Integrity static analysis of COTS/SOUP

This paper describes the integrity static analysis approach developed to support the justification of commercial off-the-shelf software (COTS) used in a safety-related system. The static analysis was part of an overall software qualification programme, which also included the work reported in our paper presented at Safecomp 2002. Integrity static analysis focuses on unsafe language constructs and “covert” flows, where one thread can affect the data or control flow of another thread. The analysis addressed two main aspects: the internal integrity of the code (especially for the more critical functions), and the intra-component integrity, checking for covert channels. The analysis process was supported by an aggregation of tools, combined and engineered to support the checks done and to scale as necessary. Integrity static analysis is feasible for industrial scale software, did not require unreasonable resources and we provide data that illustrates its contribution to the software qualification programme

Modeling the transboundary risk of feed ingredients contaminated with porcine epidemic diarrhea virus

Citation: Dee, S., Neill, C., Singrey, A., Clement, T., Cochrane, R., Jones, C., . . . Nelson, E. (2016). Modeling the transboundary risk of feed ingredients contaminated with porcine epidemic diarrhea virus. Bmc Veterinary Research, 12, 12. doi:10.1186/s12917-016-0674-zBackground: This study describes a model developed to evaluate the transboundary risk of PEDV-contaminated swine feed ingredients and the effect of two mitigation strategies during a simulated transport event from China to the US. Results: Ingredients imported to the USA from China, including organic & conventional soybeans and meal, lysine hydrochloride, D-L methionine, tryptophan, Vitamins A, D & E, choline, carriers (rice hulls, corn cobs) and feed grade tetracycline, were inoculated with PEDV. Control ingredients, and treatments (ingredients plus a liquid antimicrobial (SalCURB, Kemin Industries (LA) or a 2 % custom medium chain fatty acid blend (MCFA)) were tested. The model ran for 37 days, simulating transport of cargo from Beijing, China to Des Moines, IA, US from December 23, 2012 to January 28, 2013. To mimic conditions on land and sea, historical temperature and percent relative humidity (% RH) data were programmed into an environmental chamber which stored all containers. To evaluate PEDV viability over time, ingredients were organized into 1 of 4 batches of samples, each batch representing a specific segment of transport. Batch 1 (segment 1) simulated transport of contaminated ingredients from manufacturing plants in Beijing (day 1 post-contamination (PC)). Batch 2 (segments 1 and 2) simulated manufacturing and delivery to Shanghai, including time in Anquing terminal awaiting shipment (days 1-8 PC). Batch 3 (segments 1, 2 and 3) represented time in China, the crossing of the Pacific and entry to the US at the San Francisco, CA terminal (day 1-27 PC). Batch 4 (segments 1-4) represented the previous events, including transport to Des Moines, IA (days 1-37 PC). Across control (non-treated) ingredients, viable PEDV was detected in soybean meal (organic and conventional), Vitamin D, lysine hydrochloride and choline chloride. In contrast, viable PEDV was not detected in any samples treated with LA or MCFA. Conclusions: These results demonstrate the ability of PEDV to survive in a subset of feed ingredients using a model simulating shipment from China to the US. This is proof of concept suggesting that contaminated feed ingredients could serve as transboundary risk factors for PEDV, along with the identification of effective mitigation options

Kinematic Structure in the Galactic Halo at the North Galactic Pole: RR Lyrae and BHB Stars show different kinematics

Space motions are given for 38 RR Lyrae (RRL) stars and 79 blue horizontal branch (BHB) stars in a ~200 deg2 area around the North Galactic Pole (NGP) using a homogeneous distance scale consistent with (m-M)0=18.52 for the LMC. The kinematics of the 26 RRL and 52 BHB stars in the 10.4 cubic kpc volume that have Z<8 kpc are not homogeneous. Our BHB sample (like that of Sirko et al. 2004b) has a zero galactic rotation (V_phi) and roughly isotropic velocity dispersions. The RRL sample shows a definite retrograde rotation (V_phi = -95+/-29 km/s) and non-isotropic velocity dispersions. The combined BHB and RRL sample has a retrograde galactic rotation (V) that is similar to that found by Majewski (1992) for his sample of subdwarfs in SA 57. The velocity dispersion of the RRL stars that have a positive W motion is significantly smaller than the dispersion of those "streaming down" with a negative W. One component of our sample (rich in RRL's) shows retrograde rotation and the streaming motion that we associate with the accretion process. The other (traced by the BHB stars) shows essentially no rotation and less evidence of streaming. These two components have HB morphologies that suggest that they may be the field star equivalents of the young and old halo globular clusters respectively.Comment: Accepted for publication on MNRAS. 20 pages, 7 figures, 12 table

Developmental plasticity shapes social traits and selection in a facultatively eusocial bee

Developmental plasticity generates phenotypic variation, but how it contributes to evolutionary change is unclear. Phenotypes of individuals in caste-based (eusocial) societies are particularly sensitive to developmental processes, and the evolutionary origins of eusociality may be rooted in developmental plasticity of ancestral forms. We used an integrative genomics approach to evaluate the relationships among developmental plasticity, molecular evolution, and social behavior in a bee species (Megalopta genalis) that expresses flexible sociality, and thus provides a window into the factors that may have been important at the evolutionary origins of eusociality. We find that differences in social behavior are derived from genes that also regulate sex differentiation and metamorphosis. Positive selection on social traits is influenced by the function of these genes in development. We further identify evidence that social polyphenisms may become encoded in the genome via genetic changes in regulatory regions, specifically in transcription factor binding sites. Taken together, our results provide evidence that developmental plasticity provides the substrate for evolutionary novelty and shapes the selective landscape for molecular evolution in a major evolutionary innovation: Eusociality

The Kinematic Properties of BHB and RR Lyrae stars towards the Anticentre and the North Galactic Pole: The Transition between the Inner and the Outer Halo

We identify 51 blue horizontal branch (BHB) stars, 12 possible BHB stars and 58 RR Lyrae stars in Anticentre fields. Their selection does not depend on their kinematics. Light curves and ephemerides are given for 7 previously unknown RR Lyrae stars. All but 4 of the RR Lyrae stars are of Oosterhoff type I. Our selection criteria for BHB stars give results that agree with those used by Smith et al. (2010) and Ruhland et al. (2011). We use 5 methods to determine distances for the BHB stars and 3 methods for the RR Lyrae stars to get distances on a uniform scale. Absolute proper motions (largely derived from the GSCII and SDSS (DR7) databases) are given for these stars; radial velocities are given for 31 of the BHB stars and 37 of the RR Lyrae stars. Combining these data for BHB and RR Lyrae stars with those previously found in fields at the North Galactic Pole, we find that retrograde orbits dominate for galactocentric distances greater than 12.5 kpc. The majority of metal-poor stars in the solar neighbourhood are known to be concentrated in a Lperp vs. Lz angular momentum plot. We show that the ratio of the number of outliers to the number in the main concentration increases with galactocentric distance. The location of these outliers with Lperp and Lz shows that the halo BHB and RR Lyrae stars have more retrograde orbits and a more spherical distribution with increasing galactocentric distance. Six RR Lyrae stars are identified in the H99 group of outliers; the small spread in their [Fe/H] suggests that they could have come from a single globular cluster. Another group of outliers contains two pairs of RR Lyrae stars; the stars in each pair have similar properties.Comment: 40 pages, 19 figures, to be published in MNRA

Perceiving Nasal Patency through Mucosal Cooling Rather than Air Temperature or Nasal Resistance

Adequate perception of nasal airflow (i.e., nasal patency) is an important consideration for patients with nasal sinus diseases. The perception of a lack of nasal patency becomes the primary symptom that drives these patients to seek medical treatment. However, clinical assessment of nasal patency remains a challenge because we lack objective measurements that correlate well with what patients perceive.The current study examined factors that may influence perceived patency, including air temperature, humidity, mucosal cooling, nasal resistance, and trigeminal sensitivity. Forty-four healthy subjects rated nasal patency while sampling air from three facial exposure boxes that were ventilated with untreated room air, cold air, and dry air, respectively. In all conditions, air temperature and relative humidity inside each box were recorded with sensors connected to a computer. Nasal resistance and minimum airway cross-sectional area (MCA) were measured using rhinomanometry and acoustic rhinometry, respectively. General trigeminal sensitivity was assessed through lateralization thresholds to butanol. No significant correlation was found between perceived patency and nasal resistance or MCA. In contrast, air temperature, humidity, and butanol threshold combined significantly contributed to the ratings of patency, with mucosal cooling (heat loss) being the most heavily weighted predictor. Air humidity significantly influences perceived patency, suggesting that mucosal cooling rather than air temperature alone provides the trigeminal sensation that results in perception of patency. The dynamic cooling between the airstream and the mucosal wall may be quantified experimentally or computationally and could potentially lead to a new clinical evaluation tool

Functional Analysis of Conserved Non-Coding Regions Around the Short Stature hox Gene (shox) in Whole Zebrafish Embryos

Background: Mutations in the SHOX gene are responsible for Leri-Weill Dyschondrosteosis, a disorder characterised by mesomelic limb shortening. Recent investigations into regulatory elements surrounding SHOX have shown that deletions of conserved non-coding elements (CNEs) downstream of the SHOX gene produce a phenotype indistinguishable from Leri-Weill Dyschondrosteosis. As this gene is not found in rodents, we used zebrafish as a model to characterise the expression pattern of the shox gene across the whole embryo and characterise the enhancer domains of different CNEs associated with this gene. Methodology/Principal Findings: Expression of the shox gene in zebrafish was identified using in situ hybridization, with embryos showing expression in the blood, putative heart, hatching gland, brain pharyngeal arch, olfactory epithelium, and fin bud apical ectodermal ridge. By identifying sequences showing 65% identity over at least 40 nucleotides between Fugu, human, dog and opossum we uncovered 35 CNEs around the shox gene. These CNEs were compared with CNEs previously discovered by Sabherwal et al. ,resulting in the identification of smaller more deeply conserved sub-sequence. Sabherwal et al.’s CNEs were assayed for regulatory function in whole zebrafish embryos resulting in the identification of additional tissues under the regulatory control of these CNEs. Conclusion/Significance: Our results using whole zebrafish embryos have provided a more comprehensive picture of the expression pattern of the shox gene, and a better understanding of its regulation via deeply conserved noncoding elements. In particular, we identify additional tissues under the regulatory control of previously identified SHOX CNEs. We also demonstrate the importance of these CNEs in evolution by identifying duplicated shox CNEs and more deeply conserved sub-sequences within already identified CNEs