Miracle-dz/UniFAR-FTUs huggingface dataset:
TU-FG-207A-04: Overview of the Low Dose CT Grand Challenge.

Peer-reviewed journals and conference proceedings publish hundreds of papers that describe new medical imaging algorithms, including, for example, techniques for computer-aided diagnosis or characterization, segmentation, image registration, image reconstruction, and radiomics. It is difficult, if not impossible, to fairly compare the performance of these algorithms as investigators must either use different data sets, or if using the same data, use different implementations of competing algorithms. Grand Challenges facilitate the fair comparison of algorithms by providing a common data set to all participants and by having each participant be responsible for implementation of their own algorithm. The dissemination of findings from Grand Challenges provides important information to the scientific community and helps to determine which approaches have the greatest promise for successful translation to clinical practice. In this session we will review the outcomes and lessons learned from the 2015 SPIE-AAPM-NCI Lung Nodule Classification Challenge. We will then turn to the 2016 NIH-AAPM-Mayo Clinic Low Dose CT Grand Challenge, providing an overview of denoising and iterative reconstruction approaches and a description of the Challenge. The top 3 performing participants will be announced, and each will give a short presentation on their technique. LEARNING OBJECTIVES 1. Understand the role of Grand Challenges in the field of medical imaging 2. Be able to summarize the outcomes of the 2015 lung nodule classification challenge 3. Be able to review the primary types of noise reduction techniques used in CT 4. Be familiar with a library of patient CT projection data available to researchers 5. Learn which techniques performed best in the Low Dose CT Grand Challenge Pelc: GE Healthcare, Philips Healthcare; McCollough: Research grant, Siemens Healthcare; Low Dose CT Grand Challenge supported by the AAPM Science Council and NIH (grant EB 017185), and hosted by the Mayo Clinic; Giger: stockholder R2 technology/Hologic, royalties from Hologic, GE Medical Systems, MEDIAN Technologies, Riverain Medical, Mitsubishi/Toshiba. Cofounder/stockholder Quantitative Insights.
Tracer tests in a fractured dolomite: 2. Analysis of mass transfer in single‐well injection‐withdrawal tests

We investigated multiple‐rate diffusion as a possible explanation for observed behavior in a suite of single‐well injection‐withdrawal (SWIW) tests conducted in a fractured dolomite. We first investigated the ability of a conventional double‐porosity model and a multirate diffusion model to explain the data. This revealed that the multirate diffusion hypothesis/model is consistent with available data and is capable of matching all of the recovery curves. Second, we studied the sensitivity of the SWIW recovery curves to the distribution of diffusion rate coefficients and other parameters. We concluded that the SWIW test is very sensitive to the distribution of rate coefficients but is relatively insensitive to other flow and transport parameters such as advective porosity and dispersivity. Third, we examined the significance of the constant double‐log late time slopes (−2.1 to −2.8), which are present in several data sets. The observed late time slopes are significantly different than would be predicted by either conventional double‐porosity or single‐porosity models and are believed to be a distinctive feature of multirate diffusion. Fourth, we found that the estimated distributions of diffusion rate coefficients are very broad, with the distributions spanning a range of up to 3.6 orders of magnitude. Fifth, when both heterogeneity and solute drift are present, late time behavior similar to multirate mass transfer can occur. Although it is clear that multirate diffusion occurs in the Culebra, the number of orders of magnitude of variability may be overestimated because of the combined effects of drift and heterogeneity.
Diagnosis, Treatment, and Prevention of Congenital Toxoplasmosis in the United States

* Abbreviations: AC/HS — : differential agglutination (test) AF — : amniotic fluid CI — : confidence interval CNS — : central nervous system CSF — : cerebrospinal fluid CT — : congenital toxoplasmosis ELISA — : enzyme-linked immunosorbent assay EMSCOT — : European Multicenter Study of Congenital Toxoplasmosis EUROTOXO — : European Toxoprevention Study FDA — : US Food and Drug Administration GRADE — : Grading of Recommendations Assessment, Development, and Evaluation HR — : hazard ratio Ig — : immunoglobulin ISAGA — : immunosorbent agglutination assay MTCT — : mother-to-child transmission NCCCT — : National Collaborative Chicago-Based Congenital Toxoplasmosis Study NPV — : negative predictive value OR — : odds ratio PAMF-TSL — : Palo Alto Medical Foundation Toxoplasma Serology Laboratory PCR — : polymerase chain reaction PPV — : positive predictive value P/S — : pyrimethamine/sulfadiazine RCT — : randomized controlled trial SNHL — : sensorineural hearing loss SNSD — : serious neurologic sequelae or death SYROCOT — : Systematic Review on Congenital Toxoplasmosis Congenital toxoplasmosis (CT) is a parasitic disease that can cause significant fetal and neonatal harm. Coordinated efforts by pregnant women, researchers, physicians, and health policy makers regarding potential primary and secondary preventive measures for CT and their implementation may lead to a lower incidence of CT as well as lower morbidity and mortality rates associated with CT. In the United States, the age-adjusted seroprevalence of Toxoplasma gondii among women of childbearing age (15–44 years) has declined over time (15%, 11%, and 9% in 1988–1994, 1999–2004, and 2009–2010, respectively; among US-born women only, the seroprevalence rates during these time periods were 13%, 8%, and 6%, respectively). Thus, approximately 91% of women of childbearing age in the United States are susceptible to Toxoplasma infection. Should these women become infected during pregnancy and remain undiagnosed and untreated, they could deliver an infant with CT. However, the incidence of acute primary infection is likely very low in the current era and is probably much lower than the 1.1 in 1000 pregnant women originally reported in 1960s. There are 3 ways CT can occur. First, CT can develop through transmission of T gondii to the fetus from a previously seronegative, immunocompetent mother who acquired acute primary infection during pregnancy or within 3 months before …
The role of transient receptor potential vanilloid type-2 ion channels in innate and adaptive immune responses

The transient receptor potential vanilloid type-2 (TRPV2), belonging to the transient receptor potential channel family, is a specialized ion channel expressed in human and other mammalian immune cells. This channel has been found to be expressed in CD34+ hematopoietic stem cells, where its cytosolic Ca2+ activity is crucial for stem/progenitor cell cycle progression, growth, and differentiation. In innate immune cells, TRPV2 is expressed in granulocytes, macrophages, and monocytes where it stimulates fMet-Leu-Phe migration, zymosan-, immunoglobulin G-, and complement-mediated phagocytosis, and lipopolysaccharide-induced tumor necrosis factor-alpha and interleukin-6 production. In mast cells, activation of TRPV2 allows intracellular Ca2+ ions flux, thus stimulating protein kinase A-dependent degranulation. In addition, TRPV2 is highly expressed in CD56+ natural killer cells. TRPV2 orchestrates Ca2+ signal in T cell activation, proliferation, and effector functions. Moreover, messenger RNA for TRPV2 are expressed in CD4+ and CD8+ T lymphocytes. Finally, TRPV2 is expressed in CD19+ B lymphocytes where it regulates Ca2+ release during B cell development and activation. Overall, the specific expression of TRPV2 in immune cells suggests a role in immune-mediated diseases and offers new potential targets for immunomodulation.
Automatic Target Recognition Based on Cross-Plot

Automatic target recognition that relies on rapid feature extraction of real-time target from photo-realistic imaging will enable efficient identification of target patterns. To achieve this objective, Cross-plots of binary patterns are explored as potential signatures for the observed target by high-speed capture of the crucial spatial features using minimal computational resources. Target recognition was implemented based on the proposed pattern recognition concept and tested rigorously for its precision and recall performance. We conclude that Cross-plotting is able to produce a digital fingerprint of a target that correlates efficiently and effectively to signatures of patterns having its identity in a target repository.
Iterative Ontology Alignment Debugging Using a Scenario- and Strategy-Driven Approach

The automatic matching of entities between information repositories is essential for aligning and ontology mediation processes, but there is great ambiguity when adopting it. Data integration between repositories demands great quality of ontology alignments, and as such ambiguous correspondences must be identified and corrected beforehand. Debugging is even more relevant if the process is systematic and complete, thus allowing its formalisation and implementation and promoting its acceptance. In this paper we address the analysis and systematization of the ontology alignment debugging process, proposing the characterization of the ontology matching scenarios through ten dimensions. The resulting scenarios are categorized as Simple and Composed depending on the associated actions taken for solving the ambiguity. We suggest evolving the alignment process into an iterative matching-debugging process, where the resulting ambiguous scenarios and correction strategies are fed into the matching algorithms for supporting the resolution of the alignment problems.
Vision-based grasp planning of 3D objects by extending 2D contour based algorithms

This paper addresses the problem of grasp planning of unmodelled 3D objects with the aide of vision. The approach proposes the extension of fast 2D contour-based grasp planning algorithms, and the use of images of the target object from different points of view to recover critical 3D information like the size, location and the pose. A complete method is described, and experimental results are presented showing its feasibility.
TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei

The metabolic network of a cell represents the catabolic and anabolic reactions that interconvert small molecules (metabolites) through the activity of enzymes, transporters and non-catalyzed chemical reactions. Our understanding of individual metabolic networks is increasing as we learn more about the enzymes that are active in particular cells under particular conditions and as technologies advance to allow detailed measurements of the cellular metabolome. Metabolic network databases are of increasing importance in allowing us to contextualise data sets emerging from transcriptomic, proteomic and metabolomic experiments. Here we present a dynamic database, TrypanoCyc (http://www.metexplore.fr/trypanocyc/), which describes the generic and condition-specific metabolic network of Trypanosoma brucei, a parasitic protozoan responsible for human and animal African trypanosomiasis. In addition to enabling navigation through the BioCyc-based TrypanoCyc interface, we have also implemented a network-based representation of the information through MetExplore, yielding a novel environment in which to visualise the metabolism of this important parasite.
Model of the global distribution of the total electron content based on deep dense convolutional autoencoder

Nowadays the prediction of ionospheric parameters is an important and acute problem in the field of ensuring stable operation of radio communication and radio navigation facilities. The network of two-frequency GPS receivers data is used for monitoring the ionospheric condition. Based on these data, a number of laboratories are building global maps of total electron content (TEC). There are strong spatial and temporal correlations in the TEC maps. As a result, in order to successfully solve the problem of TEC prediction, it is advisable to perform preliminary processing of maps data with dimensionality reduction. In this paper, the problem of constructing a low-dimensional model of global distribution of the TEC is solved. In addition, the model of global distribution of the TEC can be useful for the ionosphere dynamics investigation. In this paper, it is proposed to use dense convolutional auto encoders as a base element of the model. This architecture allows us to speed up the neural network learning process and avoid the gradient-vanishing problem in error backpropagation algorithm.
Noise and Bias In Square-Root Compression Schemes

We investigate data compression schemes for proposed all-sky diffraction-limited visible/NIR sky surveys aimed at the dark-energy problem. We show that lossy square-root compression to 1 bit pixel-1 of noise, followed by standard lossless compression algorithms, reduces the images to 2.5–4 bits pixel-1, depending primarily upon the level of cosmic-ray contamination of the images. Compression to this level adds noise equivalent to ≤ 10% penalty in observing time. We derive an analytic correction to flux biases inherent to the square-root compression scheme. Numerical tests on simple galaxy models confirm that galaxy fluxes and shapes are measured with systematic biases ≲10-4 induced by the compression scheme, well below the requirements of supernova and weak gravitational lensing dark-energy experiments. In a related investigation, Vanderveld and coworkers bound the shape biases using realistic simulated images of the high-Galactic–latitude sky. The square-root preprocessing step has advantages over simple (linear) decimation when there are many bright objects or cosmic rays in the field, or when the background level will vary.
Fructo-Oligosaccharides and Calcium Absorption and Retention in Adolescent Girls

Background: Several studies have shown a positive effect of fructo-oligosaccharides on calcium absorption and retention in animals and humans. Effects of levels of these pre-biotics that can be functionally incorporated into manufactured foods, have not been studied in controlled feeding studies. Objectives: This study was designed to evaluate the effect of 9 g/d of fructo-oligosaccharides as part of a controlled diet on calcium absorption and retention in adolescent girls. Design: Fourteen healthy adolescent girls aged 11–13 y were studied in a metabolic setting for two 3-week periods separated by a 2-week washout period. In a randomized, double-blinded, crossover design, the teens received a diet containing either 9 g/d oligofructose-enriched inulin in a calcium-fortified cereal or the control cereal with no inulin. Both diets contained ∼1500 mg calcium daily. Calcium retention was determined on the third week of each period. On day 14 of the diet period, fractional calcium absorption was determined from the enrichment of 44Ca in 4-day urine collections. Results: Calcium absorption (67 ± 3 vs. 66 ± 3%) and retention (409 ± 394 vs. 464 ± 241 mg/d) were not significantly different when diets contained 9 g/d oligofructose-enriched inulin or not in a calcium-fortified cereal. Conclusions: Daily consumption of cereal containing a combination of short- and long-chain fructo-oligosaccharides as part of a controlled diet did not benefit calcium absorption or retention in adolescent girls. Lack of response to the prebiotic in this cohort may relate to their already high calcium absorption efficiency.
Delay analysis of the Max-Weight policy under heavy-tailed traffic via fluid approximations

We consider a single-hop switched queueing network with a mix of heavy-tailed (i.e., arrival processes with infinite variance) and light-tailed traffic, and study the delay performance of the Max-Weight policy, known for its throughput optimality and asymptotic delay optimality properties. Classical results in queueing theory imply that heavy-tailed queues are delay unstable, i.e., they experience infinite expected delays in steady state. Thus, we focus on the impact of heavy-tailed traffic on the light-tailed queues, using delay stability as performance metric. Recent work has shown that this impact may come in the form of subtle rate-dependent phenomena, the stochastic analysis of which is quite cumbersome. Our goal is to show how fluid approximations can facilitate the delay analysis of the Max-Weight policy under heavy-tailed traffic. More specifically, we show how fluid approximations can be combined with renewal theory in order to prove delay instability results. Furthermore, we show how fluid approximations can be combined with stochastic Lyapunov theory in order to prove delay stability results. We illustrate the benefits of the proposed approach in two ways: (i) analytically, by providing a sharp characterization of the delay stability regions of networks with disjoint schedules, significantly generalizing previous results; (ii) computationally, through a Bottleneck Identification algorithm, which identifies (some) delay unstable queues by solving the fluid model of the network from certain initial conditions.
Effect of Ebola Progression in Liberia

TO THE EDITOR: Yamin and colleagues (1) evaluated the probability of eliminating Ebola by case isolation of 50% to 100% of nonsurvivors compared with isolation of all infected persons when the type of contact is dominated by conversation or by sharing a meal or a bed. However, they do not mention the transmission of the virus during conversation, or aerosol transmission. Masks are protective only when they are of good quality and properly used. Filoviruses are classified as category A bioterrorism agents by the Centers for Disease Control and Prevention and are thought to be aerosol-mediated. Countering aerosolized filovirus infection has been a major priority of biodefense research (2). Transmission of Marburg virus by exposure to bat-inhabited caves and mines has already been reported (3). In a study by Reed and associates, when cynomolgus and rhesus macaques and African green monkeys were exposed to aerosolized Zaire ebolavirus, all 3 species developed similar clinical signs and symptoms and the outcome resembled that of parenteral inoculation with the virus for each species (4). Rhesus monkeys who experimentally inhaled droplets of 0.8 to 1.2 microns containing Ebola virus died of ebolavirus disease within a few days. Immunocytochemistry has also shown Ebola virus antigens in airway epithelium, alveolar pneumocytes, and macrophages in the lung and mediastinal lymph nodes. Aggregates of characteristic filamentous virus were present in type 1 pneumocytes, macrophages, and air spaces of the lung by electron microscopy (5). Similar lethal infections by aerosol exposure were reported in 18 rhesus macaques, including early infection of the respiratory lymphoid tissues (6), and aerosol exposure to Zaire ebolavirus has been reported to cause lethal infections in rhesus monkeys. Two rhesus monkeys were exposed to 400 plaque-forming units of the virus and 2 others to 50000 plaque-forming units; all 4 monkeys developed diseases and died 7 to 9 days after exposure (5). In a fatal disease like Ebola, where human experimentation cannot be used to prove the route of transmission, evidence available from nonhuman primates should be taken seriously. However, the absence of evidence in humans is not evidence of the absence of aerosol transmission. Demonstration of fatal aerosol transmission of Ebola virus in monkeys reinforces the importance of taking appropriate precautions to prevent its potential aerosol transmission to humans. We request that Yamin and colleagues discuss these issues related to their study to clear the air.
Investigation of Layered Structure Formation in MgB2 Wires Produced by the Internal Mg Coating Process under Low and High Isostatic Pressures

Currently, MgB2 wires made by the powder-in-tube (PIT) method are most often used in the construction and design of superconducting devices. In this work, we investigated the impact of heat treatment under both low and high isostatic pressures on the formation of a layered structure in PIT MgB2 wires manufactured using the Mg coating method. The microstructure, chemical composition, and density of the obtained superconductive wires were investigated using scanning electron microscopy (SEM) with an energy-dispersive X-ray spectroscopy (EDS) analyzer and optical microscopy with Kameram CMOS software (version 2.11.5.6). Transport measurements of critical parameters were made by using the Physical Property Measurement System (PPMS) for 100 mA and 19 Hz in a perpendicular magnetic field. We observed that the Mg coating method can significantly reduce the reactions of B with the Fe sheath. Moreover, the shape, uniformity, and continuity of the layered structure (cracks, gaps) depend on the homogeneity of the B layer before the synthesis reaction. Additionally, the formation of a layered structure depends on the annealing temperature (for Mg in the liquid or solid-state), isostatic pressure, type of boron, and density of layer B before the synthesis reaction.
On sparse matrix-vector product optimization

Summary form only given. Sparse matrices are matrices having a large number of zero elements. When such matrices are used, both computing time and memory space may be dramatically reduced by taking into account their sparsity. It is well known that the sparse matrix-vector product (SMVP) where the matrix is sparse and the vector is dense is an important kernel in many scientific applications e.g. iterative methods for linear systems and/or eigen problem. The final aim of this work is to design a kind of user-"expert system" that can be used to improve performances in computing environments, particularly grids involving heterogeneous nodes, on which the SMVP kernel is distributed. In this paper, we study the unrolling as an optimization technique and we apply it to the SMVP when the CRS sparse matrix compression format (CSF) is used. After an analysis of the problem, we detail a series of experiments achieved on three different machines. A set of conclusions could be obtained, particularly, the fact that the compiler optimization does not always lead to the best performances. Indeed, specific manual optimizations through loop unrolling could be better.