177,461 research outputs found
Meta-colored Compacted de Bruijn Graphs
No full textThe colored compacted de Bruijn graph (c-dBG) has become a fundamental tool used across several areas of genomics and pangenomics. For example, it has been widely adopted by methods that perform read mapping or alignment, abundance estimation, and subsequent downstream analyses. These applications essentially regard the c-dBG as a map from k-mers to the set of references in which they appear. The c-dBG data structure should retrieve this set—the color of the k-mer—efficiently for any given k-mer, while using little memory. To aid retrieval, the colors are stored explicitly in the data structure and take considerable space for large reference collections, even when compressed. Reducing the space of the colors is therefore of utmost importance for large-scale sequence indexing. We describe the meta-colored compacted de Bruijn graph (Mac-dBG)—a new colored de Bruijn graph data structure where colors are represented holistically, i.e., taking into account their redundancy across the whole collection being indexed, rather than individually as atomic integer lists. This allows the factorization and compression of common sub-patterns across colors. While optimizing the space of our data structure is NP-hard, we propose a simple heuristic algorithm that yields practically good solutions. Results show that the Mac-dBG data structure improves substantially over the best previous space/time trade-off, by providing remarkably better compression effectiveness for the same (or better) query efficiency . This improved space/time trade-off is robust across different datasets and query workloads. Code availability. A C++17 implementation of the Mac-dBG is publicly available on GitHub at: https://github.com/jermp/fulgor
The Kochen-Specker Theorem Based on the Kronecker Delta
No full textWe propose the Kochen-Specker theorem that relies on the properties of the Kronecker delta. We introduce the following value Sigma l=1mrl(<sigma z >)=0. The notation r(l)(<sigma(z)>) means the lth hidden outcome of quantum measurements when we would measure the expected value <sigma(z)> =0 in a thoughtful experiment. Surprisingly, we cannot define the value as zero when we accept the Kronecker delta. We cannot determine the hidden results for the expected value.
Appropriate Similarity Measures for Author Cocitation Analysis
No full textWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Malignancy risk in adults with growth hormone deficiency undergoing long-term treatment with biosimilar somatropin (Omnitrope(R)): data from the PATRO Adults study
No full textBackground: To assess the safety (particularly the occurrence of malignancies) of growth hormone (GH) replacement (Omnitrope(R)) in adults with GH deficiency, using data from the ongoing PATRO Adults post-marketing surveillance study. Methods: PATRO Adults is being conducted in hospitals and specialized endocrinology clinics across Europe. All enrolled patients who receive > 1 dose of Omnitrope(R)are included in the safety population. Malignancies are listed as adverse events under the MedDRA System Organ Class 'neoplasms, benign, malignant and unspecified (including cysts and polyps)'. Results: As of July 2018, 1293 patients had been enrolled in the study and 983 (76.0%) remained active in the study. Approximately half [n = 637 (49.3%)] of the patients were GH treatment-naive on study entry. The majority of enrolled patients had multiple pituitary hormone deficiency (n = 1128, 87.2%). A total of 41 on-study malignancies were reported in 33 patients (2.6%;incidence rate 7.94 per 1000 patient-years). The most common cancers were basal cell carcinoma (n = 13), prostate (n = 6), breast, kidney and malignant melanoma (eachn = 3). Treatment with Omnitrope(R)was discontinued following diagnosis of malignancy in 16 patients. The tumors occurred after a mean of 79.4 months of recombinant hormone GH (rhGH) treatment overall. Conclusion: Based on this snapshot of data from PATRO Adults, Omnitrope(R)treatment is tolerated in adult patients with GH deficiency in a real-life clinical practice setting. Our results do not generally support a carcinogenic effect of rhGH in adults with GH deficiency, although an increased risk of second new malignancies in patients with previous cancer cannot be excluded based on the current dataset
A Review of Unsupervised Band Selection Techniques: Land Cover Classification for Hyperspectral Earth Observation Data
No full textA hyperspectral image (HSI) is a collection of several narrow-band images that span a wide spectral range. Each band reflects the same scene, composed of various objects imaged at different wavelengths; the spatial information, however, remains generally consistent across bands. Both types of information, spectral and spatial, can be leveraged to identify and classify objects. Recently, the use of machine learning (ML) in object classification has become increasingly widespread. Regardless of the selected approach, object-specific spectral and spatial information is key to discriminating relevant categories. Whereas spatial information is usually repeated across bands, spectral information tends to be distributed more unevenly and often highly so. This poses the issue of removing redundancy, which is commonly called the band selection (BS) problem and refers to identifying an optimal subset of bands for further HSI processing
Spectrum Preserving Tilings Enable Sparse and Modular Reference Indexing
No full textThe reference indexing problem for k-mers is to pre-process a collection of reference genomic sequences so that the position of all occurrences of any queried k-mer can be rapidly identified. An efficient and scalable solution to this problem is fundamental for many tasks in bioinformatics. In this work, we introduce the spectrum preserving tiling (SPT), a general representation of that specifies how a set of tiles repeatedly occur to spell out the constituent reference sequences in. By encoding the order and positions where tiles occur, SPTs enable the implementation and analysis of a general class of modular indexes. An index over an SPT decomposes the reference indexing problem for k-mers into: (1) a k-mer-to-tile mapping; and (2) a tile-to-occurrence mapping. Recently introduced work to construct and compactly index k-mer sets can be used to efficiently implement the k-mer-to-tile mapping. However, implementing the tile-to-occurrence mapping remains prohibitively costly in terms of space. As reference collections become large, the space requirements of the tile-to-occurrence mapping dominates that of the k-mer-to-tile mapping since the former depends on the amount of total sequence while the latter depends on the number of unique k-mers in. To address this, we introduce a class of sampling schemes for SPTs that trade off speed to reduce the size of the tile-to-reference mapping. We implement a practical index with these sampling schemes in the tool pufferfish2. When indexing over 30,000 bacterial genomes, pufferfish2 reduces the size of the tile-to-occurrence mapping from 86.3 GB to 34.6 GB while incurring only a 3.6 slowdown when querying k-mers from a sequenced readset. Availability: pufferfish2 is implemented in Rust and available at https://github.com/COMBINE-lab/pufferfish2
Future perspectives of run-of-the-river hydropower and the impact of glaciers’ shrinkage: The case of Italian Alps
No full textWe assess the impacts of nine climate-change scenarios on the hydrological regime and on hydropower production of forty-two glacierized basins across the Italian Alps, assumed exemplary of similar systems in other glacierized contexts. Each of these basins includes one (or more) hydropower plant, here treated as a run-of-the-river system. We implemented a semi-distributed hydrologic model that divides each basin in elevation bands and reconstructs orographic effects on both precipitation and temperature. The nine climate-change scenarios quantify the individual and combined effects of an increase in temperature and a change in liquid-solid phase partition. The simulation horizon is 2016–2065. Thus, we avoided long-term scenarios and worked at short-medium range to maximize the relevance of this work for decision makers. Our results predict a decline of about −30% in average summer runoff across all basins compared to present. Because most of this decrease in runoff occurs during high-flow periods when the run-of-the-river capacity of these plants is exceeded, this result translates into a median decrease of about −3% in hydropower production for run-of-the-river systems through 2065, across all the basins and all scenarios. The predominant cause of this decline is glacier shrinkage, whereas different temperature or precipitation trends plays a marginal role. Run-of-the-river hydropower production in basins where the current glacier coverage is less than 10% of total area is particularly robust to climate change
"Closing the R&D Gap, Evaluating the Sources of R&D Spending"
No full textBoth spending and tax policies have been implemented in the United States with the goal of stimulating private sector research and development (R&D). Karier questions whether current R&D policy, especially the research and experimentation tax credit, can contribute to closing the gap between nondefense expenditures on R&D in the United States and such expenditures in other countries, such as Japan and Germany. He also explores possible changes to our current R&D policy to make it more effective.
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Physical properties of high performance fluoride ion conductor BaSnF4 thin films by pulsed laser deposition
No full textThis article presents the results on the growth and characterization of BaSnF4 thin films on glass substrates prepared by pulsed laser deposition technique. The structural results of BaSnF4 thin film carried out by glancing angle X-ray diffraction technique indicates the formation of the film with similar structure (tetragonal, P-4/nmm) to the bulk target material. The absorption coefficient and band gap of the film is determined by suitable analysis of the transmittance spectra. The transport properties of the thin films are studied using impedance spectroscopy in the temperature range of 323-573 K. The frequency-dependent imaginary part of impedance plot shows that the conductivity relaxation is non-Debye in nature. The scaling behavior of the imaginary part of impedance at various frequencies indicates temperature-independent relaxation behavior
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