Inverse Classification for Comparison-based Interpretability in Machine Learning

In the context of post-hoc interpretability, this paper addresses the task of explaining the prediction of a classifier, considering the case where no information is available, neither on the classifier itself, nor on the processed data (neither the training nor the test data). It proposes an instance-based approach whose principle consists in determining the minimal changes needed to alter a prediction: given a data point whose classification must be explained, the proposed method consists in identifying a close neighbour classified differently, where the closeness definition integrates a sparsity constraint. This principle is implemented using observation generation in the Growing Spheres algorithm. Experimental results on two datasets illustrate the relevance of the proposed approach that can be used to gain knowledge about the classifier.Comment: preprin

\u27Candidatus Xenohaliotis californiensis\u27, a newly described pathogen of abalone, Haliotis spp., along the west coast of North America

Withering syndrome is a fatal disease of wild and cultured abalone. Haliotis spp., that inhabit the west coast of North America. The aetiological agent of withering syndrome has recently been identified as a member of the family Rickettsiaceae in the order Rickettsiales. Using a combination of morphological, serological, life history and genomic (16S rDNA) characterization. we have identified this bacterium as a unique taxon and propose the provisional status of \u27Candidatus Xenohaliotis californiensis\u27, The Gram-negative. obligate intracellular pleomorphic bacterium is found within membrane-bound vacuoles in the cytoplasm of abalone gastrointestinal epithelial cells. The bacterium is not cultivable on synthetic media or in fish cell lines (e.g. CHSE-214) and may be controlled by tetracyclines (oxytetracycline) but not by chloramphenicol, clarithromycin or sarafloxicin. Phylogenetic analysis based on the 16S rDNA of \u27Candidatus Xenohaliotis californiensis\u27 places it in the alpha-subclass of the class Proteobacteria but not to the four recognized subtaxa of the alpha-Proteobacteria (alpha-1, alpha-2, alpha-3 and alpha-4). The bacterium can be detected in tissue squashes stained with propidium iodide, microscopic examination of stained tissue sections, PCR or in situ hybridization. \u27Candidatus Xenohaliotis californiensis\u27 can be differentiated from other closely related alpha-Proteobacteria by its unique 16S rDNA sequence

B-Cell Non-Hodgkin’s Lymphoma: viewing an aggressive neck mass in an older adult from a primary care perspective

Abstract Patients with neck masses typically present to primary care providers, but most are unfamiliar with the management of aggressively expanding neck masses. With so many varied structures in the cervical region, a rapidly growing neck mass can be a diagnostic dilemma. The broad initial differential includes infectious, inflammatory, vascular, and malignant causes. When the clinical course points to an aggressive malignancy, the location of the mass helps provide the clues to the likely etiology. Potential sites of involvement include the musculature, bone, larynx, trachea, esophagus, lymph tissue and thyroid tissue. Anterior neck masses at the level the thyroid should prompt a differential of primary thyroid lymphomas. Diffuse large B-cell lymphoma is most common, followed by mucosa-associated lymphoid tissue lymphoma, follicular lymphoma, and small lymphocytic lymphoma. Anaplastic thyroid carcinoma should be considered as well. A history of Hashimoto’s thyroiditis should lead the clinician toward the large B-cell lymphoma.Prompt diagnosis via fine-needle aspiration biopsy is essential, because compressive symptoms and airway collapse may rapidly ensue. A correct clinical and histopathologic diagnosis is essential. Primary thyroid lymphoma can often be treated with chemoimmunotherapy and radiation has a mean overall survival of 9.0 years. Anaplastic thyroid carcinoma is often locally aggressive with advanced metastatic disease at presentation, and treatment options are more limited. Primary care physicians need to be familiar with these relatively rare etiologies for an aggressively expanding neck mass in order to recognize and rapidly coordinate diagnostic and treatment options in a timely fashion

Observational measure of implementation progress in community based settings: The Stages of implementation completion (SIC)

<p>Abstract</p> <p>Background</p> <p>An increasingly large body of research is focused on designing and testing strategies to improve knowledge about how to embed evidence-based programs (EBP) into community settings. Development of strategies for overcoming barriers and increasing the effectiveness and pace of implementation is a high priority. Yet, there are few research tools that measure the implementation process itself. The Stages of Implementation Completion (SIC) is an observation-based measure that is used to track the time to achievement of key implementation milestones in an EBP being implemented in 51 counties in 53 sites (two counties have two sites) in two states in the United States.</p> <p>Methods</p> <p>The SIC was developed in the context of a randomized trial comparing the effectiveness of two implementation strategies: community development teams (experimental condition) and individualized implementation (control condition). Fifty-one counties were randomized to experimental or control conditions for implementation of multidimensional treatment foster care (MTFC), an alternative to group/residential care placement for children and adolescents. Progress through eight implementation stages was tracked by noting dates of completion of specific activities in each stage. Activities were tailored to the strategies for implementing the specific EBP.</p> <p>Results</p> <p>Preliminary data showed that several counties ceased progress during pre-implementation and that there was a high degree of variability among sites in the duration scores per stage and on the proportion of activities that were completed in each stage. Progress through activities and stages for three example counties is shown.</p> <p>Conclusions</p> <p>By assessing the attainment time of each stage and the proportion of activities completed, the SIC measure can be used to track and compare the effectiveness of various implementation strategies. Data from the SIC will provide sites with relevant information on the time and resources needed to implement MTFC during various phases of implementation. With some modifications, the SIC could be appropriate for use in evaluating implementation strategies in head-to-head randomized implementation trials and as a monitoring tool for rolling out other EBPs.</p

Tracking of dietary intakes in early childhood : the Melbourne InFANT program

Background/Objectives: The objectives of the present study were to describe food and nutrient intakes in children aged 9 and 18 months, and to assess tracking of intakes between these two ages.Subjects/Methods: Participants were 177 children of first-time mothers from the control arm of the Melbourne Infant Feeding Activity and Nutrition Trial (InFANT) Program. Dietary intake was collected at 9 and 18 months using three 24&thinsp;h diet recalls. Tracking was assessed for food and nutrient intakes using logistic regression analysis and estimating partial correlation coefficients, respectively.Results: Although overall nutrient intakes estimated in this study did not indicate a particular risk of nutrient deficiency, our findings suggest that consumption of energy-dense, nutrient-poor foods occurred as early as 9 months of age, with some of these foods tracking highly over the weaning period. Intakes of healthier foods such as fruits, vegetables, dairy products, eggs, fish and water were also relatively stable over this transition from infancy to toddlerhood, along with moderate tracking for riboflavin, iodine, fibre, calcium and iron. Tracking was low but close to &rho;=0.3 for zinc, magnesium and potassium intakes.Conclusions: The tracking of energy-dense, nutrient-poor foods has important implications for public health, given the development of early eating behaviours is likely to be modifiable. At this stage of life, dietary intakes are largely influenced by the foods parents provide, parental feeding practices and modelling. This study supports the importance of promoting healthy dietary trajectories from infancy.<br /

Impact of early applied upper limb stimulation: The EXPLICIT-stroke programme design

Main claims of the literature are that functional recovery of the paretic upper limb is mainly defined within the first month post stroke and that rehabilitation services should preferably be applied intensively and in a task-oriented way within this particular time window. EXplaining PLastICITy after stroke (acronym EXPLICIT-stroke) aims to explore the underlying mechanisms of post stroke upper limb recovery. Two randomized single blinded trials form the core of the programme, investigating the effects of early modified Constraint-Induced Movement Therapy (modified CIMT) and EMG-triggered Neuro-Muscular Stimulation (EMG-NMS) in patients with respectively a favourable or poor probability for recovery of dexterity.BioMechanical EngineeringMechanical, Maritime and Materials Engineerin

Rhizome Severing Increases Root Lifespan of Leymus chinensis in a Typical Steppe of Inner Mongolia

Root lifespan is an important trait that determines plants' ability to acquire and conserve soil resources. There have been several studies investigating characteristics of root lifespan of both woody and herbaceous species. However, most of the studies have focused on non-clonal plants, and there have been little data on root lifespan for clonal plants that occur widely in temperate grasslands.We investigated the effects of rhizome severing on overall root lifespan of Leymus chinensis, a clonal, dominant grass species in the temperate steppe in northern China, in a 2-year field study using modified rhizotron technique. More specifically, we investigated the effects of rhizome severing on root lifespan of roots born in different seasons and distributed at different soil depths. Rhizome severing led to an increase in the overall root lifespan from 81 to 103 days. The increase in root lifespan exhibited spatial and temporal characteristics such that it increased lifespan for roots distributed in the top two soil layers and for roots born in summer and spring, but it had no effect on lifespan of roots in the deep soil layer and born in autumn. We also examined the effect of rhizome severing on carbohydrate and N contents in roots, and found that root carbohydrate and N contents were not affected by rhizome severing. Further, we found that root lifespan of Stipa krylovii and Artemisia frigida, two dominant, non-clonal species in the temperate steppe, was significantly longer (118 d) than that of L. chinensis (81 d), and this value became comparable to that of L. chinensis under rhizome severing (103 d).We found that root lifespan in dominant, clonal L. chinensis was shorter than for the dominant, non-clonal species of S. krylovii and A. frigida. There was a substantial increase in the root lifespan of L. chinensis in response to severing their rhizomes, and this increase in root lifespan exhibited temporal and spatial characteristics. These findings suggest that the presence of rhizomes is likely to account for the observed short lifespan of clonal plant species in the temperate steppe

High-Resolution Positional Tracking for Long-Term Analysis of Drosophila Sleep and Locomotion Using the “Tracker” Program

Drosophila melanogaster has been used for decades in the study of circadian behavior, and more recently has become a popular model for the study of sleep. The classic method for monitoring fly activity involves counting the number of infrared beam crosses in individual small glass tubes. Incident recording methods such as this can measure gross locomotor activity, but they are unable to provide details about where the fly is located in space and do not detect small movements (i.e. anything less than half the enclosure size), which could lead to an overestimation of sleep and an inaccurate report of the behavior of the fly. This is especially problematic if the fly is awake, but is not moving distances that span the enclosure. Similarly, locomotor deficiencies could be incorrectly classified as sleep phenotypes. To address these issues, we have developed a locomotor tracking technique (the “Tracker” program) that records the exact location of a fly in real time. This allows for the detection of very small movements at any location within the tube. In addition to circadian locomotor activity, we are able to collect other information, such as distance, speed, food proximity, place preference, and multiple additional parameters that relate to sleep structure. Direct comparisons of incident recording and our motion tracking application using wild type and locomotor-deficient (CASK-β null) flies show that the increased temporal resolution in the data from the Tracker program can greatly affect the interpretation of the state of the fly. This is especially evident when a particular condition or genotype has strong effects on the behavior, and can provide a wealth of information previously unavailable to the investigator. The interaction of sleep with other behaviors can also be assessed directly in many cases with this method

Salinity and Simulated Herbivory Influence Spartina alterniflora Traits and Defense Strategy

Sea level rise is expected to push saline waters into previously fresher regions of estuaries, and higher salinities may expose oligohaline marshes to invertebrate herbivores typically constrained by salinity. The smooth cordgrass, Spartina alterniflora (syn. Sporobolus alterniflorus), can defend itself against herbivores in polyhaline marshes, however it is not known if S. alterniflora’s defense varies along the mesohaline to oligohaline marsh gradient in estuaries. I found that S. alterniflora from a mesohaline marsh is better defended than plants from an oligohaline marsh, supporting the optimal defense theory. Higher salinity treatments lowered carbon content, C:N, and new stem biomass production, traits associated with a tolerance strategy, suggesting that salinity may mediate the defense response of S. alterniflora. Further, simulated herbivory increased the nitrogen content and decreased C:N of S. alterniflora. This indicates that grazing may increase S. alterniflora susceptibility to future herbivory via improved forage quality. Simulated herbivory also decreased both belowground and new stem biomass production, highlighting a potential pathway in which herbivory can indirectly facilitate marsh loss, as S. alterniflora biomass is critical for vertical accretion and marsh stability under future sea level rise scenarios