2,738 research outputs found
A colimit decomposition for homotopy algebras in Cat
Badzioch showed that in the category of simplicial sets each homotopy algebra
of a Lawvere theory is weakly equivalent to a strict algebra. In seeking to
extend this result to other contexts Rosicky observed a key point to be that
each homotopy colimit in simplicial sets admits a decomposition into a homotopy
sifted colimit of finite coproducts, and asked the author whether a similar
decomposition holds in the 2-category of categories Cat. Our purpose in the
present paper is to show that this is the case.Comment: Some notation changed; small amount of exposition added in intr
The position and duties of the king's almoner 1255-1327
Abstract not Provide
The Drosophila genome nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 from a single ancestral range population.
Hundreds of wild-derived Drosophila melanogaster genomes have been published, but rigorous comparisons across data sets are precluded by differences in alignment methodology. The most common approach to reference-based genome assembly is a single round of alignment followed by quality filtering and variant detection. We evaluated variations and extensions of this approach and settled on an assembly strategy that utilizes two alignment programs and incorporates both substitutions and short indels to construct an updated reference for a second round of mapping prior to final variant detection. Utilizing this approach, we reassembled published D. melanogaster population genomic data sets and added unpublished genomes from several sub-Saharan populations. Most notably, we present aligned data from phase 3 of the Drosophila Population Genomics Project (DPGP3), which provides 197 genomes from a single ancestral range population of D. melanogaster (from Zambia). The large sample size, high genetic diversity, and potentially simpler demographic history of the DPGP3 sample will make this a highly valuable resource for fundamental population genetic research. The complete set of assemblies described here, termed the Drosophila Genome Nexus, presently comprises 623 consistently aligned genomes and is publicly available in multiple formats with supporting documentation and bioinformatic tools. This resource will greatly facilitate population genomic analysis in this model species by reducing the methodological differences between data sets
Chronotype differences in circadian rhythms of temperature, melatonin, and sleepiness as measured in a modified constant routine protocol
Evening chronotypes typically have sleep patterns timed 2–3 hours later than morning
chronotypes. Ambulatory studies have suggested that differences in the timing of underlying
circadian rhythms are a cause of the sleep period differences. However, differences in endogenous
circadian rhythms are best explored in laboratory protocols such as the constant routine. We used
a 27-hour modified constant routine to measure the endogenous core temperature and melatonin
circadian rhythms as well as subjective and objective sleepiness from hourly 15-minute sleep
opportunities. Ten (8f) morning type individuals were compared with 12 (8f) evening types.
All were young, healthy, good sleepers. The typical sleep onset, arising times, circadian phase
markers for temperature and melatonin and objective sleepiness were all 2–3 hours later for
the evening types than morning types. However, consistent with past studies the differences for
the subjective sleepiness rhythms were much greater (5–9 hours). Therefore, the present study
supports the important role of subjective alertness/sleepiness in determining the sleep period
differences between morning and evening types and the possible vulnerability of evening types
to delayed sleep phase disorder
Determining the origin of synchronous multifocal bladder cancer by exome sequencing
Background: Synchronous multifocal tumours are commonly observed in urothelial carcinomas of the bladder. The origin of these physically independent tumours has been proposed to occur by either intraluminal migration (clonal) or spontaneous transformation of multiple cells by carcinogens (field effect). It is unclear which model is correct, with several studies supporting both hypotheses. A potential cause of this uncertainty may be the small number of genetic mutations previously used to quantify the relationship between these tumours. Methods: To better understand the genetic lineage of these tumours we conducted exome sequencing of synchronous multifocal pTa urothelial bladder cancers at a high depth, using multiple samples from three patients. Results: Phylogenetic analysis of high confidence single nucleotide variants (SNV) demonstrated that the sequenced multifocal bladder cancers arose from a clonal origin in all three patients (bootstrap value 100 %). Interestingly, in two patients the most common type of tumour-associated SNVs were cytosine mutations of TpC*dinucleotides (Fisher's exact test p < 10-41), likely caused by APOBEC-mediated deamination. Incorporating these results into our clonal model, we found that TpC*type mutations occurred 2-5× more often among SNVs on the ancestral branches than in the more recent private branches (p < 10-4) suggesting that TpC*mutations largely occurred early in the development of the tumour. Conclusions: These results demonstrate that synchronous multifocal bladder cancers frequently arise from a clonal origin. Our data also suggests that APOBEC-mediated mutations occur early in the development of the tumour and may be a driver of tumourigenesis in non-muscle invasive urothelial bladder cancer. © 2015 Acar et al
Coalgebras, braidings, and distributive laws
We show, for a monad T, that coalgebra structures on a T-algebra can be described
in terms of ‘braidings’, provided that the monad is equipped with an invertible distributive law
satisfying the Yang-Baxter equation
The Serre spectral sequence of a noncommutative fibration for de Rham cohomology
For differential calculi on noncommutative algebras, we construct a twisted
de Rham cohomology using flat connections on modules. This has properties
similar, in some respects, to sheaf cohomology on topological spaces. We also
discuss generalised mapping properties of these theories, and relations of
these properties to corings. Using this, we give conditions for the Serre
spectral sequence to hold for a noncommutative fibration. This might be better
read as giving the definition of a fibration in noncommutative differential
geometry. We also study the multiplicative structure of such spectral
sequences. Finally we show that some noncommutative homogeneous spaces satisfy
the conditions to be such a fibration, and in the process clarify the
differential structure on these homogeneous spaces. We also give two explicit
examples of differential fibrations: these are built on the quantum Hopf
fibration with two different differential structures.Comment: LaTeX, 33 page
Head-Neck Dual-energy CT Contrast Media Reduction Using Diffusion Models
Iodinated contrast media is essential for dual-energy computed tomography
(DECT) angiography. Previous studies show that iodinated contrast media may
cause side effects, and the interruption of the supply chain in 2022 led to a
severe contrast media shortage in the US. Both factors justify the necessity of
contrast media reduction in relevant clinical applications. In this study, we
propose a diffusion model-based deep learning framework to address this
challenge. First, we simulate different levels of low contrast dosage DECT
scans from the standard normal contrast dosage DECT scans using material
decomposition. Conditional denoising diffusion probabilistic models are then
trained to enhance the contrast media and create contrast-enhanced images. Our
results demonstrate that the proposed methods can generate high-quality
contrast-enhanced results even for images obtained with as low as 12.5% of the
normal contrast dosage. Furthermore, our method outperforms selected competing
methods in a human reader study
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