Syngenetic sand veins and anti-syngenetic sand wedges, Tuktoyaktuk Coastlands, western Arctic Canada

Sand-sheet deposits of full-glacial age in the Tuktoyaktuk Coastlands, western Arctic Canada, contain syngenetic sand veins 1-21 cm wide and sometimes exceeding 9 m in height. Their tall and narrow, chimney-like morphology differs from that of known syngenetic ice wedges and indicates an unusually close balance between the rate of sand-sheet aggradation and the frequency of thermal-contraction cracking. The sand sheets also contain rejuvenated (syngenetic) sand wedges that have grown upward from an erosion surface. By contrast, sand sheets of postglacial age contain few or sometimes no intraformational sand veins and wedges, suggesting that the climatic conditions were unfavourable for thermal-contraction cracking. Beneath a postglacial sand sheet near Johnson Bay, sand wedges with unusually wide tops (3.9 m) extend down from a prominent erosion surface. The wedges grew vertically downward during deflation of the ground surface, and represent anti-syngenetic wedges. The distribution of sand veins and wedges within the sand sheets indicates that the existence of continuous permafrost during sand-sheet aggradation can be inferred confidently only during full-glacial conditions

Necessity Specifications for Robustness

Robust modules guarantee to do only what they are supposed to do - even in the presence of untrusted, malicious clients, and considering not just the direct behaviour of individual methods, but also the emergent behaviour from calls to more than one method. Necessity is a language for specifying robustness, based on novel necessity operators capturing temporal implication, and a proof logic that derives explicit robustness specifications from functional specifications. Soundness and an exemplar proof are mechanised in Coq

Encoding Featherweight Java with Assignment and Immutability using The Coq Proof Assistant

We develop a mechanized proof of Featherweight Java with Assignment and Immutability in the Coq proof assistant. This is a step towards more machine-checked proofs of a non-trivial type system. We used object immutability close to that of IGJ [8]. We describe the challenges of the mechanization and the encoding we used inside of Coq. prover. Our Coq sources are publically available 1. Example. We define a parametrized class Cell, where the mutable instantiation can get and set the interned object, whereas the immutable instantiation can only get the interned object, provided initially in the constructor. We chose to use transitive mutability in this example. 1

dCas9-based epigenome editing suggests acquisition of histone methylation is not sufficient for target gene repression.

Distinct epigenomic profiles of histone marks have been associated with gene expression, but questions regarding the causal relationship remain. Here we investigated the activity of a broad collection of genomically targeted epigenetic regulators that could write epigenetic marks associated with a repressed chromatin state (G9A, SUV39H1, Krüppel-associated box (KRAB), DNMT3A as well as the first targetable versions of Ezh2 and Friend of GATA-1 (FOG1)). dCas9 fusions produced target gene repression over a range of 0- to 10-fold that varied by locus and cell type. dCpf1 fusions were unable to repress gene expression. The most persistent gene repression required the action of several effector domains; however, KRAB-dCas9 did not contribute to persistence in contrast to previous reports. A 'direct tethering' strategy attaching the Ezh2 methyltransferase enzyme to dCas9, as well as a 'recruitment' strategy attaching the N-terminal 45 residues of FOG1 to dCas9 to recruit the endogenous nucleosome remodeling and deacetylase complex, were both successful in targeted deposition of H3K27me3. Surprisingly, however, repression was not correlated with deposition of either H3K9me3 or H3K27me3. Our results suggest that so-called repressive histone modifications are not sufficient for gene repression. The easily programmable dCas9 toolkit allowed precise control of epigenetic information and dissection of the relationship between the epigenome and gene regulation

Predicting and understanding the stability of G-quadruplexes

Motivation: G-quadruplexes are stable four-stranded guanine-rich structures that can form in DNA and RNA. They are an important component of human telomeres and play a role in the regulation of transcription and translation. The biological significance of a G-quadruplex is crucially linked with its thermodynamic stability. Hence the prediction of G-quadruplex stability is of vital interest

The chronostratigraphy of Late Pleistocene glacial and periglacial aeolian activity in the Tuktoyaktuk Coastlands, NWT, Canada

Aeolian periglacial sand deposits are common in the Tuktoyaktuk Coastlands of Western Arctic Canada. Regionally extensive and thick aeolian sand-sheet deposits have been observed in two major stratigraphic settings: within a sand unit characterized by large aeolian dune deposits; and interbedded with glaciofluvial outwash from the Laurentide Ice Sheet (LIS). Small, localized sand sheets have also been observed along the tops of sandy bluffs, within sequences of drained thermokarst lakes deposits and as an involuted veneer above buried basal ice of the LIS. On the basis of radiocarbon and optically stimulated luminescence (OSL) dates from preserved periglacial aeolian sand sheets and dunes a regional chronostratigraphy is presented which indicates that both extensive dunes and sand sheets accumulated mainly between ca 30 and 13 ka. A switch to dominantly sand-sheet aggradation at ca 14–13 ka, with sand sheets forming widely until ca 8 ka, is attributed to (a) surface armouring by glacial deposits associated with the advance of the LIS; and (b) amelioration of the climate from cold aridity. An absence of OSL dates between ca 8 and 1 ka suggests that sand sheets stabilized during much of the Holocene. Local sand-sheet aggradation during recent centuries has occurred near sandy bluffs and on the floors of drained thermokarst lakes. The OSL dates constrain the maximum extent of the LIS in the Tuktoyaktuk Coastlands to Marine Isotope Stage 2

Maximizing the potential of multi-parental crop populations.

Most agriculturally significant crop traits are quantitatively inherited which limits the ease and efficiency of trait dissection. Multi-parent populations overcome the limitations of traditional trait mapping and offer new potential to accurately define the genetic basis of complex crop traits. The increasing popularity and use of nested association mapping (NAM) and multi-parent advanced generation intercross (MAGIC) populations raises questions about the optimal design and allocation of resources in their creation. In this paper we review strategies for the creation of multi-parent populations and describe two complementary in silico studies addressing the design and construction of NAM and MAGIC populations. The first simulates the selection of diverse founder parents and the second the influence of multi-parent crossing schemes (and number of founders) on haplotype creation and diversity. We present and apply two open software resources to simulate alternate strategies for the development of multi-parent populations

Lucky imaging and speckle discrimination for the detection of faint companions with adaptive optics

We have analyzed the application of frame selection ("lucky imaging") to adaptive optics (AO), short-exposure observations of faint companions. We have used the instantaneous Strehl ratio as an image quality metric. The probability density function (PDF) of this quantity can be used to determine the outcome of frame selection in terms of optimizing the Strehl ratio and the peak-signal-to-noise-ratio of the shift-and-add image. In the presence of static speckles, frame selection can lead to both: improvement in resolution--as quantified by the Strehl ratio, as well as faint signal detectability--given by the peak-signal-to-noise-ratio. This theoretical prediction is confirmed with real data from AO observations using Lick Observatory's 3m Shane telescope, and the Palomar Observatory's 5m Hale telescope. In addition, we propose a novel statistics-based technique for the detection of faint companions from a sequence of AO-corrected exposures. The algorithm, which we call stochastic speckle discrimination, utilizes the "statistical signature" of the centre of the point spread function (PSF) to discriminate between faint companions and static speckles. The technique yields excellent results even for signals invisible in the shift-and-add images

Molecular signatures define alopecia areata subtypes and transcriptional biomarkers

AbstractAlopecia areata (AA) is an autoimmune disease typified by nonscarring hair loss with a variable clinical course. In this study, we conducted whole genome gene expression analysis of 96 human scalp skin biopsy specimens from AA or normal control subjects. Based on gene expression profiling, samples formed distinct clusters based on the presence or absence of disease as well as disease phenotype (patchy disease compared with alopecia totalis or universalis). Differential gene expression analysis allowed us to robustly demonstrate graded immune activity in samples of increasing phenotypic severity and generate a quantitative gene expression scoring system that classified samples based on interferon and cytotoxic T lymphocyte immune signatures critical for disease pathogenesis