Persistent Homology Guided Force-Directed Graph Layouts

Graphs are commonly used to encode relationships among entities, yet their abstractness makes them difficult to analyze. Node-link diagrams are popular for drawing graphs, and force-directed layouts provide a flexible method for node arrangements that use local relationships in an attempt to reveal the global shape of the graph. However, clutter and overlap of unrelated structures can lead to confusing graph visualizations. This paper leverages the persistent homology features of an undirected graph as derived information for interactive manipulation of force-directed layouts. We first discuss how to efficiently extract 0-dimensional persistent homology features from both weighted and unweighted undirected graphs. We then introduce the interactive persistence barcode used to manipulate the force-directed graph layout. In particular, the user adds and removes contracting and repulsing forces generated by the persistent homology features, eventually selecting the set of persistent homology features that most improve the layout. Finally, we demonstrate the utility of our approach across a variety of synthetic and real datasets

Analysis Without Data: Teaching Students to Tackle the VAST Challenge

The VAST Challenges have been shown to be an effective tool in visual analytics education, encouraging student learning while enforcing good visualization design and development practices. However, research has observed that students often struggle at identifying a good "starting point" when tackling the VAST Challenge. Consequently, students who could not identify a good starting point failed at finding the correct solution to the challenge. In this paper, we propose a preliminary guideline for helping students approach the VAST Challenge and identify initial analysis directions. We recruited two students to analyze the VAST 2017 Challenge using a hypothesis-driven approach, where they were required to pre-register their hypotheses prior to inspecting and analyzing the full dataset. From their experience, we developed a prescriptive guideline for other students to tackle VAST Challenges. In a preliminary study, we found that the students were able to use the guideline to generate well-formed hypotheses that could lead them towards solving the challenge. Additionally, the students reported that with the guideline, they felt like they had concrete steps that they could follow, thereby alleviating the burden of identifying a good starting point in their analysis process.Comment: IEEE Workshop on Visualization Guidelines in Research, Design, and Education (VisGuides

Visual Validation versus Visual Estimation: A Study on the Average Value in Scatterplots

We investigate the ability of individuals to visually validate statistical models in terms of their fit to the data. While visual model estimation has been studied extensively, visual model validation remains under-investigated. It is unknown how well people are able to visually validate models, and how their performance compares to visual and computational estimation. As a starting point, we conducted a study across two populations (crowdsourced and volunteers). Participants had to both visually estimate (i.e, draw) and visually validate (i.e., accept or reject) the frequently studied model of averages. Across both populations, the level of accuracy of the models that were considered valid was lower than the accuracy of the estimated models. We find that participants' validation and estimation were unbiased. Moreover, their natural critical point between accepting and rejecting a given mean value is close to the boundary of its 95% confidence interval, indicating that the visually perceived confidence interval corresponds to a common statistical standard. Our work contributes to the understanding of visual model validation and opens new research opportunities.Comment: Preprint and Author Version of a Short Paper, accepted to the 2023 IEEE Visualization Conference (VIS

Are Metrics Enough? Guidelines for Communicating and Visualizing Predictive Models to Subject Matter Experts

Presenting a predictive model's performance is a communication bottleneck that threatens collaborations between data scientists and subject matter experts. Accuracy and error metrics alone fail to tell the whole story of a model - its risks, strengths, and limitations - making it difficult for subject matter experts to feel confident in their decision to use a model. As a result, models may fail in unexpected ways or go entirely unused, as subject matter experts disregard poorly presented models in favor of familiar, yet arguably substandard methods. In this paper, we describe an iterative study conducted with both subject matter experts and data scientists to understand the gaps in communication between these two groups. We find that, while the two groups share common goals of understanding the data and predictions of the model, friction can stem from unfamiliar terms, metrics, and visualizations - limiting the transfer of knowledge to SMEs and discouraging clarifying questions being asked during presentations. Based on our findings, we derive a set of communication guidelines that use visualization as a common medium for communicating the strengths and weaknesses of a model. We provide a demonstration of our guidelines in a regression modeling scenario and elicit feedback on their use from subject matter experts. From our demonstration, subject matter experts were more comfortable discussing a model's performance, more aware of the trade-offs for the presented model, and better equipped to assess the model's risks - ultimately informing and contextualizing the model's use beyond text and numbers

Clinical and pharmaceutical applications of affinity ligands in capillary electrophoresis: A review

Affinity capillary electrophoresis (ACE) is a separation technique that combines a biologically-related binding agent with the separating power and efficiency of capillary electrophoresis. This review will examine several classes of binding agents that have been used in ACE and applications that have been described for the resulting methods in clinical or pharmaceutical analysis. Binding agents that will be considered are antibodies, aptamers, lectins, serum proteins, carbohydrates, and enzymes. This review will also describe the various formats in which each type of binding agent has been used in CE, including both homogeneous and heterogeneous methods. Specific areas of applications that will be considered are CE-based immunoassays, glycoprotein/glycan separations, chiral separations, and biointeraction studies. The general principles and formats of ACE for each of these applications will be examined, along with the potential advantages or limitations of these methods

Clioquinol Inhibits Zinc-Triggered Caspase Activation in the Hippocampal CA1 Region of a Global Ischemic Gerbil Model

Background: Excessive release of chelatable zinc from excitatory synaptic vesicles is involved in the pathogenesis of selective neuronal cell death following transient forebrain ischemia. The present study was designed to examine the neuroprotective effect of a membrane-permeable zinc chelator, clioquinol (CQ), in the CA1 region of the gerbil hippocampus after transient global ischemia. Methodology/Principal Findings: The common carotid arteries were occluded bilaterally, and CQ (10 mg/kg, i.p.) was injected into gerbils once a day. The zinc chelating effect of CQ was examined with TSQ fluorescence and autometallography. Neuronal death, the expression levels of caspases and apoptosis inducing factor (AIF) were evaluated using TUNEL, in situ hybridization and Western blotting, respectively. We were able to show for the first time that CQ treatment attenuates the ischemia-induced zinc accumulation in the CA1 pyramidal neurons, accompanied by less neuronal loss in the CA1 field of the hippocampus after ischemia. Furthermore, the expression levels of caspase-3,-9, and AIF were significantly decreased in the hippocampus of CQ-treated gerbils. Conclusions/Significance: The present study indicates that the neuroprotective effect of CQ is related to downregulation o

Paediatric leukaemia DNA methylation profiling using MBD enrichment and SOLiD sequencing on archival bone marrow smears

BACKGROUND: Acute Lymphoblastic Leukaemia (ALL) is the most common cancer in children. Over the past four decades, research has advanced the treatment of this cancer from a less than 60% chance of survival to over 85% today. The causal molecular mechanisms remain unclear. Here, we performed sequencing-based genomic DNA methylation profiling of eight paediatric ALL patients using archived bone marrow smear microscope slides. FINDINGS: SOLiD™ sequencing data was collected from Methyl-Binding Domain (MBD) enriched fractions of genomic DNA. The primary tumour and remission bone marrow sample was analysed from eight patients. Four patients relapsed and the relapsed tumour was analysed. Input and MBD-enriched DNA from each sample was sequenced, aligned to the hg19 reference genome and analysed for enrichment peaks using MACS (Model-based Analysis for ChIP-Seq) and HOMER (Hypergeometric Optimization of Motif EnRichment). In total, 3.67 gigabases (Gb) were sequenced, 2.74 Gb were aligned to the reference genome (average 74.66% alignment efficiency). This dataset enables the interrogation of differential DNA methylation associated with paediatric ALL. Preliminary results reveal concordant regions of enrichment indicative of a DNA methylation signature. CONCLUSION: Our dataset represents one of the first SOLiD™MBD-Seq studies performed on paediatric ALL and is the first to utilise archival bone marrow smears. Differential DNA methylation between cancer and equivalent disease-free tissue can be identified and correlated with existing and published genomic studies. Given the rarity of paediatric haematopoietic malignancies, relative to adult counterparts, our demonstration of the utility of archived bone marrow smear samples to high-throughput methylation sequencing approaches offers tremendous potential to explore the role of DNA methylation in the aetiology of cancer

Diet and Airway Obstruction: A Cross Sectional Study from the Second Korean National Health and Nutrition Examination Survey

Background/Aims: Several dietary factors, such as antioxidant vitamins, have potential roles in the development of obstructive lung diseases. However, the results of studies on the relationships between dietary factors and obstructive lung diseases are inconsistent. The aim of this study was to determine which nutrients are related to airway obstruction (AO) in the Korean population.&Methods: We used data obtained as part of the Korean National Health and Nutrition Examination Survey (NHANES II) in 2001. Analysis was restricted to 1,005 adults who were 18 years of age and older, who had two or more acceptable spirometry curves, and who had participated in the nutrition examination survey. AO was defined as the ratio of forced expiratory volume in one second (FEV1) to forced vital capacity (FVC) of less than 0.7.&Results: Of the 1,005 study subjects, 78 (7.8%) had AO. Statistically significant factors associated with AO were 55 years of age or older (p = 0.032), central obesity (p = 0.047), hypertension (p < 0.001), smoking of 20 pack-years or more (p < 0.001), low income (p < 0.001), and low dietary protein intake expressed as a ratio of protein to recommended dietary allowance for Koreans (p = 0.037). Multiple logistic regression analyses revealed four factors that were independently associated with AO: smoking of 20 pack-years or more (odds ratio [OR], 5.801; p < 0.001), hypertension (OR, 3.905; p < 0.001), low protein intake (OR, 0.992; p = 0.004), and low income (OR, 1.962; p = 0.018).&Conclusions: In the Korean NHANES, smoking, hypertension, and low income were related to AO. Among dietary factors, only low protein intake was associated with AO

Some exact and numerical results for plane steady sheared flow of an incompressible inviscid fluid

Analytical and numerical solutions are presented for the steady flow of an inviscid fluid about symmetric lifting profiles at an angle of attack in a plane sheared onset flow for which conformal mapping plays a critical role. For uniform shear (i.e. the onset flow speed varies linearly with position) in two dimensions, the disturbance field is potential and hence a solution based on the conformal transformation technique may be constructed. The Moriya transformation, which employs a leading-term transformation coefficient that stretches and rotates the field at great distances from the foil (as distinct from other classical transformations which leave the far field unchanged) is used and, with a limited number of terms selected for the transformation, a simple elegant solution is obtained that may be easily evaluated at arbitrary points on the foil contour. An additional investigation is reported for the field solution -- involving a locally similar but globally non-uniform sheared onset flow -- about one of the foils for which a simple O-type grid is analytically generated from the mapping function. These data indicate that the uniform-shear solution overpredicts the lift and surface speed on the suction side of the foil relative to the more realistic onset flow: the numerical solution predicts surface speeds that generally lie between those for the uniform flow and the uniformly sheared flow solutions.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/29989/1/0000356.pd