Reproducible and User-Controlled Software Environments in HPC with Guix

Support teams of high-performance computing (HPC) systems often find themselves between a rock and a hard place: on one hand, they understandably administrate these large systems in a conservative way, but on the other hand, they try to satisfy their users by deploying up-to-date tool chains as well as libraries and scientific software. HPC system users often have no guarantee that they will be able to reproduce results at a later point in time, even on the same system-software may have been upgraded, removed, or recompiled under their feet, and they have little hope of being able to reproduce the same software environment elsewhere. We present GNU Guix and the functional package management paradigm and show how it can improve reproducibility and sharing among researchers with representative use cases.Comment: 2nd International Workshop on Reproducibility in Parallel Computing (RepPar), Aug 2015, Vienne, Austria. http://reppar.org

Emission and absorption noise in the fractional quantum Hall effect

We compute the high-frequency emission and absorption noise in a fractional quantum Hall effect (FQHE) sample at arbitrary temperature. We model the edges of the FQHE as chiral Luttinger liquids (LL) and we use the non-equilibrium perturbative Keldysh formalism. We find that the non-symmetrized high frequency noise contains important signatures of the electron-electron interactions that can be used to test the Luttinger liquid physics, not only in FQHE edge states, but possibly also in other one-dimensional systems such as carbon nanotubes. In particular we find that the emission and absorption components of the excess noise (defined as the difference between the noise at finite voltage and at zero voltage) are different in an interacting system, as opposed to the non-interacting case when they are identical. We study the resonance features which appear in the noise at the Josephson frequency (proportional to the applied voltage), and we also analyze the effect of the distance between the measurement point and the backscattering site. Most of our analysis is performed in the weak backscattering limit, but we also compute and discuss briefly the high-frequency noise in the tunneling regime.Comment: 26 pages, 11 figure

DEEP: a provenance-aware executable document system

The concept of executable documents is attracting growing interest from both academics and publishers since it is a promising technology for the dissemination of scientific results. Provenance is a kind of metadata that provides a rich description of the derivation history of data products starting from their original sources. It has been used in many different e-Science domains and has shown great potential in enabling reproducibility of scientific results. However, while both executable documents and provenance are aimed at enhancing the dissemination of scientific results, little has been done to explore the integration of both techniques. In this paper, we introduce the design and development of DEEP, an executable document environment that generates scientific results dynamically and interactively, and also records the provenance for these results in the document. In this system, provenance is exposed to users via an interface that provides them with an alternative way of navigating the executable document. In addition, we make use of the provenance to offer a document rollback facility to users and help to manage the system's dynamic resources

Detecting and characterizing lateral phishing at scale

We present the first large-scale characterization of lateral phishing attacks, based on a dataset of 113 million employee-sent emails from 92 enterprise organizations. In a lateral phishing attack, adversaries leverage a compromised enterprise account to send phishing emails to other users, benefit-ting from both the implicit trust and the information in the hijacked user's account. We develop a classifier that finds hundreds of real-world lateral phishing emails, while generating under four false positives per every one-million employee-sent emails. Drawing on the attacks we detect, as well as a corpus of user-reported incidents, we quantify the scale of lateral phishing, identify several thematic content and recipient targeting strategies that attackers follow, illuminate two types of sophisticated behaviors that attackers exhibit, and estimate the success rate of these attacks. Collectively, these results expand our mental models of the 'enterprise attacker' and shed light on the current state of enterprise phishing attacks

Full counting statistics of strongly non-Ohmic transport through single molecules

We study analytically the full counting statistics of charge transport through single molecules, strongly coupled to a weakly damped vibrational mode. The specifics of transport in this regime - a hierarchical sequence of avalanches of transferred charges, interrupted by "quiet" periods - make the counting statistics strongly non-Gaussian. We support our findings for the counting statistics as well as for the frequency-dependent noise power by numerical simulations, finding excellent agreement.Comment: 4+ pages, 2 figures; minor changes, version published in Phys. Rev. Let

Efficaciousness of low affinity compared to high affinity TSPO ligands in the inhibition of hypoxic mitochondrial cellular damage induced by cobalt chloride in human lung H1299 cells

The 18 kDa translocator protein (TSPO) plays an important role in apoptotic cell death, including apoptosis induced by the hypoxia mimicking agent cobalt chloride (CoCl2). In this study, the protective effects of a high (CB86; Ki = 1.6 nM) and a low (CB204; Ki = 117.7 nM) affinity TSPO ligands were investigated in H1299 lung cancer cell line exposed to CoCl2. The lung cell line H1299 was chosen in the present study since they express TSPO and able to undergo programmed cell death. The examined cell death markers included: ATP synthase reversal, reactive oxygen species (ROS) generation, mitochondrial membrane potential (D m) depolarization, cellular toxicity, and cellular viability. Pretreatment of the cells with the low affinity ligand CB204 at a concentration of 100 μM suppressed significantly (p < 0.05 for all) CoCl2-induced cellular cytotoxicity (100%), ATP synthase reversal (67%), ROS generation (82%), D m depolarization (100%), reduction in cellular density (97%), and also increased cell viability (85%). Furthermore, the low affinity TSPO ligand CB204, was harmless when given by itself at 100 μM. In contrast, the high affinity ligand (CB86) was significantly effective only in the prevention of CoCl2-induced ROS generation (39%, p < 0.001), and showed significant cytotoxic effects when given alone at 100 μM, as reflected in alterations in ADP/ATP ratio, oxidative stress, mitochondrial membrane potential depolarization and cell death. It appears that similar to previous studies on brain-derived cells, the relatively low affinity for the TSPO target enhances the potency of TSPO ligands in the protection from hypoxic cell death. Moreover, the high affinity TSPO ligand CB86, but not the low affinity ligand CB204, was lethal to the lung cells at high concentration (100 μM). The low affinity TSPO ligand CB204 may be a candidate for the treatment of pulmonary diseases related to hypoxia, such as pulmonary ischemia and chronic obstructive pulmonary disease COPD

Cascading ecological effects from local extirpation of an ecosystem engineer in the Arava desert

The extinction of a single species from a local community may carry little cost in terms of species diversity, yet its loss eliminates its biotic and abiotic interactions. We describe such a scenario in the Arava desert, where different cultural and law enforcement practices exclude Dorcas gazelles (Gazella dorcas (Linnaeus, 1758)) from the Jordanian side of the border while protecting their populations on the Israeli side. We found that gazelles break the soil crust, formed in desert systems after annual flooding, thereby creating patches of loose and cooler sand that are used by pit-building antlions (Neuroptera: Myrmeleontidae). When we artificially broke the soil crust on both sides of the border, we found a significant increase in antlion density in these patches, but only on the Israeli side. On the Jordanian side, where no gazelles have been observed since the early 1980s, no antlions colonized either control or manipulated plots. Additional choice/no-choice feeding experiments, in which we offered antlions to lizards and birds, revealed that the effect of humans on gazelles cascades farther, as antlions serve as a palatable food source for both groups. Thus, the human-mediated loss of nontrophic interactions between gazelles and antlions cascades to the loss of trophic interactions between antlions and their predators