Molecular cloning and expression of a Toll receptor gene homologue from Zhikong Scallop, Chlamys farreri

Toll-like receptors (TLRs) are an ancient family of pattern recognition receptors, which show homology with the Drosophila Toll protein and play key roles in detecting various non-self substances and then initiating and activating immune system. In this report, the full length of the first bivalve TLR (named as CfToll-1) is presented. CfToll-1 was originally identified as an EST (expressed sequence tag) fragment from a cDNA library of Zhikong scallop (Chlamys farreri). Its complete sequence was obtained by the construction of Genome Walker library and 5' RACE (rapid amplification of cDNA end) techniques. The full length cDNA of CfToll-1 consisted of 4308 nucleotides with a polyA tail, encoding a putative protein of 1198 amino acids with a 5' UTR (untranslated region) of 211 bp and a 3'UTR of 500 bp. The predicted amino acid sequence comprised an extracellular domain with a potential signal peptide, nineteen leucine-rich repeats (LRR), two LRR-C-terminal (LRRCT) motifs, and a LRR-N-terminal (LRRNT), followed by a transmembrane segment of 20 amino acids, and a cytoplasmic region of 138 amino acids containing the Toll/IL-1R domain (TIR). The deduced amino acid sequence of CfToll-1 was homologous to Drosophila melanogaster Tolls (DmTolls) with 23-35% similarity in the full length amino acids sequence and 30-54% in the TIR domain. Phylogenetic analysis of CfToll-1 with other known TLRs revealed that CfToll-1 was closely related to DmTolls. An analysis of the tissue-specific expression of the CfToll-1 gene by Real-time PCR showed that the transcripts were constitutively expressed in tissues of haemocyte, muscle, mantle, heart, gonad and gill. The temporal expressions of CfToll-1 in the mixed primary cultured haemocytes were observed after the haemocytes were treated with 1 mu g ml(-1) and 100 ng ml(-1) lipopolysaccharide (LPS), respectively. The expression of CfToll-1 was up-regulated and increased about 2-fold at 6 h with the treatment of 1 mu g ml(-1) LPS. The expression of CfToll-1 was down-regulated with the treatment of 100 ng ml(-1) LPS. The results indicated that the expression of CfToll-1 could be regulated by LPS, and this regulation was dose-dependent. (c) 2006 Elsevier Ltd. All rights reserved.

An Empirical Study of the Use of Relevance Information in Inductive Logic Programming

Srinivasan, A., King, R. D. and Bain, M.E. (2003) An Empirical Study of the Use of Relevance Information in Inductive Logic Programming. Journal of Machine Learning Research. 4(Jul):369-383

A Type System For Safe SN Resource Allocation

snBench is a platform on which novice users compose and deploy distributed Sense and Respond programs for simultaneous execution on a shared, distributed infrastructure. It is a natural imperative that we have the ability to (1) verify the safety/correctness of newly submitted tasks and (2) derive the resource requirements for these tasks such that correct allocation may occur. To achieve these goals we have established a multi-dimensional sized type system for our functional-style Domain Specific Language (DSL) called Sensor Task Execution Plan (STEP). In such a type system data types are annotated with a vector of size attributes (e.g., upper and lower size bounds). Tracking multiple size aspects proves essential in a system in which Images are manipulated as a first class data type, as image manipulation functions may have specific minimum and/or maximum resolution restrictions on the input they can correctly process. Through static analysis of STEP instances we not only verify basic type safety and establish upper computational resource bounds (i.e., time and space), but we also derive and solve data and resource sizing constraints (e.g., Image resolution, camera capabilities) from the implicit constraints embedded in program instances. In fact, the static methods presented here have benefit beyond their application to Image data, and may be extended to other data types that require tracking multiple dimensions (e.g., image "quality", video frame-rate or aspect ratio, audio sampling rate). In this paper we present the syntax and semantics of our functional language, our type system that builds costs and resource/data constraints, and (through both formalism and specific details of our implementation) provide concrete examples of how the constraints and sizing information are used in practice.

The Sensor Network Workbench: Towards Functional Specification, Verification and Deployment of Constrained Distributed Systems

As the commoditization of sensing, actuation and communication hardware increases, so does the potential for dynamically tasked sense and respond networked systems (i.e., Sensor Networks or SNs) to replace existing disjoint and inflexible special-purpose deployments (closed-circuit security video, anti-theft sensors, etc.). While various solutions have emerged to many individual SN-centric challenges (e.g., power management, communication protocols, role assignment), perhaps the largest remaining obstacle to widespread SN deployment is that those who wish to deploy, utilize, and maintain a programmable Sensor Network lack the programming and systems expertise to do so. The contributions of this thesis centers on the design, development and deployment of the SN Workbench (snBench). snBench embodies an accessible, modular programming platform coupled with a flexible and extensible run-time system that, together, support the entire life-cycle of distributed sensory services. As it is impossible to find a one-size-fits-all programming interface, this work advocates the use of tiered layers of abstraction that enable a variety of high-level, domain specific languages to be compiled to a common (thin-waist) tasking language; this common tasking language is statically verified and can be subsequently re-translated, if needed, for execution on a wide variety of hardware platforms. snBench provides: (1) a common sensory tasking language (Instruction Set Architecture) powerful enough to express complex SN services, yet simple enough to be executed by highly constrained resources with soft, real-time constraints, (2) a prototype high-level language (and corresponding compiler) to illustrate the utility of the common tasking language and the tiered programming approach in this domain, (3) an execution environment and a run-time support infrastructure that abstract a collection of heterogeneous resources into a single virtual Sensor Network, tasked via this common tasking language, and (4) novel formal methods (i.e., static analysis techniques) that verify safety properties and infer implicit resource constraints to facilitate resource allocation for new services. This thesis presents these components in detail, as well as two specific case-studies: the use of snBench to integrate physical and wireless network security, and the use of snBench as the foundation for semester-long student projects in a graduate-level Software Engineering course.

Safe Compositional Network Sketches: Tool & Use Cases

NetSketch is a tool that enables the specification of network-flow applications and the certification of desirable safety properties imposed thereon. NetSketch is conceived to assist system integrators in two types of activities: modeling and design. As a modeling tool, it enables the abstraction of an existing system so as to retain sufficient enough details to enable future analysis of safety properties. As a design tool, NetSketch enables the exploration of alternative safe designs as well as the identification of minimal requirements for outsourced subsystems. NetSketch embodies a lightweight formal verification philosophy, whereby the power (but not the heavy machinery) of a rigorous formalism is made accessible to users via a friendly interface. NetSketch does so by exposing tradeoffs between exactness of analysis and scalability, and by combining traditional whole-system analysis with a more flexible compositional analysis approach based on a strongly-typed, Domain-Specific Language (DSL) to specify network configurations at various levels of sketchiness along with invariants that need to be enforced thereupon. In this paper, we overview NetSketch, highlight its salient features, and illustrate how it could be used in applications, including the management/shaping of traffic flows in a vehicular network (as a proxy for CPS applications) and in a streaming media network (as a proxy for Internet applications). In a companion paper, we define the formal system underlying the operation of NetSketch, in particular the DSL behind NetSketch's user-interface when used in "sketch mode", and prove its soundness relative to appropriately-defined notions of validity.

Safe Compositional Network Sketches: The Formal Framework

NetSketch is a tool for the specification of constrained-flow applications and the certification of desirable safety properties imposed thereon. NetSketch is conceived to assist system integrators in two types of activities: modeling and design. As a modeling tool, it enables the abstraction of an existing system while retaining sufficient information about it to carry out future analysis of safety properties. As a design tool, NetSketch enables the exploration of alternative safe designs as well as the identification of minimal requirements for outsourced subsystems. NetSketch embodies a lightweight formal verification philosophy, whereby the power (but not the heavy machinery) of a rigorous formalism is made accessible to users via a friendly interface. NetSketch does so by exposing tradeoffs between exactness of analysis and scalability, and by combining traditional whole-system analysis with a more flexible compositional analysis. The compositional analysis is based on a strongly-typed Domain-Specific Language (DSL) for describing and reasoning about constrained-flow networks at various levels of sketchiness along with invariants that need to be enforced thereupon. In this paper, we define the formal system underlying the operation of NetSketch, in particular the DSL behind NetSketch's user-interface when used in "sketch mode", and prove its soundness relative to appropriately-defined notions of validity. In a companion paper [6], we overview NetSketch, highlight its salient features, and illustrate how it could be used in two applications: the management/shaping of traffic flows in a vehicular network (as a proxy for CPS applications) and in a streaming media network (as a proxy for Internet applications).

Verification with Natural Contexts: Soundness of Safe Compositional Network Sketches

In research areas involving mathematical rigor, there are numerous benefits to adopting a formal representation of models and arguments: reusability, automatic evaluation of examples, and verification of consistency and correctness. However, accessibility has not been a priority in the design of formal verification tools that can provide these benefits. In earlier work [30] we attempt to address this broad problem by proposing several specific design criteria organized around the notion of a natural context: the sphere of awareness a working human user maintains of the relevant constructs, arguments, experiences, and background materials necessary to accomplish the task at hand. In this report we evaluate our proposed design criteria by utilizing within the context of novel research a formal reasoning system that is designed according to these criteria. In particular, we consider how the design and capabilities of the formal reasoning system that we employ influence, aid, or hinder our ability to accomplish a formal reasoning task – the assembly of a machine-verifiable proof pertaining to the NetSketch formalism. NetSketch is a tool for the specification of constrained-flow applications and the certification of desirable safety properties imposed thereon. NetSketch is conceived to assist system integrators in two types of activities: modeling and design. It provides capabilities for compositional analysis based on a strongly-typed domain-specific language (DSL) for describing and reasoning about constrained-flow networks and invariants that need to be enforced thereupon. In a companion paper [13] we overview NetSketch, highlight its salient features, and illustrate how it could be used in actual applications. In this paper, we define using a machine-readable syntax major parts of the formal system underlying the operation of NetSketch, along with its semantics and a corresponding notion of validity. We then provide a proof of soundness for the formalism that can be partially verified using a lightweight formal reasoning system that simulates natural contexts. A traditional presentation of these definitions and arguments can be found in the full report on the NetSketch formalism [12].

Cross-hemispheric collaboration and segregation associated with task difficulty as revealed by structural and functional connectivity.

Although it is known that brain regions in one hemisphere may interact very closely with their corresponding contralateral regions (collaboration) or operate relatively independent of them (segregation), the specific brain regions (where) and conditions (how) associated with collaboration or segregation are largely unknown. We investigated these issues using a split field-matching task in which participants matched the meaning of words or the visual features of faces presented to the same (unilateral) or to different (bilateral) visual fields. Matching difficulty was manipulated by varying the semantic similarity of words or the visual similarity of faces. We assessed the white matter using the fractional anisotropy (FA) measure provided by diffusion tensor imaging (DTI) and cross-hemispheric communication in terms of fMRI-based connectivity between homotopic pairs of cortical regions. For both perceptual and semantic matching, bilateral trials became faster than unilateral trials as difficulty increased (bilateral processing advantage, BPA). The study yielded three novel findings. First, whereas FA in anterior corpus callosum (genu) correlated with word-matching BPA, FA in posterior corpus callosum (splenium-occipital) correlated with face-matching BPA. Second, as matching difficulty intensified, cross-hemispheric functional connectivity (CFC) increased in domain-general frontopolar cortex (for both word and face matching) but decreased in domain-specific ventral temporal lobe regions (temporal pole for word matching and fusiform gyrus for face matching). Last, a mediation analysis linking DTI and fMRI data showed that CFC mediated the effect of callosal FA on BPA. These findings clarify the mechanisms by which the hemispheres interact to perform complex cognitive tasks.

Periodic FDTD analysis of a 2-D leaky-wave planar antenna based on dipole frequency selective surfaces

A periodic finite-difference time-domain (FDTD) analysis is presented and applied for the first time in the study of a two-dimensional (2-D) leaky-wave planar antenna based on dipole frequency selective surfaces (FSSs). First, the effect of certain aspects of the FDTD modeling in the modal analysis of complex waves is studied in detail. Then, the FDTD model is used for the dispersion analysis of the antenna of interest. The calculated values of the leaky-wave attenuation constants suggest that, for an antenna of this type and moderate length, a significant amount of power reaches the edges of the antenna, and thus diffraction can play an important role. To test the validity of our dispersion analysis, measured radiation patterns of a fabricated prototype are presented and compared with those predicted by a leaky-wave approach based on the periodic FDTD results.

FDTD analysis of close-coupled 418 MHz radiating devices for human biotelemetry

This paper describes the finite-difference time-domain (FDTD) analysis of antenna-body interaction effects occurring when chest-mounted 418 MHz radio transmitters are used for medical telemetry applications. Whole-body software models (homogeneous, layered and tissue-segmented) were developed for an adult male subject. Using an electrically small (300 mm(2)) planar loop antenna, calculated radiation efficiencies ranged between 33.5% and 39.2% for a whole-body model, and between 60.7% and 66.1% for a torso; radiation patterns were found to be largely independent of model composition. The computed radiation efficiency for a 21.5 kg phantom representing a six-year-old female was within 1.1 dB of measured results (actual body mass 28 kg) and well-correlated azimuthal radiation patterns were noted.

Monitoring of lineage-specific chimaerism allows early prediction of response following donor lymphocyte infusions for relapsed chronic myeloid leukaemia

Donor lymphocyte infusions (DLI) have been shown to enhance the graft-versus-leukaemia (GVL) effect and induce haematological and molecular remission in patients with relapsed CML following allogeneic bone marrow transplantation (BMT). The potent donor cell-mediated cytolysis following DLI may lead to a short period of aplasia before the re-establishment of donor haematopoiesis. The absence of detectable donor cells in patients prior to DLI infusion may result in permanent aplasia in certain patients. We report on four patients who relapsed 1, 3, 6.5 and 7 years post-BMT for chronic phase CML and were treated with DLI from their original BMT donor. Polymorphic short tandem repeats (STRs) were used to assess haematological chimaerism both prior to and following DLI. At the time of relapse, STR-PCR indicated the presence of donor cells in all four patients, at levels ranging from 1-40%. A clinical and molecular response was seen in 4/4 patients following a short period of cytopenia and all patients remain in clinical remission with a follow-up of 2 months-3 years post-DLI. STR-PCR indicated that a response was occurring during the period of pancytopenia when metaphase analysis was unsuccessful. Lineage-specific analysis of the cellular response to DLI was monitored using STR-PCR of peripheral blood (PB) and bone marrow (BM) lymphocyte-enriched fractions and CD2-positive and -negative T cell fractions. In one patient BM and PB CD34-positive and -negative fractions were also assessed. A change in the ratio of donor:recipient cells in the PB lymphocyte fraction was the earliest molecular indication of an anti-leukaemic response. Subsequent conversion to donor chimaerism occurred in the other lineages and the granulocyte fraction was the last lineage to convert. In conclusion, lineage-specific STR-PCR permits detailed monitoring of subtle changes in donor/recipient cell dynamics in specific lineages following DLI during the crucial pancytopenic phase and may be a useful predictor of haematological response to DLI therapy.

Home and Workplace Built Environment Supports for Physical Activity

BACKGROUND: Physical inactivity has been associated with obesity and related chronic diseases. Understanding built environment (BE) influences on specific domains of physical activity (PA) around homes and workplaces is important for public health interventions to increase population PA.

PURPOSE: To examine the association of home and workplace BE features with PA occurring across specific life domains (work, leisure, and travel).

METHODS: Between 2012 and 2013, telephone interviews were conducted with participants in four Missouri metropolitan areas. Questions included sociodemographic characteristics, home and workplace supports for PA, and dietary behaviors. Data analysis was conducted in 2013; logistic regression was used to examine associations between BE features and domain-specific PA.

RESULTS: In home neighborhoods, seven of 12 BE features (availability of fruits and vegetables, presence of shops and stores, bike facilities, recreation facilities, crime rate, seeing others active, and interesting things) were associated with leisure PA. The global average score of home neighborhood BE features was associated with greater odds of travel PA (AOR=1.99, 95% CI=1.46, 2.72); leisure PA (AOR=1.84, 95% CI=1.44, 2.34); and total PA (AOR=1.41, 95% CI=1.04, 1.92). Associations between workplace neighborhoods' BE features and workplace PA were small but in the expected direction.

CONCLUSIONS: This study offers empirical evidence on BE supports for domain-specific PA. Findings suggest that diverse, attractive, and walkable neighborhoods around workplaces support walking, bicycling, and use of public transit. Public health practitioners, researchers, and worksite leaders could benefit by utilizing worksite domains and measures from this study for future BE assessments.

Program slice metrics and their potential role in DSL design, position paper

The advantages a DSL and the benefits its use potentially brings imply that informed decisions on the design of a domain specific language are of paramount importance for its use. We believe that the foundations of such decisions should be informed by analysis of data empirically collected from systems to highlight salient features that should then form the basis of a DSL. To support this theory, we describe an empirical study of a large OSS called Barcode, written in C, and from which we collected two well-known 'slice' based metrics. We analyzed multiple versions of the system and sliced its functions in three separate ways (i.e., input, output and global variables). The purpose of the study was to try and identify sensitivities and traits in those metrics that might inform features of a potential slice-based DSL. Results indicated that cohesion was adversely affected through the use of global variables and that appreciation of the role of function inputs and outputs can be revealed through slicing. The study presented is motivated primarily by the problems with current tools and interfaces experienced directly by the authors in extracting slicing data and the need to promote the benefits that analysis of slice data and slicing in general can offer.

A model for information retrieval driven by conceptual spaces

A retrieval model describes the transformation of a query into a set of documents. The question is: what drives this transformation? For semantic information retrieval type of models this transformation is driven by the content and structure of the semantic models. In this case, Knowledge Organization Systems (KOSs) are the semantic models that encode the meaning employed for monolingual and cross-language retrieval. The focus of this research is the relationship between these meanings’ representations and their role and potential in augmenting existing retrieval models effectiveness. The proposed approach is unique in explicitly interpreting a semantic reference as a pointer to a concept in the semantic model that activates all its linked neighboring concepts. It is in fact the formalization of the information retrieval model and the integration of knowledge resources from the Linguistic Linked Open Data cloud that is distinctive from other approaches. The preprocessing of the semantic model using Formal Concept Analysis enables the extraction of conceptual spaces (formal contexts)that are based on sub-graphs from the original structure of the semantic model. The types of conceptual spaces built in this case are limited by the KOSs structural relations relevant to retrieval: exact match, broader, narrower, and related. They capture the definitional and relational aspects of the concepts in the semantic model. Also, each formal context is assigned an operational role in the flow of processes of the retrieval system enabling a clear path towards the implementations of monolingual and cross-lingual systems. By following this model’s theoretical description in constructing a retrieval system, evaluation results have shown statistically significant results in both monolingual and bilingual settings when no methods for query expansion were used. The test suite was run on the Cross-Language Evaluation Forum Domain Specific 2004-2006 collection with additional extensions to match the specifics of this model.

Motivation scolaire et adaptation psychosociale d'élèves du secondaire scolarisés en classe de prolongation de cycle

Depuis la mise en place de la réforme, il y a plus de dix ans, les directions d’établissement sont tenues de trouver des solutions alternatives au redoublement, afin d’aider les élèves en difficulté à rattraper leur retard. C’est afin de répondre à cet impératif que la classe de prolongation de cycle a été mise en place dans les écoles secondaires. Des élèves en fin de 1er cycle, jugés incapables de poursuivre au cycle supérieur, y sont regroupés et pendant une année, ils bénéficient de mesures de soutien afin d’atteindre le niveau de compétence attendu (plus précisément en français en en mathématiques) pour pouvoir vivre un passage réussi au second cycle. Peu de résultats de recherches sont toutefois disponibles quant à l’efficacité de cette modalité. La présente étude vise donc à estimer l’incidence de deux modèles de prolongation de cycle (co-enseignement et avec enseignant unique), sur la motivation et l’adaptation psychosociale des élèves. Ainsi, les élèves qui expérimentent un modèle de co-enseignement demeurent en groupe fermé et sont accompagnés par trois enseignants titulaires qui se partagent la responsabilité de la quasi-totalité des composantes du programme de formation. Les élèves qui expérimentent un modèle avec enseignant unique demeurent eux aussi en groupe fermé, mais sont encadrés par une seule enseignante titulaire qui assume la responsabilité des enseignements en français et en mathématiques. Les autres matières sont enseignées par des spécialistes. Cent trente-quatre élèves au total, fréquentant trois écoles secondaires francophones montréalaises situées en milieu défavorisé, ont donc formé les groupes expérimentaux et témoins. En début et en fin d’année, les participants ont répondu à un questionnaire d’enquête mesurant l’évolution de leur motivation générale pour les apprentissages, de leur motivation spécifique aux disciplines, de leur adaptation psychosociale, de même que certaines facettes de leurs relations avec leurs pairs, leurs enseignants et leurs parents. Les résultats d’analyses de variance multivariées à mesures répétées (MANOVA) et des tests univariés subséquents permettent d’observer, chez les élèves qui ont expérimenté la prolongation de cycle en co-enseignement, une augmentation de leur sentiment de compétence général vis-à-vis l’école. De plus, leurs buts de performance-évitement et leur anxiété sociale ont diminué. Chez les élèves qui ont expérimenté la prolongation de cycle avec enseignant unique, ce même sentiment de compétence vis-à-vis l’école et celui spécifique au français ont augmenté. En revanche, ces derniers s’expriment plus négativement que leurs homologues en ce qui concerne leur intérêt général envers l’école, leur sentiment d’appartenance à leur école et leurs relations avec leurs pairs. Ces résultats indiquent donc que cette mesure a un effet mitigé sur la motivation et l’adaptation psychosociale des élèves. De plus, les quelques bénéfices perçus peuvent être la conséquence du fait de se retrouver dans un environnement scolaire moins compétitif. Cela dit, il apparaît important de préciser que les enseignants qui ont testé le modèle de co-enseignement en étaient à une première expérience. Leurs pratiques sont susceptibles de se bonifier, ce qui laisse croire que des résultats plus disparates pourraient éventuellement être observés entre ces deux modèles de prolongation. Par ailleurs, la pérennité des gains observés est inconnue. En conséquence, il conviendrait de poursuivre cette étude pour être en mesure de déterminer si ceux-ci sont durables dans le temps et afin de constater la pleine mesure de l’efficacité du modèle de prolongation de co-enseignement.