Biological taxonomy and ontology development: scope and limitations

The prospects of integrating full-blown biological taxonomies into an ontological reasoning framework are reviewed. We contrast the common usage of a static 'snapshot' hierarchy in ontological representations of taxonomy with a more realistic situation that involves dynamic, piece-meal revisions of particular taxonomic groups and requires alignment with relevant preceding perspectives. Taxonomic practice is characterized by a range of phenomena that are orthogonal to the logical semantic background from which ontological entities and relationships originate, and therefore pose special challenges to ontological representation and reasoning. Among these phenomena are: (1) the notion that there is a single phylogenetic hierarchy in nature which taxonomy can only gradually approximate; (2) the evolvability of taxa which means that taxon-defining features may be lost in subordinate members or independently gained across multiple sections of the tree of life; (3) the hybrid approach of defining taxa both in reference to properties (intensional) and members (ostensive) which undermines the individual/class dichotomy sustaining conventional ontologies; (4) the idiosyncratic yet inferentially valuable usage of Linnaean ranks; (5) the indelible and semantically complex 250-year legacy of nomenclatural and taxonomic changes that characterizes the current system; (6) the insufficient taxonomic exploration of large portions of the tree of life; and the need to use a sophisticated terminology for aligning taxonomic entities in order to integrate both (7) single and (8) multiple hierarchies. We briefly such how such integration may proceed based on an initial expert alignment of concept relationship and subsequent use of first-order logic algorithms to maximize consistency, reveal implied relationships, and ultimately merge taxonomies.
 In light of the aforementioned obstacles, we suggest that research along the taxonomy/ontology interface should focus on either strictly nomenclatural entities or specialize in ontology-driven methods for producing alignments between multiple taxonomies. We furthermore suggest that the prospects of developing successful ontologies for taxonomy will largely depend on the ability of the taxonomic expert community to present their phylogenies and classifications in a way that is more compatible with ontological reasoning than concurrent practice. Minimally, this means (1) adopting rigorous standards for linking new core taxonomies to relevant peripheral taxonomies through comprehensive alignments so that their ontological/taxonomic connections are transparent; (2) using lineage-specific ontological standards for phenotype-based accounts of taxa while taking into account the phylogenetic contextuality of phenotypic descriptors; (3) presenting all nomenclatural and taxonomic novelties in an explicit, ontology-compatible format, including intensional and ostensive definitions; and (4) offering comprehensive intensional/ostensive alignments to entities in relevant preceding taxonomies

Observations of extremely thin clouds in the tropical tropopause region by a ship based lidar.

During the cruises ANT XVII/4 (Punta Arenas Bremerhaven, 2000) and ANT XX1/1 (Bremerhaven - Cape Town, 2003) continuous measurements of clouds and aerosol have been performed by a Mobile Aerosol Raman Lidar (MARL). This system measures backscatter of light at 355 nm and 532 nm and is able to detect even extremely thin layers of particles in the atmosphere. Cloud base and top height, depolarisation optical depth and color index can be deduced from this data. During the Polarstern cruises very thin layers of ice particles have been observed frequently in the tropical tropopause layer (TTL). Cases of persistent cloud layers with an optical depth below 10^-3 are reported. Based on the data of radiosondes which were launched daily aboard the vessel, the conditions at which these type of clouds form are analysed. It is shown, that these clouds form in a layer below the cold point, but above the lapse rate tropopause. The relation between cloud occurrence and temperature and wind in the TTL as well as state of the QBO are discussed

Connexin 40 promoter-based enrichment of embryonic stem cell-derived cardiovascular progenitor cells

Background: Pluripotent embryonic stem (ES) cells that can differentiate into functional cardiomyocytes as well as vascular cells in cell culture may open the door to cardiovascular cell transplantation. However, the percentage of ES cells in embryoid bodies (EBs) which spontaneously undergo cardiovascular differentiation is low (< 10%), making strategies for their specific labeling and purification indispensable. Methods: The human connexin 40 (Cx40) promoter was isolated and cloned in the vector pEGFP. The specificity of the construct was initially assessed in Xenopus embryos injected with Cx40-EGFP plasmid DNA. Stable Cx40-EGFP ES cell clones were differentiated and fluorescent cells were enriched manually as well as via fluorescence-activated cell sorting. Characterization of these cells was performed with respect to spontaneous beating as well as via RT-PCRs and immunofluorescent stainings. Results: Cx40-EGFP reporter plasmid injection led to EGFP fluorescence specifically in the abdominal aorta of frog tadpoles. After crude manual enrichment of highly Cx40-EGFP- positive EBs, the appearance of cardiac and vascular structures was increased approximately 3-fold. Immuno fluorescent stainings showed EGFP expression exclusively in vascular-like structures simultaneously expressing von Willebrand factor and in formerly beating areas expressing alpha-actinin. Cx40-EGFP-expressing EBs revealed significantly higher numbers of beating cardiomyocytes and vascular-like structures. Semiquantitative RT-PCRs confirmed an enhanced cardiovascular differentiation as shown for the cardiac markers Nkx2.5 and MLC2v, as well as the endothelial marker vascular endothelial cadherin. Conclusions: Our work shows the feasibility of specific labeling and purification of cardiovascular progenitor cells from differentiating EBs based on the Cx40 promoter. We provide proof of principle that the deleted CD4 (Delta CD4) surface marker-based method for magnetic cell sorting developed by our group will be ideally suitable for transference to this promoter. Copyright (c) 2008 S. Karger AG, Basel

Static feed water electrolysis subsystem development

This disclosure is directed to an electrolysis cell forming hydrogen and oxygen at spaced terminals. The anode terminal is porous and able to form oxygen within the cell and permit escape of the gaseous oxygen through the anode and out through a flow line in the presence of backpressure. Hydrogen is liberated in the cell at the opposing solid metal cathode which is permeable to hydrogen but not oxygen so that the migratory hydrogen formed in the cell is able to escape from the cell. The cell is maintained at an elevated pressure so that oxygen liberated by the cell is delivered at elevated pressure without pumping to raise the pressure of the oxygen

A Flexible Network Approach to Privacy of Blockchain Transactions

For preserving privacy, blockchains can be equipped with dedicated mechanisms to anonymize participants. However, these mechanism often take only the abstraction layer of blockchains into account whereas observations of the underlying network traffic can reveal the originator of a transaction request. Previous solutions either provide topological privacy that can be broken by attackers controlling a large number of nodes, or offer strong and cryptographic privacy but are inefficient up to practical unusability. Further, there is no flexible way to trade privacy against efficiency to adjust to practical needs. We propose a novel approach that combines existing mechanisms to have quantifiable and adjustable cryptographic privacy which is further improved by augmented statistical measures that prevent frequent attacks with lower resources. This approach achieves flexibility for privacy and efficency requirements of different blockchain use cases.Comment: 6 pages, 2018 IEEE 38th International Conference on Distributed Computing Systems (ICDCS

Depression and identity : Are self-constructions negative or conflictual?

Negative self-views have proved to be a consistent marker of vulnerability for depression. However, recent research has shown that a particular kind of cognitive conflict, implicative dilemma, is highly prevalent in depression. In this study, the relevance of these conflicts is assessed as compared to the cognitive model of depression of a negative view of the self. In so doing, 161 patients with major depression and 110 controls were assessed to explore negative self-construing (self-ideal discrepancy) and conflicts (implicative dilemmas), as well as severity of symptoms. Results showed specificity for the clinical group indicating a pattern of mixed positive and negative self-descriptions with a high rate of conflict. Regression analysis lent support to the conflict hypothesis in relation to clinically relevant indicators such as symptom severity, global functioning. However, self-ideal discrepancy was a stronger predictor of group membership. The findings showed the relevance of cognitive conflicts to compliment the well-consolidated theory of negative self-views. Clinical implications for designing interventions are discussed.Peer reviewedFinal Published versio

Posttraumatic Stress and Parenting Behaviors: The Mediating Role of Emotion Regulation

Maternal trauma has been linked with problematic parenting, including both harsh and permissive behaviors. However, little is known about mechanisms accounting for this association. The current study examined the potential impact of posttraumatic stress disorder (PTSD) and emotion regulation on dysfunctional parenting behaviors in a sample of community mothers. We hypothesized a mediation model wherein PTSD would be associated with dysfunctional parenting (i.e., lax and overreactive behaviors) indirectly through deficits in maternal emotion regulation. Seventy-eight community mothers of 18- to 36-month-old children were administered the Clinician Administered PTSD Scale for DSM-5 (CAPS-5) and 19 mothers met criteria for PTSD. Mothers also completed self-report measures of difficulties with emotion regulation and maternal laxness and overreactivity in parenting. Results revealed that emotion dysregulation fully mediated relations between PTSD status and lax (but not overreactive) parenting behaviors. Compared to mothers without PTSD, those with PTSD reported greater lax parenting behaviors indirectly through greater emotion dysregulation. Mothers with PTSD may struggle to parent assertively when trauma symptoms interfere with emotion regulation abilities. The current study highlights the need to design interventions focused on helping trauma-exposed mothers manage distress, ultimately aiming to enhance parenting effectiveness and improve child outcomes

Santo subito? Popes as “New Saints” in the Age of Eleventh-Century Reform

Although some popes already enjoyed saint-like veneration, papal sanctity significantly increased during the ecclesiastical reform in the eleventh century. After all, it was Pope Gregory VII (1073-1085) – one of the main protagonists of the reform – who stated in his Dictatus papae that «The Bishop of Rome, if he has been ordained according to canon law, is undoubtedly made a saint through the merits of blessed Peter […]». These ideas draw attention to general strategies of representation, especially regarding the cult of Early Christian popes (such as Clement I). The increasing worship they enjoyed can be noticed not least in contemporary pictorial programmes. The paper deals with the propagation of early popes as “new saints” and seeks to identify the driving forces behind their dissemination. Analysing monumental art such as the Enthronement scene in the Lower Church of San Clemente and the (lost) apse decoration of the Oratory of St Nicholas in Lateran Palace, it also reflects upon the intentions behind these specific commissions and the (re-)establishment of papal cults in Rome. Sebbene alcuni papi godessero già di una venerazione simile a quella di un santo, il riconoscimento della “santità papale” aumentò significativamente nel secolo XI, durante i tempi della riforma ecclesiastica. Papa Gregorio VII (1073-1085), protagonista principale della riforma, affermò infatti nel suo Dictatus papae che «Il vescovo di Roma, se è stato ordinato secondo la legge canonica, è senza dubbio di fatto un santo per i meriti del beato Pietro […]». Queste idee innescano strategie generali di rappresentazione, in particolare per quanto riguarda il culto dei papi paleocristiani (come Clemente I). La venerazione crescente di cui essi sono oggetto può essere notata anche nei programmi pittorici del tempo. L’articolo analizza la diffusione del culto dei papi come “nuovi santi”, cercando di identificare anche le forze motrici di questo fenomeno. Analizzando opere d’arte come l’Intronizzazione di Papa Clemente nella chiesa inferiore di San Clemente e la decorazione perduta dell’abside dell’oratorio di San Nicola nel Palazzo Laterano, l’autore si interroga anche sulle intenzioni che stanno alla base di queste specifiche commissioni e quindi sulla “ri-fondazione” dei culti papali a Roma