Scientific Computing Meets Big Data Technology: An Astronomy Use Case

Scientific analyses commonly compose multiple single-process programs into a dataflow. An end-to-end dataflow of single-process programs is known as a many-task application. Typically, tools from the HPC software stack are used to parallelize these analyses. In this work, we investigate an alternate approach that uses Apache Spark -- a modern big data platform -- to parallelize many-task applications. We present Kira, a flexible and distributed astronomy image processing toolkit using Apache Spark. We then use the Kira toolkit to implement a Source Extractor application for astronomy images, called Kira SE. With Kira SE as the use case, we study the programming flexibility, dataflow richness, scheduling capacity and performance of Apache Spark running on the EC2 cloud. By exploiting data locality, Kira SE achieves a 2.5x speedup over an equivalent C program when analyzing a 1TB dataset using 512 cores on the Amazon EC2 cloud. Furthermore, we show that by leveraging software originally designed for big data infrastructure, Kira SE achieves competitive performance to the C implementation running on the NERSC Edison supercomputer. Our experience with Kira indicates that emerging Big Data platforms such as Apache Spark are a performant alternative for many-task scientific applications

Usefulness of BATF3 immunohistochemistry in diagnosing classical Hodgkin lymphoma

It is well recognized that the AP-1 transcription factor BATF3 is constitutively expressed in Hodgkin/Reed-Sternberg (HRS) cells, but its potential as a diagnostic marker for classical Hodgkin lymphoma (cHL) has not yet been addressed. In this study, we performed immunohistochemistry and analyzed the BATF3 expression in lymphoma cells on 218 lymphoma samples belonging to 14 different lymphoma entities. We observed varying degrees of BATF3 expression in nearly half of the cases (n = 100) with BATF3 expression being a constitutive feature of cHL (n = 53) and anaplastic large cell lymphoma (ALCL). By scoring BATF3 expression (BATF3-score) we observed constitutively high BATF3-scores in cHL and ALCL and low to moderate BATF3-scores in all other entities examined. Western blot analysis confirmed BATF3 protein expression in cell lysates from cHL cell lines (n = 7). Thus, BATF3 can be considered a useful IHC marker for the diagnosis of cHL as it is highly sensitive and sufficiently specific when analyzed by BATF3-scoring

Correction of severe valgus osteoarthritis by total knee arthroplasty is associated with increased postoperative ankle symptoms

Purpose: The aim of this study was to assess the mid-term clinical outcome of the ankle joint after total knee arthroplasty (TKA) in high-grade valgus osteoarthritis. Methods: In this case–control study, n=36 patients with a preoperative mechanical tibiofemoral angle (mTFA)≥15° who underwent TKA between December 2002 and December 2012 were included. The control group (mTFA<15°) of n=60 patients was created using case matching. Radiological [mechanical tibiofemoral angle (mTFA) and ankle joint orientation to the ground (G-AJLO)] and clinical parameters [Foot Function Index (FFI), Knee Society Score, Forgotten Joint Score, and Range of Motion (ROM)] were analysed. The mean follow-up time was 59 months (IQR [56, 62]). Results: The degree of correcting the mTFA by TKA signifcantly correlated with the postoperative FFI (R=0.95, p<0.05), although the knee and ankle joint lines were corrected to neutral orientations. A cut-of value of 16.5° [AUC 0.912 (0.85–0.975 95% CI), sensitivity=0.8, specifcity=0.895] was calculated, above which the odds ratio (OR) for developing ankle symptoms increased vastly [OR 34.0 (9.10–127.02 95% CI)]. ROM restrictions of the subtalar joint displayed a strong sig nifcant correlation with the FFI (R=0.74, p<0.05), demonstrating that decreased ROM of the subtalar joint was associated with aggravated outcomes of the ankle joint. Conclusions: In this study, higher degrees of leg axis correction in TKA were associated with increased postoperative ankle symptoms. When TKA is performed in excessive valgus knee osteoarthritis, surgeons should be aware that this might trigger the onset or progression of ankle symptoms, particularly in cases of a stif subtalar joint. Level of evidence III

On continuum driven winds from rotating stars

We study the dynamics of continuum driven winds from rotating stars, and develop an approximate analytical model. We then discuss the evolution of stellar angular momentum, and show that just above the Eddington limit, the winds are sufficiently concentrated towards the poles to spin up the star. A twin-lobe structure of the ejected nebula is seen to be a generic consequence of critical rotation. We find that if the pressure in such stars is sufficiently dominated by radiation, an equatorial ejection of mass will occur during eruptions. These results are then applied to {\eta}-Carinae. We show that if it began its life with a high enough angular momentum, the present day wind could have driven the star towards critical rotation, if it is the dominant mode of mass loss. We find that the shape and size of the Homunculus nebula, as given by our model, agree with recent observations. Moreover, the contraction expected due to the sudden increase in luminosity at the onset of the Great Eruption explains the equatorial "skirt" as well.Comment: 8 pages, 4 figure

3D printed measurement phantoms for evaluation of magnetic particle imaging scanner

To assess the potential and capability of different MPI scanner designs and architectures, defined reference phantoms for imaging studies are required. For the preparation of well-defined structures as well as realistic vessel structures, 3D printed molds were filled with magnetic nanoparticles embedded into a long term stable polymeric matrix or perfused with a flowing ferrofluid. Different types and layouts of 3D printed phantoms will be presented which were imaged by means of MPI successfully

Repeat late instent-stenosis after an interval of four years in the same lesion after bare-metal and drug-eluting stent: a case report

In 2001, a 71-year old male was admitted to our hospital with unstable angina. The angiography revealed 2-vessel disease with a 90% stenosis of the proximal LAD. A bare-metal stent was implanted. Four years later the angiography showed a 80% instent-stenosis in the bare-metal stent but no progress at the other coronary arteries. A DES was implanted. Again, four years later, the patient presented with non-ST-elevation myocardial infarction. Angiography showed a 90% instent-restenosis, again without any progession of coronary artery disease in the other vessels. Again a DES implanted. Therefore the processes involved in the late instent-stenosis were not influenced by the antiproliferative agent sirolimu

Internal Structure and Apsidal Motions of Polytropic Stars in Close Binaries

We consider a synchronized, circular-orbit binary consisting of a polytrope with index n and a point-mass object, and use a self-consistent field method to construct the equilibrium structure of the polytrope under rotational and tidal perturbations. Our self-consistent field method is distinct from others in that the equilibrium orbital angular velocity is calculated automatically rather than being prescribed, which is crucial for obtaining apsidal motion rates accurately. We find that the centrifugal and tidal forces make perturbed stars more centrally condensed and larger in size. For n=1.5 polytopes with fixed entropy, the enhancement factor in stellar radii is about 23% and 4-8% for mu=1 and sim0.1-0.9, respectively, where mu is the fractional mass of the polytrope relative to the total. The centrifugal force dominates the tidal force in determining the equilibrium structure provided mu > 0.13-0.14 for n > 1.5. The shape and size of rotationally- and tidally-perturbed polytropes are well described by the corresponding Roche models as long as n > 2. The apsidal motion rates calculated for circular-orbit binaries under the equilibrium tide condition agree well with the predictions of the classical formula only when the rotational and tidal perturbations are weak. When the perturbations are strong as in critical configurations, the classical theory underestimates the real apsidal motion rates by as much as 50% for n=1.5 polytropes, although the discrepancy becomes smaller as n increases. For practical uses, we provide fitting formulae for various quantities including the density concentration, volume radius, and effective internal structure constant, as functions of mu and the perturbation parameters.Comment: 48 pages, 17 figures, 9 Tables. To appear in the ApJ (v699 issue

Altruistic decisions following penetrating traumatic brain injury

Abstract The cerebral correlates of altruistic decisions have increasingly attracted the interest of neuroscientists. To date, investigations on the neural underpinnings of altruistic decisions have primarily been conducted in healthy adults undergoing functional neuroimaging as they engaged in decisions to punish third parties. The chief purpose of the present study was to investigate altruistic decisions following focal brain damage with a novel altruistic decision task. In contrast to studies that have focused either on altruistic punishment or donation, the Altruistic Decision Task allows players to anonymously punish or donate to 30 charitable organizations involved with salient societal issues such as abortion, nuclear energy and civil rights. Ninety-four Vietnam War veterans with variable patterns of penetrating traumatic brain injury and 28 healthy veterans who also served in combat participated in the study as normal controls. Participants were asked to invest $1 to punish or reward real societal organizations, or keep the money for themselves. Associations between lesion distribution and performance on the task were analysed with multivariate support vector regression, which enables the assessment of the joint contribution of multiple regions in the determination of a given behaviour of interest. Our main findings were: (i) bilateral dorsomedial prefrontal lesions increased altruistic punishment, whereas lesions of the right perisylvian region and left temporo-insular cortex decreased punishment; (ii) altruistic donations were increased by bilateral lesions of the dorsomedial parietal cortex, whereas lesions of the right posterior superior temporal sulcus and middle temporal gyri decreased donations; (iii) altruistic punishment and donation were only weakly correlated, emphasizing their dissociable neuroanatomical associations; and (iv) altruistic decisions were not related to post-traumatic personality changes. These findings indicate that altruistic punishment and donation are determined by largely non-overlapping cerebral regions, which have previously been implicated in social cognition and moral experience such as evaluations of intentionality and intuitions of justice and morality. 10.1093/brain/awy064_video1 awy064media1 5758316955001</jats:p