Toward Optimal Fingerprint Indexing for Large Scale Genomics

Motivation. To keep up with the scale of genomic databases, several methods rely on local sensitive hashing methods to efficiently find potential matches within large genome collections. Existing solutions rely on Minhash or Hyperloglog fingerprints and require reading the whole index to perform a query. Such solutions can not be considered scalable with the growing amount of documents to index. Results. We present NIQKI, a novel structure with well-designed fingerprints that lead to theoretical and practical query time improvements, outperforming state-of-the-art by orders of magnitude. Our contribution is threefold. First, we generalize the concept of Hyperminhash fingerprints in (h,m)-HMH fingerprints that can be tuned to present the lowest false positive rate given the expected sub-sampling applied. Second, we provide a structure able to index any kind of fingerprints based on inverted indexes that provide optimal queries, namely linear with the size of the output. Third, we implemented these approaches in a tool dubbed NIQKI that can index and calculate pairwise distances for over one million bacterial genomes from GenBank in a few days on a small cluster. We show that our approach can be orders of magnitude faster than state-of-the-art with comparable precision. We believe this approach can lead to tremendous improvements, allowing fast queries and scaling on extensive genomic databases

Procédé et machine de fomation de capsules contenant un fluide

Selon un procédé de fabrication de capsules (16) contenant un fluide, procède par pas aux étapes suivantes; réception de deux pans (11, 12) de film (1) thermoplastique, chaque pan (11, 12) comportant au moins une colonne (14a, 14b, 14c, 14d) de cavités (10) formées; rapprochement des deux pans (11, 12) pour mettre en correspondance les cavités (10) respectives de chaque pan et placage des pans (11, 12) par des paires de barres (301, 302, 303) qui pincent successivement les pans (11, 12) de part et d'autre des paires de colonnes de cavités (10), remplissage de la poche délimitée entre deux paires de barres (301, 302, 303) par le fluide pour remplir les cavités (10); soudure des pans (11, 12) autour des cavités (10) pour former les capsules (16). Machine mettant en œuvre le procéd

Behavior of epoxy bonded bars in concrete affected by alkali-silica reaction

Installation of drilled-in epoxy-bonded reinforcing bars is generally an effective strengthening method to increase the flexural and shear capacities of deficient concrete structures. However, most of the available studies characterizing the bond behavior of epoxy bonded bars in concrete have been carried out on sound concrete elements—that is, without any pathological material damage. This raises the question of bond capacities in existing damaged elements. This study investigates the influence of alkali-silica reaction (ASR) on the capacity of post-installed reinforcing bars. ASR is a deleterious mechanism that causes expansion and cracking in the affected concrete elements. Pullout tests on post-installed reinforcing bars having embedded lengths of 2db, 4db, and 5db with 15M reinforcing bars (db = 15.9 mm [0.626 in.]) have demonstrated a drop-in bond strength when concrete is affected by ASR. In addition, the study revealed that the progression of concrete expansion due to ASR may lead to some confinement of the post-installed reinforcing bar and possibly increases the bond strength

Study of bond between epoxy, steel reinforcing bars and concrete affected by alkali-silica reaction

Installation of drilled-in epoxy bonded reinforcing barsis generally an effective strengthening method for deficient concretestructures. However, this method of rehabilitation has largely been studied and tested on sound concrete elements, i.e. without any pathological damage, which raisesthe question of bond capabilities inexisting damaged elements. This investigation studies the influence of alkali-silica reaction (ASR) onthe capacity of epoxy bonded anchors. ASR, which is very common in eastern Canada, results from the chemical reaction between the alkali hydroxides in the concrete’s pore solution and some siliceous mineral phases inthe aggregates. Pull-out tests on epoxy bonded anchors havingembedded lengths offourtimes the bar diameter(Ø= 16 mm)have demonstrated a drop in bond strength when concrete is affected by ASR. In addition, the study revealed that the progression of concrete expansion due to ASR, leads to a confinement of the epoxy bonded anchor and increases the bond strength. These conclusions are therefore considered for the development of a model for the design of epoxy bonded anchors in existing concrete infrastructure affected by ASR

A review of potential impacts of submarine power cables on the marine environment:Knowledge gaps, recommendations and future directions

Submarine power cables (SPC) have been in use since the mid-19th century, but environmental concerns about them are much more recent. With the development of marine renewable energy technologies, it is vital to understand their potential impacts. The commissioning of SPC may temporarily or permanently impact the marine environment through habitat damage or loss, noise, chemical pollution, heat and electromagnetic field emissions, risk of entanglement, introduction of artificial substrates, and the creation of reserve effects. While growing numbers of scientific publications focus on impacts of the marine energy harnessing devices, data on impacts of associated power connections such as SPC are scarce and knowledge gaps persist. The present study (1) examines the different categories of potential ecological effects of SPC during installation, operation and decommissioning phases and hierarchizes these types of interactions according to their ecological relevance and existing scientific knowledge, (2) identifies the main knowledge gaps and needs for research, and (3) sets recommendations for better monitoring and mitigation of the most significant impacts. Overall, ecological impacts associated with SPC can be considered weak or moderate, although many uncertainties remain, particularly concerning electromagnetic effects

Les beautés de la nature ou Description des arbres, plantes, cataractes, fointaines ... qui se trouvents dans les cinq parties du monde

Copia digital. España : Ministerio de Educación, Cultura y Deporte. Subdirección General de Coordinación Bibliotecaria, 201

Analog programming of CMOS-compatible Al2_2O3_3/TiO2-x_\textrm{2-x} memristor at 4.2 K after metal-insulator transition suppression by cryogenic reforming

The exploration of memristors' behavior at cryogenic temperatures has become crucial due to the growing interest in quantum computing and cryogenic electronics. In this context, our study focuses on the characterization at cryogenic temperatures (4.2 K) of TiO$_\textrm{2-x}$-based memristors fabricated with a CMOS-compatible etch-back process. We demonstrate a so-called cryogenic reforming (CR) technique performed at 4.2 K to overcome the well-known metal-insulator transition (MIT) which limits the analog behavior of memristors at low temperatures. This cryogenic reforming process was found to be reproducible and led to a durable suppression of the MIT. This process allowed to reduce by approximately 20% the voltages required to perform DC resistive switching at 4.2 K. Additionally, conduction mechanism studies of memristors before and after cryogenic reforming from 4.2 K to 300 K revealed different behaviors above 100 K, indicating a potential change in the conductive filament stoichiometry. The reformed devices exhibit a conductance level that is 50 times higher than ambient-formed memristor, and the conduction drop between 300 K and 4.2 K is 100 times smaller, indicating the effectiveness of the reforming process. More importantly, CR enables analog programming at 4.2 K with typical read voltages. Suppressing the MIT improved the analog switching dynamics of the memristor leading to approximately 250% larger on/off ratios during long-term depression (LTD)/long-term potentiation (LTP) resistance tuning. This enhancement opens up the possibility of using TiO$_{\textrm{2-x}}$-based memristors to be used as synapses in neuromorphic computing at cryogenic temperatures

Behavior of Post-Installed Bonded Bars as Shear Reinforcement

Post-installed epoxy-bonded shear reinforcement is a promising technique to increase shear capacity of reinforced concrete (RC) structures. However, the behavior of epoxy-bonded bars largely affects the shear strengthening efficiency. To better predict the behavior of epoxy-bonded bars, a bond model is developed in this paper. This model appears to adequately predict the behavior of epoxy-bonded bars observed in experimental pullout tests and beam loading tests. Based on numerical results, a simplified model is proposed to predict the epoxy-bonded bars’ stress according to the crack width. It appears that the behavior of long embedded bars is similar to stirrups in terms of crack width and bar stress. However, a large diagonal crack is required to reach the bar yielding strength when the bar embedment length is below a transition length, which differs from stirrups. Embedment length below the epoxy-bonded bar development length leads to pullout failure and bar capacity lower than the bar yielding strength

Effect of temperature on high pressure cellulose compression

The effect of temperature during cellulose compression has been studied using mechanical testing, particle size analysis, density and Pressure-Volume-Temperature (PVT) measurements, crystallinity index, SEM photographs and water sorption isotherms. Commercial cellulose powder samples with different crystallinity levels were compacted at high pressure (177 MPa) for 10 minutes at two different temperatures: 25 and 160 °C. 3 point bending test results for compressed samples are discussed. When pressure was applied directly to powders at room temperature, the cellulose sample with the highest level of crystallinity showed an increase in its crystallinity index of about 5 %, while this was about 22 % for the sample with the lowest level. These increases were even higher at 160 °C attaining 8 and 33 % respectively. Using density measurements, a densification phase related to this crystallinization was observed, and the PVT diagrams from different cellulose samples showed that this was associated with high temperatures. Water sorption isotherms were made on cellulose samples before and after compression. They showed a diminution of cellulose sorption capacity after compression at 160 °C, revealing the effect of temperature on high-pressure cellulose compression, reducing specific surface area. Events of this nature suggest a sintering mechanism, when temperature is associated with high pressure during cellulose compression

Effet de la réaction alcalis-silice (RAS) sur l'adhérence des ancrages époxydiques de barres d'armature

L’installation d’ancrages époxydiques à l’aide d’armatures conventionnelles constitue une méthode généralement efficace de renforcement d’infrastructures en béton armé. Toutefois, cette méthode de réhabilitation a été étudiée, puis testée sur des éléments de béton sain, c’est-à-dire sans endommagement pathologique. Le projet de recherche étudie donc l’effet de l’endommagement dû au développement de la réaction alcalis-silice (RAS) sur la capacité des ancrages époxydiques. La RAS, très présente à l’est du Canada, résulte de la réaction chimique entre les hydroxydes alcalins à l’intérieur de la solution interstitielle du béton et certaines phases minérales siliceuses qui composent les granulats. Des essais d’arrachement réalisés sur des ancrages époxydiques de longueur 5ø(~80 mm) ont montré une diminution de leur résistance en adhérence avec l’augmentation de l’endommagement causé par la RAS. Cette perte de capacité doit donc être considérée lors du calcul d’un renforcement de structures atteintes de RAS à l’aide de ce type d’ancrage adhésif