General Purpose Audio Effect Removal

Although the design and application of audio effects is well understood, the inverse problem of removing these effects is significantly more challenging and far less studied. Recently, deep learning has been applied to audio effect removal; however, existing approaches have focused on narrow formulations considering only one effect or source type at a time. In realistic scenarios, multiple effects are applied with varying source content. This motivates a more general task, which we refer to as general purpose audio effect removal. We developed a dataset for this task using five audio effects across four different sources and used it to train and evaluate a set of existing architectures. We found that no single model performed optimally on all effect types and sources. To address this, we introduced RemFX, an approach designed to mirror the compositionality of applied effects. We first trained a set of the best-performing effect-specific removal models and then leveraged an audio effect classification model to dynamically construct a graph of our models at inference. We found our approach to outperform single model baselines, although examples with many effects present remain challenging

Chemical Addressability of Ultraviolet-Inactivated Viral Nanoparticles (VNPs)

. Thus, inactivation of the virus RNA genome is important for biosafety considerations, however the surface characteristics and chemical reactivity of the particles must be maintained in order to preserve chemical and structural functionality. were shown to maintain particle structure and chemical reactivity, and cellular binding properties were similar to CPMV-WT. applications

Consequences of converting graded to action potentials upon neural information coding and energy efficiency

Information is encoded in neural circuits using both graded and action potentials, converting between them within single neurons and successive processing layers. This conversion is accompanied by information loss and a drop in energy efficiency. We investigate the biophysical causes of this loss of information and efficiency by comparing spiking neuron models, containing stochastic voltage-gated Na+ and K+ channels, with generator potential and graded potential models lacking voltage-gated Na+ channels. We identify three causes of information loss in the generator potential that are the by-product of action potential generation: (1) the voltage-gated Na+ channels necessary for action potential generation increase intrinsic noise and (2) introduce non-linearities, and (3) the finite duration of the action potential creates a ‘footprint’ in the generator potential that obscures incoming signals. These three processes reduce information rates by ~50% in generator potentials, to ~3 times that of spike trains. Both generator potentials and graded potentials consume almost an order of magnitude less energy per second than spike trains. Because of the lower information rates of generator potentials they are substantially less energy efficient than graded potentials. However, both are an order of magnitude more efficient than spike trains due to the higher energy costs and low information content of spikes, emphasizing that there is a two-fold cost of converting analogue to digital; information loss and cost inflation

Chloroplast DNA sequences integrated into an intron of a tomato nuclear gene

DNA sequences capable of hybridizing with chloroplast DNA have previously been reported to exist in the nuclear genome of higher plants. Here we show that the third intron of the cultivated tomato ( Lycopersicon esculentum ) nuclear gene Cab -7, which resides on chromosome 10 and which we recently cloned and sequenced, contains two DNA fragments derived from the coding region of the chloroplast gene psb G. The first fragment, 133 bp long, is located at a site 63 bp from the 3′ end of the 833 bp intron. The exact sequence of the 11 nucleotides at the 3′ end of the inserting chloroplast sequence is also found at the 5′ border of the insertion. A small (107 bp) chloroplast DNA fragment is inserted near the middle of the intron, again with the 3′ end of the inserting element (6 bp) duplicated at the 5′ border of the insertion. The second insert is a subfragment of the first insert, and is most likely directly derived from it. The psb G insertion sequence was found to be present in the Cab -7 gene of all tomato species examined but not in species from related genera (e.g. Solanum, Petunia, Nicotiana ), suggesting that the original transposition event (chloroplast to nucleus) occurred relatively recently-since the divergence of the genus Lycopersicon from other genera in the family Solanaceae, but before radiation of species in that genus.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47568/1/438_2004_Article_BF00331304.pd

Mapping gene associations in human mitochondria using clinical disease phenotypes

Nuclear genes encode most mitochondrial proteins, and their mutations cause diverse and debilitating clinical disorders. To date, 1,200 of these mitochondrial genes have been recorded, while no standardized catalog exists of the associated clinical phenotypes. Such a catalog would be useful to develop methods to analyze human phenotypic data, to determine genotype-phenotype relations among many genes and diseases, and to support the clinical diagnosis of mitochondrial disorders. Here we establish a clinical phenotype catalog of 174 mitochondrial disease genes and study associations of diseases and genes. Phenotypic features such as clinical signs and symptoms were manually annotated from full-text medical articles and classified based on the hierarchical MeSH ontology. This classification of phenotypic features of each gene allowed for the comparison of diseases between different genes. In turn, we were then able to measure the phenotypic associations of disease genes for which we calculated a quantitative value that is based on their shared phenotypic features. The results showed that genes sharing more similar phenotypes have a stronger tendency for functional interactions, proving the usefulness of phenotype similarity values in disease gene network analysis. We then constructed a functional network of mitochondrial genes and discovered a higher connectivity for non-disease than for disease genes, and a tendency of disease genes to interact with each other. Utilizing these differences, we propose 168 candidate genes that resemble the characteristic interaction patterns of mitochondrial disease genes. Through their network associations, the candidates are further prioritized for the study of specific disorders such as optic neuropathies and Parkinson disease. Most mitochondrial disease phenotypes involve several clinical categories including neurologic, metabolic, and gastrointestinal disorders, which might indicate the effects of gene defects within the mitochondrial system. The accompanying knowledgebase (http://www.mitophenome.org/) supports the study of clinical diseases and associated genes

The R-Process Alliance: Fourth Data Release from the Search for R-process-enhanced Stars in the Galactic Halo

This compilation is the fourth data release from the R-Process Alliance (RPA) search for r-process-enhanced stars and the second release based on "snapshot" high-resolution (R ~ 30,000) spectra collected with the du Pont 2.5 m Telescope. In this data release, we propose a new delineation between the r-I and r-II stellar classes at $[\mathrm{Eu}/\mathrm{Fe}]=+0.7$, instead of the empirically chosen $[\mathrm{Eu}/\mathrm{Fe}]=+1.0$ level previously in use, based on statistical tests of the complete set of RPA data released to date. We also statistically justify the minimum level of [Eu/Fe] for definition of the r-I stars, [Eu/Fe] > +0.3. Redefining the separation between r-I and r-II stars will aid in the analysis of the possible progenitors of these two classes of stars and determine whether these signatures arise from separate astrophysical sources at all. Applying this redefinition to previous RPA data, the number of identified r-II and r-I stars changes to 51 and 121, respectively, from the initial set of data releases published thus far. In this data release, we identify 21 new r-II, 111 new r-I (plus 3 re-identified), and 7 new (plus 1 re-identified) limited-r stars out of a total of 232 target stars, resulting in a total sample of 72 new r-II stars, 232 new r-I stars, and 42 new limited-r stars identified by the RPA to date

Kefir consumption does not alter plasma lipid levels or cholesterol fractional synthesis rates relative to milk in hyperlipidemic men: a randomized controlled trial [ISRCTN10820810]

BACKGROUND: Fermented milk products have been shown to affect serum cholesterol concentrations in humans. Kefir, a fermented milk product, has been traditionally consumed for its potential health benefits but has to date not been studied for its hypocholesterolemic properties. METHODS: Thirteen healthy mildly hypercholesterolemic male subjects consumed a dairy supplement in randomized crossover trial for 2 periods of 4 wk each. Subjects were blinded to the dairy supplement consumed. Blood samples were collected at baseline and after 4 wk of supplementation for measurement of plasma total, low-density lipoprotein, and high-density lipoprotein cholesterol and triglyceride concentrations, as well as fatty acid profile and cholesterol synthesis rate. Fecal samples were collected at baseline and after 2 and 4 wk of supplementation for determination of fecal short chain fatty acid level and bacterial content. RESULTS: Kefir had no effect on total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglyceride concentrations nor on cholesterol fractional synthesis rates after 4 wk of supplementation. No significant change on plasma fatty acid levels was observed with diet. However, both kefir and milk increased (p < 0.05) fecal isobutyric, isovaleric and propionic acids as well as the total amount of fecal short chain fatty acids. Kefir supplementation resulted in increased fecal bacterial content in the majority of the subjects. CONCLUSIONS: Since kefir consumption did not result in lowered plasma lipid concentrations, the results of this study do not support consumption of kefir as a cholesterol-lowering agent

The stellar halo of the Galaxy

Stellar halos may hold some of the best preserved fossils of the formation history of galaxies. They are a natural product of the merging processes that probably take place during the assembly of a galaxy, and hence may well be the most ubiquitous component of galaxies, independently of their Hubble type. This review focuses on our current understanding of the spatial structure, the kinematics and chemistry of halo stars in the Milky Way. In recent years, we have experienced a change in paradigm thanks to the discovery of large amounts of substructure, especially in the outer halo. I discuss the implications of the currently available observational constraints and fold them into several possible formation scenarios. Unraveling the formation of the Galactic halo will be possible in the near future through a combination of large wide field photometric and spectroscopic surveys, and especially in the era of Gaia.Comment: 46 pages, 16 figures. References updated and some minor changes. Full-resolution version available at http://www.astro.rug.nl/~ahelmi/stellar-halo-review.pd