BI-LAVA: Biocuration with Hierarchical Image Labeling through Active Learning and Visual Analysis

In the biomedical domain, taxonomies organize the acquisition modalities of scientific images in hierarchical structures. Such taxonomies leverage large sets of correct image labels and provide essential information about the importance of a scientific publication, which could then be used in biocuration tasks. However, the hierarchical nature of the labels, the overhead of processing images, the absence or incompleteness of labeled data, and the expertise required to label this type of data impede the creation of useful datasets for biocuration. From a multi-year collaboration with biocurators and text-mining researchers, we derive an iterative visual analytics and active learning strategy to address these challenges. We implement this strategy in a system called BI-LAVA Biocuration with Hierarchical Image Labeling through Active Learning and Visual Analysis. BI-LAVA leverages a small set of image labels, a hierarchical set of image classifiers, and active learning to help model builders deal with incomplete ground-truth labels, target a hierarchical taxonomy of image modalities, and classify a large pool of unlabeled images. BI-LAVA's front end uses custom encodings to represent data distributions, taxonomies, image projections, and neighborhoods of image thumbnails, which help model builders explore an unfamiliar image dataset and taxonomy and correct and generate labels. An evaluation with machine learning practitioners shows that our mixed human-machine approach successfully supports domain experts in understanding the characteristics of classes within the taxonomy, as well as validating and improving data quality in labeled and unlabeled collections.Comment: 15 pages, 6 figure

Disgust implicated in obsessive-compulsive disorder

Psychiatric classificatory systems consider obsessions and compulsions as forms of anxiety disorder. However, the neurology of diseases associated with obsessive-compulsive symptoms suggests the involvement of fronto-striatal regions likely to be involved in the mediation of the emotion of disgust, suggesting that dysfunctions of disgust should be considered alongside anxiety in the pathogenesis of obsessive-compulsive behaviours. We therefore tested recognition of facial expressions of basic emotions (including disgust) by groups of participants with obsessive-compulsive disorder (OCD) and with Gilles de la Tourette's syndrome (GTS) with and without co-present obsessive-compulsive behaviours (GTS with OCB; GTS without OCB). A group of people suffering from panic disorder and generalized anxiety were also included in the study. Both groups with obsessive-compulsive symptoms (OCD; GTS with OCB) showed impaired recognition of facial expressions of disgust. Such problems were not evident in participants with panic disorder and generalized anxiety, or for participants with GTS without obsessions or compulsions, indicating that the deficit is closely related to the presence of obsessive-compulsive symptoms. Participants with OCD were able to assign words to emotion categories without difficulty, showing that their problem with disgust is linked to a failure to recognize this emotion in others and not a comprehension or response criterion effect. Impaired recognition of disgust is consistent with the neurology of OCD and with the idea that abnormal experience of disgust may be involved in the genesis of obsessions and compulsions

Integrating Engineering Data Systems for NASA Spaceflight Projects

NASA has a large range of custom-built and commercial data systems to support spaceflight programs. Some of the systems are re-used by many programs and projects over time. Management and systems engineering processes require integration of data across many of these systems, a difficult problem given the widely diverse nature of system interfaces and data models. This paper describes an ongoing project to use a central data model with a web services architecture to support the integration and access of linked data across engineering functions for multiple NASA programs. The work involves the implementation of a web service-based middleware system called Data Aggregator to bring together data from a variety of systems to support space exploration. Data Aggregator includes a central data model registry for storing and managing links between the data in disparate systems. Initially developed for NASA's Constellation Program needs, Data Aggregator is currently being repurposed to support the International Space Station Program and new NASA projects with processes that involve significant aggregating and linking of data. This change in user needs led to development of a more streamlined data model registry for Data Aggregator in order to simplify adding new project application data as well as standardization of the Data Aggregator query syntax to facilitate cross-application querying by client applications. This paper documents the approach from a set of stand-alone engineering systems from which data are manually retrieved and integrated, to a web of engineering data systems from which the latest data are automatically retrieved and more quickly and accurately integrated. This paper includes the lessons learned through these efforts, including the design and development of a service-oriented architecture and the evolution of the data model registry approaches as the effort continues to evolve and adapt to support multiple NASA programs and priorities

Scientific Visualization to Study Flux Transfer Events at the Community Coordinated Modeling Center

In this paper we present results of modeling of reconnection at the dayside magnetopause with subsequent development of flux transfer event signatures. The tools used include new methods that have been added to the suite of visualization methods that are used at the Community Coordinated Modeling Center (CCMC). Flux transfer events result from localized reconnection that connect magnetosheath magnetic field and plasma with magnetospheric fields and plasma and results in flux rope structures that span the dayside magnetopause. The onset of flux rope formation and the three-dimensional structure of flux ropes are studied as they have been modeled by high-resolution magnetohydrodynamic simulations of the dayside magnetosphere of the Earth. We show that flux transfer events are complex three-dimensional structures that require modern visualization and analysis techniques. Two suites of visualization methods are presented and we demonstrate the usefulness of those methods through the CCMC web site to the general science user

Therapeutic approach in glioblastoma multiforme with primitive neuroectodermal tumor components: case report and review of the literature

Glioblastoma multiforme (GBM) is the most common and aggressive malignant glioma that is treated with first-line therapy, using surgical resection followed by local radiotherapy and concomitant/adjuvant temozolomide (TMZ) treatment. GBM is characterised by a high local recurrence rate and a low response to therapy. Primitive neuroectodermal tumour (PNET) of the brain revealed a low local recurrence rate; however, it also exhibited a high risk of cerebrospinal fluid (CSF) dissemination. PNET is treated with surgery followed by craniospinal irradiation (CSI) and platinum-based chemotherapy in order to prevent CSF dissemination. GBM with PNET-like components (GBM/PNET) is an emerging variant of GBM, characterised by a PNET-like clinical behaviour with an increased risk of CSF dissemination; it also may benefit from platinum-based chemotherapy upfront or following failure of GBM therapy. The results presented regarding the management of GBM/PNET are based on case reports or case series, so a standard therapeutic approach for GBM/PNET is not defined, constituing a challenging diagnostic and therapeutic dilemma. In this report, a case of a recurrent GBM/PNET treated with surgical resection and radiochemotherapy as Stupp protocol, and successive platinum-based chemotherapy due to the development of leptomeningeal dissemintation and an extracranial metastasis, is discussed. A review of the main papers regarding this rare GBM variant and its therapeutic approach are also reported. In conclusion, GBM/PNET should be treated with a multimodal approach including surgery, chemoradiotherapy, and/or the early introduction of CSI and platinum-based chemotherapy upfront or at recurrence

Habitat occupancy of the threatened Diademed Plover (Phegornis mitchellii) is not affected by llama grazing or peatland size, but declines with peatland humidity

Fil: Pietrek, Alejandro G. University of California Santa Cruz. Ecology and Evolutionary Biology Department. Santa Cruz, CA; United States of America.Fil: Pietrek, Alejandro G. Universidad Nacional de Salta; Argentina.Fil: Pietrek, Alejandro G. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Bio y Geociencias del NOA; Argentina.Fil: Cockle, Kristina L. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología Subtropical, Puerto Iguazú, Misiones; Argentina.Fil: Izquierdo, Andrea E. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; Argentina.Fil: Izquierdo, Andrea E. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Berrios, Viviana S. Universidad Nacional de Salta. Facultad de Ciencias Naturales; Argentina.Fil: Berrios, Viviana S. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Lyon, Bruce E. University of California Santa Cruz. Ecology and Evolutionary Biology Department. Santa Cruz, CA; United States of America.Fil: Lyon, Bruce E. Universidad Nacional de Salta; Argentina.Fil: Lyon, Bruce E. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Bio y Geociencias del NOA; Argentina.Many habitat-specialist organisms occur in distinct, patchy habitat, yet do not occupy all patches, and an important question is why apparently suitable habitat remains unoccupied. We examined factors influencing patch occupancy in near-threatened, little-known Diademed Plovers (Phegornis mitchellii), arguably the bird most specialized to life in High Andean peatlands. Andean peatlands are well-suited to occupancy modelling because they are discrete patches of humid habitat within a matrix of high-altitude steppe. We hypothesized that Diademed Plovers occupy preferably larger and more humid peatlands, and avoid peatlands used for grazing by llamas and vicuñas, which may trample vegetation and nests. From December 2021 to February 2022 (breeding season), we conducted plover occupancy surveys (2–4) on 40 peatlands at Lagunas de Vilama, a landscape of arid steppe and wetlands above 4,500 m in NW Argentina. We measured peatland size, grazing pressure, topographic and remotely-sensed variables that correlate with humidity, and incorporated these as covariates in occupancy models. Occupancy models showed that more than 50% of the studied peatlands were used by Diademed Plovers and most showed signs of reproduction, highlighting the importance of the Vilama Wetlands for Diademed Plover conservation. Within peatlands, Diademed Plovers were most often associated with headwaters. The top ranked occupancy model included constant detection, random spatial effects, and a single occupancy covariate: mean NDWI (Normalized Difference Water Index, an index correlated with water content and humidity) over the previous three years. Contrary to our prediction, Diademed Plovers preferred less water-saturated peatlands (lower NDWI), possibly to avoid nest flooding. This may be especially important in wet years, like the year when we conducted our surveys. Neither peatland size nor grazing by llamas and vicuñas affected peatland use by Diademed Plovers, suggesting that llama grazing at current levels may be compatible with plover conservation. For organisms that specialize on humid habitats, such as peatlands, factors affecting occupancy may vary temporally with variation in climate, and we recommend follow-up surveys across multi-year timescales to untangle the impact of climate on animals’ use of humid habitats.info:eu-repo/semantics/publishedVersionFil: Pietrek, Alejandro G. University of California Santa Cruz. Ecology and Evolutionary Biology Department. Santa Cruz, CA; United States of America.Fil: Pietrek, Alejandro G. Universidad Nacional de Salta; Argentina.Fil: Pietrek, Alejandro G. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Bio y Geociencias del NOA; Argentina.Fil: Cockle, Kristina L. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología Subtropical, Puerto Iguazú, Misiones; Argentina.Fil: Izquierdo, Andrea E. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; Argentina.Fil: Izquierdo, Andrea E. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Berrios, Viviana S. Universidad Nacional de Salta. Facultad de Ciencias Naturales; Argentina.Fil: Berrios, Viviana S. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Lyon, Bruce E. University of California Santa Cruz. Ecology and Evolutionary Biology Department. Santa Cruz, CA; United States of America.Fil: Lyon, Bruce E. Universidad Nacional de Salta; Argentina.Fil: Lyon, Bruce E. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Bio y Geociencias del NOA; Argentina