HMMER cut-off threshold tool (HMMERCTTER): Supervised classification of superfamily protein sequences with a reliable cut-off threshold

Background: Protein superfamilies can be divided into subfamilies of proteins with different functional characteristics. Their sequences can be classified hierarchically, which is part of sequence function assignation. Typically, there are no clear subfamily hallmarks that would allow pattern-based function assignation by which this task is mostly achieved based on the similarity principle. This is hampered by the lack of a score cut-off that is both sensitive and specific. Results: HMMER Cut-off Threshold Tool (HMMERCTTER) adds a reliable cut-off threshold to the popular HMMER. Using a high quality superfamily phylogeny, it clusters a set of training sequences such that the cluster-specific HMMER profiles show cluster or subfamily member detection with 100% precision and recall (P&R), thereby generating a specific threshold as inclusion cut-off. Profiles and thresholds are then used as classifiers to screen a target dataset. Iterative inclusion of novel sequences to groups and the corresponding HMMER profiles results in high sensitivity while specificity is maintained by imposing 100% P&R self detection. In three presented case studies of protein superfamilies, classification of large datasets with 100% precision was achieved with over 95% recall. Limits and caveats are presented and explained. Conclusions: HMMERCTTER is a promising protein superfamily sequence classifier provided high quality training datasets are used. It provides a decision support system that aids in the difficult task of sequence function assignation in the twilight zone of sequence similarity. All relevant data and source codes are available from the Github repository at the following.Fil: Pagnuco, Inti Anabela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Científicas y Tecnológicas en Electrónica. Universidad Nacional de Mar del Plata. Facultad de Ingeniería. Instituto de Investigaciones Científicas y Tecnológicas en Electrónica; ArgentinaFil: Revuelta, María Victoria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Biológicas. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Biológicas; ArgentinaFil: Bondino, Hernán Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Biológicas. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Biológicas; ArgentinaFil: Brun, Marcel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Científicas y Tecnológicas en Electrónica. Universidad Nacional de Mar del Plata. Facultad de Ingeniería. Instituto de Investigaciones Científicas y Tecnológicas en Electrónica; ArgentinaFil: Ten Have, Arjen. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Biológicas. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Biológicas; Argentin

When Credit Dries Up: Job Losses in the Great Recession

We use a unique dataset to estimate the impact of a large credit supply shock on employment in Spain. We exploit marked differences in banks' health at the onset of the Great Recession. Several weak banks were rescued by the State and they reduced credit more than other banks. We compare employment changes from 2006 to 2010 at firms heavily indebted to weak banks before the crisis and the rest. Our estimates imply that these firms suffered an additional employment drop between 3 and 13.5 percentage points due to weak-bank attachment, representing between 8% and 36% of aggregate job losses

Functional Nanopores: A Solid-state Concept for Artificial Reaction Compartments and Molecular Factories

On the road towards the long-term goal of the NCCR Molecular Systems Engineering to create artificial molecular factories, we aim at introducing a compartmentalization strategy based on solid-state silicon technology targeting zeptoliter reaction volumes and simultaneous electrical contact to ensembles of well-oriented molecules. This approach allows the probing of molecular building blocks under a controlled environment prior to their use in a complex molecular factory. Furthermore, these ultra-sensitive electrical conductance measurements allow molecular responses to a variety of external triggers to be used as sensing and feedback mechanisms. So far, we demonstrate the proof-of-concept by electrically contacting self-assembled mono-layers of alkane-dithiols as an established test system. Here, the molecular films are laterally constrained by a circular dielectric confinement, forming a so-called `nanopore`. Device yields above 85% are consistently achieved down to sub-50 nm nanopore diameters. This generic platform will be extended to create distributed, cascaded reactors with individually addressable reaction sites, including interconnecting micro-fluidic channels for electrochemical communication among nanopores and sensing sites for reaction control and feedback. In this scientific outlook, we will sketch how such a solid-state nanopore concept can be used to study various aspects of molecular compounds tailored for operation in a molecular factory

Densely integrated photonic devices based on microring resonators for use in access networks

A reconfigurable optical add-drop multiplexer as well as a 1x4x4 reconfigurable λ router, designed for use in the second telecom window, are demonstrated. The devices that each have a footprint less than 2 mm$_{2}$ are based on thermally tunable vertically coupled microring resonators fabricated in $Si_{3}N_{4}$/$SiO_{2}$

When Credit Dries Up: Job Losses in the Great Recession

We use a unique dataset to estimate the impact of a large credit supply shock on employment in Spain. We exploit marked differences in banks' health at the onset of the Great Recession. Several weak banks were rescued by the State and they reduced credit more than other banks. We compare employment changes from 2006 to 2010 at firms heavily indebted to weak banks before the crisis and the rest. Our estimates imply that these firms suffered an additional employment drop between 3 and 13.5 percentage points due to weak-bank attachment, representing between 8% and 36% of aggregate job losses

Stages of health behavior change and factors associated with physical activity in patients with intermittent claudication

OBJECTIVE: To analyze, in people with intermittent claudication, the frequency of individuals who are in each of stages of health behavior change to practice physical activity, and analyze the association of these stages with the walking capacity. METHODS: We recruited 150 patients with intermittent claudication treated at a tertiary center, being included those > 30-year-old-individuals and who had ankle-arm index < 0.90. We obtained socio-demographic information, presence of comorbidities and cardiovascular risk factors and stages of health behavior change to practice physical activity through a questionnaire, they being pre-contemplation, contemplation, preparation, action and maintenance. Moreover, the walking capacity was measured in a treadmill test (Gardner protocol). RESULTS: Most individuals were in the maintenance stage (42.7%), however, when the stages of health behavior change were categorized into active (action and maintenance) and inactive (pre-contemplation, contemplation and preparation), 51.3% of the individuals were classified as inactive behavior. There was no association between stages of health behavior change, sociodemographic factors and cardiovascular risk factors. However, patients with intermittent claudication who had lower total walking distance were three times more likely to have inactive behavior. CONCLUSION: Most patients with intermittent claudication showed an inactive behavior and, in this population, lower walking capacity was associated with this behavior

Innovative method for reducing uninformative calls in non-invasive prenatal testing

Non-invasive prenatal testing or NIPT is currently among the top researched topic in obstetric care. While the performance of the current state-of-the-art NIPT solutions achieve high sensitivity and specificity, they still struggle with a considerable number of samples that cannot be concluded with certainty. Such uninformative results are often subject to repeated blood sampling and re-analysis, usually after two weeks, and this period may cause a stress to the future mothers as well as increase the overall cost of the test. We propose a supplementary method to traditional z-scores to reduce the number of such uninformative calls. The method is based on a novel analysis of the length profile of circulating cell free DNA which compares the change in such profiles when random-based and length-based elimination of some fragments is performed. The proposed method is not as accurate as the standard z-score; however, our results suggest that combination of these two independent methods correctly resolves a substantial portion of healthy samples with an uninformative result. Additionally, we discuss how the proposed method can be used to identify maternal aberrations, thus reducing the risk of false positive and false negative calls. Keywords: Next-generation sequencing, Cell-free DNA, Uninformative result, Method, Trisomy, Prenatal testin

Wasteland Beautiful : o estatuto ontológico da imagem nos mundos tridimensionais dos games

The paper presents the concept of the digital image in games as the result of an artistic process, digital and personified in the figure of the craftsman, which focuses its activity on a make-believe. The article is located within a proposed phenomenological thought that seeks to show the ontological structure that underlies the work with digital images and drawing / painting / color / dash / form in target quality, considering the production of games. Shows that the ontological contexts outlined are present unintentionally in public displays of development teams, analyzing and illustrating two exemplary examples in which the game chasing a homoiosis produced in relation to digital and historical tradition. Culminates in the defense of a research on the artistic production in games coupled with production processes and understanding games as an art form that speaks to today's man

Toward the understanding of fungal mixed culture solid substrate fermentation for cellulolytic enzyme production

博士論文 (Doctoral dissertation)doctoral thesi

Revue d'histoire du Bas-Saint-Laurent, vol. 14 (2)

Éditorial -- Enseignement -- Archéologie -- Mont Commis ou Mont Camille? -- Joachim Vautour, pêcheur résidant à Rimouski au XVIIIe siècle -- Les guerres du bois -- L'incorporation de Trois-Pistoles a donné lieu à une série de conflits (1916-1924) -- Chroniques rimouskoises -- Histoire orale -- Patrimoine -- Archives -- Des livres à lire! -- Photos ancienne