Decidability of the Monadic Shallow Linear First-Order Fragment with Straight Dismatching Constraints

The monadic shallow linear Horn fragment is well-known to be decidable and has many application, e.g., in security protocol analysis, tree automata, or abstraction refinement. It was a long standing open problem how to extend the fragment to the non-Horn case, preserving decidability, that would, e.g., enable to express non-determinism in protocols. We prove decidability of the non-Horn monadic shallow linear fragment via ordered resolution further extended with dismatching constraints and discuss some applications of the new decidable fragment.Comment: 29 pages, long version of CADE-26 pape

On Functionality of Visibly Pushdown Transducers

Visibly pushdown transducers form a subclass of pushdown transducers that (strictly) extends finite state transducers with a stack. Like visibly pushdown automata, the input symbols determine the stack operations. In this paper, we prove that functionality is decidable in PSpace for visibly pushdown transducers. The proof is done via a pumping argument: if a word with two outputs has a sufficiently large nesting depth, there exists a nested word with two outputs whose nesting depth is strictly smaller. The proof uses technics of word combinatorics. As a consequence of decidability of functionality, we also show that equivalence of functional visibly pushdown transducers is Exptime-Complete.Comment: 20 page

Single-molecule real-time sequencing combined with optical mapping yields completely finished fungal genome

Next-generation sequencing (NGS) technologies have increased the scalability, speed, and resolution of genomic sequencing and, thus, have revolutionized genomic studies. However, eukaryotic genome sequencing initiatives typically yield considerably fragmented genome assemblies. Here, we assessed various state-of-the-art sequencing and assembly strategies in order to produce a contiguous and complete eukaryotic genome assembly, focusing on the filamentous fungus Verticillium dahliae. Compared with Illumina-based assemblies of the V. dahliae genome, hybrid assemblies that also include PacBio- generated long reads establish superior contiguity. Intriguingly, provided that sufficient sequence depth is reached, assemblies solely based on PacBio reads outperform hybrid assemblies and even result in fully assembled chromosomes. Furthermore, the addition of optical map data allowed us to produce a gapless and complete V. dahliae genome assembly of the expected eight chromosomes from telomere to telomere. Consequently, we can now study genomic regions that were previously not assembled or poorly assembled, including regions that are populated by repetitive sequences, such as transposons, allowing us to fully appreciate an organism’s biological complexity. Our data show that a combination of PacBio-generated long reads and optical mapping can be used to generate complete and gapless assemblies of fungal genomes. IMPORTANCE Studying whole-genome sequences has become an important aspect of biological research. The advent of nextgeneration sequencing (NGS) technologies has nowadays brought genomic science within reach of most research laboratories, including those that study nonmodel organisms. However, most genome sequencing initiatives typically yield (highly) fragmented genome assemblies. Nevertheless, considerable relevant information related to genome structure and evolution is likely hidden in those nonassembled regions. Here, we investigated a diverse set of strategies to obtain gapless genome assemblies, using the genome of a typical ascomycete fungus as the template. Eventually, we were able to show that a combination of PacBiogenerated long reads and optical mapping yields a gapless telomere-to-telomere genome assembly, allowing in-depth genome sanalyses to facilitate functional studies into an organism’s biology

Absorption and photoluminescence spectroscopy on a single self-assembled charge-tunable quantum dot

We have performed detailed photoluminescence (PL) and absorption spectroscopy on the same single self-assembled quantum dot in a charge-tunable device. The transition from neutral to charged exciton in the PL occurs at a more negative voltage than the corresponding transition in absorption. We have developed a model of the Coulomb blockade to account for this observation. At large negative bias, the absorption broadens as a result of electron and hole tunneling. We observe resonant features in this regime whenever the quantum dot hole level is resonant with two-dimensional hole states located at the capping layer-blocking barrier interface in our structure.Comment: 6 pages, 6 figure

Enforcing Termination of Interprocedural Analysis

Interprocedural analysis by means of partial tabulation of summary functions may not terminate when the same procedure is analyzed for infinitely many abstract calling contexts or when the abstract domain has infinite strictly ascending chains. As a remedy, we present a novel local solver for general abstract equation systems, be they monotonic or not, and prove that this solver fails to terminate only when infinitely many variables are encountered. We clarify in which sense the computed results are sound. Moreover, we show that interprocedural analysis performed by this novel local solver, is guaranteed to terminate for all non-recursive programs --- irrespective of whether the complete lattice is infinite or has infinite strictly ascending or descending chains

The spatial coverage of dairy cattle urine patches in an intensively grazed pasture system

Accurate field data on the paddock area affected by cow urine depositions are critical to the estimation and modelling of nitrogen (N) losses and N management in grazed pasture systems. A new technique using survey-grade global positioning system (GPS) technology was developed to precisely measure the paddock spatial area coverage, diversity and distribution of dairy cattle urine patches in grazed paddocks over time. A 4-year study was conducted on the Lincoln University Dairy Farm (LUDF), Canterbury, New Zealand, from 2003 to 2007. Twelve field plots, each 100m² in area, were established on typical grazing areas of the farm. All urine and dung deposits within the plots were visually identified, the pasture response area (radius) measured and position marked with survey-grade GPS. The plots were grazed as part of the normal grazing rotation of the farm and urine and dung deposits measured at 12-week intervals. The data were collated using spatial (GIS) software and an assessment of annual urine patch coverage and spatial distribution was made. Grazing intensities ranged from 17645 to 30295 cow grazing h/ha/yr. Mean annual areas of urine patches ranged from 0·34 to 0·40m² (4-year mean 0·37±0·009m²), with small but significant variation between years and seasons. Mean annual urine patch numbers were 6240±124 patches/ha/yr. The mean proportional area coverage for a single sampling event or season was 0·058 and the mean proportional annual urine patch coverage was 0·232±0·0071. There was a strong linear relationship between annual cow grazing h/ha and urine patch numbers/ha (R²=0·69) and also annual urine patch area coverage (R²=0·77). Within the stocking densities observed in this study, an annual increase of 10 000 cow grazing h/ha increased urine patch numbers by 1800 urine patches/ha/yr and annual urine patch area coverage by 0·07. This study presents new quantitative data on urine patch size, numbers and the spatial coverage of patches on a temporal basis

Unpaired and spin-singlet paired states of a two-dimensional electron gas in a perpendicular magnetic field

We present a variational study of both unpaired and spin-singlet paired states induced in a two-dimensional electron gas at low density by a perpendicular magnetic field. It is based on an improved circular-cell approximation which leads to a number of closed analytical results. The ground-state energy of the Wigner crystal containing a single electron per cell in the lowest Landau level is obtained as a function of the filling factor $\nu$: the results are in good agreement with those of earlier approaches and predict $\nu_{c} \approx 0.25$ for the upper filling factor at which the solid-liquid transition occurs. A novel localized state of spin-singlet electron pairs is examined and found to be a competitor of the unpaired state for filling factor $\nu >1$. The corresponding phase boundary is quantitatively displayed in the magnetic field-electron density plane.Comment: 19 pages, 8 figures, submitted to Phys. Rev. B on 7th April 2001. to appear in Phys. Rev.