Some genus 3 curves with many points

Using an explicit family of plane quartic curves, we prove the existence of a genus 3 curve over any finite field of characteristic 3 whose number of rational points stays within a fixed distance from the Hasse-Weil-Serre upper bound. We also provide an intrinsic characterization of so-called Legendre elliptic curves

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics.

Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies and expanding data volumes make evaluation of completeness a challenging task. Technical sequencing quality metrics can be complemented by quantifying completeness of genomic data sets in terms of the expected gene content of Benchmarking Universal Single-Copy Orthologs (BUSCO, http://busco.ezlab.org). The latest software release implements a complete refactoring of the code to make it more flexible and extendable to facilitate high-throughput assessments. The original six lineage assessment data sets have been updated with improved species sampling, 34 new subsets have been built for vertebrates, arthropods, fungi, and prokaryotes that greatly enhance resolution, and data sets are now also available for nematodes, protists, and plants. Here, we present BUSCO v3 with example analyses that highlight the wide-ranging utility of BUSCO assessments, which extend beyond quality control of genomics data sets to applications in comparative genomics analyses, gene predictor training, metagenomics, and phylogenomics

Gauss Sums and Quantum Mechanics

By adapting Feynman's sum over paths method to a quantum mechanical system whose phase space is a torus, a new proof of the Landsberg-Schaar identity for quadratic Gauss sums is given. In contrast to existing non-elementary proofs, which use infinite sums and a limiting process or contour integration, only finite sums are involved. The toroidal nature of the classical phase space leads to discrete position and momentum, and hence discrete time. The corresponding `path integrals' are finite sums whose normalisations are derived and which are shown to intertwine cyclicity and discreteness to give a finite version of Kelvin's method of images.Comment: 14 pages, LaTe

Insights into an unexplored component of the mosquito repeatome: Distribution and variability of viral sequences integrated into the genome of the arboviral vector aedes albopictus

The Asian tiger mosquito Aedes albopictus is an invasive mosquito and a competent vector for public-health relevant arboviruses such as Chikungunya (Alphavirus), Dengue and Zika (Flavivirus) viruses. Unexpectedly, the sequencing of the genome of this mosquito revealed an unusually high number of integrated sequences with similarities to non-retroviral RNA viruses of the Flavivirus and Rhabdovirus genera. These Non-retroviral Integrated RNA Virus Sequences (NIRVS) are enriched in piRNA clusters and coding sequences and have been proposed to constitute novel mosquito immune factors. However, given the abundance of NIRVS and their variable viral origin, their relative biological roles remain unexplored. Here we used an analytical approach that intersects computational, evolutionary and molecular methods to study the genomic landscape of mosquito NIRVS. We demonstrate that NIRVS are differentially distributed across mosquito genomes, with a core set of seemingly the oldest integrations with similarity to Rhabdoviruses. Additionally, we compare the polymorphisms of NIRVS with respect to that of fast and slow-evolving genes within the Ae. albopictus genome. Overall, NIRVS appear to be less polymorphic than slow-evolving genes, with differences depending on whether they occur in intergenic regions or in piRNA clusters. Finally, two NIRVS that map within the coding sequences of genes annotated as Rhabdovirus RNA-dependent RNA polymerase and the nucleocapsid-encoding gene, respectively, are highly polymorphic and are expressed, suggesting exaptation possibly to enhance the mosquito's antiviral responses. These results greatly advance our understanding of the complexity of the mosquito repeatome and the biology of viral integrations in mosquito genomes

The Rapid Methylation of T-DNAs Upon Agrobacterium Inoculation in Plant Leaves

Agrobacterium tumefaciens has been foundational in the development of transgenic plants for both agricultural biotechnology and plant molecular research. However, the transformation efficiency and level of transgene expression obtained for any given construct can be highly variable. These inefficiencies often require screening of many lines to find one with consistent and heritable transgene expression. Transcriptional gene silencing is known to affect transgene expression, and is associated with DNA methylation, especially of cytosines in symmetric CG and CHG contexts. While the specificity, heritability and silencing-associated effects of DNA methylation of transgene sequences have been analyzed in many stably transformed plants, the methylation status of transgene sequences in the T-DNA during the transformation process has not been well-studied. Here we used agro-infiltration of the eGFP reporter gene in Nicotiana benthamiana leaves driven by either an AtEF1α-A4 or a CaMV-35S promoter to study early T-DNA methylation patterns of these promoter sequences. The T-DNA was examined by amplicon sequencing following sodium bisulfite treatment using three different sequencing platforms: Sanger sequencing, Ion Torrent PGM, and the Illumina MiSeq. Rapid DNA methylation was detectable in each promoter region just 2–3 days post-infiltration and the levels continued to rapidly accumulate over the first week, then steadily up to 21 days later. Cytosines in an asymmetric context (CHH) were the most heavily and rapidly methylated. This suggests that early T-DNA methylation may be important in determining the epigenetic and transcriptional fate of integrated transgenes. The Illumina MiSeq platform was the most sensitive and robust way of detecting and following the methylation profiles of the T-DNA promoters. The utility of the methods was then used to show a subtle but significant difference in promoter methylation during intron-mediated enhancement. In addition, the method was able to detect an increase in promoter methylation when the eGFP reporter gene was targeted by siRNAs generated by co-infiltration of a hairpin RNAi construct

Pulmonary function in patients with trophoblastic disease treated with low-dose methotrexate

The Sheffield Trophoblastic Disease Centre treats about 25 patients with persistent trophoblastic disease each year. A total of 75% of patients are classified as low risk according to the Charing Cross Hospital prognostic scoring system and receive methotrexate (MTX) 50 mg, i.m., on days 1, 3, 5, 7 with folinic acid 7.5 mg orally 24 h after each methotrexate injection. There is a 7-day rest between treatment cycles. Remission is achieved in 85% of cases. Approximately 20% of patients experienced pleuritic chest pain and dyspnoea. We have evaluated prospectively lung function in 16 low-risk patients receiving methotrexate. All patients had pulmonary function tests [spirometry-forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC), peak expiratory flow rate (PEFR), and transfer factor - TLCO, kCO] performed before and after completed treatment. A mean of 7.5 cycles of MTX were administered (range 4-11). There was a significant reduction in the mean TLCO (mean pre/post 8.15/7.38 mmol min-1 kPa-1, P = 0.01), but there were no other statistically significant changes. Three patients experienced respiratory symptoms and were found to have a 39%, 28%, and 11% reduction in TLCO from baseline, improving on follow up to pretreatment levels. Low-dose MTX is an effective therapy but may cause troublesome pulmonary toxicity

Ultrasonic assisted creep feed grinding of Inconel 718

AbstractThe paper details the effects of depth of cut and vibration amplitude when ultrasonic assisted (US) creep feed grinding Inconel 718 with an open structured alumina based wheel. The workpiece was actuated at a constant frequency (∼20.5kHz) via a block sonotrode attached to a 1kW piezoelectric transducer-generator system. A full factorial experimental array comprising 12 tests was conducted involving variation in depth of cut (0.1, 0.5 and 1.0mm), amplitude of vibration (high and low) and grinding condition (with and without vibration). Wheel speed and table feed were fixed at 30m/s and 600mm/min respectively for all tests. Application of ultrasonic vibration resulted in reductions in vertical (Fv) and horizontal (Fh) force components by up to 28% and 37% respectively, however greater wheel wear (30-60% lower G-ratio) occurred under hybrid operation due to increased grit/bond fracture. SEM micrographs of the slots machined with US assistance revealed higher levels of side flow/ploughing in comparison to standard creep feed ground specimens. Additionally, more overlapping grit marks were visible on surfaces subject to ultrasonic assisted grinding. Increasing amplitude of vibration produced lower grinding forces (up to 30% for Fv and 43% for Fh) but higher workpiece surface roughness (up to 24%). Topographic maps of grinding wheel surface replicas indicated that use of US vibration generally led to an increase in the number of active cutting points on the wheel

Cubic Curves, Finite Geometry and Cryptography

Some geometry on non-singular cubic curves, mainly over finite fields, is surveyed. Such a curve has 9,3,1 or 0 points of inflexion, and cubic curves are classified accordingly. The group structure and the possible numbers of rational points are also surveyed. A possible strengthening of the security of elliptic curve cryptography is proposed using a `shared secret' related to the group law. Cubic curves are also used in a new way to construct sets of points having various combinatorial and geometric properties that are of particular interest in finite Desarguesian planes.Comment: This is a version of our article to appear in Acta Applicandae Mathematicae. In this version, we have corrected a sentence in the third paragraph. The final publication is available at springerlink.com at http://www.springerlink.com/content/xh85647871215644

Tannakian duality for Anderson-Drinfeld motives and algebraic independence of Carlitz logarithms

We develop a theory of Tannakian Galois groups for t-motives and relate this to the theory of Frobenius semilinear difference equations. We show that the transcendence degree of the period matrix associated to a given t-motive is equal to the dimension of its Galois group. Using this result we prove that Carlitz logarithms of algebraic functions that are linearly independent over the rational function field are algebraically independent.Comment: 39 page

Taxonbridge: an R package to create custom taxonomies based on the NCBI and GBIF taxonomies

Biological taxonomies establish conventions by which researchers can catalogue and systematically compare their work using nomenclature such as species binomial names and reference identifiers. The ideal taxonomy is unambiguous and exhaustive; however, no such single taxonomy exists, partly due to continuous changes and contributions made to existing taxonomies. The degree to which a taxonomy is useful furthermore depends on context provided by such variables as the taxonomic neighbourhood of a species (e.g., selecting arthropod or vertebrate species) or the geological time frame of the study (e.g., selecting extinct versus extant species). Collating the most relevant taxonomic information from multiple taxonomies is hampered by arbitrarily defined identifiers, ambiguity in scientific names, as well as duplicated and erroneous entries. The goal of taxonbridge is to provide tools for merging the Global Biodiversity Information Facility (GBIF) Backbone Taxonomy and the United States National Center for Biotechnology Information (NCBI) Taxonomy in order to create consistent, deduplicated and disambiguated custom taxonomies that reference both extant and extinct species