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

Modeling BCR-ABL and MLL-AF9 leukemia in a human bone marrow-like scaffold based xenograft model

While NOD-SCID IL2Rγ(-/-) (NSG) xenograft mice are currently the most frequently used model to study human leukemia in vivo, the absence of a human niche severely hampers faithful recapitulation of the disease. We used NSG mice in which ceramic scaffolds seeded with human mesenchymal stromal cells were implanted to generate a human bone marrow (huBM-sc)-like niche. We observed that, in contrast to the murine bone marrow (mBM) niche, expression of BCR-ABL or MLL-AF9 was sufficient to induce both primary AML and ALL. Stemness was preserved within the human niches as demonstrated by serial transplantation assays. Efficient engraftment of AML MLL-AF9 and blast-crisis CML patient cells was also observed, whereby the immature blast-like phenotype was maintained in the huBM-sc niche, but to a much lesser extent in mBM niches. We compared transcriptomes of leukemias derived from mBM niches versus leukemias from huBM-like scaffold-based niches, which revealed striking differences in expression of genes associated with hypoxia, mitochondria and metabolism. Finally, we utilized the huBM-sc MLL-AF9 B-ALL model to evaluate the efficacy of the I-BET151 inhibitor in vivo. In conclusion, we have established human niche models in which the myeloid and lymphoid features of BCR-ABL(+) and MLL-AF9(+) leukemias can be studied in detail. Accepted article preview online 29 April 2016; Advance online publication 17 May 2016This work was supported by grants from the Dutch Cancer Society (2009-4411; VU2011-5127) and by the EU (ITN EuroCSC). I-BET151 was kindly provided by Nicholas Smithers (GSK R&D, UK)

Dynamics of fully coupled rotators with unimodal and bimodal frequency distribution

We analyze the synchronization transition of a globally coupled network of N phase oscillators with inertia (rotators) whose natural frequencies are unimodally or bimodally distributed. In the unimodal case, the system exhibits a discontinuous hysteretic transition from an incoherent to a partially synchronized (PS) state. For sufficiently large inertia, the system reveals the coexistence of a PS state and of a standing wave (SW) solution. In the bimodal case, the hysteretic synchronization transition involves several states. Namely, the system becomes coherent passing through traveling waves (TWs), SWs and finally arriving to a PS regime. The transition to the PS state from the SW occurs always at the same coupling, independently of the system size, while its value increases linearly with the inertia. On the other hand the critical coupling required to observe TWs and SWs increases with N suggesting that in the thermodynamic limit the transition from incoherence to PS will occur without any intermediate states. Finally a linear stability analysis reveals that the system is hysteretic not only at the level of macroscopic indicators, but also microscopically as verified by measuring the maximal Lyapunov exponent.Comment: 22 pages, 11 figures, contribution for the book: Control of Self-Organizing Nonlinear Systems, Springer Series in Energetics, eds E. Schoell, S.H.L. Klapp, P. Hoeve

Self-Affirmation Improves Problem-Solving under Stress

High levels of acute and chronic stress are known to impair problem-solving and creativity on a broad range of tasks. Despite this evidence, we know little about protective factors for mitigating the deleterious effects of stress on problem-solving. Building on previous research showing that self-affirmation can buffer stress, we tested whether an experimental manipulation of self-affirmation improves problem-solving performance in chronically stressed participants. Eighty undergraduates indicated their perceived chronic stress over the previous month and were randomly assigned to either a self-affirmation or control condition. They then completed 30 difficult remote associate problem-solving items under time pressure in front of an evaluator. Results showed that self-affirmation improved problem-solving performance in underperforming chronically stressed individuals. This research suggests a novel means for boosting problem-solving under stress and may have important implications for understanding how self-affirmation boosts academic achievement in school settings. © 2013 Creswell et al

Bone Morphogenetic Protein 4 Gene Therapy in Mice Inhibits Myeloma Tumor Growth, But Has a Negative Impact on Bone.

Multiple myeloma is characterized by accumulation of malignant plasma cells in the bone marrow. Most patients suffer from an osteolytic bone disease, caused by increased bone degradation and reduced bone formation. Bone morphogenetic protein 4 (BMP4) is important for both pre- and postnatal bone formation and induces growth arrest and apoptosis of myeloma cells. BMP4-treatment of myeloma patients could have the potential to reduce tumor growth and restore bone formation. We therefore explored BMP4 gene therapy in a human-mouse model of multiple myeloma where humanized bone scaffolds were implanted subcutaneously in RAG2-/- γC-/-mice. Mice were treated with adeno-associated virus serotype 8 BMP4 vectors (AAV8-BMP4) to express BMP4 in the liver. When mature BMP4 was detectable in the circulation, myeloma cells were injected into the scaffolds and tumor growth was examined by weekly imaging. Strikingly, the tumor burden was reduced in AAV8-BMP4 mice compared with the AAV8-CTRL mice, suggesting that increased circulating BMP4 reduced tumor growth. BMP4-treatment also prevented bone loss in the scaffolds, most likely due to reduced tumor load. To delineate the effects of BMP4 overexpression on bone per se, without direct influence from cancer cells, we examined the unaffected, non-myeloma femurs by μCT. Surprisingly, the AAV8-BMP4 mice had significantly reduced trabecular bone volume, trabecular numbers, as well as significantly increased trabecular separation compared with the AAV8-CTRL mice. There was no difference in cortical bone parameters between the two groups. Taken together, BMP4 gene therapy inhibited myeloma tumor growth, but also reduced the amount of trabecular bone in mice. Our data suggest that care should be taken when considering using BMP4 as a therapeutic agent. © 2019 The Authors. JBMR Plus published by Wiley Periodicals, Inc. on behalf of American Society for Bone and Mineral Research

Steady-state modulation of voltage-gated K+ channels in rat arterial smooth muscle by cyclic AMP-dependent protein kinase and protein phosphatase 2B

Voltage-gated potassium channels (Kv) are important regulators of membrane potential in vascular smooth muscle cells, which is integral to controlling intracellular Ca2+ concentration and regulating vascular tone. Previous work indicates that Kv channels can be modulated by receptor-driven alterations of cyclic AMP-dependent protein kinase (PKA) activity. Here, we demonstrate that Kv channel activity is maintained by tonic activity of PKA. Whole-cell recording was used to assess the effect of manipulating PKA signalling on Kv and ATP-dependent K+ channels of rat mesenteric artery smooth muscle cells. Application of PKA inhibitors, KT5720 or H89, caused a significant inhibition of Kv currents. Tonic PKA-mediated activation of Kv appears maximal as application of isoprenaline (a β-adrenoceptor agonist) or dibutyryl-cAMP failed to enhance Kv currents. We also show that this modulation of Kv by PKA can be reversed by protein phosphatase 2B/calcineurin (PP2B). PKA-dependent inhibition of Kv by KT5720 can be abrogated by pre-treatment with the PP2B inhibitor cyclosporin A, or inclusion of a PP2B auto-inhibitory peptide in the pipette solution. Finally, we demonstrate that tonic PKA-mediated modulation of Kv requires intact caveolae. Pre-treatment of the cells with methyl-β-cyclodextrin to deplete cellular cholesterol, or adding caveolin-scaffolding domain peptide to the pipette solution to disrupt caveolae-dependent signalling each attenuated PKA-mediated modulation of the Kv current. These findings highlight a novel, caveolae-dependent, tonic modulatory role of PKA on Kv channels providing new insight into mechanisms and the potential for pharmacological manipulation of vascular tone

An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data

<p>Abstract</p> <p>Background</p> <p>The ecological niche occupied by a fungal species, its pathogenicity and its usefulness as a microbial cell factory to a large degree depends on its secretome. Protein secretion usually requires the presence of a N-terminal signal peptide (SP) and by scanning for this feature using available highly accurate SP-prediction tools, the fraction of potentially secreted proteins can be directly predicted. However, prediction of a SP does not guarantee that the protein is actually secreted and current <it>in silico </it>prediction methods suffer from gene-model errors introduced during genome annotation.</p> <p>Results</p> <p>A majority rule based classifier that also evaluates signal peptide predictions from the best homologs of three neighbouring <it>Aspergillus </it>species was developed to create an improved list of potential signal peptide containing proteins encoded by the <it>Aspergillus niger </it>genome. As a complement to these <it>in silico </it>predictions, the secretome associated with growth and upon carbon source depletion was determined using a shotgun proteomics approach. Overall, some 200 proteins with a predicted signal peptide were identified to be secreted proteins. Concordant changes in the secretome state were observed as a response to changes in growth/culture conditions. Additionally, two proteins secreted via a non-classical route operating in <it>A. niger </it>were identified.</p> <p>Conclusions</p> <p>We were able to improve the <it>in silico </it>inventory of <it>A. niger </it>secretory proteins by combining different gene-model predictions from neighbouring Aspergilli and thereby avoiding prediction conflicts associated with inaccurate gene-models. The expected accuracy of signal peptide prediction for proteins that lack homologous sequences in the proteomes of related species is 85%. An experimental validation of the predicted proteome confirmed <it>in silico </it>predictions.</p

Early readmission and length of hospitalization practices in the Dialysis Outcomes and Practice Patterns Study (DOPPS)

Background:  Rising hospital care costs have created pressure to shorten hospital stays and emphasize outpatient care. This study tests the hypothesis that shorter median length of stay (LOS) as a dialysis facility practice is associated with higher rates of early readmission. Methods:  Readmission within 30 days of each hospitalization was evaluated for participants in the Dialysis Outcomes and Practice Patterns Study, an observational study of randomly selected hemodialysis patients in the United States (142 facilities, 5095 patients with hospitalizations), five European countries (101 facilities, 2281 patients with hospitalizations), and Japan (58 facilities, 883 patients with hospitalizations). Associations between median facility LOS (estimated from all hospitalizations at the facility and interpreted as a dialysis facility practice pattern) and odds of readmission were assessed using logistic regression, adjusted for patient characteristics and the LOS of each index hospitalization. Results:  Risk of readmission was directly and significantly associated with LOS of the index hospitalization (adjusted odds ratio [AOR] 1.005 per day in median facility LOS, p = 0.007) and inversely associated with median facility LOS (AOR = 0.974 per day, p = 0.016). This latter association was strongest for US hemodialysis centers (AOR = 0.954 per day, p = 0.015). Conclusions:  Dialysis facilities with shorter median hospital LOS for their patients have higher odds of readmission, particularly in the United States, where there is greater pressure to shorten LOS. The determinants and consequences of practices related to hospital LOS for hemodialysis patients should be further studied.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73641/1/j.1492-7535.2004.01107.x.pd

A cluster randomized controlled trial aimed at implementation of local quality improvement collaboratives to improve prescribing and test ordering performance of general practitioners: Study Protocol

<p>Abstract</p> <p>Background</p> <p>The use of guidelines in general practice is not optimal. Although evidence-based methods to improve guideline adherence are available, variation in physician adherence to general practice guidelines remains relatively high. The objective for this study is to transfer a quality improvement strategy based on audit, feedback, educational materials, and peer group discussion moderated by local opinion leaders to the field. The research questions are: is the multifaceted strategy implemented on a large scale as planned?; what is the effect on general practitioners' (GPs) test ordering and prescribing behaviour?; and what are the costs of implementing the strategy?</p> <p>Methods</p> <p>In order to evaluate the effects, costs and feasibility of this new strategy we plan a multi-centre cluster randomized controlled trial (RCT) with a balanced incomplete block design. Local GP groups in the south of the Netherlands already taking part in pharmacotherapeutic audit meeting groups, will be recruited by regional health officers. Approximately 50 groups of GPs will be randomly allocated to two arms. These GPs will be offered two different balanced sets of clinical topics. Each GP within a group will receive comparative feedback on test ordering and prescribing performance. The feedback will be discussed in the group and working agreements will be created after discussion of the guidelines and barriers to change. The data for the feedback will be collected from existing and newly formed databases, both at baseline and after one year.</p> <p>Discussion</p> <p>We are not aware of published studies on successes and failures of attempts to transfer to the stakeholders in the field a multifaceted strategy aimed at GPs' test ordering and prescribing behaviour. This pragmatic study will focus on compatibility with existing infrastructure, while permitting a certain degree of adaptation to local needs and routines.</p> <p>Trial registration</p> <p>Nederlands Trial Register ISRCTN40008171</p

The Potential for pathogenicity was present in the ancestor of the Ascomycete subphylum Pezizomycotina

<p>Abstract</p> <p>Background</p> <p>Previous studies in Ascomycetes have shown that the function of gene families of which the size is considerably larger in extant pathogens than in non-pathogens could be related to pathogenicity traits. However, by only comparing gene inventories in extant species, no insights can be gained into the evolutionary process that gave rise to these larger family sizes in pathogens. Moreover, most studies which consider gene families in extant species only tend to explain observed differences in gene family sizes by gains rather than by losses, hereby largely underestimating the impact of gene loss during genome evolution.</p> <p>Results</p> <p>In our study we used a selection of recently published genomes of Ascomycetes to analyze how gene family gains, duplications and losses have affected the origin of pathogenic traits. By analyzing the evolutionary history of gene families we found that most gene families with an enlarged size in pathogens were present in an ancestor common to both pathogens and non-pathogens. The majority of these families were selectively maintained in pathogenic lineages, but disappeared in non-pathogens. Non-pathogen-specific losses largely outnumbered pathogen-specific losses.</p> <p>Conclusions</p> <p>We conclude that most of the proteins for pathogenicity were already present in the ancestor of the Ascomycete lineages we used in our study. Species that did not develop pathogenicity seemed to have reduced their genetic complexity compared to their ancestors. We further show that expansion of gained or already existing families in a species-specific way is important to fine-tune the specificities of the pathogenic host-fungus interaction.</p