Abelian covers of surfaces and the homology of the level L mapping class group

We calculate the first homology group of the mapping class group with coefficients in the first rational homology group of the universal abelian $\Z / L \Z$-cover of the surface. If the surface has one marked point, then the answer is \Q^{\tau(L)}, where $\tau(L)$ is the number of positive divisors of $L$. If the surface instead has one boundary component, then the answer is \Q. We also perform the same calculation for the level $L$ subgroup of the mapping class group. Set $H_L = H_1(\Sigma_g;\Z/L\Z)$. If the surface has one marked point, then the answer is \Q[H_L], the rational group ring of $H_L$. If the surface instead has one boundary component, then the answer is \Q.Comment: 32 pages, 10 figures; numerous corrections and simplifications; to appear in J. Topol. Ana

Herbicide impacts on exotic grasses and a population of the critically endangered herb "Calystegia affinis" (Convolvulaceae) on Lord Howe Island

Introduced perennial grasses are capable of altering the habitat of native species, causing reductions in population size and vigour, and potentially affecting life-history processes such as survival, pollination and seedling recruitment. We examined the utility of herbicide treatment on two exotic grasses, Pennisetum clandestinum (Kikuyu) and Stenotaphrum secundatum (Buffalo grass) to restore the habitat of Calystegia affinis, a critically endangered species endemic to Lord Howe and Norfolk Islands. Using two herbicides, Asset (designed to affect only grasses) and Glyphosate (a general herbicide), we compared effectiveness in reducing grass cover on a population of Calystegia affinis. We protected Calystegia plants from the herbicides by ensuring their leaves were covered by plastic bags during herbicide application. Both herbicides were similarly effective in reducing grass cover after four weeks and had no noticeable adverse affect on Calystegia (suggesting the plastic bag protection was effective). After 26 weeks, Glyphosate was more effective in maintaining a reduced grass cover. Plots treated with either herbicide had a greater relative increase in abundance of Calystegia stems compared to untreated controls. The Glyphosate treatment resulted in the greatest relative increase in stem abundance, but this was not significantly greater than in the Asset treatment. We consider that spraying with Glyphosate treatment, with follow-up monitoring and spot-spraying, will assist the recovery of the Calystegia affinis population. Ultimately, the maintenance of a weed-free zone at the forest edge will provide suitable habitat for additional recruitment of this and other native species

Synthetic lethal analysis of Caenorhabditis elegans posterior embryonic patterning genes identifies conserved genetic interactions

Phenotypic robustness is evidenced when single-gene mutations do not result in an obvious phenotype. It has been suggested that such phenotypic stability results from 'buffering' activities of homologous genes as well as non-homologous genes acting in parallel pathways. One approach to characterizing mechanisms of phenotypic robustness is to identify genetic interactions, specifically, double mutants where buffering is compromised. To identify interactions among genes implicated in posterior patterning of the Caenorhabditis elegans embryo, we measured synthetic lethality following RNA interference of 22 genes in 15 mutant strains. A pair of homologous T-box transcription factors (tbx-8 and tbx-9) is found to interact in both C. elegans and C. briggsae, indicating that their compensatory function is conserved. Furthermore, a muscle module is defined by transitive interactions between the MyoD homolog hlh-1, another basic helix-loop-helix transcription factor, hnd-1, and the MADS-box transcription factor unc-120. Genetic interactions within a homologous set of genes involved in vertebrate myogenesis indicate broad conservation of the muscle module and suggest that other genetic modules identified in C. elegans will be conserved

A cancer cell-line titration series for evaluating somatic classification.

BackgroundAccurate detection of somatic single nucleotide variants and small insertions and deletions from DNA sequencing experiments of tumour-normal pairs is a challenging task. Tumour samples are often contaminated with normal cells confounding the available evidence for the somatic variants. Furthermore, tumours are heterogeneous so sub-clonal variants are observed at reduced allele frequencies. We present here a cell-line titration series dataset that can be used to evaluate somatic variant calling pipelines with the goal of reliably calling true somatic mutations at low allele frequencies.ResultsCell-line DNA was mixed with matched normal DNA at 8 different ratios to generate samples with known tumour cellularities, and exome sequenced on Illumina HiSeq to depths of >300×. The data was processed with several different variant calling pipelines and verification experiments were performed to assay >1500 somatic variant candidates using Ion Torrent PGM as an orthogonal technology. By examining the variants called at varying cellularities and depths of coverage, we show that the best performing pipelines are able to maintain a high level of precision at any cellularity. In addition, we estimate the number of true somatic variants undetected as cellularity and coverage decrease.ConclusionsOur cell-line titration series dataset, along with the associated verification results, was effective for this evaluation and will serve as a valuable dataset for future somatic calling algorithm development. The data is available for further analysis at the European Genome-phenome Archive under accession number EGAS00001001016. Data access requires registration through the International Cancer Genome Consortium's Data Access Compliance Office (ICGC DACO)

Structure and dielectric response in the high TcT_c ferroelectric Bi(Zn,Ti)O3_3-PbTiO3_3 solid solutions

Theoretical {\em ab initio} and experimental methods were used to investigate the $x$Bi(Zn,Ti)O$_3$-(1-$x$)PbTiO$_3$ (BZT-PT) solid solution. We find that hybridization between Zn 4$p$ and O 2$p$ orbitals allows the formation of short, covalent Zn-O bonds, enabling favorable coupling between A-site and B-site displacements. This leads to large polarization, strong tetragonality and an elevated ferroelectric to paraelectric phase transition temperature. nhomogeneities in local structure near the 90$^\circ$ domain boundaries can be deduced from the asymetric peak broadening in the neutron and x-ray diffraction spectra. These extrinsic effects make the ferroelectric to paraelectric phase transition diffuse in BZT-PT solid solutions

The homeodomain protein PAL-1 specifies a lineage-specific regulatory network in the C. elegans embryo

Maternal and zygotic activities of the homeodomain protein PAL-1 specify the identity and maintain the development of the multipotent C blastomere lineage in the C. elegans embryo. To identify PAL-1 regulatory target genes, we used microarrays to compare transcript abundance in wild-type embryos with mutant embryos lacking a C blastomere and to mutant embryos with extra C blastomeres. pal-1-dependent C-lineage expression was verified for select candidate target genes by reporter gene analysis, though many of the target genes are expressed in additional lineages as well. The set of validated target genes includes 12 transcription factors, an uncharacterized wingless ligand and five uncharacterized genes. Phenotypic analysis demonstrates that the identified PAL-1 target genes affect specification, differentiation and morphogenesis of C-lineage cells. In particular, we show that cell fate-specific genes (or tissue identity genes) and a posterior HOX gene are activated in lineage-specific fashion. Transcription of targets is initiated in four temporal phases, which together with their spatial expression patterns leads to a model of the regulatory network specified by PAL-1

Photon Diffusion in Microscale Solids

This paper presents a theoretical and experimental investigation of photon diffusion in highly absorbing microscale graphite. An Nd:YAG continuous wave (CW) laser is used to heat the graphite samples with thicknesses of 40 microns and 100 microns. Optical intensities of 10 kW/cm^2 and 20 kW/cm^2 are used in laser heating. The graphite samples are heated to temperatures of thousands of kelvins within milliseconds, which are recorded by a 2-color, high-speed pyrometer. To compare the observed temperatures, the differential equation of heat conduction is solved across the samples with proper initial and boundary conditions. In addition to lattice vibrations, photon diffusion is incorporated into the analytical model of thermal conductivity for solving the heat equation. The numerical simulations showed close matching between experiment and theory only when including the photon diffusion equations and existing material properties data found in the previously published works with no fitting constants. The results indicate that the commonly-overlooked mechanism of photon diffusion dominates the heat transfer of many microscale structures near their evaporation temperatures. In addition, the treatment explains the discrepancies between thermal conductivity measurements and theory that were previously described in the scientific literature.Comment: 8 pages, 7 figures, (N.B. there is a typo and minor correction in Table 1 and References in the online version of the journal, corrected and highlighted in this PDF