Morpho-MNIST: Quantitative Assessment and Diagnostics for Representation Learning

Revealing latent structure in data is an active field of research, having brought exciting new models such as variational autoencoders and generative adversarial networks, and is essential to push machine learning towards unsupervised knowledge discovery. However, a major challenge is the lack of suitable benchmarks for an objective and quantitative evaluation of learned representations. To address this issue we introduce Morpho-MNIST. We extend the popular MNIST dataset by adding a morphometric analysis enabling quantitative comparison of different models, identification of the roles of latent variables, and characterisation of sample diversity. We further propose a set of quantifiable perturbations to assess the performance of unsupervised and supervised methods on challenging tasks such as outlier detection and domain adaptation

Optimal Scheduling of Multiproduct Pipeline System Using MILP Continuous Approach

Part 5: Planning and Scheduling; International audience; To date, the multiproduct pipeline transportation mode has nationally and internationally considerably evolved thanks to his efficiently and effectively of transporting several products. In this paper, we focus our study on the scheduling of a multiproduct pipeline system that receives a number of petroleum products (fuels) from a single refinery source in order to be distributed to several storage and distribution centers (depots). Mixed Integer Linear Programming (MILP) continuous mathematical approach is presented to solve this problem. The sequence of injected products in the same pipeline should be carefully studied, in order to meet market demands and ensure storage autonomy of the marketable pure products in the fuels depots on the one hand and to minimize the number of interfaces; Birth zone of mixture between two products in contact and in sequential flow, which may hinder the continuous operation of the pipeline system, by the necessity of additional storage capacity for this last mixture, that is in no way marketable and requires special processing operations. This work is applied on a real case of a multiproduct pipeline that feeds the western and southwestern region of Algeria with fuels. The obtained results based on the MILP continuous approach give an optimal scheduling of the multiproduct transport system with a minimized number of interfaces. Document type: Conference objec

Electric Field Effects on Graphene Materials

Understanding the effect of electric fields on the physical and chemical properties of two-dimensional (2D) nanostructures is instrumental in the design of novel electronic and optoelectronic devices. Several of those properties are characterized in terms of the dielectric constant which play an important role on capacitance, conductivity, screening, dielectric losses and refractive index. Here we review our recent theoretical studies using density functional calculations including van der Waals interactions on two types of layered materials of similar two-dimensional molecular geometry but remarkably different electronic structures, that is, graphene and molybdenum disulphide (MoS$_2$). We focus on such two-dimensional crystals because of they complementary physical and chemical properties, and the appealing interest to incorporate them in the next generation of electronic and optoelectronic devices. We predict that the effective dielectric constant ($\varepsilon$) of few-layer graphene and MoS$_2$ is tunable by external electric fields ($E_{\rm ext}$). We show that at low fields ($E_{\rm ext}^{}<0.01$ V/\AA) $\varepsilon$ assumes a nearly constant value $\sim$4 for both materials, but increases at higher fields to values that depend on the layer thickness. The thicker the structure the stronger is the modulation of $\varepsilon$ with the electric field. Increasing of the external field perpendicular to the layer surface above a critical value can drive the systems to an unstable state where the layers are weakly coupled and can be easily separated. The observed dependence of $\varepsilon$ on the external field is due to charge polarization driven by the bias, which show several similar characteristics despite of the layer considered.Comment: Invited book chapter on Exotic Properties of Carbon Nanomatter: Advances in Physics and Chemistry, Springer Series on Carbon Materials. Editors: Mihai V. Putz and Ottorino Ori (11 pages, 4 figures, 30 references

Phosphorylation of eIF2α on Threonine 169 is not required for Trypanosoma brucei cell cycle arrest during differentiation.

The trypanosome life cycle consists of a series of developmental forms each adapted to an environment in the relevant insect and/or mammalian host. The differentiation process from the mammalian bloodstream form to the insect-midgut procyclic form in Trypanosoma brucei occurs in two steps in vivo. First proliferating 'slender' bloodstream forms differentiate to non-dividing 'stumpy' forms arrested in G1. Second, in response to environmental cues, stumpy bloodstream forms re-enter the cell cycle and start to proliferate as procyclic forms after a lag during which both cell morphology and gene expression are modified. Nearly all arrested cells have lower rates of protein synthesis when compared to the proliferating equivalent. In eukaryotes, one mechanism used to regulate the overall rate of protein synthesis involves phosphorylation of the alpha subunit of initiation factor eIF2 (eIF2α). The effect of eIF2α phosphorylation is to prevent the action of eIF2B, the guanine nucleotide exchange factor that activates eIF2 for the next rounds of initiation. To investigate the role of the phosphorylation of eIF2α in the life cycle of T. brucei, a cell line was made with a single eIF2α gene that contained the phosphorylation site, threonine 169, mutated to alanine. These cells were capable of differentiating from proliferating bloodstream form cells into arrested stumpy forms in mice and into procyclic forms in vitro and in tsetse flies. These results indicate that translation attenuation mediated by the phosphorylation of eIF2α on threonine 169 is not necessary for the cell cycle arrest associated with these differentiation processes.This work was supported by Fapesp grants 09/52047-5 and 11/51973-3 to B.A.C. and S. S., respectively, and CNPq grants 309860/2011-3 and 478903/2012-0 to B.A.C. and 477143/2011-3 and 445655/2014-3 to S.S.. C.C.A. was supported by a Fapesp doctoral fellowship (2007/59753-7) and a CAPES-PSDE fellowship. Work in Cambridge and Bristol was supported by Wellcome Trust Project, Grants 085956 and 088099 respectively.This is the final version of the article. It first appeared from Elsevier via https://doi.org/10.1016/j.molbiopara.2016.03.00

Assistência pré-natal à adolescente e os atributos da Atenção Primária à Saúde

OBJECTIVE: evaluate prenatal care for adolescents in health units, in accordance with the attributes of Primary Health Care (PHC) guidelines. METHOD: quantitative study conducted with health professionals, using the Primary Care Assessment Tool-Brazil to assess the presence and extent of PHC attributes. RESULTS: for all the participating units, the attribute Access scored =6.6; the attributes Longitudinality, Coordination (integration of care), Coordination (information systems) and Integrality scored =6.6, and the Essential Score =6.6. Comparing basic units with family health units, the attribute scores were equally distributed; Accessibility scored =6.6, the others attributes scored =6.6; however, in the basic units, the Essential Score was =6.6 and, in the family health units, =6.6. CONCLUSION: expanding the coverage of family health units and the training of professionals can be considered strategies to qualify health care.OBJETIVO: evaluar la atención prenatal a las adolescentes en unidades de salud, según los atributos de la Atención Primaria a la Salud. MÉTODO: estudio de abordaje cuantitativo, realizado con profesionales de la salud, utilizando el instrumento Primary Care Assessment Tool-Brasil para analizar la presencia y extensión de los atributos vinculados a la APS en las unidades de salud. RESULTADOS: para todas las unidades participantes, el atributo Acceso obtuvo un puntaje =6,6; los atributos Longitudinalidad, Coordinación (integración de cuidados), Coordinación (sistemas de información) e Integralidad obtuvieron puntajes =6,6 y el Puntaje Esencial fue =6,6. Comparando las unidades básicas de salud y las unidades de salud de la familia, los puntajes están igualmente distribuidos: Accesibilidad =6,6 y los demás atributos con puntajes =6,6; sin embargo, el puntaje Esencial en las unidades básicas fue =6,6 y el de las unidades de salud de la familia fue =6,6. CONCLUSIÓN: la ampliación de la cobertura de las unidades de salud de la familia y la capacitación profesional pueden ser estrategias para calificar la atención a la salud.OBJETIVO: avaliar a atenção pré-natal às adolescentes em unidades de saúde, segundo os atributos da Atenção Primária à Saúde. MÉTODO: estudo de abordagem quantitativa, realizado com profissionais de saúde, utilizando-se o instrumento Primary Care Assessment Tool-Brasil, para analisar a presença e extensão dos atributos. RESULTADOS: para todas as unidades participantes, o atributo acesso obteve escore =6,6; os atributos longitudinalidade, coordenação (integração de cuidados), coordenação (sistemas de informação) e integralidade obtiveram escores =6,6 e escore essencial =6,6. Comparando-se as unidades básicas e as unidades de saúde da família, os escores estão igualmente distribuídos: acessibilidade: =6,6 e os demais atributos com escores =6,6, no entanto, o escore essencial nas unidades básicas foi =6,6 e nas unidades de saúde da família foi =6,6. CONCLUSÃO: a ampliação da cobertura das unidades de saúde da família e a capacitação profissional podem ser estratégias para qualificar a atenção à saúde

Diffusion microscopic MRI of the mouse embryo: Protocol and practical implementation in the splotch mouse model

Advanced methodologies for visualizing novel tissue contrast are essential for phenotyping the ever-increasing number of mutant mouse embryos being generated. Although diffusion microscopic MRI (μMRI) has been used to phenotype embryos, widespread routine use is limited by extended scanning times, and there is no established experimental procedure ensuring optimal data acquisition

One-point functions in massive integrable QFT with boundaries

We consider the expectation value of a local operator on a strip with non-trivial boundaries in 1+1 dimensional massive integrable QFT. Using finite volume regularisation in the crossed channel and extending the boundary state formalism to the finite volume case we give a series expansion for the one-point function in terms of the exact form factors of the theory. The truncated series is compared with the numerical results of the truncated conformal space approach in the scaling Lee-Yang model. We discuss the relevance of our results to quantum quench problems.Comment: 43 pages, 20 figures, v2: typos correcte

Light and the outcome of the critically ill: An observational cohort study

Introduction: Light before and during acute illness has been associated with both benefit and harm in animal models and small human studies. Our objective was to determine the associations of light duration (photoperiod) and intensity (insolation) before and during critical illness with hospital mortality in ICU patients. Based on the 'winter immunoenhancement' theory, we tested the hypothesis that a shorter photoperiod before critical illness is associated with improved survival.Methods: We analyzed data from 11,439 patients admitted to 8 ICUs at the University of Pittsburgh Medical Center between June 30, 1999 and July 31, 2004. Daily photoperiod and insolation prior to and after ICU admission were estimated for each patient by using data provided by the United States Naval Observatory and National Aeronautics and Space Administration and direct measurement of light gradient from outside to bedside for each ICU room. Our primary outcome was hospital mortality. The association between light and risk of death was analyzed using multivariate analyses, adjusting for potential confounders, including severity of illness, case mix, and ICU type.Results: The cohort had an average APACHE III of 52.9 and a hospital mortality of 10.7%. In total, 128 ICU beds were analyzed; 108 (84%) had windows. Pre-illness photoperiod ranged from 259 to 421 hours in the prior month. A shorter photoperiod was associated with a reduced risk of death: for each 1-hour decrease, the adjusted OR was 0.997 (0.994 to 0.999, p = 0.03). In the ICU, there was near complete (99.6%) degradation of natural light from outside to the ICU bed. Thus, light exposure once in the ICU approached zero; the 24-hour insolation was 0.005 ± 0.003 kWh/m 2 with little diurnal variation. There was no association between ICU photoperiod or insolation and mortality.Conclusions: Consistent with the winter immunoenhancement theory, a shorter photoperiod in the month before critical illness is associated with a reduced risk of death. Once in the ICU, patients are exposed to near negligible natural light despite the presence of windows. Further studies are warranted to determine the underlying mechanisms and whether manipulating light exposure, before or during ICU admission, can enhance survival. © 2012 Castro et al.; licensee BioMed Central Ltd

Image-level harmonization of multi-site data using image-and-spatial transformer networks

We investigate the use of image-and-spatial transformer networks (ISTNs) to tackle domain shift in multi-site medical imaging data. Commonly, domain adaptation (DA) is performed with little regard for explainability of the inter-domain transformation and is often conducted at the feature-level in the latent space. We employ ISTNs for DA at the image-level which constrains transformations to explainable appearance and shape changes. As proof-of-concept we demonstrate that ISTNs can be trained adversarially on a classification problem with simulated 2D data. For real-data validation, we construct two 3D brain MRI datasets from the Cam-CAN and UK Biobank studies to investigate domain shift due to acquisition and population differences. We show that age regression and sex classification models trained on ISTN output improve generalization when training on data from one and testing on the other site

Rare germline variants in DNA repair genes and the angiogenesis pathway predispose prostate cancer patients to develop metastatic disease

Background Prostate cancer (PrCa) demonstrates a heterogeneous clinical presentation ranging from largely indolent to lethal. We sought to identify a signature of rare inherited variants that distinguishes between these two extreme phenotypes. Methods We sequenced germline whole exomes from 139 aggressive (metastatic, age of diagnosis < 60) and 141 non-aggressive (low clinical grade, age of diagnosis ≥60) PrCa cases. We conducted rare variant association analyses at gene and gene set levels using SKAT and Bayesian risk index techniques. GO term enrichment analysis was performed for genes with the highest differential burden of rare disruptive variants. Results Protein truncating variants (PTVs) in specific DNA repair genes were significantly overrepresented among patients with the aggressive phenotype, with BRCA2, ATM and NBN the most frequently mutated genes. Differential burden of rare variants was identified between metastatic and non-aggressive cases for several genes implicated in angiogenesis, conferring both deleterious and protective effects. Conclusions Inherited PTVs in several DNA repair genes distinguish aggressive from non-aggressive PrCa cases. Furthermore, inherited variants in genes with roles in angiogenesis may be potential predictors for risk of metastases. If validated in a larger dataset, these findings have potential for future clinical application