Software Product Line Engineering via Software Transplantation

Software Product Lines (SPLs) improve time-to-market, enhance software quality, and reduce maintenance costs. Current SPL reengineering practices are largely manual and require domain knowledge. Thus, adopting and, to a lesser extent, maintaining SPLs are expensive tasks, preventing many companies from enjoying their benefits. To address these challenges, we introduce Foundry, an approach utilizing software transplantation to reduce the manual effort of SPL adoption and maintenance. Foundry enables integrating features across different codebases, even codebases that are unaware that they are contributing features to a software product line. Each product produced by Foundry is pure code, without variability annotation, unlike feature flags, which eases variability management and reduces code bloat. We realise Foundry in prodScalpel, a tool that transplants multiple organs (i.e., a set of interesting features) from donor systems into an emergent product line for codebases written in C. Given tests and lightweight annotations identifying features and implantation points, prodScalpel automates feature extraction and integration. To evaluate its effectiveness, our evaluation compares feature transplantation using prodScalpel to the current state of practice: on our dataset, prodScalpel’s use speeds up feature migration by an average of 4.8 times when compared to current practice

Kepler and TESS observations of PG 1159-035

PG 1159-035 is the prototype of the PG 1159 hot (pre-)white dwarf pulsators. This important object was observed during the Kepler satellite K2 mission for 69 days in 59 s cadence mode and by the TESS satellite for 25 days in 20 s cadence mode. We present a detailed asteroseismic analysis of those data. We identify a total of 107 frequencies representing 32 ℓ = 1 modes, 27 frequencies representing 12 ℓ = 2 modes, and eight combination frequencies. The combination frequencies and the modes with very high k values represent new detections. The multiplet structure reveals an average splitting of 4.0 ± 0.4 μHz for ℓ = 1 and 6.8 ± 0.2 μHz for ℓ = 2, indicating a rotation period of 1.4 ± 0.1 days in the region of period formation. In the Fourier transform of the light curve, we find a significant peak at 8.904 ± 0.003 μHz suggesting a surface rotation period of 1.299 ± 0.002 days. We also present evidence that the observed periods change on timescales shorter than those predicted by current evolutionary models. Our asteroseismic analysis finds an average period spacing for ℓ = 1 of 21.28 ± 0.02 s. The ℓ = 2 modes have a mean spacing of 12.97 ± 0.4 s. We performed a detailed asteroseismic fit by comparing the observed periods with those of evolutionary models. The best-fit model has Teff = 129, 600 ± 11 100 K, M* = 0.565 ± 0.024M⊙, and $\mathrm{log}g={7.41}_{-0.54}^{+0.38}$, within the uncertainties of the spectroscopic determinations. We argue for future improvements in the current models, e.g., on the overshooting in the He-burning stage, as the best-fit model does not predict excitation for all of the pulsations detected in PG 1159-035

Preliminary genetic evidence of two different populations of Opisthorchis viverrini in Lao PDR

Opisthorchis viverrini is a major public health concern in Southeast Asia. Various reports have suggested that this parasite may represent a species complex, with genetic structure in the region perhaps being dictated by geographical factors and different species of intermediate hosts. We used four microsatellite loci to analyze O. viverrini adult worms originating from six species of cyprinid fish in Thailand and Lao PDR. Two distinct O. viverrini populations were observed. In Ban Phai, Thailand, only one subgroup occurred, hosted by two different fish species. Both subgroups occurred in fish from That Luang, Lao PDR, but were represented to very different degrees among the fish hosts there. Our data suggest that, although geographical separation is more important than fish host specificity in influencing genetic structure, it is possible that two species of Opisthorchis, with little interbreeding, are present near Vientiane in Lao PDR

Evaluation of an interactive, case-based review session in teaching medical microbiology

<p>Abstract</p> <p>Background</p> <p>Oklahoma State University-Center for Health Sciences (OSU-CHS) has replaced its microbiology wet laboratory with a variety of tutorials including a case-based interactive session called Microbial Jeopardy!. The question remains whether the time spent by students and faculty in the interactive case-based tutorial is worthwhile? This study was designed to address this question by analyzing both student performance data and assessing students' perceptions regarding the tutorial.</p> <p>Methods</p> <p>Both quantitative and qualitative data were used in the current study. Part One of the study involved assessing student performance using archival records of seven case-based exam questions used in the 2004, 2005, 2006, and 2007 OSU-CHS Medical Microbiology course. Two sample t-tests for proportions were used to test for significant differences related to tutorial usage. Part Two used both quantitative and qualitative means to assess student's perceptions of the Microbial Jeopardy! session. First, a retrospective survey was administered to students who were enrolled in Medical Microbiology in 2006 or 2007. Second, responses to open-ended items from the 2008 course evaluations were reviewed for comments regarding the Microbial Jeopardy! session.</p> <p>Results</p> <p>Both student performance and student perception data support continued use of the tutorials. Quantitative and qualitative data converge to suggest that students like and learn from the interactive, case-based session.</p> <p>Conclusion</p> <p>The case-based tutorial appears to improve student performance on case-based exam questions. Additionally, students perceived the tutorial as helpful in preparing for exam questions and reviewing the course material. The time commitment for use of the case-based tutorial appears to be justified.</p

Optimising the Duration of Adjuvant Trastuzumab in Early Breast Cancer in the UK.

Adjuvant trastuzumab for patients with HER2 positive early breast cancer demonstrated significant improvements in both disease-free and overall survival with 12 months treatment (1, 2), and this was NICE approved in the UK in 2006. When the FinHer trial demonstrated similar results with nine weeks trastuzumab (3), there was significant interest in whether shorter durations might be as effective. Additional benefits for patients could be less toxicity, fewer hospital visits and a more rapid return to normal life, with considerable societal benefits of reduced costs. PERSEPHONE was the pragmatic UK duration trial funded by the NIHR HTA, which showed that 6 months adjuvant trastuzumab was non-inferior to 12 months with 4-year disease-free survival rate of 89.4% compared with 89.8% respectively (non-inferiority p = 0.01) (4). Less toxicity was reported with 6 months particularly cardiac toxicity and there were cost savings over the first 2 years (5), which were maintained over an average patient’s lifetime when extrapolated using an economic model. After the publication of these results in June 2019, the Optimal Duration of Adjuvant Trastuzumab Working Group was convened, comprising a diverse, multi-disciplinary membership. There were representatives from the PERSEPHONE Trial Management Group including patient advocates, the NCRI Breast Group, the Association of Cancer Physicians (ACP), the Royal College of Radiologists (RCR), and the Independent Cancer Patients’ Voice (ICPV). By November 2019, both dual antibody treatment with trastuzumab and pertuzumab (https://www.nice.org.uk/guidance/ta569) and extended neratinib after single agent trastuzumab (https://www.nice.org.uk/guidance/ta612) had been approved by NICE only for those at high risk of recurrence. Therefore, single agent trastuzumab remained standard of care for those at lower risk of recurrence and recommendations were made for these patients.Funded by NIHR HTA

Environmental variables, habitat discontinuity and life history shaping the genetic structure of Pomatoschistus marmoratus

Coastal lagoons are semi-isolated ecosystems exposed to wide fluctuations of environmental conditions and showing habitat fragmentation. These features may play an important role in separating species into different populations, even at small spatial scales. In this study, we evaluate the concordance between mitochondrial (previous published data) and nuclear data analyzing the genetic variability of Pomatoschistus marmoratus in five localities, inside and outside the Mar Menor coastal lagoon (SE Spain) using eight microsatellites. High genetic diversity and similar levels of allele richness were observed across all loci and localities, although significant genic and genotypic differentiation was found between populations inside and outside the lagoon. In contrast to the FST values obtained from previous mitochondrial DNA analyses (control region), the microsatellite data exhibited significant differentiation among samples inside the Mar Menor and between lagoonal and marine samples. This pattern was corroborated using Cavalli-Sforza genetic distances. The habitat fragmentation inside the coastal lagoon and among lagoon and marine localities could be acting as a barrier to gene flow and contributing to the observed genetic structure. Our results from generalized additive models point a significant link between extreme lagoonal environmental conditions (mainly maximum salinity) and P. marmoratus genetic composition. Thereby, these environmental features could be also acting on genetic structure of coastal lagoon populations of P. marmoratus favoring their genetic divergence. The mating strategy of P. marmoratus could be also influencing our results obtained from mitochondrial and nuclear DNA. Therefore, a special consideration must be done in the selection of the DNA markers depending on the reproductive strategy of the species

Experimental Infection of Cynomolgus Macaques (Macaca fascicularis) with Aerosolized Monkeypox Virus

Monkeypox virus (MPXV) infection in humans results in clinical symptoms very similar to ordinary smallpox. Aerosol is a route of secondary transmission for monkeypox, and a primary route of smallpox transmission in humans. Therefore, an animal model for aerosol exposure to MPXV is needed to test medical countermeasures. To characterize the pathogenesis in cynomolgus macaques (Macaca fascicularis), groups of macaques were exposed to four different doses of aerosolized MPXV. Blood was collected the day before, and every other day after exposure and assessed for complete blood count (CBC), clinical chemistry analysis, and quantitative PCR. Macaques showed mild anorexia, depression, and fever on day 6 post-exposure. Lymphadenopathy, which differentiates monkeypox from smallpox, was observed in exposed macaques around day 6 post-exposure. CBC and clinical chemistries showed abnormalities similar to human monkeypox cases. Whole blood and throat swab viral loads peaked around day 10, and in survivors, gradually decreased until day 28 post-exposure. Survival was not dose dependent. As such, doses of 4×104 PFU, 1×105 PFU, or 1×106 PFU resulted in lethality for 70% of the animals, whereas a dose of 4×105 PFU resulted in 85% lethality. Overall, cynomolgus macaques exposed to aerosolized MPXV develop a clinical disease that resembles that of human monkeypox. These findings provide a strong foundation for the use of aerosolized MPXV exposure of cynomolgus macaques as an animal model to test medical countermeasures against orthopoxviruses

Differential Influence of Clonal Integration on Morphological and Growth Responses to Light in Two Invasive Herbs

Background and aims: In contrast to seeds, high sensitivity of vegetative fragments to unfavourable environments may limit the expansion of clonal invasive plants. However, clonal integration promotes the establishment of propagules in less suitable habitats and may facilitate the expansion of clonal invaders into intact native communities. Here, we examine the influence of clonal integration on the morphology and growth of ramets in two invasive plants, Alternanthera philoxeroides and Phyla canescens, under varying light conditions. Methods: In a greenhouse experiment, branches, connected ramets and severed ramets of the same mother plant were exposed under full sun and 85 % shade and their morphological and growth responses were assessed. Key results: The influence of clonal integration on the light reaction norm (connection6light interaction) of daughter ramets was species-specific. For A. philoxeroides, clonal integration evened out the light response (total biomass, leaf mass per area, and stem number, diameter and length) displayed in severed ramets, but these connection6light interactions were largely absent for P. canescens. Nevertheless, for both species, clonal integration overwhelmed light effect in promoting the growth of juvenile ramets during early development. Also, vertical growth, as an apparent shade acclimation response, was more prevalent in severed ramets than in connected ramets. Finally, unrooted branches displayed smaller organ size and slower growth than connected ramets, but the pattern of light reaction was similar, suggesting mothe