Weighted Pointer: Error-aware Gaze-based Interaction through Fallback Modalities.

Gaze-based interaction is a fast and ergonomic type of hands-free interaction that is often used with augmented and virtual reality when pointing at targets. Such interaction, however, can be cumbersome whenever user, tracking, or environmental factors cause eye tracking errors. Recent research has suggested that fallback modalities could be leveraged to ensure stable interaction irrespective of the current level of eye tracking error. This work thus presents Weighted Pointer interaction, a collection of error-aware pointing techniques that determine whether pointing should be performed by gaze, a fallback modality, or a combination of the two, depending on the level of eye tracking error that is present. These techniques enable users to accurately point at targets when eye tracking is accurate and inaccurate. A virtual reality target selection study demonstrated that Weighted Pointer techniques were more performant and preferred over techniques that required the use of manual modality switching.

Breaking the Rebellion: Photodynamic Inactivation against Erwinia amylovora Resistant to Streptomycin.

Global crop production depends on strategies to counteract the ever-increasing spread of plant pathogens. Antibiotics are often used for large-scale treatments. As a result, Erwinia amylovora, causal agent of the contagious fire blight disease, has already evolved resistance to streptomycin (Sm). Photodynamic Inactivation (PDI) of microorganisms has been introduced as innovative method for plant protection. The aim of this study is to demonstrate that E. amylovora resistant to Sm (E. amylovoraSmR) can be killed by PDI. Two photosensitizers, the synthetic B17-0024, and the natural derived anionic sodium magnesium chlorophyllin (Chl) with cell-wall-permeabilizing agents are compared in terms of their photo-killing efficiency in liquid culture with or without 100 µg/mL Sm. In vitro experiments were performed at photosensitizer concentrations of 1, 10 or 100 µM and 5 or 30 min incubation in the dark, followed by illumination at 395 nm (radiant exposure 26.6 J/cm2). The highest inactivation of seven log steps was achieved at 100 µM B17-0024 after 30 min incubation. Shorter incubation (5 min), likely to represent field conditions, reduced the photo-killing to 5 log steps. Chlorophyllin at 100 µM in combination with 1.2% polyaspartic acid (PASA) reduced the number of bacteria by 6 log steps. While PASA itself caused some light independent toxicity, an antibacterial effect (3 log reduction) was achieved only in combination with Chl, even at concentrations as low as 10 µM. Addition of 100 µg/mL Sm to media did not significantly increase the efficacy of the photodynamic treatment. This study proves principle that PDI can be used to treat plant diseases even if causative bacteria are resistant to conventional treatment. Therefore, PDI based on natural photosensitizers might represent an eco-friendly treatment strategy especially in organic farming.

Determination of the Efficiency of Photodynamic Decontamination of Food.

Unsafe food causes more than 200 diseases and therefore poses a threat to the health of millions of people worldwide. Children under 5 years of age carry about 40% of the foodborne disease burden. With a rapidly growing world population, the supply of nutritious, safe, and healthy food represents a high challenge for the coming centuries. Photodynamic decontamination of food (PDc) is based on the photosensitizer (PS)-mediated and light-induced overproduction of reactive oxygen species, which kill microorganisms irrespective of their resistance to conventional treatment. Several natural substances approved as food additives such as curcumin or chlorophyllin are photoactive. Thus, PDc based on these compounds is a promising approach to improve food safety.In this chapter, two experimental protocols to investigate the antimicrobial efficacy of PDc on flat objects like lettuce or slices of cucumber or round objects like mung beans in situ are described in detail, which allow for quantitative analysis of the decontamination effect. Both methods are also applicable for other radiation-based decontamination, such as UV- or γ-treatment of food.

Photodynamic Inactivation of plant pathogens part II: fungi.

The constantly increasing demand for agricultural produce from organic and conventional farming calls for new, sustainable, and biocompatible solutions for crop protection. The overuse of fungicides leading to contamination of both produce and environment and the emergence of plant pathogenic fungi that are resistant to conventional treatments warrant the need for new methods to combat fungal infections in the field. We here deliver the follow-up study to our research on the Photodynamic Inactivation (PDI) of plant pathogenic bacteria (Glueck et al. in Photochem Photobiol Sci 18(7):1700-1708, 2019) by expanding the scope to fungal pathogens. Both fungal species employed in this study-Alternaria solani and Botrytis cinerea-cause substantial crop and economic losses. Sodium magnesium chlorophyllin (Chl, approved as food additive E140) in combination with Na2EDTA and the chlorin e6 derivative B17-0024 holding cationic moieties serve as eco-friendly photoactive compounds. Effectiveness of the antifungal PDI was measured by inhibition of growth of mycelial spheres (average diameter 2-3 mm) after incubation with the photosensitizer for 100 min and subsequent illumination using a LED array (395 nm, 106.6 J cm-2). One hundred micromolar Chl combined with 5 mM Na2EDTA was able to successfully photokill 94.1% of A. solani and 91.7% of B. cinerea samples. PDI based on B17-0024 can completely inactivate A. solani at 10 times lower concentration (10 µM); however, for B. cinerea, the concentration required for complete eradication was similar to that of Chl with Na2EDTA (100 µM). Using a plant compatibility assay based on Fragaria vesca, we further demonstrate that both photosensitizers neither affect host plant development nor cause significant leaf damage. The plants were sprayed with 300 µL of treatment solution used for PDI (one or three treatments on consecutive days) and plant growth was monitored for 21 days. Only minor leaf damage was observed in samples exposed to the chelators Na2EDTA and polyaspartic acid, but overall plant development was unaffected. In conclusion, our results suggest that sodium magnesium chlorophyllin in combination with EDTA and B17-0024 could serve as effective and safe photofungicides.

A Cross-Sectional Study of Nemaline Myopathy.

OBJECTIVE: Nemaline myopathy (NM) is a rare neuromuscular condition with clinical and genetic heterogeneity. To establish disease natural history, we performed a cross-sectional study of NM, complemented by longitudinal assessment and exploration of pilot outcome measures. METHODS: Fifty-seven individuals with NM were recruited at 2 family workshops, including 16 examined at both time points. Participants were evaluated by clinical history and physical examination. Functional outcome measures included the Motor Function Measure (MFM), pulmonary function tests (PFTs), myometry, goniometry, and bulbar assessments. RESULTS: The most common clinical classification was typical congenital (54%), whereas 42% had more severe presentations. Fifty-eight percent of individuals needed mechanical support, with 26% requiring wheelchair, tracheostomy, and feeding tube. The MFM scale was performed in 44 of 57 participants and showed reduced scores in most with little floor/ceiling effect. Of the 27 individuals completing PFTs, abnormal values were observed in 65%. Last, bulbar function was abnormal in all patients examined, as determined with a novel outcome measure. Genotypes included mutations in ACTA1 (18), NEB (20), and TPM2 (2). Seventeen individuals were genetically unresolved. Patients with pathogenic ACTA1 and NEB variants were largely similar in clinical phenotype. Patients without genetic resolution had more severe disease. CONCLUSION: We present a comprehensive cross-sectional study of NM. Our data identify significant disabilities and support a relatively stable disease course. We identify a need for further diagnostic investigation for the genetically unresolved group. MFM, PFTs, and the slurp test were identified as promising outcome measures for future clinical trials.

Save the crop: Photodynamic Inactivation of plant pathogens I: bacteria.

The ever growing world-population poses challenges concerning the need for more food free of pesticide residues. The most common means to control plant pathogens is through the application of pesticides, which raises concerns over safety for humans and the environment. Recently, Photodynamic Inactivation (PDI) of microorganisms using natural photosensitizers has shown itself to be a powerful tool to combat bacteria and fungi. This study investigates the efficacy of PDI against the Gram(+) bacterial plant pathogen Rhodococcus fascians and Gram(-) Xanthomonas axonopodis and Erwinia amylovora using two chlorin e6 derivatives as photosensitizers: anionic sodium magnesium chlorophyllin (Chl, approved as food additive E140) in combination with cell wall permeabilizing agents (Na2EDTA or Polyaspartic acid sodium salt (PA)) and B17-0024, a mixture of chlorin e6 derivatives with cationic moieties at physiological pH. Both photosensitizers show excellent efficacy against R. fascians, whereby B17-0024 is phototoxic at a one order of magnitude lower concentration than Chl (10 µM B17-0024: relative inactivation (r.i.) >7.5 × 106, 100 µM Chl: r.i. 2.2 × 106, illumination with 26.6 J cm-2, 395 nm). The phototreatment of Gram(-) bacteria with Chl requires the obligatory use of cell wall permeabilizing agents like Na2EDTA (X. axonopodis) or PA (E. amylovora) to induce significant killing (more than 7 log units at 100 µM). On the other hand, B17-0024 proves to be a highly effective photosensitizer inducing bacterial inactivation at very low concentrations (10 µM for R. fascians and X. axonopodis, 100 µM for E. amylovora) without additives. In summary, PDI using both the natural photosensitizer Chl in combination with cell wall permeabilizing agents is effective and environmentally friendly. As an alternative, B17-0024 is highly photoactive against all model strains tested - even without cell wall permeabilizing agents. The photodynamic approach based on chlorin e6 derivatives should add to the growers' toolbox as a preferred alternative for the control of phytopathogens.

A Phenotypic Description of Congenital Myotonic Dystrophy using PhenoStacks.

BACKGROUND: Congenital Myotonic Dystrophy (CDM1) is a rare neuromuscular condition caused by a triplet repeat expansion in the DMPK gene. Despite there being a well-recognized clinical syndrome, there has not been an effort to use a standardized ontology system to describe the disease characteristics in existing literature. Thus, comparing or contrasting different cohorts from the literature can be challenging, and coding disease features for clinical research or for registry data items is not uniform. PhenoStacks is a visualization analytics tool which helps graphically illustrate phenotypes of patients with genetic disorders using Human Phenotype Ontology (HPO) terms and can sort phenotypes by different disease characteristics. OBJECTIVE: To demonstrate the efficacy of PhenoStacks and the HPO system as clinical research tools when describing CDM1 cohorts. METHODS: Health Endpoints and Longitudinal progression in congenital myotonic dystrophy (HELP-CDM) is an ongoing study which longitudinally follows patients with CDM1. Items from the HELP-CDM data sheet were matched to corresponding HPO terms and analyzed using PhenoStacks. RESULTS: In total 40 subjects' phenotypes were visualized through PhenoStacks and 73 HPO terms were used for the analysis. Frequent phenotypic features included "high narrow palate", "facial palsy", "ptosis", "hyporeflexia", and "weak voice". Contractures were associated with higher repeat sizes. Hypoplastic muscles and infantile axial hypotonia were more frequently observed in infants. CONCLUSIONS: PhenoStacks is a valuable clinical and scientific tool as it identifies variability within cohorts and highlights significant phenotypic features.

PhenoLines: Phenotype Comparison Visualizations for Disease Subtyping via Topic Models.

PhenoLines is a visual analysis tool for the interpretation of disease subtypes, derived from the application of topic models to clinical data. Topic models enable one to mine cross-sectional patient comorbidity data (e.g., electronic health records) and construct disease subtypes-each with its own temporally evolving prevalence and co-occurrence of phenotypes-without requiring aligned longitudinal phenotype data for all patients. However, the dimensionality of topic models makes interpretation challenging, and de facto analyses provide little intuition regarding phenotype relevance or phenotype interrelationships. PhenoLines enables one to compare phenotype prevalence within and across disease subtype topics, thus supporting subtype characterization, a task that involves identifying a proposed subtype's dominant phenotypes, ages of effect, and clinical validity. We contribute a data transformation workflow that employs the Human Phenotype Ontology to hierarchically organize phenotypes and aggregate the evolving probabilities produced by topic models. We introduce a novel measure of phenotype relevance that can be used to simplify the resulting topology. The design of PhenoLines was motivated by formative interviews with machine learning and clinical experts. We describe the collaborative design process, distill high-level tasks, and report on initial evaluations with machine learning experts and a medical domain expert. These results suggest that PhenoLines demonstrates promising approaches to support the characterization and optimization of topic models.

Supporting Handoff in Asynchronous Collaborative Sensemaking Using Knowledge-Transfer Graphs.

During asynchronous collaborative analysis, handoff of partial findings is challenging because externalizations produced by analysts may not adequately communicate their investigative process. To address this challenge, we developed techniques to automatically capture and help encode tacit aspects of the investigative process based on an analyst's interactions, and streamline explicit authoring of handoff annotations. We designed our techniques to mediate awareness of analysis coverage, support explicit communication of progress and uncertainty with annotation, and implicit communication through playback of investigation histories. To evaluate our techniques, we developed an interactive visual analysis system, KTGraph, that supports an asynchronous investigative document analysis task. We conducted a two-phase user study to characterize a set of handoff strategies and to compare investigative performance with and without our techniques. The results suggest that our techniques promote the use of more effective handoff strategies, help increase an awareness of prior investigative process and insights, as well as improve final investigative outcomes.

New horizons in microbiological food safety: Photodynamic Decontamination based on a curcumin derivative.

Outbreaks of foodborne diseases are regularly reported worldwide. In particular, uncooked plant food is considered risky in terms of microbiological safety. Food is also the most important transmission route for resistant microorganisms from animals to humans. Photodynamic Decontamination (PDc) of foodstuff was recently introduced as a novel approach for increasing microbiological food safety. We investigated the efficiency of PDc on plant food with different geometries (flat, spherical and complex) using a two-dimensional LED array as a light source (435 nm, 33.8 J cm-2) and the cationic curcumin derivative SACUR-3 as a photosensitiser. A photoantibacterial effect (>3 log10 CFU reduction) was achieved on all flat substrates (slices of cucumber, tomato and lettuce) with 10 µM, 50 µM or 100 µM SACUR-3. The maximal photokilling with a relative inactivation of 5.6 log10 was measured on lettuce using 50 µM of the photoactive compound. Phototreatment of non-germinated fenugreek seeds and mung beans was successful if the spherical objects were rotated while under illumination (antibacterial effect at 100 µM SACUR-3). The decontamination of mung bean germlings with a more complex geometry using the PDc approach was ineffective with the two-dimensional light source. In conclusion, PDc based on the cationic curcumin derivative SACUR-3 is very effective at improving the microbiological safety of plant food with a flat or spherical geometry. More complex objects will require the development of novel illumination devices.

A natural history study of X-linked myotubular myopathy.

OBJECTIVE: To define the natural history of X-linked myotubular myopathy (MTM). METHODS: We performed a cross-sectional study that included an online survey (n = 35) and a prospective, 1-year longitudinal investigation using a phone survey (n = 33). RESULTS: We ascertained data from 50 male patients with MTM and performed longitudinal assessments on 33 affected individuals. Consistent with existing knowledge, we found that MTM is a disorder associated with extensive morbidities, including wheelchair (86.7% nonambulant) and ventilator (75% requiring >16 hours of support) dependence. However, unlike previous reports and despite the high burden of disease, mortality was lower than anticipated (approximate rate 10%/y). Seventy-six percent of patients with MTM enrolled (mean age 10 years 11 months) were alive at the end of the study. Nearly all deaths in the study were associated with respiratory failure. In addition, the disease course was more stable than expected, with few adverse events reported during the prospective survey. Few non-muscle-related morbidities were identified, although an unexpectedly high incidence of learning disability (43%) was noted. Conversely, MTM was associated with substantial burdens on patient and caregiver daily living, reflected by missed days of school and lost workdays. CONCLUSIONS: MTM is one of the most severe neuromuscular disorders, with affected individuals requiring extensive mechanical interventions for survival. However, among study participants, the disease course was more stable than predicted, with more individuals surviving infancy and early childhood. These data reflect the disease burden of MTM but offer hope in terms of future therapeutic intervention.

Annotation Graphs: A Graph-Based Visualization for Meta-Analysis of Data Based on User-Authored Annotations.

User-authored annotations of data can support analysts in the activity of hypothesis generation and sensemaking, where it is not only critical to document key observations, but also to communicate insights between analysts. We present annotation graphs, a dynamic graph visualization that enables meta-analysis of data based on user-authored annotations. The annotation graph topology encodes annotation semantics, which describe the content of and relations between data selections, comments, and tags. We present a mixed-initiative approach to graph layout that integrates an analyst's manual manipulations with an automatic method based on similarity inferred from the annotation semantics. Various visual graph layout styles reveal different perspectives on the annotation semantics. Annotation graphs are implemented within C8, a system that supports authoring annotations during exploratory analysis of a dataset. We apply principles of Exploratory Sequential Data Analysis (ESDA) in designing C8, and further link these to an existing task typology in the visualization literature. We develop and evaluate the system through an iterative user-centered design process with three experts, situated in the domain of analyzing HCI experiment data. The results suggest that annotation graphs are effective as a method of visually extending user-authored annotations to data meta-analysis for discovery and organization of ideas.

PhenoStacks: Cross-Sectional Cohort Phenotype Comparison Visualizations.

Cross-sectional phenotype studies are used by genetics researchers to better understand how phenotypes vary across patients with genetic diseases, both within and between cohorts. Analyses within cohorts identify patterns between phenotypes and patients (e.g., co-occurrence) and isolate special cases (e.g., potential outliers). Comparing the variation of phenotypes between two cohorts can help distinguish how different factors affect disease manifestation (e.g., causal genes, age of onset, etc.). PhenoStacks is a novel visual analytics tool that supports the exploration of phenotype variation within and between cross-sectional patient cohorts. By leveraging the semantic hierarchy of the Human Phenotype Ontology, phenotypes are presented in context, can be grouped and clustered, and are summarized via overviews to support the exploration of phenotype distributions. The design of PhenoStacks was motivated by formative interviews with genetics researchers: we distil high-level tasks, present an algorithm for simplifying ontology topologies for visualization, and report the results of a deployment evaluation with four expert genetics researchers. The results suggest that PhenoStacks can help identify phenotype patterns, investigate data quality issues, and inform data collection design.

Methylsulfonyl Zn phthalocyanine: A polyvalent and powerful hydrophobic photosensitizer with a wide spectrum of photodynamic applications.

BACKGROUND: The biomedical photodynamic principle is based on the light-induced and photosensitizer-mediated killing of unwanted or harmful cells by overproduction of reactive oxygen species. Motivated by the success of photodynamic therapy (PDT) against several types of tumors, further applications of this approach are constantly identified which require the design and synthesis of novel photosensitizers with specifically tailored properties for a particular clinical application. METHODS: Hydrophobic photosensitizers are currently gaining attention and hence a tetramethylsulfonyl Zn(II) phthalocyanine (2) was designed with respect to the desired photoproperties. The photodynamic potential of 2 was assessed by the determination of its photophysical and photochemical properties, and by a large range of biological tests including its phototoxicity against cancer cells and Gram(+) bacteria. Unsubstituted ZnPc was used as a reference compound for comparison purposes. RESULTS: Phthalocyanine 2 has a better oxygen generation and is more photostable than ZnPc. 2 is a polyvalent and powerful hydrophobic photosensitizer with a wide spectrum of photodynamic applications against cancer (tested on A431 cells) and for Gram(+) PDI. Against Staphylococcus aureus, a maximum photokilling efficiency of more than 6 log10 steps was induced by a 5µM concentration of 2, outperforming the 3 log10 criterion for an antimicrobial effect (according to the recommendation of the American Society for Microbiology) by more than three orders of magnitude. CONCLUSIONS: Phthalocyanine 2 has attractive photophysical and -chemical characteristics. Initial evaluation of its application in anti-tumor PDT and PDI suggest potential for further pre-clinical and clinical development of this compound.

PhenoBlocks: Phenotype Comparison Visualizations.

The differential diagnosis of hereditary disorders is a challenging task for clinicians due to the heterogeneity of phenotypes that can be observed in patients. Existing clinical tools are often text-based and do not emphasize consistency, completeness, or granularity of phenotype reporting. This can impede clinical diagnosis and limit their utility to genetics researchers. Herein, we present PhenoBlocks, a novel visual analytics tool that supports the comparison of phenotypes between patients, or between a patient and the hallmark features of a disorder. An informal evaluation of PhenoBlocks with expert clinicians suggested that the visualization effectively guides the process of differential diagnosis and could reinforce the importance of complete, granular phenotypic reporting.