Reflections on the Ethical Content of the IT Honours Program Project Module

Part 4: Syllabus DesignInternational audienceHonours programs in South African universities must include a research project module. There are external pressures from professional bodies and government that influences the nature of the project module. This paper presents a reflection on the process of managing the project module at a South African university taking into account internal and external demands. The focus for this paper is on the ethical content of the projects. Examples of projects are presented after which the ethical awareness of the students is discussed. Not all projects have ethical, legal or social issues, however ethical aspects need to be reflected upon and awareness of these issues is essential during the planning of the project. The awareness that students have on ethical, social and legal issues is investigated in this paper

Feeding in the dark: lateral-line-mediated prey detection in the peacock cichlid \u3cem\u3eAulonocara stuartgranti\u3c/em\u3e

The cranial lateral line canal system of teleost fishes is morphologically diverse and is characterized by four patterns. One of these, widened lateral line canals, has evolved convergently in a wide range of teleosts, including the Lake Malawi peacock cichlids (Aulonocara), and has been attributed to its role in prey detection. The ability to study Aulonocara in the laboratory provides an opportunity to test the hypothesis that their reported ability to feed on invertebrate prey living in sandy substrates in their natural habitat is the result of lateral-line-mediated prey detection. The goal of this study was to determine whether Aulonocara stuartgranti could detect hydrodynamic stimuli generated by tethered brine shrimp (visualized using digital particle image velocimetry) under light and dark conditions, with and without treatment with cobalt chloride, which is known to temporarily inactivate the lateral line system. Fish were presented with six pairs of tethered live and dead adult brine shrimp and feeding behavior was recorded with HD digital video. Results demonstrate that A. stuartgranti: (1) uses the same swimming/feeding strategy as they do in the field; (2) detects and consumes invertebrate prey in the dark using its lateral line system; (3) alters prey detection behavior when feeding on the same prey under light and dark conditions, suggesting the involvement of multiple sensory modalities; and (4) after treatment with cobalt chloride, exhibits a reduction in their ability to detect hydrodynamic stimuli produced by prey, especially in the dark, thus demonstrating the role of the lateral line system in prey detection

Profiling the Mismatch Tolerance of Argonaute 2 through Deep Sequencing of Sliced Polymorphic Viral RNAs

Low allelic and clonal variability among endogenous RNA interference (RNAi) targets has focused mismatch tolerance studies to RNAi-active guide strands. However, the inherent genomic instability of RNA viruses such as hepatitis C virus (HCV) gives rise to quasi-species mutants within discrete clones: this facilitates mismatch tolerance studies from a target perspective. We recently quantified the slicing imprecision of Argonaute 2 using small interfering RNA (siRNA) analogues of the DNA-directed RNAi drug TT-034 and next generation sequencing of 5’ RNA Ligase-Mediated Rapid Amplification of cDNA Ends (RACE-SEQ). Here, we present an open source, customizable, and computationally light RACE-SEQ bioinformatic pipeline, describing adaptations that semi-quantitatively report the impact of RNAi hybridisation site mismatches from the target perspective. The analysis shows Argonaute 2 has a substitution-specific, 3-5 log activity window between fully complementary targets and targets with mismatches across positions 10-11. It further focuses the endonucleotic Slicer imprecision around positions 13-17, demonstrating its dependence on guide strand central region complementarity, and potentiation by even a single mismatch. We further propose pharmacogenomics value in testing endogenous targets using recombinant replicon systems and RACE-SEQ to report the pharmacodynamics of sequence-specific oligonucleotide therapeutics against all possible polymorphisms in a population, in a minimally-biased, patient-free manner

Lars Vegard:key communicator and pioneer crystallographer

The Norwegian physicist Lars Vegard studied with William H. Bragg in Leeds and then with Wilhelm Wien in Würzburg. There, in 1912, he heard a lecture by Max Laue describing the first X-ray diffraction experiments and took accurate notes which he promptly sent to Bragg. Although now remembered mainly for his work on the physics of the aurora borealis, Vegard also did important pioneering work in three areas of crystallography. He derived chemical insight from a series of related crystal structures that he determined, Vegard's Law relates the unit-cell dimensions of mixed crystals to those of the pure components, and he determined some of the first crystal structures of gases solidified at cryogenic temperatures

Gut microbiota transplantation drives the adoptive transfer of colonic genotype-phenotype characteristics between mice lacking catestatin and their wild type counterparts

The gut microbiota is in continuous interaction with the intestinal mucosa via metabolic, neuro-immunological, and neuroendocrine pathways. Disruption in levels of antimicrobial peptides produced by the enteroendocrine cells, such as catestatin, has been associated with changes in the gut microbiota and imbalance in intestinal homeostasis. However, whether the changes in the gut microbiota have a causational role in intestinal dyshomeostasis has remained elusive. To this end, we performed reciprocal fecal microbial transplantation in wild-type mice and mice with a knockout in the catestatin coding region of the chromogranin-A gene (CST-KO mice). Combined microbiota phylogenetic profiling, RNA sequencing, and transmission electron microscopy were employed. Fecal microbiota transplantation from mice deficient in catestatin (CST-KO) to microbiota-depleted wild-type mice induced transcriptional and physiological features characteristic of a distorted colon in the recipient animals, including impairment in tight junctions, as well as an increased collagen area fraction indicating colonic fibrosis. In contrast, fecal microbiota transplantation from wild-type mice to microbiota-depleted CST-KO mice reduced collagen fibrotic area, restored disrupted tight junction morphology, and altered fatty acid metabolism in recipient CST-KO mice. This study provides a comprehensive overview of the murine metabolic- and immune-related cellular pathways and processes that are co-mediated by the fecal microbiota transplantation and supports a prominent role for the gut microbiota in the colonic distortion associated with the lack of catestatin in mice. Overall, the data show that the gut microbiota may play a causal role in the development of features of intestinal inflammation and metabolic disorders, known to be associated with altered levels of catestatin and may, thus, provide a tractable target in the treatment and prevention of these disorders

Equilibria-based Probabilistic Model Checking for Concurrent Stochastic Games

Probabilistic model checking for stochastic games enables formal verification of systems that comprise competing or collaborating entities operating in a stochastic environment. Despite good progress in the area, existing approaches focus on zero-sum goals and cannot reason about scenarios where entities are endowed with different objectives. In this paper, we propose probabilistic model checking techniques for concurrent stochastic games based on Nash equilibria. We extend the temporal logic rPATL (probabilistic alternating-time temporal logic with rewards) to allow reasoning about players with distinct quantitative goals, which capture either the probability of an event occurring or a reward measure. We present algorithms to synthesise strategies that are subgame perfect social welfare optimal Nash equilibria, i.e., where there is no incentive for any players to unilaterally change their strategy in any state of the game, whilst the combined probabilities or rewards are maximised. We implement our techniques in the PRISM-games tool and apply them to several case studies, including network protocols and robot navigation, showing the benefits compared to existing approaches

GW170104: Observation of a 50-Solar-Mass Binary Black Hole Coalescence at Redshift 0.2

We describe the observation of GW170104, a gravitational-wave signal produced by the coalescence of a pair of stellar-mass black holes. The signal was measured on January 4, 2017 at 10∶11:58.6 UTC by the twin advanced detectors of the Laser Interferometer Gravitational-Wave Observatory during their second observing run, with a network signal-to-noise ratio of 13 and a false alarm rate less than 1 in 70 000 years. The inferred component black hole masses are 31.2 þ8.4 −6.0M⊙ and 19.4 þ5.3 −5.9M⊙ (at the 90% credible level). The black hole spins are best constrained through measurement of the effective inspiral spin parameter, a mass-weighted combination of the spin components perpendicular to the orbital plane, χeff ¼ −0.12 þ0.21 −0.30. This result implies that spin configurations with both component spins positively aligned with the orbital angular momentum are disfavored. The source luminosity distance is 880 þ450 −390 Mpc corresponding to a redshift of z ¼ 0.18 þ0.08 −0.07 .We constrain the magnitude of modifications to the gravitational-wave dispersion relation and perform null tests of general relativity. Assuming that gravitons are dispersed in vacuum like massive particles, we bound the graviton mass to mg ≤ 7.7 × 10−23 eV=c2. In all cases, we find that GW170104 is consistent with general relativity

Upper Limits on Gravitational Waves from Scorpius X-1 from a Model-Based Cross-Correlation Search in Advanced LIGO Data

We present the results of a semicoherent search for continuous gravitational waves from the low-mass X-ray binary Scorpius X-1, using data from the first Advanced LIGO observing run. The search method uses details of the modeled, parametrized continuous signal to combine coherently data separated by less than a specified coherence time, which can be adjusted to trade off sensitivity against computational cost. A search was conducted over the frequency range 25–$2000\,\mathrm{Hz}$, spanning the current observationally constrained range of binary orbital parameters. No significant detection candidates were found, and frequency-dependent upper limits were set using a combination of sensitivity estimates and simulated signal injections. The most stringent upper limit was set at $175\,\mathrm{Hz}$, with comparable limits set across the most sensitive frequency range from 100 to $200\,\mathrm{Hz}$. At this frequency, the 95% upper limit on the signal amplitude h 0 is $2.3\times {10}^{-25}$ marginalized over the unknown inclination angle of the neutron star\u27s spin, and $8.0\times {10}^{-26}$ assuming the best orientation (which results in circularly polarized gravitational waves). These limits are a factor of 3–4 stronger than those set by other analyses of the same data, and a factor of ~7 stronger than the best upper limits set using data from Initial LIGO science runs. In the vicinity of $100\,\mathrm{Hz}$, the limits are a factor of between 1.2 and 3.5 above the predictions of the torque balance model, depending on the inclination angle; if the most likely inclination angle of 44° is assumed, they are within a factor of 1.7

First Search for Nontensorial Gravitational Waves From Known Pulsars

We present results from the first directed search for nontensorial gravitational waves. While general relativity allows for tensorial (plus and cross) modes only, a generic metric theory may, in principle, predict waves with up to six different polarizations. This analysis is sensitive to continuous signals of scalar, vector, or tensor polarizations, and does not rely on any specific theory of gravity. After searching data from the first observation run of the advanced LIGO detectors for signals at twice the rotational frequency of 200 known pulsars, we find no evidence of gravitational waves of any polarization. We report the first upper limits for scalar and vector strains, finding values comparable in magnitude to previously published limits for tensor strain. Our results may be translated into constraints on specific alternative theories of gravity