Automating Reproducibility - Challenges and what it takes to meet them

Computational reproducibility is a building block for transparent and cumulative science. It enables the originator and other researchers, on other computers and later in time, to reproduce and thus understand how results came about while avoiding various errors that may lead to erroneous reporting of statistical and computational results. But what does it take to make something reproducible? Until recently, detailed descriptions of methods and analyses were the primary instrument for ensuring scientific reproducibility. Such manual description fails to ensure reproduction due to four different reasons that get more likely the more central computational methods are for research. To meet these challenges, we propose that researchers take advantage of four technological advancements—version control, dynamic document generation, workflow automation, and containerization. Our workflow enables scientists to achieve a more comprehensive standard that allows anyone to access a digital research repository and reproduce all computational steps from raw data to final report with a single command

The string tension in SU(N) gauge theory from a careful analysis of smearing parameters

We report a method to select optimal smearing parameters before production runs and discuss the advantages of this selection for the determination of the string tension.Comment: Contribution to Lat97 poster session, title was 'How to measure the string tension', 3 pages, 5 colour eps figure

Development and test of a planar R-band accelerating structure

Planar accelerating structures, so called muffin tins, are of great interest for new accelerating techniques which are operating at high frequencies. At present the upper frequency limit for high power sources is 29.9855 GHz available at CERN. Therefore a new design of a planar traveling wave constant impedance accelerating structure is presented. A fully engineered 37-cell prototype with an operating frequency of 29.9855 GHz, which is designed for the 2 pi /3-mode, was fabricated by CNC milling technology. The design includes a power coupler, a cavity geometry optimized to compensate the effect of transverse forces, vacuum flanges and beam pipe flanges. Shown are the frequency scan of transmission and reflection measurements compared to numerical simulations with GdfidL. Further, a non resonant bead pull measurement was made to determine and verify the fundamental modes of the structure. The cavity is planned to be powered at the CLIC test stand at CERN. (4 refs)

Future Challenges and Unsolved Problems in Multi-field Visualization

Evaluation, solved and unsolved problems, and future directions are popular themes pervading the visualization community over the last decade. The top unsolved problem in both scientific and information visualization was the subject of an IEEE Visualization Conference panel in 2004. The future of graphics hardware was another important topic of discussion the same year. The subject of how to evaluate visualization returned a few years later. Chris Johnson published a list of 10 top problems in scientific visualization research. This was followed up by report of both past achievements and future challenges in visualization research as well as financial support recommendations to the National Science Foundation (NSF) and National Institute of Health (NIH). Chen recently published the first list of top unsolved information visualization problems. Future research directions of topology-based visualization was also a major theme of a workshop on topology-based methods. Laramee and Kosara published a list of top future challenges in human-centered visualization

One-Flavour Hybrid Monte Carlo with Wilson Fermions

The Wilson fermion determinant can be written as product of the determinants of two hermitian positive definite matrices. This formulation allows to simulate non-degenerate quark flavors by means of the hybrid Monte Carlo algorithm. A major numerical difficulty is the occurrence of nested inversions. We construct a Uzawa iteration scheme which treats the nested system within one iterative process.Comment: 11 pages, to appear in proceedings of the workshop "Numerical Challenges in Lattice QCD", Springer Verla

Improved staggered quark actions with reduced flavour symmetry violations for lattice QCD

We introduce a new class of actions for staggered quarks in lattice QCD which significantly reduce flavour symmetry violations in the pion mass spectrum. An action introduced by the MILC collaboration for the same purpose is seen to be a special case. We discus how such actions arise from a systematic attempt to reduce flavour symmetry violations in the weak coupling limit. It is shown that for quenched lattice QCD at 6/g^2=5.7, representative actions of this class give a considerable reduction in flavour symmetry violation over the standard staggered action, and a significant reduction over what is achieved by the MILC action.Comment: RevTeX 18 pages with 3 postscript figure

Ausbringung von Abwasser aus der Olivenölproduktion auf Böden - Eine Screening studie

Olivenplantagen sind von großer Bedeutung für die Israelische und Palestinensische Agrarwirtschaft. Bei der continuierlichen 3-Phasen-Extraktion wird der Olivenpresskuchen mit Wasser versetzt. Nach Abtrennung des Öls fallen große Mengen Abwasser an. Es ist stark sauer, besitzt eine hohe Konzentration an organischen Stoffen und ist aufgrund toxischer Effekte durch überwiegend phenolische Verbindungen nur schwer mikrobiologisch abbaubar. Augrund dieser Eigenschaften kann es sich negative auf den wasseraufbereitenden Vorgang in Kläranlagen auswirken. Alternative Entsorgungsmethoden sind kaum vorhanden, weshalb es oft zu einer unkontrollierten Entsorgung des Abwassers kommt. Wir untersuchten verschiedenen Böden im Westjordanland und Israel, die in der Vergangenheit unkontrolliert mit Abwasser aus der Olivenölproduktion versetzt wurden in einer Screening Studie. Alle contaminierten Böden enthielten signifant mehr Nährstoffe, wie z.B. Chlorid, Kalium, organischen Kohlenstoff und Stickstoff. Allerdings waren die Mehrzahl der contaminierten Proben hydrophober als vergleichbare unkontaminierte Proben. Dies konnte durch Kontaktwinkelmessungen und die Bestimmung der Water Drop Penetration Time gezeigt werden. Vielversprechend wäre es, das Abwasser als Dünger einzusetzen und gleichzeitig hydrophobisierenden Auswirkungen zu reduzieren

Changes in Blood Cell Deformability in Chorea-Acanthocytosis and Effects of Treatment With Dasatinib or Lithium

Misshaped red blood cells (RBCs), characterized by thorn-like protrusions known as acanthocytes, are a key diagnostic feature in Chorea-Acanthocytosis (ChAc), a rare neurodegenerative disorder. The altered RBC morphology likely influences their biomechanical properties which are crucial for the cells to pass the microvasculature. Here, we investigated blood cell deformability of five ChAc patients compared to healthy controls during up to 1-year individual off-label treatment with the tyrosine kinase inhibitor dasatinib or several weeks with lithium. Measurements with two microfluidic techniques allowed us to assess RBC deformability under different shear stresses. Furthermore, we characterized leukocyte stiffness at high shear stresses. The results showed that blood cell deformability–including both RBCs and leukocytes - in general was altered in ChAc patients compared to healthy donors. Therefore, this study shows for the first time an impairment of leukocyte properties in ChAc. During treatment with dasatinib or lithium, we observed alterations in RBC deformability and a stiffness increase for leukocytes. The hematological phenotype of ChAc patients hinted at a reorganization of the cytoskeleton in blood cells which partly explains the altered mechanical properties observed here. These findings highlight the need for a systematic assessment of the contribution of impaired blood cell mechanics to the clinical manifestation of ChAc

Chosen-ciphertext security from subset sum

We construct a public-key encryption (PKE) scheme whose security is polynomial-time equivalent to the hardness of the Subset Sum problem. Our scheme achieves the standard notion of indistinguishability against chosen-ciphertext attacks (IND-CCA) and can be used to encrypt messages of arbitrary polynomial length, improving upon a previous construction by Lyubashevsky, Palacio, and Segev (TCC 2010) which achieved only the weaker notion of semantic security (IND-CPA) and whose concrete security decreases with the length of the message being encrypted. At the core of our construction is a trapdoor technique which originates in the work of Micciancio and Peikert (Eurocrypt 2012