Experience Implementing a Performant Category-Theory Library in Coq

We describe our experience implementing a broad category-theory library in Coq. Category theory and computational performance are not usually mentioned in the same breath, but we have needed substantial engineering effort to teach Coq to cope with large categorical constructions without slowing proof script processing unacceptably. In this paper, we share the lessons we have learned about how to represent very abstract mathematical objects and arguments in Coq and how future proof assistants might be designed to better support such reasoning. One particular encoding trick to which we draw attention allows category-theoretic arguments involving duality to be internalized in Coq's logic with definitional equality. Ours may be the largest Coq development to date that uses the relatively new Coq version developed by homotopy type theorists, and we reflect on which new features were especially helpful.Comment: The final publication will be available at link.springer.com. This version includes a full bibliography which does not fit in the Springer version; other than the more complete references, this is the version submitted as a final copy to ITP 201

Spatio-temporal patterns of earthworm abundance suggest time-limited food availability for a subalpine bird species

Changes in food availability may act as a major mechanism by which global change impacts populations of birds, especially in seasonal environments at high elevations or latitudes. Systematic sampling of invertebrates, which constitute the diet of many bird species during the breeding season, is however largely missing in mountain ecosystems and is overall very rare for soil-dwelling species or stages. Here, we repeatedly sampled earthworms (Lumbricidae), the staple prey of the Ring Ouzel Turdus torquatus, over a whole breeding season in a study area in the Swiss Alps. Our main goal was to finely characterise spatio-temporal patterns of food availability for this declining bird species, in relation to elevation, habitat type and snowmelt stage. In 24 sampling plots, we extracted two soil cores every week for 6–10 weeks and hand-sorted soil invertebrates separately for two 5-cm soil layers. We then analysed the abundance of earthworms in those two layers in relation to various environmental parameters. We show that within our study area, edaphic and topographical parameters are poor predictors of the mean abundance of earthworms over the breeding season. Ground vegetation cover and soil moisture, however, are suitable predictors for the number of earthworms within the soil profile at each sampling time, i.e., of their availability for Ring Ouzels. Moreover, we provide evidence for a clear seasonal peak in earthworm availability, which was more pronounced in open grasslands compared to forested areas and happened later in the season where snow lingered. This study, by improving our understanding of the factors driving food availability for a mountain bird species, provides insights into how shifts in land-use and climate might lead to altered predator-prey interactions

Seasonal and daily movement patterns of an alpine passerine suggest high flexibility in relation to environmental conditions

Mountains naturally offer variable habitat conditions, but their biodiversity is currently facing the extra challenge of adapting to rapid environmental shifts that are much more pronounced than in the lowlands. Among adaptive responses, intra- and inter-seasonal movements represent potentially important coping strategies for wildlife that remain largely unexplored. We investigated the seasonal and daily movements of the ring ouzel Turdus torquatus, a European mountain bird species that is declining in many parts of its distribution. We tracked individuals breeding in the Swiss Alps using light-level geolocators and multi-sensor loggers. Of the birds traced to their nonbreeding grounds, two-thirds reached the Atlas Mountains while one-third stayed in Spain, a region potentially more significant for overwintering than previously thought. The birds remained mostly above 1000 m throughout the annual cycle, highlighting a strict association of ring ouzels with mountain habitats. We also evidenced flexible daily elevational movements, especially upon spring arrival on the breeding grounds in relation to date and snowfall occurrence, suggesting adaptive potential in response to environmental variation. This study shows how modern technology can deliver deeper and valuable insights into movements, behavioural patterns and life-history strategies for relatively little-studied animal species. By doing so, it paves the way for refined assessments of species’ vulnerability to ongoing global change while providing basic conservation guidance

Inhibition of cell migration and invasion mediated by the TAT-RasGAP317-326 peptide requires the DLC1 tumor suppressor.

TAT-RasGAP317-326, a peptide corresponding to the 317-326 sequence of p120 RasGAP coupled with a cell-permeable TAT-derived peptide, sensitizes the death response of various tumor cells to several anticancer treatments. We now report that this peptide is also able to increase cell adherence, prevent cell migration and inhibit matrix invasion. This is accompanied by a marked modification of the actin cytoskeleton and focal adhesion redistribution. Interestingly, integrins and the small Rho GTP-binding protein, which are well-characterized proteins modulating actin fibers, adhesion and migration, do not appear to be required for the pro-adhesive properties of TAT-RasGAP317-326. In contrast, deleted in liver cancer-1, a tumor suppressor protein, the expression of which is often deregulated in cancer cells, was found to be required for TAT-RasGAP317-326 to promote cell adherence and inhibit migration. These results show that TAT-RasGAP317-326, besides its ability to favor tumor cell death, hampers cell migration and invasion

Living small-sized (63-150 µm) foraminifera from mid-shelf to mid-slope environments in the Bay of Bisca

Live (rose Bengal stained) foraminiferal faunas of the 63–150 μm size fraction have been investigated in surficial sediment (0–1 cm) from mid-shelf to mid-slope environments in the Bay of Biscay. Eleven stations were sampled in April 2002 and March 2004 between 80 and 2000 m water depth (mwd). Earlier studies on the temporal variability of phytoplankton primary production suggest that our stations were sampled at the most eutrophic period of the year. In response to the decrease of exported organic matter flux to the seafloor along our bathymetric transect, foraminiferal standing stocks decrease from ~1400–2000 specimens per 50 cm3 on the continental shelf (100–140 mwd) and upper slope (550 mwd) to about 400 specimens per 50 cm3 at mid-slope stations (2000 mwd). At all stations, the faunas contain an important amount of small opportunistic species that are favored by seasonal phytodetritus input. On the continental shelf where phytoplankton bloom, events may be geographically restricted; the foraminiferal response is dependent on the distance to the surface-water primary-production cells. Textularia porrecta is very abundant at an 80-m-deep station that is close to the coast and characterized by a high sedimentation rate of fine-grained particles. Foraminiferal faunas are dominated by Nonionella iridea, Cassidulina carinata and Bolivina ex. gr. dilatata at the outer-shelf stations (110–140 mwd) that are under the direct influence of spring bloom phytodetritus input in the northern Bay of Biscay. A fauna dominated by Bolivina dilatata/spathulata and Bolivina subaenariensis is found in the southeastern Bay of Biscay at a 140-m-deep outer-shelf station located seaward of the Adour River estuary, where the sediment is probably enriched in terrestrial organic matter. Apparently, differences in foraminiferal composition between outer-shelf areas in the northern and southeastern Bay of Biscay are related to differences in organic matter quality. On the continental slope, a bathymetric zonation of taxa is observed from upper-slope sites (550–1000 mwd) rich in Epistominella exigua and Uvigerina peregrina to mid-slope stations (1600–2000 mwd), where Nuttallides pusillus and Gavelinopsis translucens dominate the small-sized living fauna. This bathymetric foraminiferal zonation probably reflects a trophic gradient between upper-slope eutrophic stations and mid-slope, more oligotrophic sites. Our zonal description of small-sized living foraminifera (63–150 μm) is new for the Bay of Biscay and may provide the basis to reconstruct former export production regimes in marginal paleo-environments from temperate latitude areas

Variation in Demography and Life-History Strategies Across the Range of a Declining Mountain Bird Species

Species- and population-specific responses to their environment may depend to a large extent on the spatial variation in life-history traits and in demographic processes of local population dynamics. Yet, those parameters and their variability remain largely unknown for many cold-adapted species, which are exposed to particularly rapid rates of environmental change. Here, we compared the demographic traits and dynamics for an emblematic bird species of European mountain ecosystems, the ring ouzel (Turdus torquatus). Using integrated population models fitted in a Bayesian framework, we estimated the survival probability, productivity and immigration of two populations from the Western European Alps, in France (over 11 years) and Switzerland (over 6 years). Juvenile apparent survival was lower and immigration rate higher in the Swiss compared to the French population, with the temporal variation in population growth rate driven by different demographic processes. Yet, when compared to populations in the northwestern part of the range, in Scotland, these two Alpine populations both showed a much lower productivity and higher adult survival, indicating a slower life-history strategy. Our results suggest that demographic characteristics can substantially vary across the discontinuous range of this passerine species, essentially due to contrasted, possibly locally evolved life-history strategies. This study therefore raises the question of whether flexibility in life-history traits is widespread among boreo-alpine species and if it might provide adaptive potential for coping with current environmental change

Bayesian estimation of tobramycin exposure in cystic fibrosis

Fixed tobramycin (mg/kg) dosing is often inappropriate in patients with cystic fibrosis (CF), as pharmacokinetics are highly variable. The area under the concentration-time curve (AUC) is an exposure metric suited to monitoring in this population. Bayesian strategies to estimate AUC have been available for over 20 years but are not standard practice in the clinical setting. To assess their suitability for use in clinical practice, three AUC estimation methods using limited sampling were compared to measured true exposure by using intensive sampling tobramycin data. Adults prescribed once daily intravenous tobramycin had eight concentrations taken over 24 h. An estimate of true exposure within one dosing interval was calculated using the trapezoidal method and compared to three alternate estimates determined using (i) a two-sample log-linear regression (LLR) method (local hospital practice); (ii) a Bayesian estimate using one concentration (AUC(1)); and (iii) a Bayesian estimate using two concentrations (AUC(2)). Each method was evaluated against the true measured exposure by a Bland-Altman analysis. Twelve patients with a median (range) age and weight of 25 (18 to 36) years and 66.5 (51 to 76) kg, respectively, were recruited. There was good agreement between the true exposure and the three alternate estimates of AUC, with a mean AUC bias of < 10 mg/liter center dot h in each case, i.e., -8.2 (LLR), 3.8 (AUC(1)), and 1.0 (AUC(2)). Bayesian analysis-based and LLR estimation methods of tobramycin AUC are equivalent to true exposure estimation. All three methods may be suitable for use in the clinical setting; however, a one-sample Bayesian method may be most useful in ambulatory patients for which coordinating blood samples is difficult. Suitably powered, randomized clinical trials are required to assess patient outcomes

"Come i secchi nel pozzo". Scienza ed etica negli scritti contro la vivisezione delle femministe britanniche (1870-1910)

Il saggio ripercorre le riflessioni teoriche delle femministe britanniche su scienza ed etica in relazione al dibattito sulla vivisezion