Biological order provided by α-helical secondary protein structures is an important resource exploitable by living organisms for increasing the efficiency of energy transport. In particular, self-trapping of amide I energy quanta by the induced phonon deformation of the hydrogen-bonded lattice of peptide groups is capable of generating either pinned or moving solitary waves following the Davydov quasiparticle/soliton model. The effect of applied in-phase Gaussian pulses of amide I energy, however, was found to be strongly dependent on the site of (...) application. Moving solitons were only launched when the amide I energy was applied at one of the α-helix ends, whereas pinned solitons were produced in the α-helix interior. In this paper, we describe a general mechanism that launches moving solitons in the interior of the α-helix through phase-modulated Gaussian pulses of amide I energy. We also compare the predicted soliton velocity based on effective soliton mass and the observed soliton velocity in computer simulations for different parameter values of the isotropy of the exciton-phonon interaction. The presented results demonstrate the capacity for explicit control of soliton velocity in protein α-helices, and further support the plausibility of gradual optimization of quantum dynamics for achieving specialized protein functions through natural selection. (shrink)

The essential biological processes that sustain life are catalyzed by protein nano-engines, which maintain living systems in far-from-equilibrium ordered states. To investigate energetic processes in proteins, we have analyzed the system of generalized Davydov equations that govern the quantum dynamics of multiple amide I exciton quanta propagating along the hydrogen-bonded peptide groups in α-helices. Computational simulations have confirmed the generation of moving Davydov solitons by applied pulses of amide I energy for protein α-helices of varying length. The stability (...) and mobility of these solitons depended on the uniformity of dipole-dipole coupling between amide I oscillators, and the isotropy of the exciton-phonon interaction. Davydov solitons were also able to quantum tunnel through massive barriers, or to quantum interfere at collision sites. The results presented here support a nontrivial role of quantum effects in biological systems that lies beyond the mechanistic support of covalent bonds as binding agents of macromolecular structures. Quantum tunneling and interference of Davydov solitons provide catalytically active macromolecular protein complexes with a physical mechanism allowing highly efficient transport, delivery, and utilization of free energy, besides the evolutionary mandate of biological order that supports the existence of such genuine quantum phenomena, and may indeed demarcate the quantum boundaries of life. (shrink)

Applying mild methods of preparation, part of the ribosomes of rabbit reticulocytes are found in aggregates (later called polyribosomes) of up to six ribosomal units. Upon treatment with RNA-ase, they desintegrate into single ribosomes. The fast-sedimenting aggregates are found to be more active in protein synthesis in terms of incorporation of radioactive amino acids, whereas the single ribosomes are more receptive to stimulation by the artificial messenger RNA poly-U. The findings indicate that the linkage of ribosomes into aggregates is (...) due to the messenger RNA. They support a tape-reading mechanism of protein synthesis whereby growth of the peptide chain is accompanied by shifting the active site of the ribosome from one coding group of nucleotides of the messenger RNA to the next. (shrink)

Macromolecular protein complexes catalyze essential physiological processes that sustain life. Various interactions between protein subunits could increase the effective mass of certain peptide groups, thereby compartmentalizing protein α-helices. Here, we study the differential effects of applied massive barriers upon the soliton-assisted energy transport within proteins. We demonstrate that excentric barriers, localized onto a single spine in the protein α-helix, reflect or trap three-spine solitons as effectively as concentric barriers with comparable total mass. Furthermore, wider protein (...) solitons, whose energy is lower, require heavier massive barriers for soliton reflection or trapping. Regulation of energy transport, delivery and utilization at protein active sites could thus be achieved through control of the soliton width, or of the effective mass of the protein subunits. (shrink)

Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid (...) class='Hi'>sites shared by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

This article presents a newly discovered votive inscription found during the course of the 2013 survey conducted at the ancient city of Phaselis and in its territory. The inscription was found where the stairs to the acropolis from the southwest of the theatre end, in front of the west wall of the tower structure give access to the acropolis. This inscription in the Doric dialect, on a limestone block measuring 0.315 x 0.77 x 0.61 m., records a dedication to Athena (...) Polias. The letters 0.03 m. high, exhibit Late Archaic - Early Classical Period features ( - - - - ) and, consequently the inscription can be dated to the Vth century B.C. -/- Phaselis and its Chief Goddess Athena Polias From the earliest times of Athena worship, especially in the Aegean Islands and Hellas, this goddess was the protectress of cities, institutions and mythological heroes and she manifested this function in various ways. In one of the earliest recorded examples she carries the epithet ἐρυσίπτολις (guardian of the cities), and in another example, in a Linear B inscription discovered in the Palace of Knossos on Crete as Atana Potnia (a-ta-na-po-ti-ni-ja), the mistress of the palace. But perhaps the most striking myth relating to this role of Athena is undoubtedly that of the Palladion statue, the reason for the fall of Troy and for defeat in the Trojan War. In this context, Troy could resist the Achaeans for as long as it was protected by the Palladion, but after it was stolen by Odysseus and Diomedes, the city was captured by the Achaeans. Subsequently, Athens, Argos and Sparta, the most powerful Greek cities, as later the city of Rome, in order to obtain Athena’s protection and so to gain legitimization for the expansion of their empires, invented their own myths claiming that the Palladion statue from Troy was brought to their cities. In another myth the Goddess became the protectress of Tegea through giving Medusa’s hair as a protective image to a hero of the city. Athena’s frequently used epithets, Polias (Πολιάς), Poliouchos (Πολιοῦχος), and the epithet the protectress of the Athenians (Ἀθηνᾶ Ἀθηνῶν μεδέουσα), employed as a means of religious propaganda by the city of Athens when it established the Delian League which subsequently evolved into an empire, clearly indicate Athena was regarded as guardian of the cities. Particularly during the Archaic and Classical Periods, it was this aspect of Athena that, politically placed the Goddess amongst the most important of deities with Zeus and Apollo, and she is most commonly found with the epithet Polias. The epithet Polias or similar, refers in particular to the heart of these cities, to their acropoleis, where Athena Polias was usually worshipped. Her temples located on the heights of the cities made her role particularly visible as the main protecting goddess. One of the best examples of this “visibility”concerns the earliest record of the epithet Polias as, although she wasn’t the chief deity of Argos, within the sanctuary of Athena Polias located on Larisa hill an inscription was found which supplies us with the text of a cult regulation which is datable to the VIth century. B.C.. The Anatolian goddess of Malija, equal to Athena (in Lycia), was attested in Hittite texts from IInd millennium B.C.. This goddess worshipped in Lycia, close to the city of Phaselis, is similarly in a relationship with cities and acropoleis. The Inscribed Pillar of Ksanthos dating from the Vth century B.C. records that many acropoleis were seized with the help of Athena ptoliporthos (πτολίπορθος) “Sacker of Cities”. In the same inscription the city of Patara was named together with Malija and it may refer to the Patara of Malija as in the example of the Lindian Athena (Lindos, city of Athena). Moreover, the goddess Malija was named with the epithet Wedrẽñni (regional, municipal) the equivalent of the epithet Polias in Rhodiapolis. During the great colonization movements (750-550 B.C.) the colonists brought the cult of Athena Polias to many Mediterranean cities, as was the case for example for Lindos on the island of Rhodos. As a matter of fact the strongest ties between Lindos and the colonies which Rhodes founded was the cult of Athena. In consequence, these cities offered precious gifts to the Temple of Athena in Lindos as a demonstration of both their veneration of the goddess and of loyalty. According to myth, the city of Phaselis was colonized in 691/690 B.C. by a group under the leadership of Lakios from Lindos and the Athena cult of the mother city was brought to Phaselis. Thereafter the Phaselitai dedicated the helmets and sickles to Athena Lindia upon which was inscribed, “Having taken them from the Solymoi, the Phaselitai offered them to Athena Lindia, when Lakios was the leader of the colonists”. In addition to this, the other evidence concerning the presence of Athena in the city confirms that this deity was the chief goddess of Phaselis. During the Classical, and especially in the Hellenistic Period, depictions of Athena’s owl, of her Palladion and of Athena Promachos are found. As mentioned above, the epithet Polias usually draws attention to a city’s acropolis with the temple of Athena Polias located there. In the case of Phaselis, the find spot of these votive inscriptions, reused in a wall of a tower that was built in defense of the acropolis, provides an additional indication for the localization of Athena’s temple to the acropolis. This temple most probably was on the acropolis where there are the ruins of a columned building and large ashlar blocks possibly indicating the site of a temple; however, due to the dense vegetation and in the absence of excavations, at present this localisation cannot be stated with certainty. Another reference indicating that Athena Polias was the chief deity of the city was the presence of a holy relic in the Temple of Athena, the spear of the hero of the Trojan War Achilles. During his campaign against the Persians, Alexander the Great stayed in Phaselis in the winter of 334/333 B.C. and he left Achilles’ spear in the Temple of Athena at Phaselis. During the Hellenistic Period, Hellenistic Kings were mentioned with the chief deities of the Archaic and Classical periods as were the emperors in Roman Imperial Period. And according with this practice, the boule and demos of Phaselis worshipped Athena Polias together with the deified emperors, known from an honorific inscription for a certain Ptolemaios. Evidence from the Late Roman Period, especially from the IIIrd century A.D., records the Palladeios agons (ἀγὼν Παλλάδειος) were held in the city in honour of the Goddess Athena. Consequently, philological, epigraphic as well as numismatic evidence shows the Goddess Athena was the chief deity of the city of Phaselis from the Archaic Period into the Late Roman Period. As the epithet Polias on this votive inscription indicates, the goddess had a temple which should be located on the acropolis where the holy relic (Achilles’ spear) was kept and where the officials of the goddess conducted their functions. This new votive inscription provides record of the role Athena occupied in this early post-colonisation period of the city’s political and socio-cultural history. Further, it is also a physical document dating from the city’s Late Archaic-Early Classical Period, aiding in the evaluation of both Phaselis and of the wider region’s history of settlement. (shrink)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

This paper describes one style of functional analysis commonly used in the neurosciences called task-bound functional analysis. The concept of function invoked by this style of analysis is distinctive in virtue of the dependence relations it bears to transient environmental properties. It is argued that task-bound functional analysis cannot explain the presence of structural properties in nervous systems. An alternative concept of neural function is introduced that draws on the theoretical neuroscience literature, and an argument is given to show that (...) this alternative concept of may help to overcome the explanatory limitations of task-bound functional analysis. (shrink)

In this paper I argue for the following two related claims. First, the science of phoronomy from Kant's Metaphysical Foundations of Natural Science is grounded in the duplication of space. Second, this duplication is made possible through the self-localization of the subject, as Kant shows in the "Gegnden-Schrift". The thesis of this paper is that the self-localization transforms space into an object that can be cinematically moved and that this action sets the ground for a science of phoronomy, (...) which presupposes the existence of at least two spaces. In the end, the other endpoint of the Kantian determination of space is discussed, namely space understood as an idea of reason. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to (...) enhance accessibility to results of protein research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides (...) a framework for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and (...) modified forms. Because proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

It is widely understood that protein functions can be exhaustively described in terms of no single parameter, whether this be amino acid sequence or the three-dimensional structure of the underlying protein molecule. This means that a number of different attributes must be used to create an ontology of protein functions. Certainly much of the required information is already stored in databases such as Swiss-Prot, Protein Data Bank, SCOP and MIPS. But the latter have been developed for (...) different purposes and the separate data-structures which they employ are not conducive to the needed data integration. When we attempt to classify the entities in the domain of proteins, we find ourselves faced with a number of cross-cutting principles of classification. Our question here is: how can we bring together these separate taxonomies in order to describe protein functions? Our proposed answer is: via a careful top-level ontological analysis of the relevant principles of classification, combined with a new framework for the simultaneous manipulation of classifications constructed for different purposes. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (...) (GO). PRO relates to UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

In the late 19th century, physiologists such as David Ferrier, Eduard Hitzig, and Hermann Munk argued that cerebral brain functions are localized in discrete structures. By the early 20th century, this became the dominant position. However, another prominent physiologist, Friedrich Goltz, rejected theories of cerebral localization and argued against these physiologists until his death in 1902. I argue in this paper that previous historical accounts have failed to comprehend why Goltz rejected cerebral localization. I show that Goltz adhered (...) to a falsificationist methodology, and I reconstruct how he designed his experiments and weighted different kinds of evidence. I then draw on the exploratory experimentation literature from recent philosophy of science to trace one root of the debate to differences in how the German localizers designed their experiments and reasoned about evidence. While Goltz designed his experiments to test hypotheses about the functions of predetermined cerebral structures, the localizers explored new functions and structures in the process of constructing new theories. I argue that the localizers relied on untested background conjectures to justify their inferences about functional organization. These background conjectures collapsed a distinction between phenomena they produced direct evidence for (localized symptoms) and what they reached conclusions about (localized functions). (shrink)

What are the relationships between an entity and the space at which it is located? And between a region of space and the events that take place there? What is the metaphysical structure of localization? What its modal status? This paper addresses some of these questions in an attempt to work out at least the main coordinates of the logical structure of localization. Our task is mostly taxonomic. But we also highlight some of the underlying structural features and (...) we single out the interactions between the notion of localization and nearby notions, such as the notions of part and whole, or of necessity and possibility. A theory of localization—we argue—is needed in order to account for the basic relations between objects and space, and runs afoul a pure part-whole theory. We also provide an axiomatization of the relation of localization and examine cases of localization involving entities different from material objects. (shrink)

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD (...) as a post-translational modification reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a (...) class='Hi'>PRotein Ontology (PRO) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

To discover affects within Husserl’s texts designates a difficult investigation; it points to a theme of which these texts were forced to speak, even as they were explicitly speaking of regional ontologies and the foundations of sciences. For we may at first wonder: where can affection find a positive role in the rigor of a pure philosophy that seeks to account for its phenomena from within the immanence of consciousness? Does this not mean that the very passivity and foreignness of (...) affect will be overlooked; will it not be continually linked to a Vorstellung that issues as a ray of the pure ego? That is, will the phenomenological account of affect be reduced to the cognition of an object, as Emmanuel Levinas suggests? Yet there are affects in Husserl’s texts that maintain their autonomy and resist subsumption to an objectivating intentionality.We may see this in the Lectures On the Phenomenology of the Consciousness of Internal Time: in the longitudinal intentionality of retention, through which consciousness becomes aware of its elapsed phases without making them into objects—a passive synthesis that gives the flow of time-constituting consciousness the form of a continually deferred auto-affection.1We find it again as early as the fifth Logical Investigation, 2 providing us with the impetus to radicalize Husserlian phenomenology. (shrink)

The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data (...) set has allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (shrink)

In the beginning of the 20th century the groundbreaking work of Ramon y Cajal firmly established the neuron doctrine, according to which neurons are the basic structural and functional units of the nervous system. Von Weldeyer coined the term “neuron” in 1891, but the huge leap forward in neuroscience was due to Cajal’s meticulous microscopic observations of brain sections stained with an improved version of Golgi’s la reazione nera (black reaction). The latter improvement of Golgi’s technique made it possible to (...) visualize the arborizations of single neurons that were “colored brownish black even to their finest branchlets, standing out with unsurpassable clarity upon a transparent yellow background. All was sharp as a sketch with Chinese ink”. The high quality of both the visualization of individual nerve cells and the work performed on studying the anatomy of the central nervous system lead Ramon y Cajal to the conclusion that axons output the nervous impulses to the dendrites or the soma of other target neurons. (shrink)

Mitchell & Gronenborn propose that we account for the presence of multiple models of protein structure, each produced in different contexts, through the framework of integrative pluralism. I argue that two interpretations of this framework are available, neither of which captures the relationship between a model and the protein structure it represents or between multiple models of protein structure. Further, it inclines us toward concluding prematurely that models of protein structure are right in their contexts and (...) makes extrapolation of findings from one context to another seem unwarranted. Instead, protein structure determination ought to be understood as modestly monistic. There is one model for every protein in each physicochemical context, and models of the same protein produced in different contexts are compatible with one another. ‘Integrating’ multiple models amounts to extrapolating from one context to another; this is possible because the effect of context on protein folding is relatively weak and predictable. Modest monism better describes the practice of protein structure determination than integrative pluralism and enables greater attention to how context affects protein folding. (shrink)

Several contemporary architects have designed architectural objects that are closely linked to their particular sites. An in-depth study of the relevant relationship holding between those objects and their sites is, however, missing. This paper addresses the issue, arguing that those architectural objects are akin to works of site-specific art. In section (1), I introduce the topic of the paper. In section (2), I critically analyse the debate on the categorisation of artworks as site-specific. In section (3), I apply (...) to architecture the lesson learned from the analysis of the art debate. (shrink)

Biochemical kinds such as proteins pose interesting problems for philosophers of science, as they can be studied from the points of view of both biology and chemistry. The relationship between the biological functions of biochemical kinds and the microstructures that they are related to is the key question. This leads us to a more general discussion about ontological reductionism, microstructuralism, and multiple realization at the biology-chemistry interface. On the face of it, biochemical kinds seem to pose a challenge for ontological (...) reductionism and hence motivate a dual theory of chemical and biological kinds, a type of pluralism about natural kinds. But it will be argued that the challenge, which is based on multiple realization, can be addressed. The upshot is that there are reasonable prospects for ontological reductionism about biochemical kinds, which corroborates natural kind monism. (shrink)

This research explores the effects of globalization to the Malaysian architectural practice in the current situation. The research explores three issues, firstly what are the reasons local architects are taking projects locally (localization) only, and, secondly, what are the factors which motivate local architects to venture into international projects (termed as globalization). It also explores, thirdly, what are the factors which influence foreign architects coming to Malaysia to practice. Research was qualitative in nature using semi-structured interviews. The interviews were (...) transcribed and a thematic analysis was carried out. An online survey was conducted towards the end to a different group from the architecture fraternity to supplement the research and findings. Overall, the reasons uncovered for the first issue are the total lack of opportunities and insufficient capacity due to small practices. Reasons for the second issue are due to the more lucrative fees and the experience and technology transfer which are advancements to their practices. For the third issue, the factors were found to more personal reasons based rather than solely applying to practice. In summary, to go global or stay local is actually up to the individual preference of the architect and also the capacity of their practices. The findings can be used as a resource for architects and architectural students who are still deciding whether to globalize or localize their careers. As it currently the case, many architects are practicing in other countries to replicate architectural styles which may be more conducive to sustainable tourism, for example, hotel designs. (shrink)

The short paper introduces the concept of possible branches of double-stranded DNA (later sometimes called palindromes): Certain sequences of nucleotides may be followed, after a short unpaired stretch, by a complementary sequence in reversed order, such that each DNA strand can fold back on itself, and the DNA assumes a cruciform or tree-like structure. This is postulated to interact with regulatory proteins. -/- .

This paper examines G. W. F. Hegel’s interpretation of Plato from his Lectures on the History of Philosophy, situating his interpretation historically and noting features that resonate with contemporary Plato scholarship. Hegel forms his interpretation prior to stylometric studies of the dialogues, and distinguishes his Plato from Wilhelm Gottlieb Tennemann and Friedrich Daniel Ernst Schleiermacher’s views. Hegel responds to important interpretive concerns: 1) the relationship between Socratic and Platonic thought, 2) the dialogue form, 3) Platonic Anonymity and 4) Platonic myth. (...) His treatment of these issues is illustrative with respect to understanding Hegelian philosophy and the history of Plato interpretation. (shrink)

The aim of this article is to examine Edmund Husserl’s theory of aesthetic consciousness and the possibility to apply it to site-specific art. The central focus will be on the idea of the limited synthetic unity of the aesthetic object that is introduced by Husserl in order to differentiate positional and aesthetic attitude towards the object. I claim that strongly site-specific art, which is a work of art about a place and in the place, challenges the view that the synthetic (...) unity of the aesthetic object is limited. Moreover, following Husserl’s theory, it becomes questionable whether strongly site-specific art is art at all. I try to answer these objections by explaining how the artist prescribes the appearances and boundaries of a strongly site-specific object of art, thereby satisfying the demand for the limitedness of the synthetic unity of the aesthetic object. (shrink)

This paper is a study about Philadelphia’s comprehensive user engagement sites (CUESs) as the authors address and examine issues related to the upcoming implementation of a CUES while seeking solutions for its disputed questions and plans. Beginning with the federal drug schedules, the authors visit some of the medical and public health issues vis-à-vis safe injection facilities (SIFs). Insite, a successful Canadian SIF, has been thoroughly researched as it represents a paradigm for which a Philadelphia CUES can expand upon. (...) Also, the existing criticisms against SIFs are revisited while critically unpackaged and responded to in favor of the establishment. In the main section, the authors propose the layout and services of the upcoming CUES, much of which would be in congruent to Vancouver’s Insite. On the other hand, the CUES would be distinct from Insite, as the authors emphasize, in that it will offer an information center run by individuals in recovery and place additional emphasis on early education for young healthcare professionals by providing them a platform to work at the site. The paper will also briefly investigate the implementation of a CUES site under an ethical scope of the Harm Reduction Theory. Lastly, the authors recommend some strategic plans that the Philadelphia City government may consider employing at this crucial stage. (shrink)

Abstract: Sickle cell disease (SCD) comprises an inherited blood disorder that is life long and affects many people globally. Despite progress in therapy, SCA is a considerable cause of mortality and morbidity. This study was designed to measure the immunological and inflammatory parameters of patients with sickle cell disease (SCD) and to found if there is any role of it in the pathogenicity of the disease. This study included A total of 32 patients, their ages ranged from 16 to 55 (...) years patients with Sickle cell disease who have been evaluated during vaso occlusive crisis and had been followed up till they attained steady state, and there are 32 normal control subjects matched with patients in age and sex. In general there was elevation in all parameters the study were included in patients than control and particularly in crisis, despite the IgM value which was insignificantly decrease, but the statically significant elevation reported only in CRP, IgG, IgA. (shrink)

Protein α-helices provide an ordered biological environment that is conducive to soliton-assisted energy transport. The nonlinear interaction between amide I excitons and phonon deformations induced in the hydrogen-bonded lattice of peptide groups leads to self-trapping of the amide I energy, thereby creating a localized quasiparticle (soliton) that persists at zero temperature. The presence of thermal noise, however, could destabilize the protein soliton and dissipate its energy within a finite lifetime. In this work, we have computationally solved the system (...) of stochastic differential equations that govern the quantum dynamics of protein solitons at physiological temperature, T=310 K, for either a single isolated α-helix spine of hydrogen bonded peptide groups or the full protein α-helix comprised of three parallel α-helix spines. The simulated stochastic dynamics revealed that although the thermal noise is detrimental for the single isolated α-helix spine, the cooperative action of three amide I exciton quanta in the full protein α-helix ensures soliton lifetime of over 30 ps, during which the amide I energy could be transported along the entire extent of an 18-nm-long α-helix. Thus, macromolecular protein complexes, which are built up of protein α-helices could harness soliton-assisted energy transport at physiological temperature. Because the hydrolysis of a single adenosine triphosphate molecule is able to initiate three amide I exciton quanta, it is feasible that multiquantal protein solitons subserve a variety of specialized physiological functions in living systems. (shrink)

This article explores the norms that govern regular users’ acts of sharing content on social networking sites. Many debates on how to counteract misinformation on Social Networking Sites focus on the epistemic norms of testimony, implicitly assuming that the users’ acts of sharing should fall under the same norms as those for posting original content. I challenge this assumption by proposing a non-epistemic interpretation of (mis) information sharing on social networking sites which I construe as infrastructures for (...) forms of life found online. Misinformation sharing belongs more in the realm of rumour spreading and gossiping rather than in the information-giving language games. However, the norms for sharing cannot be fixed in advance, as these emerge at the interaction between the platforms’ explicit rules, local norms established by user practices, and a meta-norm of sociality. This unpredictability does not leave us with a normative void as an important user responsibility still remains, namely that of making the context of the sharing gesture explicit. If users will clarify how their gestures of sharing are meant to be interpreted by others, they will implicitly assume responsibility for possible misunderstandings based on omissions, and the harms of shared misinformation can be diminished. (shrink)

Within siting literature there is strong agreement that compensation for environmental risks is a necessary condition for local acceptance of waste treatment facilities. In-kind compensation is commonly pushed forward as being more effective than financial benefits in reducing local opposition. By forcusing on the siting of a sanitary landfill in Santiago, Chile, this paper explores the performance of both types of compensation and relates the analysis to the notion of social norms of exchange. These are understood as being based on (...) three main types of social relations: care, justice and freedom. Whereas monetary compensation is associated with market relations based on freedom and the offer of in-kind compensation to egalitarian relations based on justice, the absence of compensation is linked to fraternal relations based on care. It is argued that in-kind compensation is more acceptable than monetary payments or not compensation because people tend to understand siting conflicts more as matters of justice rather than as matters of freedom or care. (shrink)

During the rapid process of deindustrialization in Iran, the term ‘industrial heritage’ has recently emerged as a new subject into public realm. In order to integrate the methodologies for the protection and adaptive reuse strategies, the ‘industrial heritage’ itself needs to be divided into various categories. UNESCO has begun inscribing increasing numbers of local industrial legacies such as railway, mines, factories, assembly plants, agricultural production and manufacturing production in its World Heritage List. However, in the process of their adaptive reuse (...) the question of heritage meanings arises. Over the past century in Iran, powerful corporate and governmental actors have created a broad range of oil imaginaries that changed over time and in line with local cultures. Starting from 1920s and after the nationalization of oil industry in Iran, oil cities such as Abadan and Masjid Suleiman saw massive expansion to house labors and oil-industry specialists who had arrived from the United States, Europe, India, and the Persian Gulf states. This research aims to clarify how the oil industry, in close collaboration with national governments, has materially shaped the oil cities through oil-specific architecture like company headquarters, gas stations, retail and infrastructure buildings. The current legacy of oil industry continues to reshape the industry, society and politics as well. This research uses a critical and analytical problem-based approach to examine the current policies that build a new image and identity through adaptive reuse strategies to promote sustainable local development in Iran’s industrial heritage. (shrink)

GianCarlo Ghirardi passed away on June 1st, 201. He would have turned 83 on October 28, 2018. He was without any doubt one of the most prominent theoretical physicists working on the foundation and the philosophy of quantum mechanics. In this paper I review some of his achievements and underline how his research influenced the philosophy of physics community.

All over the Internet, many websites operate dealing with collective and personal memory. The sites relevant to collective memory deal with structuring the memory of social groups and they comprise part of “civil religion”. The sites that deal with personal memory memorialize people who have died and whose family members or friends or other members of their community have an interest in preserving their memory. This article offers an analysis of an expanded philosophical discourse that took place over (...) a two-year period with three groups of young people who had experienced loss in their families or their communities and who were partners in writing texts on memorial sites or had established websites as part of coping with the loss. This article seeks to offer a narrative analysis of the philosophical discourse and to contribute to an expansion of the discussion regarding the connection between Philosophy with Children and its methods and the social networks where entire lives involving philosophical dimensions are conducted. (shrink)

A topological model of elementary semiotic schemes is presented. Implications are discussed with respect to the establishment of abstract terms and the search for ultimate meaning.

The construction of railways has been one of the symbols of advanced technology and modernity in various societies and is known as a means of expanding and transferring goods, men, and their ideas. During the political-economic circumstances of the second half of the 19th century, the first rail line of Iran was built under the Qajar rule. This was an 8 km railway to connect Tehran to Rey with some small wagons, most local people tended to call it Mashin-Doodi, which (...) translates as Smokey Machine. The railway then appeared in southwest Iran as a means of transport for the oil industry which was booming after oil discoveries in Khuzestan. The intercity railway started to operate in 1923 and was 57 km long, connecting Masjed-i-Soleyman to Dar-i-Kahzineh. It was established for exploitative purposes of foreign states resulting in a few small-scale and temporary projects, but the idea of constructing and expanding rail lines based on national investments finally materialized with the first national railroad. (shrink)

This study discusses foreign tourists' perceptions of Toraja which is a cultural tourism site in South Sulawesi, Indonesia. Every year, tourists visit Toraja to participate in their yearly rituals of death take time to visit the graves inside the mountain cliffs (in caves) as they feel the rich cultural heritage and have a view of the traditional houses. Data were collected by interviewing these tourists through the use of questionnaires with randomly selected respondents. The results obtained showed that knowledge about (...) Toraja cultural tourism gained by foreign tourists before their visit creates curiosity and willingness to obtain experiences in Toraja ethnic culture. Foreign tourists get to experience Toraja's rich cultural heritage. According to them, Toraja is one of the most unique, special and outstanding tourism centers in the world. The uniqueness of Toraja culture creates greater curiosity among tourists so that they want to have a cultural experience by conducting a tour to Toraja and through direct communication with Toraja people. However, they also stated the importance of some objects other than those previously listed. Tourist objects that are all related to grief such as graves, however, cause some boredom. Some tourists frowned upon the mismanagement of some tourist centers such as the natural agrotourism center which is known to produce the ingredients used in Toraja products and they suggested ways to manage these areas more effectively. (shrink)

The main purpose of this study is to revisit the backgrounds and problems of the colonial-era cemeteries in Tayabas, Quezon, and analyze their potential as local cultural heritage sites. Data for this study was collected through walk surveys and documentation of the intended heritage sites. The findings of the study indicated the rich historical background as well as the existence of potential heritage structures in the cemeteries. Finally, it is deemed that these cemeteries and their adjoining colonial-era burial (...) structures must also be regarded as cultural heritage sites alongside churches, bridges, and buildings and called for preserving these cemeteries for future generations to see for themselves. (shrink)

There is increasing appreciation for the role that location plays in the experience of a musical event. This paper seeks to understand this role in terms of our habitual relationships to place, asking whether and how being musical somewhere can expand and transform our habituated comportment there, and with what consequences. This inquiry is anchored in a series of site-specific improvised performances by Jen Reimer and Max Stein, and the theory and practice of the late experimental music pioneer Pauline Oliveros. (...) The argument made interpreting these performances is grounded in Maurice Merleau-Ponty’s phenomenology of embodiment, and Alia Al-Saji’s reception of it. This paper claims that such site-specific improvised performances can elicit a sort of hesitation in our everyday style of sensory-motor conditioning, and, concomitantly, awaken a layer of sensory living amenable to radically new sonic and behavioural configurations. (shrink)

Industrial heritage has become a very matter of debate among experts as the most significant reminder of the industrial era, it also is of great examples of 20th-century heritage. Nowadays, industrial heritage sites are suffering from intense physical conditions and are being intruded by massive economic projects since they are located in favorable places of towns and possess vast spaces. Conservation methods have mostly been limited to the surroundings of industrial heritage sites and have not considered the extended (...) areas connected to the site. The resolutions should be sought throughout these questions: How do outstanding values of an industrial heritage site affect its buffer zone mapping? Or what should a buffer zone map encompass to protect specific values of an industrial heritage site? During this research ample of evidence is seen which firstly depicts the appreciation of industrial heritage and the tendency to conserve them among the host countries. The main result concluded is a guideline based on the similarities and differences between various types of industrial heritage and their impacts on determining boundaries and zones. In case of increasing the number of case studies, the results of this paper can aid in charge organizations to take more effective measure in developing plans to determine boundaries and zones for different types of industrial heritage sites. The data gathered for this paper was collected through library resources about industrial heritage and basically from academic and universal management manuals of buffer zones. The information chiefly is adopted from registration files received by the world heritage committee of UNESCO. The method of this research is case study research and the method for analysis is descriptive-analytical. (shrink)

The role of the cultural assets as one of the pillars of sustainable development is undeniably of great significance in the cultural sustainability of cities. Indeed, the way users understand and interpret cultural heritage sites would be highly critical to managing cultural organizations properly. It means by improving users’ perception of these sites, it can expect a fair distribution of comprehensive awareness among generations about the values of cultural assets. Past studies in spatial psychology have demonstrated that environmental (...) properties can positively Influence human emotions. On the other hand, using computational–mathematical methods used to examine spatio-visual properties have rarely been compared to human perceptions. This paper examines the impact of spatio-visual properties on human perception as a clever cultural management strategy to promote cultural sustainability. It is discussed how environmental features in general, and visibility in particular, can shape the way users interpret cultural heritage. Results indicate that not only visibility of users’ paths within cultural heritage sites can be an influential factor for the development of users’ perception, but also the visibility of the entrance of these complexes can change their understanding. This means that decision-makers, architects, and managers of the cultural organizations can apply these findings as cultural management framework by defining predefined paths in these sites in the way that they possess high visibility and visible entrance. Consequently, the distribution of public awareness among generations can be improved to strengthen the role of cultural aspects in sustainable development. (shrink)

As Derrida showed in a later essay on Foucault’s relationship to psychoanalysis, Foucault displayed a marked ambivalence toward Freud, sometimes putting him on the side of the exclusion of madness and sometimes putting him on the side of those eager to listen to it. Yet, in the final stages of Foucault’s work, this ambivalence hardened into a resistance. By the time of The History of Sexuality, Volume 1, Freud is situated squarely on the side of power. It is precisely in (...) leaving Freud behind, Foucault suggests in Volume 1’s final pages, that we might begin to imagine “a different economy of bodies and pleasures”. In the late Foucault, what is necessary is thus not a reinvigorated... (shrink)

Interest in just war theory has boomed in recent years, as a revisionist school of thought has challenged the orthodoxy of international law, most famously defended by Michael Walzer [1977]. These revisionist critics have targeted the two central principles governing the conduct of war (jus in bello): combatant equality and noncombatant immunity. The first states that combatants face the same permissions and constraints whether their cause is just or unjust. The second protects noncombatants from intentional attack. In response to these (...) critics, some philosophers have defended aspects of the old orthodoxy on novel grounds. Revisionists counter. As things stand, the prospects for progress are remote. In this paper, we offer a way forward. We argue that exclusive focus on first-order moral principles, such as combatant equality and noncombatant immunity, has led revisionist and orthodox just war theorists to engage in “proxy battles.” Their first-order moral disagreements are at least partly traceable to second-order disagreements about the nature and purpose of political theory. These deeper disputes have been central to the broader discipline of political theory for several years; we hope that bringing them to bear on the ethics of war will help us move beyond the present impasse. (shrink)