underwent either Endoscopic Retrograde Cholangiopancreatography (ERCP) or Percutaneous Transhepatic Cholangiogram (PTC). Variable regions (V3-V4) of the 16S rRNA genes of microorganisms present in the samples were amplified by Polymerase Chain Reaction (PCR) and sequenced. The cohort consisted of 12 PDAC, 10 choledocholithiasis, seven gallstone pancreatitis and two primary sclerosing cholangitis patients. Using the 16S rRNA method, we identified a total of 135 genera from 29 individuals (12 PDAC and 17 benign). The bile microbial beta diversity significantly differed between patients with PDAC vs. benign disease (Permanova p = 0.0173). The separation of PDAC from benign samples is clearly seen through unsupervised clustering of Aitchison distance. We found three genera to be of significantly lower abundance among PDAC samples vs. benign, adjusting for false discovery rate (FDR). These were Escherichia (FDR = 0.002) and two unclassified genera, one from Proteobacteria (FDR = 0.002) and one from Enterobacteriaceae (FDR = 0.011). In the same samples, the genus Streptococcus (FDR = 0.033) was found to be of increased abundance in the PDAC group. We show that patients with obstructive jaundice caused by PDAC have an altered microbiome composition in the bile compared to those with benign disease. These bile-based microbes could be developed into potential diagnostic and prognostic biomarkers for PDAC and warrant further investigation