Pruning GHSOM to create an explainable intrusion detection system

Intrusion Detection Systems (IDS) that provide high detection rates but are black boxes leadto models that make predictions a security analyst cannot understand. Self-Organizing Maps(SOMs) have been used to predict intrusion to a network, while also explaining predictions throughvisualization and identifying significant features. However, they have not been able to compete withthe detection rates of black box models. Growing Hierarchical Self-Organizing Maps (GHSOMs)have been used to obtain high detection rates on the NSL-KDD and CIC-IDS-2017 network trafficdatasets, but they neglect creating explanations or visualizations, which results in another blackbox model.This paper offers a high accuracy, Explainable Artificial Intelligence (XAI) based on GHSOMs.One obstacle to creating a white box hierarchical model is the model growing too large and complexto understand. Another contribution this paper makes is a pruning method used to cut down onthe size of the GHSOM, which provides a model that can provide insights and explanation whilemaintaining a high detection rate

Development and Assessment of a Diagnostic DNA Oligonucleotide Microarray for Detection and Typing of Meningitis-Associated Bacterial Species.

Meningitis is commonly caused by infection with a variety of bacterial or viral pathogens. Acute bacterial meningitis (ABM) can cause severe disease, which can progress rapidly to a critical life-threatening condition. Rapid diagnosis of ABM is critical, as this is most commonly associated with severe sequelae with associated high mortality and morbidity rates compared to viral meningitis, which is less severe and self-limiting. We have designed a microarray for detection and diagnosis of ABM. This has been validated using randomly amplified DNA targets (RADT), comparing buffers with or without formamide, in glass slide format or on the Alere ArrayTubeTM (Alere Technologies GmbH) microarray platform. Pathogen-specific signals were observed using purified bacterial nucleic acids and to a lesser extent using patient cerebral spinal fluid (CSF) samples, with some technical issues observed using RADT and glass slides. Repurposing the array onto the Alere ArrayTubeTM platform and using a targeted amplification system increased specific and reduced nonspecific hybridization signals using both pathogen nucleic and patient CSF DNA targets, better revealing pathogen-specific signals although sensitivity was still reduced in the latter. This diagnostic microarray is useful as a laboratory diagnostic tool for species and strain designation for ABM, rather than for primary diagnosis

Point of care testing for urinary tract infection in primary care (POETIC): protocol for a randomised controlled trial of the clinical and cost effectiveness of FLEXICULT (TM) informed management of uncomplicated UTI in primary care

BACKGROUND: Urinary tract infections (UTI) are the most frequent bacterial infection affecting women and account for about 15% of antibiotics prescribed in primary care. However, some women with a UTI are not prescribed antibiotics or are prescribed the wrong antibiotics, while many women who do not have a microbiologically confirmed UTI are prescribed antibiotics. Inappropriate antibiotic prescribing unnecessarily increases the risk of side effects and the development of antibiotic resistance, and wastes resources. POETIC is a randomised controlled trial of a Point Of Care Test (POCT) (Flexicult™) guided UTI management strategy for use in primary care, which may help General Practitioners more effectively decide both whether or not to prescribe antibiotics, and if so, to select the most appropriate antibiotic. METHODS/DESIGN: 614 adult female patients will be recruited from four primary care research networks (Wales, England, Spain, the Netherlands) and individually randomised to either POCT guided care or the guideline-informed ‘standard care’ arm. Urine and stool samples (where possible) will be obtained at presentation (day 1) and two weeks later for microbiological analysis. All participants will be followed up on the course of their illness and their quality of life, using a 2 week self-completed symptom diary. At 3 months, a primary care notes review will be conducted for evidence of further evidence of treatment failures, recurrence, complications, hospitalisations and health service costs. The primary objective is to compare appropriate antibiotic use on day 3 between the POCT and standard care arms using multi-level logistic regression to produce an odds ratio and associated 95% confidence interval. Costs of the two management approaches will be assessed in terms of the primary outcome. DISCUSSION: Although the Flexicult™ POCT is used in some countries in routine primary care, it’s clinical and cost effectiveness has never been evaluated in a randomised clinical trial. If shown to be effective, the use of this POCT could benefit individual sufferers and provide evidence for health care authorities to develop evidence based policies to combat the spread and impact of the unprecedented rise of infections caused by antibiotic resistant bacteria in Europe. TRIAL REGISTRATION NUMBER: ISRCTN65200697 (Registered 10 September 2013)

Long-term effects of chronic light pollution on seasonal functions of European blackbirds (turdus merula)

Light pollution is known to affect important biological functions of wild animals, including daily and annual cycles. However, knowledge about long-term effects of chronic exposure to artificial light at night is still very limited. Here we present data on reproductive physiology, molt and locomotor activity during two-year cycles of European blackbirds (Turdus merula) exposed to either dark nights or 0.3 lux at night. As expected, control birds kept under dark nights exhibited two regular testicular and testosterone cycles during the two-year experiment. Control urban birds developed testes faster than their control rural conspecifics. Conversely, while in the first year blackbirds exposed to light at night showed a normal but earlier gonadal cycle compared to control birds, during the second year the reproductive system did not develop at all: both testicular size and testosterone concentration were at baseline levels in all birds. In addition, molt sequence in light-treated birds was more irregular than in control birds in both years. Analysis of locomotor activity showed that birds were still synchronized to the underlying light-dark cycle. We suggest that the lack of reproductive activity and irregular molt progression were possibly the results of i) birds being stuck in a photorefractory state and/or ii) chronic stress. Our data show that chronic low intensities of light at night can dramatically affect the reproductive system. Future studies are needed in order to investigate if and how urban animals avoid such negative impact and to elucidate the physiological mechanisms behind these profound long-term effects of artificial light at night. Finally we call for collaboration between scientists and policy makers to limit the impact of light pollution on animals and ecosystems

First radial velocity results from the MINiature Exoplanet Radial Velocity Array (MINERVA)

The MINiature Exoplanet Radial Velocity Array (MINERVA) is a dedicated observatory of four 0.7m robotic telescopes fiber-fed to a KiwiSpec spectrograph. The MINERVA mission is to discover super-Earths in the habitable zones of nearby stars. This can be accomplished with MINERVA's unique combination of high precision and high cadence over long time periods. In this work, we detail changes to the MINERVA facility that have occurred since our previous paper. We then describe MINERVA's robotic control software, the process by which we perform 1D spectral extraction, and our forward modeling Doppler pipeline. In the process of improving our forward modeling procedure, we found that our spectrograph's intrinsic instrumental profile is stable for at least nine months. Because of that, we characterized our instrumental profile with a time-independent, cubic spline function based on the profile in the cross dispersion direction, with which we achieved a radial velocity precision similar to using a conventional "sum-of-Gaussians" instrumental profile: 1.8 m s$^{-1}$ over 1.5 months on the RV standard star HD 122064. Therefore, we conclude that the instrumental profile need not be perfectly accurate as long as it is stable. In addition, we observed 51 Peg and our results are consistent with the literature, confirming our spectrograph and Doppler pipeline are producing accurate and precise radial velocities.Comment: 22 pages, 9 figures, submitted to PASP, Peer-Reviewed and Accepte

The Milky Way's bright satellites as an apparent failure of LCDM

We use the Aquarius simulations to show that the most massive subhalos in galaxy-mass dark matter halos in LCDM are grossly inconsistent with the dynamics of the brightest Milky Way dwarf spheroidal galaxies. While the best-fitting hosts of the dwarf spheroidals all have 12 < Vmax < 25 km/s, LCDM simulations predict at least ten subhalos with Vmax > 25 km/s. These subhalos are also among the most massive at earlier times, and significantly exceed the UV suppression mass back to z ~ 10. No LCDM-based model of the satellite population of the Milky Way explains this result. The problem lies in the satellites' densities: it is straightforward to match the observed Milky Way luminosity function, but doing so requires the dwarf spheroidals to have dark matter halos that are a factor of ~5 more massive than is observed. Independent of the difficulty in explaining the absence of these dense, massive subhalos, there is a basic tension between the derived properties of the bright Milky Way dwarf spheroidals and LCDM expectations. The inferred infall masses of these galaxies are all approximately equal and are much lower than standard LCDM predictions for systems with their luminosities. Consequently, their implied star formation efficiencies span over two orders of magnitude, from 0.2% to 20% of baryons converted into stars, in stark contrast with expectations gleaned from more massive galaxies. We explore possible solutions to these problems within the context of LCDM and find them to be unconvincing. In particular, we use controlled simulations to demonstrate that the small stellar masses of the bright dwarf spheroidals make supernova feedback an unlikely explanation for their low inferred densities.Comment: 18 pages, 10 figures; matches version published in MNRA

Biomarker and Geochemical Assay Validation in Mars Analog Sites: Lessons from the FELDSPAR (Field Exploration and Life Detection Sampling for Planetary Analog Research) Project

Missions looking for signs of life on other worlds can often only take a few samples once they arrive. Making sense of these "few and far between" observations is easier if we know what a "normal" level of variation for that kind of planet is. Recent eruption sites in Iceland are good places to learn about this, because they have very little life present and the same types of rocks as many places on Mars. We have visited several of these sites in Iceland and tested many different kinds of measurements: the energy available for life, the amount of DNA (an important biological molecule) present, the relative amounts of different kinds of micro-organisms, and the specific minerals that make up the rocks and ground. In addition to recommendations for future expeditions, we have also shown that using early on-site measurements to choose later on-site sample sites is very helpful in reducing the number of sample sites needed

Genetic Variants of Ehrlichia phagocytophila1, Rhode Island and Connecticut

Primers were used to amplify a 561-bp region of the 16S rRNA gene of Ehrlichia phagocytophila from Ixodes scapularis ticks and small mammals collected in Rhode Island and Connecticut. DNA sequences for all 50 E. phagocytophila-positive samples collected from 1996 through 1998 in southwestern Connecticut were identical to the sequence reported for E. phagocytophila DNA from confirmed human cases. In contrast, the sequences from 92 of 123 E. phagocytophila-positive Rhode Island samples collected from 1996 through 1999 included several variants differing by 1-2 nucleotides from that in the agent infecting humans. While 11.9% of 67 E. phagocytophila-positive ticks collected during 1997 in Rhode Island harbored ehrlichiae with sequences identical to that of the human agent, 79.1% had a variant sequence not previously described. The low incidence of human ehrlichiosis in Rhode Island may in part result from interference by these variant ehrlichiae with maintenance and transmission of the true agent of human disease

Combining biodiversity resurveys across regions to advance global change research

More and more ecologists have started to resurvey communities sampled in earlier decades to determine long-term shifts in community composition and infer the likely drivers of the ecological changes observed. However, to assess the relative importance of and interactions among multiple drivers, joint analyses of resurvey data from many regions spanning large environmental gradients are needed. In this article, we illustrate how combining resurvey data from multiple regions can increase the likelihood of driver orthogonality within the design and show that repeatedly surveying across multiple regions provides higher representativeness and comprehensiveness, allowing us to answer more completely a broader range of questions. We provide general guidelines to aid the implementation of multiregion resurvey databases. In so doing, we aim to encourage resurvey database development across other community types and biomes to advance global environmental change research