The CKC Challenge: Exploring Tools for Collaborative Knowledge Construction

The great success of Web 2.0 is mainly fuelled by an infrastructure that allows web users to create, share, tag, and connect content and knowledge easily. The tools for developing structured knowledge in this manner have started to appear as well. However, there are few, if any, user studies that are aimed at understanding what users expect from such tools, what works and what doesn't. We organized the Collaborative Knowledge Construction (CKC) Challenge to assess the state of the art for the tools that support collaborative processes for creation of various forms of structured knowledge. The goal of the Challenge was to get users to try out different tools and to learn what users expect from such tools /features that users need, features that they like or dislike. The Challenge task was to construct structured knowledge for a portal that would provide information about research. The Challenge design contained several incentives for users to participate. Forty-nine users registered for the Challenge; thirty three of them participated actively by using the tools. We collected extensive feedback from the users where they discussed their thoughts on all the tools that they tried. In this paper, we present the results of the Challenge, discuss the features that users expect from tools for collaborative knowledge constructions, the features on which Challenge participants disagreed, and the lessons that we learned

Winnowing ontologies based on application use

The requirements of specific applications and services are often over estimated when ontologies are reused or built. This sometimes results in many ontologies being too large for their intended purposes. It is not uncommon that when applications and services are deployed over an ontology, only a few parts of the ontology are queried and used. Identifying which parts of an ontology are being used could be helpful to winnow the ontology, i.e., simplify or shrink the ontology to smaller, more fit for purpose size. Some approaches to handle this problem have already been suggested in the literature. However, none of that work showed how ontology-based applications can be used in the ontology-resizing process, or how they might be affected by it. This paper presents a study on the use of the AKT Reference Ontology by a number of applications and services,and investigates the possibility of relying on this usage information to winnow that ontology

Working out a common task: design and evaluation of user-intelligent system collaboration

This paper describes the design and user evaluation of an intelligent user interface intended to mediate between users and an Adaptive Information Extraction (AIE) system. The design goal was to support a synergistic and cooperative work. Laboratory tests showed the approach was efficient and effective; focus groups were run to assess its ease of use. Logs, user satisfaction questionnaires, and interviews were exploited to investigate the interaction experience. We found that user’ attitude is mainly hierarchical with the user wishing to control and check the system’s initiatives. However when confidence in the system capabilities rises, a more cooperative interaction is adopted

Error Analysis in Surfaces Reconstruction by Fitting and Interpolation Technique

Error between surfaces is the measurement to give us information how similar or different they are. Moreover, since the data associated with error between two matching surfaces are too huge and further need to be filtered into meaningful information. This research shows the suitable ways to represent error, to achieve data reduction and how detailed. Surfacerepresentations that may then be used as a part of many applications in engineering, clinic, virtual and other CAD applications. The statistical tools analysis of error has been developed to provide effective visual inputs that the designer can interpret of meaningful information. The comparison between two matching surfaces was done by using the differences in elevation techniquesthat called distance error between surfaces. A comparison has been made between the two adopted techniques of surface generation (fitting and interpolation) depending on several standard functions (sine-cosine functions, exponential functions and power functions), where the two techniques (fitting and interpolation) have been applied to analyze the representing error statistically. Then the design results have been implemented in manufacturing three of these surfaces using three axis vertical CNC milling machine tool with ball end mill cutter. By applying the proposed surface models, the similarity factor was found to be ranged between 84.86% for one of the models to 100% for other models that are reconstructed by the adopted fitting and interpolating techniques

On the emergent Semantic Web and overlooked issues

The emergent Semantic Web, despite being in its infancy, has already received a lotof attention from academia and industry. This resulted in an abundance of prototype systems and discussion most of which are centred around the underlying infrastructure. However, when we critically review the work done to date we realise that there is little discussion with respect to the vision of the Semantic Web. In particular, there is an observed dearth of discussion on how to deliver knowledge sharing in an environment such as the Semantic Web in effective and efficient manners. There are a lot of overlooked issues, associated with agents and trust to hidden assumptions made with respect to knowledge representation and robust reasoning in a distributed environment. These issues could potentially hinder further development if not considered at the early stages of designing Semantic Web systems. In this perspectives paper, we aim to help engineers and practitioners of the Semantic Web by raising awareness of these issues

Evaluating the semantic web: a task-based approach

The increased availability of online knowledge has led to the design of several algorithms that solve a variety of tasks by harvesting the Semantic Web, i.e. by dynamically selecting and exploring a multitude of online ontologies. Our hypothesis is that the performance of such novel algorithms implicity provides an insight into the quality of the used ontologies and thus opens the way to a task-based evaluation of the Semantic Web. We have investigated this hypothesis by studying the lessons learnt about online ontologies when used to solve three tasks: ontology matching, folksonomy enrichment, and word sense disambiguation. Our analysis leads to a suit of conclusions about the status of the Semantic Web, which highlight a number of strengths and weaknesses of the semantic information available online and complement the findings of other analysis of the Semantic Web landscape

Essential Role for OspA/B in the Life Cycle of the Lyme Disease Spirochete

The molecular basis of how Borrelia burgdorferi (Bb), the Lyme disease spirochete, maintains itself in nature via a complex life cycle in ticks and mammals is poorly understood. Outer surface (lipo)protein A (OspA) of Bb has been the most intensively studied of all borrelial molecular constituents, and hence, much has been speculated about the potential role(s) of OspA in the life cycle of Bb. However, the precise function of OspA (along with that of its close relative and operonic partner, outer surface [lipo]protein B [OspB]) heretofore has not been directly determined, due primarily to the inability to generate an OspA/B-deficient mutant from a virulent strain of Bb. In this study, we created an OspA/B-deficient mutant of an infectious human isolate of Bb (strain 297) and found that OspA/B function was not required for either Bb infection of mice or accompanying tissue pathology. However, OspA/B function was essential for Bb colonization of and survival within tick midguts, events crucial for sustaining Bb in its natural enzootic life cycle

Concurrent regulation of LKB1 and CaMKK2 in the activation of AMPK in castrate-resistant prostate cancer by a well-defined polyherbal mixture with anticancer properties

Abstract Background Zyflamend, a blend of herbal extracts, effectively inhibits tumor growth using preclinical models of castrate-resistant prostate cancer mediated in part by 5′-adenosine monophosphate-activated protein kinase (AMPK), a master energy sensor of the cell. Clinically, treatment with Zyflamend and/or metformin (activators of AMPK) had benefits in castrate-resistant prostate cancer patients who no longer responded to treatment. Two predominant upstream kinases are known to activate AMPK: liver kinase B1 (LKB1), a tumor suppressor, and calcium-calmodulin kinase kinase-2 (CaMKK2), a tumor promotor over-expressed in many cancers. The objective was to interrogate how Zyflamend activates AMPK by determining the roles of LKB1 and CaMKK2. Methods AMPK activation was determined in CWR22Rv1 cells treated with a variety of inhibitors of LKB1 and CaMKK2 in the presence and absence of Zyflamend, and in LKB1-null HeLa cells that constitutively express CaMKK2, following transfection with wild type LKB1 or catalytically-dead mutants. Upstream regulation by Zyflamend of LKB1 and CaMKK2 was investigated targeting protein kinase C-zeta (PKCζ) and death-associated protein kinase (DAPK), respectively. Results Zyflamend’s activation of AMPK appears to be LKB1 dependent, while simultaneously inhibiting CaMKK2 activity. Zyflamend failed to rescue the activation of AMPK in the presence of pharmacological and molecular inhibitors of LKB1, an effect not observed in the presence of inhibitors of CaMKK2. Using LKB1-null and catalytically-dead LKB1-transfected HeLa cells that constitutively express CaMKK2, ionomycin (activator of CaMKK2) increased phosphorylation of AMPK, but Zyflamend only had an effect in cells transfected with wild type LKB1. Zyflamend appears to inhibit CaMKK2 by DAPK-mediated phosphorylation of CaMKK2 at Ser511, an effect prevented by a DAPK inhibitor. Alternatively, Zyflamend mediates LKB1 activation via increased phosphorylation of PKCζ, where it induced translocation of PKCζ and LKB1 to their respective active compartments in HeLa cells following treatment. Altering the catalytic activity of LKB1 did not alter this translocation. Discussion Zyflamend’s activation of AMPK is mediated by LKB1, possibly via PKCζ, but independent of CaMKK2 by a mechanism that appears to involve DAPK. Conclusions Therefore, this is the first evidence that natural products simultaneously and antithetically regulate upstream kinases, known to be involved in cancer, via the activation of AMPK.https://deepblue.lib.umich.edu/bitstream/2027.42/144515/1/12906_2018_Article_2255.pd

The Ecm11-Gmc2 complex promotes synaptonemal complex formation through assembly of transverse filaments in budding yeast

During meiosis, homologous chromosomes pair at close proximity to form the synaptonemal complex (SC). This association is mediated by transverse filament proteins that hold the axes of homologous chromosomes together along their entire length. Transverse filament proteins are highly aggregative and can form an aberrant aggregate called the polycomplex that is unassociated with chromosomes. Here, we show that the Ecm11-Gmc2 complex is a novel SC component, functioning to facilitate assembly of the yeast transverse filament protein, Zip1. Ecm11 and Gmc2 initially localize to the synapsis initiation sites, then throughout the synapsed regions of paired homologous chromosomes. The absence of either Ecm11 or Gmc2 substantially compromises the chromosomal assembly of Zip1 as well as polycomplex formation, indicating that the complex is required for extensive Zip1 polymerization. We also show that Ecm11 is SUMOylated in a Gmc2-dependent manner. Remarkably, in the unSUMOylatable ecm11 mutant, assembly of chromosomal Zip1 remained compromised while polycomplex formation became frequent. We propose that the Ecm11-Gmc2 complex facilitates the assembly of Zip1 and that SUMOylation of Ecm11 is critical for ensuring chromosomal assembly of Zip1, thus suppressing polycomplex formation