A Purely Functional Computer Algebra System Embedded in Haskell

We demonstrate how methods in Functional Programming can be used to implement a computer algebra system. As a proof-of-concept, we present the computational-algebra package. It is a computer algebra system implemented as an embedded domain-specific language in Haskell, a purely functional programming language. Utilising methods in functional programming and prominent features of Haskell, this library achieves safety, composability, and correctness at the same time. To demonstrate the advantages of our approach, we have implemented advanced Gr\"{o}bner basis algorithms, such as Faug\`{e}re's $F_4$ and $F_5$, in a composable way.Comment: 16 pages, Accepted to CASC 201

A Upf3b-mutant mouse model with behavioral and neurogenesis defects.

Nonsense-mediated RNA decay (NMD) is a highly conserved and selective RNA degradation pathway that acts on RNAs terminating their reading frames in specific contexts. NMD is regulated in a tissue-specific and developmentally controlled manner, raising the possibility that it influences developmental events. Indeed, loss or depletion of NMD factors have been shown to disrupt developmental events in organisms spanning the phylogenetic scale. In humans, mutations in the NMD factor gene, UPF3B, cause intellectual disability (ID) and are strongly associated with autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD) and schizophrenia (SCZ). Here, we report the generation and characterization of mice harboring a null Upf3b allele. These Upf3b-null mice exhibit deficits in fear-conditioned learning, but not spatial learning. Upf3b-null mice also have a profound defect in prepulse inhibition (PPI), a measure of sensorimotor gating commonly deficient in individuals with SCZ and other brain disorders. Consistent with both their PPI and learning defects, cortical pyramidal neurons from Upf3b-null mice display deficient dendritic spine maturation in vivo. In addition, neural stem cells from Upf3b-null mice have impaired ability to undergo differentiation and require prolonged culture to give rise to functional neurons with electrical activity. RNA sequencing (RNAseq) analysis of the frontal cortex identified UPF3B-regulated RNAs, including direct NMD target transcripts encoding proteins with known functions in neural differentiation, maturation and disease. We suggest Upf3b-null mice serve as a novel model system to decipher cellular and molecular defects underlying ID and neurodevelopmental disorders

High Resolution HST-STIS Spectra of CI and CO in the Beta Pictoris Circumstellar Disk

High resolution FUV echelle spectra showing absorption features arising from CI and CO gas in the Beta Pictoris circumstellar (CS) disk were obtained on 1997 December 6 and 19 using the Space Telescope Imaging Spectrograph (STIS). An unsaturated spin-forbidden line of CI at 1613.376 A not previously seen in spectra of Beta Pictoris was detected, allowing for an improved determination of the column density of CI at zero velocity relative to the star (the stable component), N = (2-4) x 10^{16} cm^{-2}. Variable components with multiple velocities, which are the signatures of infalling bodies in the Beta Pictoris CS disk, are observed in the CI 1561 A and 1657 A multiplets. Also seen for the first time were two lines arising from the metastable singlet D level of carbon, at 1931 A and 1463 A The results of analysis of the CO A-X (0-0), (1-0), and (2-0) bands are presented, including the bands arising from {13}^CO, with much better precision than has previously been possible, due to the very high resolution provided by the STIS echelle gratings. Only stable CO gas is observed, with a column density N(CO) = (6.3 +/- 0.3) x 10^{14} cm{-2}. An unusual ratio of the column densities of {12}^CO to {13}^CO is found (R = 15 +/- 2). The large difference between the column densities of CI and CO indicates that photodissociation of CO is not the primary source of CI gas in the disk, contrary to previous suggestion.Comment: 13 pages, including 6 figures. LaTex2e (emulateapj5.sty). Accepted for publication in Ap

Combining Double Fluorescence In Situ Hybridization with Immunolabelling for Detection of the Expression of Three Genes in Mouse Brain Sections

Detection of gene expression in different types of brain cells e.g., neurons, astrocytes, oligodendrocytes, oligodendrocyte precursors and microglia, can be hampered by the lack of specific primary or secondary antibodies for immunostaining. Here we describe a protocol to detect the expression of three different genes in the same brain section using double fluorescence in situ hybridization with two gene-specific probes followed by immunostaining with an antibody of high specificity directed against the protein encoded by a third gene. The Aspartoacyclase (ASPA) gene, mutations of which can lead to a rare human white matter disease - Canavan disease - is thought to be expressed in oligodendrocytes and microglia but not in astrocytes and neurons. However, the precise expression pattern of ASPA in the brain has yet to be established. This protocol has allowed us to determine that ASPA is expressed in a subset of mature oligodendrocytes and it can be generally applied to a wide range of gene expression pattern studies