299 research outputs found
A Categorical Normalization Proof for the Modal Lambda-Calculus
We investigate a simply typed modal -calculus,
, due to Pfenning, Wong and Davies, where we define a
well-typed term with respect to a context stack that captures the possible
world semantics in a syntactic way. It provides logical foundation for
multi-staged meta-programming. Our main contribution in this paper is a
normalization by evaluation (NbE) algorithm for which we
prove sound and complete. The NbE algorithm is a moderate extension to the
standard presheaf model of simply typed -calculus. However, central to
the model construction and the NbE algorithm is the observation of Kripke-style
substitutions on context stacks which brings together two previously separate
concepts, structural modal transformations on context stacks and substitutions
for individual assumptions. Moreover, Kripke-style substitutions allow us to
give a formulation for contextual types, which can represent open code in a
meta-programming setting. Our work lays the foundation for extending the
logical foundation by Pfenning, Wong, and Davies towards building a practical,
dependently typed foundation for meta-programming
A Category Theoretic View of Contextual Types: from Simple Types to Dependent Types
We describe the categorical semantics for a simply typed variant and a
simplified dependently typed variant of Cocon, a contextual modal type theory
where the box modality mediates between the weak function space that is used to
represent higher-order abstract syntax (HOAS) trees and the strong function
space that describes (recursive) computations about them. What makes Cocon
different from standard type theories is the presence of first-class contexts
and contextual objects to describe syntax trees that are closed with respect to
a given context of assumptions. Following M. Hofmann's work, we use a presheaf
model to characterise HOAS trees. Surprisingly, this model already provides the
necessary structure to also model Cocon. In particular, we can capture the
contextual objects of Cocon using a comonad that restricts presheaves
to their closed elements. This gives a simple semantic characterisation of the
invariants of contextual types (e.g. substitution invariance) and identifies
Cocon as a type-theoretic syntax of presheaf models. We further extend this
characterisation to dependent types using categories with families and show
that we can model a fragment of Cocon without recursor in the Fitch-style
dependent modal type theory presented by Birkedal et. al.
Near-Infrared Photometric Survey of Proto-Planetary Nebula Candidates
We present JHK' photometric measurements of 78 objects mostly consisting of
proto-planetary nebula candidates. Photometric magnitudes are determined by
means of imaging and aperture photometry. Unlike the observations with a
photometer with a fixed-sized beam, the method of imaging photometry permits
accurate derivation of photometric values because the target sources can be
correctly identified and confusion with neighboring sources can be easily
avoided. Of the 78 sources observed, we report 10 cases in which the source
seems to have been misidentified or confused by nearby bright sources. We also
present nearly two dozen cases in which the source seems to have indicated a
variability which prompts a follow-up monitoring. There are also a few sources
that show previously unreported extendedness. In addition, we present H band
finding charts of the target sources.Comment: 3 tables, 1 figur
Genomorama: genome visualization and analysis
<p>Abstract</p> <p>Background</p> <p>The ability to visualize genomic features and design experimental assays that can target specific regions of a genome is essential for modern biology. To assist in these tasks, we present Genomorama, a software program for interactively displaying multiple genomes and identifying potential DNA hybridization sites for assay design.</p> <p>Results</p> <p>Useful features of Genomorama include genome search by DNA hybridization (probe binding and PCR amplification), efficient multi-scale display and manipulation of multiple genomes, support for many genome file types and the ability to search for and retrieve data from the National Center for Biotechnology Information (NCBI) Entrez server.</p> <p>Conclusion</p> <p>Genomorama provides an efficient computational platform for visualizing and analyzing multiple genomes.</p
Introductory programming: a systematic literature review
As computing becomes a mainstream discipline embedded in the school curriculum and acts as an enabler for an increasing range of academic disciplines in higher education, the literature on introductory programming is growing. Although there have been several reviews that focus on specific aspects of introductory programming, there has been no broad overview of the literature exploring recent trends across the breadth of introductory programming.
This paper is the report of an ITiCSE working group that conducted a systematic review in order to gain an overview of the introductory programming literature. Partitioning the literature into papers addressing the student, teaching, the curriculum, and assessment, we explore trends, highlight advances in knowledge over the past 15 years, and indicate possible directions for future research
Empirical comparison of cross-platform normalization methods for gene expression data
<p>Abstract</p> <p>Background</p> <p>Simultaneous measurement of gene expression on a genomic scale can be accomplished using microarray technology or by sequencing based methods. Researchers who perform high throughput gene expression assays often deposit their data in public databases, but heterogeneity of measurement platforms leads to challenges for the combination and comparison of data sets. Researchers wishing to perform cross platform normalization face two major obstacles. First, a choice must be made about which method or methods to employ. Nine are currently available, and no rigorous comparison exists. Second, software for the selected method must be obtained and incorporated into a data analysis workflow.</p> <p>Results</p> <p>Using two publicly available cross-platform testing data sets, cross-platform normalization methods are compared based on inter-platform concordance and on the consistency of gene lists obtained with transformed data. Scatter and ROC-like plots are produced and new statistics based on those plots are introduced to measure the effectiveness of each method. Bootstrapping is employed to obtain distributions for those statistics. The consistency of platform effects across studies is explored theoretically and with respect to the testing data sets.</p> <p>Conclusions</p> <p>Our comparisons indicate that four methods, DWD, EB, GQ, and XPN, are generally effective, while the remaining methods do not adequately correct for platform effects. Of the four successful methods, XPN generally shows the highest inter-platform concordance when treatment groups are equally sized, while DWD is most robust to differently sized treatment groups and consistently shows the smallest loss in gene detection. We provide an R package, CONOR, capable of performing the nine cross-platform normalization methods considered. The package can be downloaded at <url>http://alborz.sdsu.edu/conor</url> and is available from CRAN.</p
The state of the Martian climate
60°N was +2.0°C, relative to the 1981â2010 average value (Fig. 5.1). This marks a new high for the record. The average annual surface air temperature (SAT) anomaly for 2016 for land stations north of starting in 1900, and is a significant increase over the previous highest value of +1.2°C, which was observed in 2007, 2011, and 2015. Average global annual temperatures also showed record values in 2015 and 2016. Currently, the Arctic is warming at more than twice the rate of lower latitudes
LSST: from Science Drivers to Reference Design and Anticipated Data Products
(Abridged) We describe here the most ambitious survey currently planned in
the optical, the Large Synoptic Survey Telescope (LSST). A vast array of
science will be enabled by a single wide-deep-fast sky survey, and LSST will
have unique survey capability in the faint time domain. The LSST design is
driven by four main science themes: probing dark energy and dark matter, taking
an inventory of the Solar System, exploring the transient optical sky, and
mapping the Milky Way. LSST will be a wide-field ground-based system sited at
Cerro Pach\'{o}n in northern Chile. The telescope will have an 8.4 m (6.5 m
effective) primary mirror, a 9.6 deg field of view, and a 3.2 Gigapixel
camera. The standard observing sequence will consist of pairs of 15-second
exposures in a given field, with two such visits in each pointing in a given
night. With these repeats, the LSST system is capable of imaging about 10,000
square degrees of sky in a single filter in three nights. The typical 5
point-source depth in a single visit in will be (AB). The
project is in the construction phase and will begin regular survey operations
by 2022. The survey area will be contained within 30,000 deg with
, and will be imaged multiple times in six bands, ,
covering the wavelength range 320--1050 nm. About 90\% of the observing time
will be devoted to a deep-wide-fast survey mode which will uniformly observe a
18,000 deg region about 800 times (summed over all six bands) during the
anticipated 10 years of operations, and yield a coadded map to . The
remaining 10\% of the observing time will be allocated to projects such as a
Very Deep and Fast time domain survey. The goal is to make LSST data products,
including a relational database of about 32 trillion observations of 40 billion
objects, available to the public and scientists around the world.Comment: 57 pages, 32 color figures, version with high-resolution figures
available from https://www.lsst.org/overvie
Association of Six Single Nucleotide Polymorphisms with Gestational Diabetes Mellitus in a Chinese Population
To investigate whether the candidate genes that confer susceptibility to type 2 diabetes mellitus are also correlated with gestational diabetes mellitus (GDM) in pregnant Chinese women.In this study, 1764 unrelated pregnant women were recruited, of which 725 women had GDM and 1039 served as controls. Six single nucleotide polymorphisms (rs7754840 in CDKAL1, rs391300 in SRR, rs2383208 in CDKN2A/2B, rs4402960 in IGF2BP2, rs10830963 in MTNR1B, rs4607517 in GCK) were genotyped using TaqMan allelic discrimination assays. The genotype and allele distributions of each SNP between the GDM cases and controls and the combined effects of alleles for the risk of developing GDM were analyzed. We found that the rs4402960, rs2383208 and rs391300 were statistically associated with GDM (ORâ=â1.207, 95%CIâ=â1.029-1.417, pâ=â0.021; ORâ=â1.242, 95%CIâ=â1.077-1.432, pâ=â0.003; ORâ=â1.202, 95%CIâ=â1.020-1.416, Pâ=â0.028, respectively). In addition, the effect was greater under a recessive model in rs391300 (ORâ=â1.820, 95%CIâ=â1.226-2.701, pâ=â0.003). Meanwhile, the joint effect of these three loci indicated an additive effect of multiple alleles on the risk of developing GDM with an OR of 1.196 per allele (pâ=â1.08Ă10(-4)). We also found that the risk alleles of rs2383208 (bâ=â-0.085, pâ=â0.003), rs4402960 (bâ=â-0.057, pâ=â0.046) and rs10830963 (bâ=â-0.096, pâ=â0.001) were associated with HOMA-B, while rs7754840 was associated with decrease in insulin AUC during a 100 g OGTT given at the time of GDM diagnosis (bâ=â-0.080, pâ=â0.007).Several risk alleles of type 2 diabetes were associated with GDM in pregnant Chinese women. The effects of these SNPs on GDM might be through the impairment of beta cell function and these risk loci contributed additively to the disease
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