Pim-1 kinase inhibits the activation of reporter gene expression in Elk-1 and c-Fos reporting systems but not the endogenous gene expression: an artifact of the reporter gene assay by transient co-transfection

We have studied the molecular mechanism and signal transduction of pim-1, an oncogene encoding a serine-threonine kinase. This is a true oncogene which prolongs survival and inhibits apoptosis of hematopoietic cells. In order to determine whether the effects of Pim-1 occur by regulation of the mitogen-activated protein kinase pathway, we used a transcriptional reporter assay by transient co-transfection as a screening method. In this study, we found that Pim-1 inhibited the Elk-1 and NFkappaB transcriptional activities induced by activation of the mitogen-activated protein kinase cascade in reporter gene assays. However, Western blots showed that the induction of Elk-1-regulated expression of endogenous c-Fos was not affected by Pim-1. The phosphorylation and activation of neither Erk1/2 nor Elk-1 was influenced by Pim-1. Also, in the gel shift assay, the pattern of endogenous NFkappaB binding to its probe was not changed in any manner by Pim-1. These data indicate that Pim-1 does not regulate the activation of Erk1/2, Elk-1 or NFkappaB. These contrasting results suggest a pitfall of the transient co-transfection reporter assay in analyzing the regulation of transcription factors outside of the chromosome context. It ensures that results from reporter gene expression assay should be verified by study of endogenous gene expression.

Detecting the node-density artifact in phylogeny reconstruction

The node-density effect is an artifact of phylogeny reconstruction that can cause branch lengths to be underestimated in areas of the tree with fewer taxa. Webster, Payne, and Pagel (2003, Science 301:478) introduced a statistical procedure (the "delta" test) to detect this artifact, and here we report the results of computer simulations that examine the test's performance. In a sample of 50,000 random data sets, we find that the delta test detects the artifact in 94.4% of cases in which it is present. When the artifact is not present (n = 10,000 simulated data sets) the test showed a type I error rate of approximately 1.69%, incorrectly reporting the artifact in 169 data sets. Three measures of tree shape or "balance" failed to predict the size of the node-density effect. This may reflect the relative homogeneity of our randomly generated topologies, but emphasizes that nearly any topology can suffer from the artifact, the effect not being confined only to highly unevenly sampled or otherwise imbalanced trees. The ability to screen phylogenies for the node-density artifact is important for phylogenetic inference and for researchers using phylogenetic trees to infer evolutionary processes, including their use in molecular clock dating. [Delta test; molecular clock; molecular evolution; node-density effect; phylogenetic reconstruction; speciation; simulation.]

Automated artifact removal from the electroencephalogram; a comparative study

Contamination of the electroencephalogram (EEG) by artifacts greatly reduces the quality of the recorded signals. There is a need for automated artifact removal methods. However, such methods are rarely evaluated against one another via rigorous criteria, with results often presented based upon visual inspection alone. This work presents a comparative study of automatic methods for removing blink, electrocardiographic, and electromyographic artifacts from the EEG. Three methods are considered; wavelet, blind source separation (BSS), and multivariate singular spectrum analysis (MSSA)-based correction. These are applied to data sets containing mixtures of artifacts. Metrics are devised to measure the performance of each method. The BSS method is seen to be the best approach for artifacts of high signal to noise ratio (SNR). By contrast, MSSA performs well at low SNRs but at the expense of a large number of false positive corrections.

FORCe: fully online and automated artifact removal for brain-computer interfacing

A fully automated and online artifact removal method for the electroencephalogram (EEG) is developed for use in brain-computer interfacing. The method (FORCe) is based upon a novel combination of wavelet decomposition, independent component analysis, and thresholding. FORCe is able to operate on a small channel set during online EEG acquisition and does not require additional signals (e.g. electrooculogram signals). Evaluation of FORCe is performed offline on EEG recorded from 13 BCI particpants with cerebral palsy (CP) and online with three healthy participants. The method outperforms the state-of the-art automated artifact removal methods Lagged auto-mutual information clustering (LAMIC) and Fully automated statistical thresholding (FASTER), and is able to remove a wide range of artifact types including blink, electromyogram (EMG), and electrooculogram (EOG) artifacts.

The ratio bias phenomenon: fact or artifact?

The ratio bias—according to which individuals prefer to bet on probabilities expressed as a ratio of large numbers to normatively equivalent or superior probabilities expressed as a ratio of small numbers—has recently gained momentum, with researchers especially in health economics emphasizing the policy importance of the phenomenon. Although the bias has been replicated several times, some doubts remain about its economic significance. Our two experiments show that the bias disappears once order effects are excluded, and once salient and dominant incentives are provided. This holds true for both choice and valuation tasks. Also, adding context to the decision problem does not alter this finding. No ratio bias could be found in between-subject tests either, which leads us to the conclusion that the policy relevance of the phenomenon is doubtful at best.

Periacinar Retraction Clefting in Nonneoplastic and Neoplastic Prostatic Glands: Artifact or Molecular Involvement

A space between neoplastic acini and prostatic stroma is not rare and studies have interpreted this as an artifact, considering the absence of endothelial cells indicating vascular invasion. Thus, the aims of this work were to characterize and correlate the occurrence and extent of retraction clefting with the reactivities of alpha and beta dystroglycan (alpha DG, beta DG), laminin, matrix metalloproteinase 2 (MMP-2), p63, insulin-like growth factor 1(IGF-1), vimentin, and fibroblast growth factor 2 (FGF-2). The study was based on nonneoplastic and neoplastic prostatic tissues obtained from necropsies and retropubic radical prostatectomies. The results showed that periacinar retraction clefting was significantly more frequent in prostatic carcinoma samples than in normal prostatic acini. Most of the neoplastic acini (72.0%) showed retraction clefting of more than 50% of circumference, which were significantly more frequent in Gleason score 7 and 6. Decreased collagen and reticular and elastic fibers were verified in the stroma around neoplastic acini. Weak and discontinuous alpha DG, beta DG, and laminin immunoreactivities and intensified MMP-2, vimentin, IGF-1 and FGF-2 immunoreactivities were verified in the neoplastic acini; p63 immunoreactivity was negative in all carcinomas. Thus, these findings showed that the lack of epithelial basal cells, DGs, and laminin and increased MMP-2, IGF-1, and FGF-7 could be considered important pathways in periacinar retraction occurrence. This study demonstrated the origin of and the biological mechanisms responsible for periacinar retraction clefting in prostatic carcinoma.

Ceramic technology of the Asurini do Xingu, Brazil: An ethnoarchaeological study of artifact variability

This article presents some of the results of ethnoarchaeological research on ceramic technology I have conducted among the Asurini do Xingu, an Amazonian indigenous population inhabiting a village in the margins of the Xingu River, Para, Brazil. Based on collected data, presented throughout the article, I discuss the reasons behind the formal, quantitative, spatial and relational variability of the Asurini ceramic vessels. This work will demonstrate that these distinct dimensions of variability are related to the potters` technological choices during the vessels` production process, the ceramic teaching-learning structure, and the type, frequency, method and context of use of the same vessels. I try to make clear the different practical and symbolic aspects that may influence the production, use, reuse, storage and discard processes of the vessels. Furthermore, I compare the Asurini context with other ethnographic contexts and try to distinguish regularities that may serve as interpretative references to the study of archaeological ceramic assemblages.

Designing and Programming Organizational Infrastructures for Agents situated in Artifact-based Environments

Actual trends in software development are pushing the need to face a multiplicity of diverse activities and interaction styles characterizing complex and distributed application domains, in such a way that the resulting dynamics exhibits some grade of order, i.e. in terms of evolution of the system and desired equilibrium. Autonomous agents and Multiagent Systems are argued in literature as one of the most immediate approaches for describing such a kind of challenges. Actually, agent research seems to converge towards the definition of renewed abstraction tools aimed at better capturing the new demands of open systems. Besides agents, which are assumed as autonomous entities purposing a series of design objectives, Multiagent Systems account new notions as first-class entities, aimed, above all, at modeling institutional/organizational entities, placed for normative regulation, interaction and teamwork management, as well as environmental entities, placed as resources to further support and regulate agent work. The starting point of this thesis is recognizing that both organizations and environments can be rooted in a unifying perspective. Whereas recent research in agent systems seems to account a set of diverse approaches to specifically face with at least one aspect within the above mentioned, this work aims at proposing a unifying approach where both agents and their organizations can be straightforwardly situated in properly designed working environments. In this line, this work pursues reconciliation of environments with sociality, social interaction with environment based interaction, environmental resources with organizational functionalities with the aim to smoothly integrate the various aspects of complex and situated organizations in a coherent programming approach. Rooted in Agents and Artifacts (A&A) meta-model, which has been recently introduced both in the context of agent oriented software engineering and programming, the thesis promotes the notion of Embodied Organizations, characterized by computational infrastructures attaining a seamless integration between agents, organizations and environmental entities.

Time course based artifact identification for independent components of resting-state FMRI

In functional magnetic resonance imaging (fMRI) coherent oscillations of the blood oxygen level-dependent (BOLD) signal can be detected. These arise when brain regions respond to external stimuli or are activated by tasks. The same networks have been characterized during wakeful rest when functional connectivity of the human brain is organized in generic resting-state networks (RSN). Alterations of RSN emerge as neurobiological markers of pathological conditions such as altered mental state. In single-subject fMRI data the coherent components can be identified by blind source separation of the pre-processed BOLD data using spatial independent component analysis (ICA) and related approaches. The resulting maps may represent physiological RSNs or may be due to various artifacts. In this methodological study, we propose a conceptually simple and fully automatic time course based filtering procedure to detect obvious artifacts in the ICA output for resting-state fMRI. The filter is trained on six and tested on 29 healthy subjects, yielding mean filter accuracy, sensitivity and specificity of 0.80, 0.82, and 0.75 in out-of-sample tests. To estimate the impact of clearly artifactual single-subject components on group resting-state studies we analyze unfiltered and filtered output with a second level ICA procedure. Although the automated filter does not reach performance values of visual analysis by human raters, we propose that resting-state compatible analysis of ICA time courses could be very useful to complement the existing map or task/event oriented artifact classification algorithms.

Sound As Artifact

A distinguishing feature of the discipline of archaeology is its reliance upon sensory dependant investigation. As perceived by all of the senses, the felt environment is a unique area of archaeological knowledge. It is generally accepted that the emergence of industrial processes in the recent past has been accompanied by unprecedented sonic extremes. The work of environmental historians has provided ample evidence that the introduction of much of this unwanted sound, or "noise" was an area of contestation. More recent research in the history of sound has called for more nuanced distinctions than the noisy/quiet dichotomy. Acoustic archaeology tends to focus upon a reconstruction of sound producing instruments and spaces with a primary goal of ascertaining intentionality. Most archaeoacoustic research is focused on learning more about the sonic world of people within prehistoric timeframes while some research has been done on historic sites. In this thesis, by way of a meditation on industrial sound and the physical remains of the Quincy Mining Company blacksmith shop (Hancock, MI) in particular, I argue for an acceptance and inclusion of sound as artifact in and of itself. I am introducing the concept of an individual sound-form, or sonifact, as a reproducible, repeatable, representable physical entity, created by tangible, perhaps even visible, host-artifacts. A sonifact is a sound that endures through time, with negligible variability. Through the piecing together of historical and archaeological evidence, in this thesis I present a plausible sonifactual assemblage at the blacksmith shop in April 1916 as it may have been experienced by an individual traversing the vicinity on foot: an 'historic soundwalk.' The sensory apprehension of abandoned industrial sites is multi-faceted. In this thesis I hope to make the case for an acceptance of sound as a primary heritage value when thinking about the industrial past, and also for an increased awareness and acceptance of sound and listening as a primary mode of perception.

Artifact exhibit and storage box

Plaster death mask. Goal To design a box that can store and exhibit the death mask without requiring the removal or re-positioning of the mask. Treatment A custom, cloth-covered box with a drop-front was constructed to fit the dimensions of the mask and foam filler. Foam was carved to accommodate the mask and then covered with unbleached muslin.