Miracle-dz/UniFAR-FTUs huggingface dataset:
Iterative Refinement and Quality Checking of Annotation Guidelines — How to Deal Effectively with Semantically Sloppy Named Entity Types, such as Pathological Phenomena

We here discuss a methodology for dealing with the annotation of semantically hard to delineate, i.e., sloppy, named entity types. To illustrate sloppiness of entities, we treat an example from the medical domain, namely pathological phenomena. Based on our experience with iterative guideline refinement we propose to carefully characterize the thematic scope of the annotation by positive and negative coding lists and allow for alternative, short vs. long mention span annotations. Short spans account for canonical entity mentions (e.g., standardized disease names), while long spans cover descriptive text snippets which contain entity-specific elaborations (e.g., anatomical locations, observational details, etc.). Using this stratified approach, evidence for increasing annotation performance is provided by kappa-based inter-annotator agreement measurements over several, iterative annotation rounds using continuously refined guidelines. The latter reflects the increasing understanding of the sloppy entity class both from the perspective of guideline writers and users (annotators). Given our data, we have gathered evidence that we can deal with sloppiness in a controlled manner and expect inter-annotator agreement values around 80% for PathoJen, the pathological phenomena corpus currently under development in our lab.
Conceptualizing participation in context for children and youth with disabilities: an activity setting perspective

Abstract This article considers the conceptualization, operationalization and implications of “activity settings” for research on the recreation and leisure participation of children and youth with disabilities. Activity settings are contextualized settings that situate child and youth activities and their participation experiences. We discuss activity settings as an important construct for considering environmental qualities that provide opportunities for beneficial participation experiences for children and youth with disabilities. The article considers existing research using the concept of activity settings, the conceptualization of environment and contemporary issues in the measurement of participation and environment, indicating how these are addressed by an activity settings approach. We then describe the development of two quantitative measures of recreation and leisure activity settings – one assessing environmental qualities and the other assessing youth experiences – that have the potential to inform researchers, managers and clinicians about relationships between environmental qualities and participation experiences. Finally, we consider the implications of an activity settings approach for research, theory building and clinical practice. Implications for Rehabilitation An activity setting perspective can enhance understanding of the recreation and leisure participation of children and youth with disabilities. The Measure of Environmental Qualities of Activity Settings (MEQAS) and Self-reported Experiences of Activity Settings (SEAS) provide unique assessments of environmental qualities and experiences from an activity setting perspective. Clinicians might use the SEAS alone to understand particular youth experiences in certain types of settings, which may be limiting or facilitating development. The combined use of the SEAS and MEQAS can provide experiential profiles linked to activity setting qualities such as structure, type of activity and social partners, providing a valuable source of information about youth programs.
Combined gamma‐irradiation and subsequent cisplatin treatment in human squamous carcinoma cell lines sensitive and resistant to cisplatin

Purpose: To investigate the effects of combined radiation and subsequent cisplatin treatment on the human squamous carcinoma cell line SCC‐25 and its cisplatin‐resistant derivative SCC‐25/CP. Materials and methods: SCC‐25 and SCC‐25/CP cells were treated with various gamma‐ray doses (5 cGy–7 Gy) followed 60 min later by cisplatin treatment and subsequently assayed for survival using a conventional colony assay. For SCC‐25, the subsequent cisplatin treatment was 0.1, 1, 10 and 20 µM for 1 h. For the more cisplatin‐resistant SCC‐25/CP cells, the subsequent cisplatin treatment was 10 and 50 µM for 1 h. Results: The cisplatin‐resistant SCC‐25/CP cells were not cross‐resistant to gamma‐irradiation. Subsequent treatment with an LD50 concentration of cisplatin (10 and 50 µM for SCC‐25 and SCC‐25/CP, respectively) resulted in radiosensitization for SCC‐25/CP but not for SCC‐25 cells. Gamma‐irradiation of SCC‐25/CP cells followed by treatment with 10 and 50 µM cisplatin for 1 h resulted in radiation survival curves displaying a significant low‐dose hypersensitive region followed by increased radioresistance at higher doses. A total of 10 µM cisplatin resulted in radiosensitization confined to the low‐dose region (0.05 and 0.25 Gy), whereas the higher cisplatin treatment of 50 µM resulted in the appearance of a hypersensitive region together with a reduction of the increased radioresistance region. In contrast, cisplatin treatment (0.1, 1, 10 and 20 µM for 1 h) of SCC‐25 cells had no significant effect on survival following 2.5 or 7.0 Gy and actually resulted in an increased low‐dose radiation survival (0.05, 0.25 and 1 Gy) when survival was corrected for cisplatin treatment (p<0.01 for all cisplatin concentrations tested). Conclusions: The significant radiosensitization for SCC‐25/CP given subsequent treatment with 50 µM cisplatin indicates cisplatin can inhibit the increased radioresistance response in SCC‐25/CP cells. In contrast, the subsequent cisplatin treatment of SCC‐25 cells can enhance their survival following low radiation doses.
A KEYHOLE PLAN RECOGNITION MODEL FOR ALZHEIMER'S PATIENTS: FIRST RESULTS

This article addresses the problem of recognizing the behavior of a person suffering from Alzheimer's disease at early-intermediate stages. We present a keyhole plan recognition model, based on lattice theory and action description logic, which transforms the recognition problem into a classification issue. This approach allows us to formalize the plausible incoherent intentions of the patient, resulting from the symptoms of his cognitive impairment, such as disorientation, memory lapse, etc. An implementation of this model was tested in our smart home laboratory, by simulating a set of real case scenarios.
An Immunocytochemical Approach to Detection of Mitochondrial Disorders

Mitochondrial disorders can lead to a confusing array of symptoms, which frequently makes a diagnosis difficult. Traditional approaches to such diagnoses are based on enzyme activity assays, with further characterization provided by genetic analysis. However, these methods require relatively large sample sizes, are time-consuming, labor-intensive, and show variability between laboratories. Here, we report an immunocytochemical test that makes use of monoclonal antibodies to subunits from each of the oxidative phosphorylation complexes and pyruvate dehydrogenase to aid in the detection of mitochondrial disorders. It can be completed and data analyzed in less than 4 hr. We have used this test to study fibroblast cultures from patients with mitochondrial disorders arising from both mitochondrial DNA and nuclear DNA defects. We have also examined cases of Leigh syndrome arising from different genetic causes. We show that patients can be categorized on the basis of which complexes are affected and whether or not the defect being studied shows a mosaic distribution, an indicator of whether the causal mutation(s) is/are in the mitochondrial or nuclear genome. Immunocytochemical analysis as described here should be considered as an initial screen for mitochondrial disorders by which to direct (and limit) the subsequent enzymatic and genetic tests required to make an unambiguous diagnosis.
DYNAMIC BEHAVIOR OF GENERALIZED INVERTIBLE HÉNON MAP

Interesting dynamic behavior of Generalized Invertible Henon Map has been observed under different feasible conditions in the framework of nonlinear dynamics. Evolutionary phenomena are discussed through bifurcation analysis leading to period doubling and chaos. Appearance of chaos in the system, within certain range of parameter, is detected by plotting Lyapunov characteristic exponents (LCE). The plot of indicators, Fast Lyapunov indicators (FLI), Smaller Alignment Indices (SALI), and Dynamic Lyapunov Indicator (DLI), have been obtained for further identification of regular and chaotic motions of the invertible Henon map. The numerical results clearly show the merits and demerits of these recently discovered indicators. For the dimension of the chaotic attractor, correlation dimension has been calculated numerically.
Direct and Indirect Effects of Cumulative Trauma, PTSD, and Substance Use Disorder on Probability of Arrest Among Lower Income African American and Latina Women

We conducted a secondary analysis of cross-sectional data to examine the association of cumulative trauma, post-traumatic stress disorder (PTSD), and substance use disorder (SUD) with the probability of arrest in a sample of socioeconomically disadvantaged African American and Latino mothers (N = 158). Results revealed that 34% of the sample had a history of arrest. Logistic regression revealed that cumulative trauma was significantly and positively associated with the likelihood of arrest. Exposure to increasing numbers of traumas contributed to greater odds of arrest, as much as 62% for each additional trauma exposure. Moreover, binary mediation analyses revealed that PTSD and SUD exerted an intervening influence on the pathway between cumulative trauma and the probability of arrest. Women with a lifetime history of PTSD or SUD were 5–6 times more likely to be arrested than women without either disorder. Lifetime PTSD and lifetime SUD were partial mediators of the association between cumulative trauma exposure and arrest, accounting for 63% of the variance. These findings have important implications for intervention efforts geared toward helping young racial/ethnic minority mothers, especially those with PTSD and SUD, manage the distress and impairment that may contribute to criminal justice involvement.
Imaging vector field using SMP images

This paper presents a new concept of texture image method for displaying divergent-free vector field on surfaces, sine modulated potential (SMP) map. A scalar potential for such vector field is first defined. Field vectors are then mapped to a grayscale image through its scalar potential modulated with a sine function. The image visualizes a soft appearance of flux tubes instead of flux lines, whose orientation and width reflect the direction and amplitude of field vectors respectively. Animated SMP images can identify the exact "flow" direction inside each flux tube for the vector field at a specific moment, which is often missed in other visualization techniques. SMP images can also be animated for visualization of time-varying field, in which the variation of the field in space and the variation with time can be revealed simultaneously.
Occurrence and Hyperthyroidism Spontaneous Preceded by Remission of Graves ' Painless Thyroiditis

A 45-year-old woman was referred to our hospital because of discomfort in the cervical region. Laboratory findings revealed thyrotoxicosis with positive TSH receptor antibodies, but acute inflammatory data were absent. After three weeks the thyroid hormone levels spontaneously decreased to hypothyroid levels, and thyroidal radioactive iodine uptake (RAID) was below normal. A needlebiopsy specimen of the thyroid gland obtained two months later showed diffuse lymphocytic thyroiditis, and she was therefore diagnosed as having had painless thyroiditis. Two months after returning to euthyroidism, a second thyrotoxicosis developed. TSH receptor antibodies remained positive, but RAIU was slightly above normal, indicating Graves' hyperthyroidism. Treatment with antithyroidal drugs was commenced but was soon discontinued due to an allergic reaction. Although only f3-adrenergic antagonist was administered for treating the thyrotoxicosis, thyroid function was gradually normalized in parallel with the reduction in TSH receptor antibody. In this case, painless thyroiditis would be followed by Graves' disease and subsequent spontaneous remission.
An Improved Multiple Objectives Optimization of QoS Routing Algorithm Base on Genetic Algorithm

Providing quality of service (QoS) guarantees in packet networks gives rise to several challenging issues. One of them is how to determine a feasible path that satisfies a set of constraints. Multi-constrained QoS routing finds a feasible route in the network that satisfies multiple independent constraints. In general, multi-constrained path selection is a NP-complete problem that cannot be exactly solved in polynomial time. The existing routing algorithms usually optimize a single objective, which have some inherent drawbacks. An improved genetic algorithm based on multi-objective optimization algorithm for multiple QoS routing constraints is proposed in this paper, which search for the set of Pareto optimal solutions of QoS routing. Simulation results show that this algorithm has a high success ratio, and can obtain a set of QoS routing which satisfy all constraints in finite evolutionary generations. Those Qos routing overcomes the drawbacks of single objective optimization.
HIF 1 β C / EBP Responses by the Transcription Factors Cord Factor Recognition and Macrophage Differential Control of Mincle-Dependent Bronte and Roland

Trehalose-6,6-dimycolate (TDM), the mycobacterial cord factor, and its synthetic analog Trehalose-6,6-dibehenate (TDB) bind to the C-type lectin receptors macrophage-inducible C-type lectin (Mincle) and Mcl to activate macrophages. Genetically, the tran-scriptional response to TDB/TDM has been defined to require FcRg-Syk-Card9 signaling. However, TDB/TDM-triggered kinase activation has not been studied well, and it is largely unknown which transcriptional regulators bring about inflammatory gene expression. In this article, we report that TDB/TDM caused only weak Syk-phosphorylation in resting macrophages, consistent with low basal Mincle expression. However, LPS-priming caused MYD88-dependent upregulation of Mincle, resulting in enhanced TDB/TDM-induced kinase activation and more rapid inflammatory gene expression. TLR-induced Mincle expression partially circumvented the requirement for Mcl in the response to TDB/TDM. To dissect transcriptional responses to TDB/TDM, we mined microarray data and identified early growth response (Egr) family transcription factors as direct Mincle target genes, whereas upregulation of Cebpb and Hif1a required new protein synthesis. Macrophages and dendritic cells lacking C/EBPb showed nearly complete abrogation of TDB/TDM responsiveness, but also failed to upregulate Mincle. Retroviral rescue of Mincle expression in Cebpb-deficient cells restored induction of Egr1, but not of G-CSF. This pattern of C/EBPb dependence was also observed after stimulation with the Dectin-1 ligand Curdlan. Inducible expression of hypoxia-inducible factor 1a (HIF1a) also required C/EBPb. In turn, HIF1a was not required for Mincle expression, kinase activation, and Egr1 or Csf3 expression, but critically contributed to NO production. Taken together, we identify C/EBPb as central hub in Mincle expression and inflam-matory gene induction, whereas HIF1a controls Nos2 expression. C/EBPb also connects TLR signals to cord factor responsiveness through MYD88-dependent upregulation of Mincle. T he intracellular pathogen Mycobacterium tuberculosis survives and multiplies in the phagosome of macro-phages, which become activated and are recruited along with other cells to the site of infection to form typical granulomas. Mycobacteria are a rich source of pathogen-associated molecular patterns that include mycobacterial DNA triggering TLR9, the 19-kDa lipopeptide that activates TLR2, and several cell-wall lipids and glycolipids (1). The mycobacterial cord factor, Tre-halose-6,6-dimycolate (TDM), is abundant in the mycobacterial cell and has long been known to be a major virulence factor of mycobacteria and a potent inducer of inflammation in animal models (2). Geisel et al. (3) demonstrated that TDM is the major cell-wall glycolipid inducing inflammatory responses by macro-phages in vitro. Importantly, TDM per se is sufficient to induce formation of granulomas when injected in oil droplets (4). TDM (5) and …
Towards Efficient Component-Based Software Development of Distributed Embedded Systems

The paper presents Save-IDE, an Integrated Development Environment for thedevelopment of component-based embedded systems. Save-IDE supports efficient development of dependable embedded systems by providing tools for design of embedded software systems using a dedicated component model, formal specification and analysis of component and system behaviors already in early development phases, and a fully automated transformation of the system of components into an executable image.
You’ve Got Mail

Email is a primary method of communication for organizations, clients, and customers. The goal of this study is to examine the effects of a brief implementation of an online, less expensive, and less time consuming training session on writing a professional email. The findings suggest that conscientiousness predicts comfort with training which, in turn, predicts motivation to transfer. In other words, we found evidence to support the notion that individual characteristics can predict affective reactions which then predict utility reactions. The data, however, do not support the link between motivation to transfer and objective learning. Overall, practitioners and researchers need to measure and account for individual characteristics (e.g., conscientiousness) as well as affective (e.g., comfort with the training) and utility reactions (e.g., motivation to transfer) when evaluating training programs.
Genome-Wide Transcriptome Directed Pathway Analysis of Maternal Pre-Eclampsia Susceptibility Genes

Background Preeclampsia (PE) is a serious hypertensive pregnancy disorder with a significant genetic component. Numerous genetic studies, including our own, have yielded many susceptibility genes from distinct functional groups. Additionally, transcriptome profiling of tissues at the maternal-fetal interface has likewise yielded many differentially expressed genes. Often there is little overlap between these two approaches, although genes identified in both approaches are significantly associated with PE. We have thus taken a novel integrative bioinformatics approach of analysing pathways common to the susceptibility genes and the PE transcriptome. Methods Using Illumina Human Ht12v4 and Wg6v3 BeadChips, transcriptome profiling was conducted on n = 65 normotensive and n = 60 PE decidua basalis tissues collected at delivery. The R software package libraries lumi and limma were used to preprocess transcript data for pathway analysis. Pathways were analysed and constructed using Pathway Studio. We examined ten candidate genes, which are from these functional groups: activin/inhibin signalling—ACVR1, ACVR1C, ACVR2A, INHA, INHBB; structural components—COL4A1, COL4A2 and M1 family aminopeptidases—ERAP1, ERAP2 and LNPEP. Results/Conclusion Major common regulators/targets of these susceptibility genes identified were AGT, IFNG, IL6, INHBA, SERPINE1, TGFB1 and VEGFA. The top two categories of pathways associated with the susceptibility genes, which were significantly altered in the PE decidual transcriptome, were apoptosis and cell signaling (p < 0.001). Thus, susceptibility genes from distinct functional groups share similar downstream pathways through common regulators/targets, some of which are altered in PE. This study contributes to a better understanding of how susceptibility genes may interact in the development of PE. With this knowledge, more targeted functional analyses of PE susceptibility genes in these key pathways can be performed to examine their contributions to the pathogenesis and severity of PE.
Classification on the Monogenic Scale Space: Application to Target Recognition in SAR Image

This paper introduces a novel classification strategy based on the monogenic scale space for target recognition in Synthetic Aperture Radar (SAR) image. The proposed method exploits monogenic signal theory, a multidimensional generalization of the analytic signal, to capture the characteristics of SAR image, e.g., broad spectral information and simultaneous spatial localization. The components derived from the monogenic signal at different scales are then applied into a recently developed framework, sparse representation-based classification (SRC). Moreover, to deal with the data set, whose target classes are not linearly separable, the classification via kernel combination is proposed, where the multiple components of the monogenic signal are jointly considered into a unifying framework for target recognition. The novelty of this paper comes from: the development of monogenic feature via uniformly downsampling, normalization, and concatenation of the components at various scales; the development of score-level fusion for SRCs; and the development of composite kernel learning for classification. In particular, the comparative experimental studies under nonliteral operating conditions, e.g., structural modifications, random noise corruption, and variations in depression angle, are performed. The comparative experimental studies of various algorithms, including the linear support vector machine and the kernel version, the SRC and the variants, kernel SRC, kernel linear representation, and sparse representation of monogenic signal, are performed too. The feasibility of the proposed method has been successfully verified using Moving and Stationary Target Acquiration and Recognition database. The experimental results demonstrate that significant improvement for recognition accuracy can be achieved by the proposed method in comparison with the baseline algorithms.
3D object classification for mobile robots in home-environments using web-data

Building knowledge for robots can be tedious, especially if focused on object class recognition in home environments where hundreds of everyday-objects - some with a huge intra class variability - can be found. Object recognition and especially object class recognition is a key capability in home-robotics. Achieving deployable results from state-of-. the-art algorithms is not yet achievable when the number of classes increases and near real-time is the goal. Hence, we propose to exploit contextual knowledge by using sensor and hardware constraints from the robotics and home domains and show how to use the internet as a source for obtaining the required data for building a fast, vision based object categorization system for robotics. In this paper, we give an overview of the available constraints and advantages of using a robot to set priors for object classification and propose a system which covers automated model acquisition from the web, domain simulation, descriptor generation, 3D data processing from dense stereo and classification for a - not too far - robot scenario in an internet-connected home-environment. In this work we show that this system is capable of being used in home robotics in a fast and robust way for recognition of object classes commonly found in such environments, including but not limited to chairs and mugs. We also discuss challenges and missing pieces in the framework and useful extensions.