Combined SVM-CRFs for Biological Named Entity Recognition with Maximal Bidirectional Squeezing

Biological named entity recognition, the identification of biological terms in text, is essential for biomedical information extraction. Machine learning-based approaches have been widely applied in this area. However, the recognition performance of current approaches could still be improved. Our novel approach is to combine support vector machines (SVMs) and conditional random fields (CRFs), which can complement and facilitate each other. During the hybrid process, we use SVM to separate biological terms from non-biological terms, before we use CRFs to determine the types of biological terms, which makes full use of the power of SVM as a binary-class classifier and the data-labeling capacity of CRFs. We then merge the results of SVM and CRFs. To remove any inconsistencies that might result from the merging, we develop a useful algorithm and apply two rules. To ensure biological terms with a maximum length are identified, we propose a maximal bidirectional squeezing approach that finds the longest term. We also add a positive gain to rare events to reinforce their probability and avoid bias. Our approach will also gradually extend the context so more contextual information can be included. We examined the performance of four approaches with GENIA corpus and JNLPBA04 data. The combination of SVM and CRFs improved performance. The macro-precision, macro-recall, and macro-F1 of the SVM-CRFs hybrid approach surpassed conventional SVM and CRFs. After applying the new algorithms, the macro-F1 reached 91.67% with the GENIA corpus and 84.04% with the JNLPBA04 data

The Global Diversity of Parasitic Isopods Associated with Crustacean Hosts (Isopoda: Bopyroidea and Cryptoniscoidea)

Parasitic isopods of Bopyroidea and Cryptoniscoidea (commonly referred to as epicarideans) are unique in using crustaceans as both intermediate and definitive hosts. In total, 795 epicarideans are known, representing ∼7.7% of described isopods. The rate of description of parasitic species has not matched that of free-living isopods and this disparity will likely continue due to the more cryptic nature of these parasites. Distribution patterns of epicarideans are influenced by a combination of their definitive (both benthic and pelagic species) and intermediate (pelagic copepod) host distributions, although host specificity is poorly known for most species. Among epicarideans, nearly all species in Bopyroidea are ectoparasitic on decapod hosts. Bopyrids are the most diverse taxon (605 species), with their highest diversity in the North West Pacific (139 species), East Asian Sea (120 species), and Central Indian Ocean (44 species). The diversity patterns of Cryptoniscoidea (99 species, endoparasites of a diverse assemblage of crustacean hosts) are distinct from bopyrids, with the greatest diversity of cryptoniscoids in the North East Atlantic (18 species) followed by the Antarctic, Mediterranean, and Arctic regions (13, 12, and 8 species, respectively). Dajidae (54 species, ectoparasites of shrimp, mysids, and euphausids) exhibits highest diversity in the Antarctic (7 species) with 14 species in the Arctic and North East Atlantic regions combined. Entoniscidae (37 species, endoparasites within anomuran, brachyuran and shrimp hosts) show highest diversity in the North West Pacific (10 species) and North East Atlantic (8 species). Most epicarideans are known from relatively shallow waters, although some bopyrids are known from depths below 4000 m. Lack of parasitic groups in certain geographic areas is likely a sampling artifact and we predict that the Central Indian Ocean and East Asian Sea (in particular, the Indo-Malay-Philippines Archipelago) hold a wealth of undescribed species, reflecting our knowledge of host diversity patterns

Petri Net computational modelling of Langerhans cell Interferon Regulatory Factor Network predicts their role in T cell activation

Langerhans cells (LCs) are able to orchestrate adaptive immune responses in the skin by interpreting the microenvironmental context in which they encounter foreign substances, but the regulatory basis for this has not been established. Utilising systems immunology approaches combining in silico modelling of a reconstructed gene regulatory network (GRN) with in vitro validation of the predictions, we sought to determine the mechanisms of regulation of immune responses in human primary LCs. The key role of Interferon regulatory factors (IRFs) as controllers of the human Langerhans cell response to epidermal cytokines was revealed by whole transcriptome analysis. Applying Boolean logic we assembled a Petri net-based model of the IRF-GRN which provides molecular pathway predictions for the induction of different transcriptional programmes in LCs. In silico simulations performed after model parameterisation with transcription factor expression values predicted that human LC activation of antigen-specific CD8 T cells would be differentially regulated by epidermal cytokine induction of specific IRF-controlled pathways. This was confirmed by in vitro measurement of IFN-g production by activated T cells. As a proof of concept, this approach shows that stochastic modelling of a specific immune networks renders transcriptome data valuable for the prediction of functional outcomes of immune responses

More than one way of being a moa: differences in leg bone robustness map divergent evolutionary trajectories in Dinornithidae and Emeidae (Dinornithiformes).

The extinct moa of New Zealand included three families (Megalapterygidae; Dinornithidae; Emeidae) of flightless palaeognath bird, ranging in mass from 200 kg. They are perceived to have evolved extremely robust leg bones, yet current estimates of body mass have very wide confidence intervals. Without reliable estimators of mass, the extent to which dinornithid and emeid hindlimbs were more robust than modern species remains unclear. Using the convex hull volumetric-based method on CT-scanned skeletons, we estimate the mass of a female Dinornis robustus (Dinornithidae) at 196 kg (range 155-245 kg) and of a female Pachyornis australis (Emeidae) as 50 kg (range 33-68 kg). Finite element analysis of CT-scanned femora and tibiotarsi of two moa and six species of modern palaeognath showed that P. australis experienced the lowest values for stress under all loading conditions, confirming it to be highly robust. In contrast, stress values in the femur of D. robustus were similar to those of modern flightless birds, whereas the tibiotarsus experienced the highest level of stress of any palaeognath. We consider that these two families of Dinornithiformes diverged in their biomechanical responses to selection for robustness and mobility, and exaggerated hindlimb strength was not the only successful evolutionary pathway

Magnesium isotope evidence that accretional vapour loss shapes planetary compositions

It has long been recognized that Earth and other differentiated planetary bodies are chemically fractionated compared to primitive, chondritic meteorites and, by inference, the primordial disk from which they formed. However, it is not known whether the notable volatile depletions of planetary bodies are a consequence of accretion1 or inherited from prior nebular fractionation2. The isotopic compositions of the main constituents of planetary bodies can contribute to this debate3, 4, 5, 6. Here we develop an analytical approach that corrects a major cause of measurement inaccuracy inherent in conventional methods, and show that all differentiated bodies have isotopically heavier magnesium compositions than chondritic meteorites. We argue that possible magnesium isotope fractionation during condensation of the solar nebula, core formation and silicate differentiation cannot explain these observations. However, isotopic fractionation between liquid and vapour, followed by vapour escape during accretionary growth of planetesimals, generates appropriate residual compositions. Our modelling implies that the isotopic compositions of magnesium, silicon and iron, and the relative abundances of the major elements of Earth and other planetary bodies, are a natural consequence of substantial (about 40 per cent by mass) vapour loss from growing planetesimals by this mechanism

L'immagine di Napoli dopo il movimento dei disoccupati organizzati

"L'alfabeto urbano", marzo 198

Within-Subject Variation in Hemoglobin Mass in Elite Athletes

C1 - Journal Articles RefereedUNLABELLED: Illicit autologous blood transfusion to improve performance in elite sport is currently undetectable, but the stability of longitudinal profiles of an athlete's hemoglobin mass (Hbmass) might be used to detect such practices. PURPOSE: Our aim was to quantify within-subject variation of Hbmass in elite athletes, and the effects of potentially confounding factors such as reduced training or altitude exposure. METHODS: A total of 130 athletes (43 females and 87 males) were measured for Hbmass an average of six times during a period of approximately 1 yr using carbon monoxide rebreathing. Linear mixed models were used to quantify within-subject variation of Hbmass and its associated analytical and biological components for males and females, as well as the effects of reduced training and moderate altitude exposure in certain athletes. RESULTS: The maximum within-subject coefficient of variation (CV) for Hbmass was 3.4% for males and 4.0% for females. The analytical CV was ~2.0% for both males and females, and the long-term biological CV, after allowing for analytical variation, was 2.8% for males and 3.5% for females. On average, self-reported reduced training resulted in a 2.8% decrease in Hbmass and altitude exposure increased Hbmass by 1.5% to 2.9%, depending on the duration and type of exposure. CONCLUSIONS: The within-subject CV for Hbmass of ~4% indicates that athletes may experience changes up to ~20% with a 1-in-1000 probability. Changes of this magnitude for measures taken a few months apart suggest that Hbmass has a limited capacity to detect autologous blood doping. However, changes in Hbmass may be a useful indicator when combined with other measures of blood manipulation