M3G: Maximum Margin Microarray Gridding

<p>Abstract</p> <p>Background</p> <p>Complementary DNA (cDNA) microarrays are a well established technology for studying gene expression. A microarray image is obtained by laser scanning a hybridized cDNA microarray, which consists of thousands of spots representing chains of cDNA sequences, arranged in a two-dimensional array. The separation of the spots into distinct cells is widely known as microarray image gridding.</p> <p>Methods</p> <p>In this paper we propose M³G, a novel method for automatic gridding of cDNA microarray images based on the maximization of the margin between the rows and the columns of the spots. Initially the microarray image rotation is estimated and then a pre-processing algorithm is applied for a rough spot detection. In order to diminish the effect of artefacts, only a subset of the detected spots is selected by matching the distribution of the spot sizes to the normal distribution. Then, a set of grid lines is placed on the image in order to separate each pair of consecutive rows and columns of the selected spots. The optimal positioning of the lines is determined by maximizing the margin between these rows and columns by using a maximum margin linear classifier, effectively facilitating the localization of the spots.</p> <p>Results</p> <p>The experimental evaluation was based on a reference set of microarray images containing more than two million spots in total. The results show that M³G outperforms state of the art methods, demonstrating robustness in the presence of noise and artefacts. More than 98% of the spots reside completely inside their respective grid cells, whereas the mean distance between the spot center and the grid cell center is 1.2 pixels.</p> <p>Conclusions</p> <p>The proposed method performs highly accurate gridding in the presence of noise and artefacts, while taking into account the input image rotation. Thus, it provides the potential of achieving perfect gridding for the vast majority of the spots.</p

Negotiating the Meaning of Team Expertise: A Firefighter Team’s Epistemic Denial

In this case study, we report how a team of firefighters critiqued one of its member’s decisions to facilitate learning and process improvement. The study is supported by 500+ hr of ethnographic observations, documents, and 11 retrospective interviews, which captured how the team’s talk about the member’s decision shaped their interpretations of their own and others’ expertise—interpretations that ironically undermined learning. Constant comparative analysis revealed that these firefighters positioned themselves as experts by crediting either personal experience or technical knowledge and then discrediting the alternative way of knowing. We labeled this process epistemic denial. The process of epistemic denial was rooted in identity concern; specifically, veteran team members relied on personal experience and newer members relied on technical information gained from training to assert their expertise, and to devalue others’ expertise. The article concludes with recommendations for avoiding problems associated with epistemic denial in high-reliability teams.Yeshttps://us.sagepub.com/en-us/nam/manuscript-submission-guideline

A nonspeech investigation of tongue function in Parkinson's disease

Background. Nonspeech investigations of tongue function in persons with Parkinson's disease (PD) have generally reported impaired tongue strength, endurance, and fine force control. However, these investigations did not specifically evaluate the relative contribution of age effects to the deficits in tongue function observed. Furthermore, the relationship between these nonspeech measures of tongue function and the speech disorder present in PD remains equivocal. Therefore, the current study investigated the strength, rate of repetitive movement, fine force control, and endurance of the tongue in three groups of participants. Methods. Participants in the study included 14 older adults with PD and imprecise consonant articulation, 11 neurologically healthy older adults, and 15 neurologically healthy young adults. All participants were assessed using a comprehensive nonspeech assessment battery of tongue function. Results. The results of the investigation revealed similar levels of tongue strength, rate of repetitive movement, and endurance between the persons with PD and the older control participants. Significant age effects were noted, with both groups demonstrating significantly reduced functioning on those measures when compared to young control participants. However, the three participant groups had similar levels of fine force control. No relationship was found between the nonspeech measures of tongue function employed and the severity of consonant imprecision. Conclusion. The nonspeech measures used failed to provide useful diagnostic information regarding the physiologic basis of perceived articulatory dysfunction in the persons with PD who were examined

Trust-Building in a Patient Forum: The Interplay of Professional and Personal Expertise

Online discussion forums for patients offer the benefits of community but the risks of misinformation. A physician-moderated forum may help to mitigate this tension. How do both the professional expertise of a physician moderator and the personal, experiential expertise of patients contribute to trust in a forum? A rhetorical analysis of a year of postings in an online Parkinson’s community reveals that both forms of expertise were trusted, demonstrating the possibility for them to complement each other. This study illustrates the broader ways trust is established in patient communities and offers implications for technical communicators as forum designers or moderators

Long-Term Phonatory Instability in Individuals With Multiple Sclerosis

This paper uses a new approach to describe and quantify the long-term phonatory instability of speakers with MS. Sustained vowel phonations of 20 individuals with a definite diagnosis of multiple sclerosis (MS) and 20 age- and gender-matched individuals with normal speech were recorded. The phonations were f0 and intensity analyzed and subjected to spectral analysis using the Fast Fourier Transform. Three methods for analyzing the instabilities are presented, compared, and related to perceptual judgments: (a) coefficients of variation, (b) magnitude-based analysis of spectral energy, and (c) frequency-based analysis of spectral components. All measures reliably distinguished between individuals with MS and persons with normal speech. A single factor based on a linear discriminant analysis of the frequency-based measures was especially useful in distinguishing these groups. Critical frequency bands of instability, corresponding to wow (1-2 Hz), tremor (around 8 Hz), and flutter (17-18 Hz), distinguished the MS group from those of the control group