Miracle-dz/UniFAR-FTUs huggingface dataset:
Solvation in protein (un)folding of melittin tetramer–monomer transition

Protein structural integrity and flexibility are intimately tied to solvation. Here, we examine the effect that changes in bulk and local solvent properties have on protein structure and stability. We observe the change in solvation of an unfolding of the protein model, melittin, in the presence of a denaturant, trifluoroethanol. The peptide system displays a well defined transition in that the tetramer unfolds without disrupting the secondary or tertiary structure. In the absence of local structural perturbation, we are able to reveal exclusively the role of solvation dynamics in protein structure stabilization and the (un)folding pathway. A sudden retardation in solvent dynamics, which is coupled to the change in protein structure, is observed at a critical trifluoroethanol concentration. The large amplitude conformational changes are regulated by the local solvent hydrophobicity and bulk solvent viscosity.
Coffee residues as substrates for aroma production by Ceratocystis fimbriata in solid state fermentation

The ability of two different strains of Ceratocystis fimbriata for fruity aroma production by solid state fermentation (SSF) was tested on coffee pulp and coffee husk complemented with glucose as substrates. Experiments were carried out in 250 mL Erlenmeyer flasks and the experimental conditions were: 70% of initial moisture, 20% of glucose addition and pH 6.0. Aeration was made by passive diffusion through the gauze covering the flasks. Headspace analysis of the culture by gas chromatography (GC) showed that 12 compounds were produced with coffee husk. Maximum total volatiles (TV) concentration was reached after 72 h of culture with coffee husk as substrate (28 µmol.L-1.g-1). Ethyl acetate, ethanol and acetaldehyde were the major compounds produced, representing 84.7%, 7.6% and 2.0% of TV, respectively. A pre-treatment with heat (100oC/ 40 min) of substrates did not improve TV production. Respirometry analysis was used to determine the growth of the culture by measuring carbon dioxide produced. Results showed that the CO2 production follows the aroma production. This result shows the great potential for the use coffee pulp and coffee husk as substrates to microbial aroma production by solid state fermentation.
Influences on gene expression in vivo by a Shine–Dalgarno sequence

The Shine–Dalgarno (SD+: 5′‐AAGGAGG‐3′) sequence anchors the mRNA by base pairing to the 16S rRNA in the small ribosomal subunit during translation initiation. We have here compared how an SD+ sequence influences gene expression, if located upstream or downstream of an initiation codon. The positive effect of an upstream SD+ is confirmed. A downstream SD+ gives decreased gene expression. This effect is also valid for appropriately modified natural Escherichia coli genes. If an SD+ is placed between two potential initiation codons, initiation takes place predominantly at the second start site. The first start site is activated if the distance between this site and the downstream SD+ is enlarged and/or if the second start site is weakened. Upstream initiation is eliminated if a stable stem‐loop structure is placed between this SD+ and the upstream start site. The results suggest that the two start sites compete for ribosomes that bind to an SD+ located between them. A minor positive contribution to upstream initiation resulting from 3′ to 5′ ribosomal diffusion along the mRNA is suggested. Analysis of the E. coli K12 genome suggests that the SD+ or SD‐like sequences are systematically avoided in the early coding region suggesting an evolutionary significance.
The use of genre analysis in the design of electronic meeting systems

Introduccion. El analisis del genero es una aproximacion al estudio de los modelos de comunicacion y en consecuencia puede aplicarse al contexto especifico de las reuniones. Este estudio investiga el uso de analisis del genero en el diseno de sistemas de la reunion electronica. Fondo. El objetivo principal de analisis del genero es comprender como usan las comunidades virtuales la comunicacion digital para la colaboracion. Este conocimiento es fundamental para influenciar (informar) el diseno de sistemas de informacion, particularmente en areas donde son primordiales la comunicacion e informalidad. Sin embargo, la bibliografia de investigacion no informa sobre ningun experimento donde haya sido usado el analisis del genero para influenciar el diseno de sistemas de reunion electronicos. Problemas. El articulo aborda los siguientes problemas muy comunes encontrados en sistemas de reunion electronica actuales: (1) integracion organizativa reducida, descuidando muchas claves (senales) contextuales y factores explicativos necesarios para hacer utilizables los resultados de la reunion dentro de la organizacion; (2) falta de soporte para comunidades especificas de usuarios, haciendo hincapie en la dependencia de un facilitador para configurar y gestionar la tecnologia; y (3) falta de soporte para reuniones que abarcan largos periodos de tiempo. Conclusiones. El trabajo describe como se uso el analisis del genero para desarrollar sistemas de reunion electronicos para algunas organizaciones y reuniones de genero. Cubre el proceso de diseno completo, desde la elicitacion de genero a la validacion. Los resultados obtenidos demuestran que el enfoque de genero produce sistemas de reunion electronica enfocados en la integracion organizativa, pre-configurados a comunidades de usuarios, con soporte para el uso a largo plazo, y valor anadido organizativo.
High efficiency planar microcavity LED's: comparison of design and experiment

This paper describes the design of substrate emitting microcavity LED's and a comparison of experimental results with modeling results. The modeling is based on a simulation tool which accounts for guided modes, quantum well reabsorption and photon recycling. The overall quantum efficiencies of /spl lambda//2 and /spl lambda/ cavities both with a 60% and a 90% reflecting DBR mirror are compared and a good qualitative correspondence is found between theory and experiment. The maximum theoretical overall quantum efficiency for the considered structures is expected to be around 14%, whereas the best experimental value amounts to 10.2%. <<ETX>>
A Novel Multiplex Real-Time PCR Assay for the Concurrent Detection of Hepatitis A, B and C Viruses in Patients with Acute Hepatitis

A novel multiplex real-time PCR assay for concurrent detection of hepatitis viruses was evaluated for its clinical performance in screening patients with acute hepatitis. A total of 648 serum samples were collected from patients with acute symptoms of hepatitis. Concurrent detection of nucleic acids of HAV, HBV and HCV was performed using the Magicplex™ HepaTrio Real-time Detection test. Serum nucleic acid levels of HBV and HCV were also quantified by the Cobas® AmpliPrep/Cobas® TaqMan® (CAP/CTM) HBV and HCV tests. Patients’ medical records were also reviewed. Concordance rates between the results from the HepaTrio and the CAP/CTM tests for the detection of HBV and HCV were 94.9% (k = 0.88) and 99.2% (k = 0.98), respectively. The cycle threshold values with the HepaTrio test were also correlated well with the levels of HBV DNA (r = −0.9230) and HCV RNA (r = −0.8458). The sensitivity and specificity of the HepaTrio test were 93.8% and 98.2%, respectively, for detecting HBV infection, and 99.1% and 100.0%, respectively, for HCV infection. For the HepaTrio test, 21 (3.2%) cases were positive for both HBV and HCV. Among the positive cases, 6 (0.9%) were true coinfections. This test also detected 18 (2.8%) HAV positives. The HepaTrio test demonstrated good clinical performance and produced results that agreed well with those of the CAP/CTM assays, especially for the detection of HCV. This assay was also able to detect HAV RNA from anti-HAV IgM-positive individuals. Therefore, this new multiplex PCR assay could be useful for the concurrent detection of the three hepatitis viruses.
Learning Multiple Tasks using Shared Hypotheses

In this work we consider a setting where we have a very large number of related tasks with few examples from each individual task. Rather than either learning each task individually (and having a large generalization error) or learning all the tasks together using a single hypothesis (and suffering a potentially large inherent error), we consider learning a small pool of shared hypotheses. Each task is then mapped to a single hypothesis in the pool (hard association). We derive VC dimension generalization bounds for our model, based on the number of tasks, shared hypothesis and the VC dimension of the hypotheses class. We conducted experiments with both synthetic problems and sentiment of reviews, which strongly support our approach.
Estimating Reaction Plan Size

The Shannon/Ginsberg circuit size estimate, by assuming independence of Boolean inputs, is not usable as a plan size estimate. By re-estimating circuit size as a function of the number of combinations w of Boolean inputs, I show that a reaction plan over w world states should grow as O(w/log w), on average. However, in a Blocks World containing N blocks and w ≈ NN world states, actual Universal Plans grow only as O(N3). This difference is shown to be attributable to the Universal Plans' use of dynamically bound object variables. Finally I obtain the general domain-independent result that for a domain containing w world states, the expected size of a reaction plan with variables is O((w/log w)1/log p(p+(b-1)v)) where p is the number of preconditions per operator, v is the number of those preconditions that introduce an unbound variable, and b is the number of possible bindings per variable. The exponent is ≤ 1 and allows this formula to predict plan size reductions of many orders of magnitude.
The Printed Reverberation Board and the Extraction of IC Noise Models Above 1 GHz

A new approach to integrated circuit (IC) noise modeling using a single current source for the whole area below the IC on a printed circuit board (PCB) is proposed. This approach extends the frequency of application of similar models in the literature by focusing on the current and power injected into the region outside the IC perimeter. A new measurement equipment for IC electromagnetic compatibility tests above 1 GHz is proposed; the printed reverberation board (PRB). A statistical model for characterizing the PRB is presented and confirmed by measurement results. Limitations of the fabricated PRB prototype and possible improvements are discussed. A new random IC model that includes the random properties of the IC noise is introduced. A methodology to extract the IC model by means of the PRB is presented. An active test PCB has been designed and fabricated to verify the feasibility of the modeling and measurement methods. Measurement results corroborated the validity of the new measurement and modeling approaches on one side, and on the other side showed that further studies are required.
Describing the hexapeptide identity platform between the influenza A H5N1 and Homo sapiens proteomes

We searched the primary sequence of influenza A H5N1 polyprotein for hexamer amino acid sequences shared with human proteins using the Protein International Resource database and the exact peptide matching analysis program. We find that the viral polyprotein shares numerous hexapeptides with the human proteome. The human proteins involved in the viral overlap are represented by antigens associated with basic cell functions such as proliferation, development, and differentiation. Of special importance, many human proteins that share peptide sequences with influenza A polyprotein are antigens such as reelin, neurexin I-α, myosin-IXa, Bardet–Biedl syndrome 10 protein, Williams syndrome transcription factor, disrupted in schizophrenia 1 protein, amyotrophic lateral sclerosis 2 chromosomal region candidate gene 17 protein, fragile X mental retardation 2 protein, and jouberin. That is, the viral-vs-human overlap involves human proteins that, when altered, have been reported to be potentially associated with multiple neurological disorders that can include autism, epilepsy, obesity, dystonia, ataxia–telangiectasia, amyotrophic lateral sclerosis, sensorineural deafness, sudden infant death syndrome, Charcot-Marie-Tooth disease, and myelination. The present data are discussed as a possible molecular basis for understanding influenza A viral escape from immunosurveillance and for defining anti-influenza immune-therapeutic approaches devoid of collateral adverse events.
Classification of Sparse and Irregularly Sampled Time Series with Mixtures of Expected Gaussian Kernels and Random Features

This paper presents a kernel-based framework for classification of sparse and irregularly sampled time series. The properties of such time series can result in substantial uncertainty about the values of the underlying temporal processes, while making the data difficult to deal with using standard classification methods that assume fixed-dimensional feature spaces. To address these challenges, we propose to first re-represent each time series through the Gaussian process (GP) posterior it induces under a GP regression model. We then define kernels over the space of GP posteriors and apply standard kernel-based classification. Our primary contributions are (i) the development of a kernel between GPs based on the mixture of kernels between their finite marginals, (ii) the development and analysis of extensions of random Fourier features for scaling the proposed kernel to large-scale data, and (iii) an extensive empirical analysis of both the classification performance and scalability of our proposed approach.
Algebraic Multigrid Preconditioner for the Cardiac Bidomain Model

The bidomain equations are considered to be one of the most complete descriptions of the electrical activity in cardiac tissue, but large scale simulations, as resulting from discretization of an entire heart, remain a computational challenge due to the elliptic portion of the problem, the part associated with solving the extracellular potential. In such cases, the use of iterative solvers and parallel computing environments are mandatory to make parameter studies feasible. The preconditioned conjugate gradient (PCG) method is a standard choice for this problem. Although robust, its efficiency greatly depends on the choice of preconditioner. On structured grids, it has been demonstrated that a geometric multigrid preconditioner performs significantly better than an incomplete LU (ILU) preconditioner. However, unstructured grids are often preferred to better represent organ boundaries and allow for coarser discretization in the bath far from cardiac surfaces. Under these circumstances, algebraic multigrid (AMG) methods are advantageous since they compute coarser levels directly from the system matrix itself, thus avoiding the complexity of explicitly generating coarser, geometric grids. In this paper, the performance of an AMG preconditioner (BoomerAMG) is compared with that of the standard ILU preconditioner and a direct solver. BoomerAMG is used in two different ways, as a preconditioner and as a standalone solver. Two 3-D simulation examples modeling the induction of arrhythmias in rabbit ventricles were used to measure performance in both sequential and parallel simulations. It is shown that the AMG preconditioner is very well suited for the solution of the bidomain equation, being clearly superior to ILU preconditioning in all regards, with speedups by factors in the range 5.9-7.7
Analytic Phase-based Representation for Face Recognition

A representation based on the phase of analytic image is proposed to address the issue of illumination variation in face recognition task. The problem of unwrapping in the computation of analytic phase is avoided by using trigonometric functions of phase. Template matching is used to compare the functions of analytic phase for face recognition. For template matching, the functions of the analytic phase are compressed using eigenanalysis. Performance of the face recognition is improved by using weights derived from the eigenvalues in the template matching.
Transapical implantation of a Melody valve in a degenerated low-diameter prosthetic aortic valve.

78-year-old woman had undergone a biological aortic valve replacement (Mitroflow Pericardial, Sorin Inc, Burnaby, BC, Canada) and coronary artery bypass graft surgery 8 years previously. Acute exacerbation of her symptoms resulting from prosthetic aortic valve stenosis caused respiratory failure, necessitating resuscitation and mechanical ventilation. A transthoracic Doppler echocardiogram demonstrated peak and mean prosthetic aortic valve gradients of 70 and 51 mm Hg, respectively, and a calculated valve area of 0.5cm 2 (Figure 1). Coronary angiography demonstrated triple-vessel disease and 3 patent grafts to all coronary territories. Although the need for a tracheostomy and the seeming adherence of patent grafts to the sternal plate precluded conventional surgical intervention, the prosthetic valve size of 19 mm deemed the patient unsuitable for a conventional transcatheter aortic valve implantation. A Melody valve (Medtronic Inc, Santa Ana, CA), because of its suitability for annular diameters of 16 to 22 mm, was a possible solution. A surgical transapical approach was chosen because of the limitations of the Melody transvenous delivery system, poor vascular access, and the need for absolute control during the procedure. A pediatric cardiologist (E.B.) familiar with the Melody system was integrated into the team. The valve delivery system, Ensemble, is a balloon-in-balloon over-the-wire catheter onto which the valve is hand crimped. The level of expansion of the valve is determined by the size of the outer balloon used for inflation (range, 18–22 mm). The balloon and Melody valve are covered by a movable sleeve that is retracted before positioning and deployment with 22F profile that could easily be advanced through a 24F Ascendra-2 transapical sheath (Ascendra Inc, Reston, VA) originally designed for Edwards-XT transcatheter aortic valve implantation with its radiopaque markers and a reliable hemostatic seal. The femoral vessels were accessed for transvenous pacing and an aortic root marker pigtail catheter. The working angle was determined to be perpendicular to the Mitroflow ring (Figures 2 and 3). To avoid unequal valve expansion and to verify the true inner diameter of Mitroflow, we predilated the stenotic valve with a Nucleus 18-mm balloon (NuMed Inc, Hopkington, NY; Figure 4). After the valvuloplasty, the Melody delivery system was introduced via the Ascendra-2 sheath and positioned in a 50:50 position through the valve
Association Between Posterior Left Atrial Adipose Tissue Mass and Atrial Fibrillation

Background— Epicardial adipose tissue located close to the atrial wall can change the electric conduction of the left atrium, potentially leading to atrial fibrillation (AF). The aim of this study was to assess whether an increased atrial adipose tissue mass posterior to the left atrium is related to AF independent of demographical and cardiovascular risk factors. Methods and Results— Two hundred patients with AF and 200 patients without AF who underwent computed tomographic angiography were included. The posterior left atrial adipose tissue mass was quantified on computed tomographic angiography images as tissue with Hounsfield Units between −195 and −45. The adipose tissue mass was significantly larger in patients with AF compared with patients with sinus rhythm: 10.6±5.5 versus 4.7±3.5 g, P<0.001. In a multiple variable model (including age, body mass index, sex, coronary artery calcium score, diabetes mellitus, hypertension, hypercholesterolemia, family history of coronary artery disease, and known coronary artery disease), each gram increase of posterior left atrial adipose tissue was associated with 1.32 odds ratio of having AF (95% confidence interval, 1.22–1.43; P<0.001). Furthermore, the addition of the adipose tissue mass to the multiple variable analysis significantly increased the discriminatory ability to predict AF: increase in the area under the receiver operating characteristic, 0.88 (95% confidence interval, 0.84–0.91) versus 0.81 (0.76–0.85), P<0.001. Conclusions— Posterior left atrial adipose tissue mass is significantly larger in patients with AF versus without AF. An increase in adipose tissue was independently associated with AF and provided incremental value over well-known predictors of AF. These findings add to the hypothesis that the posterior left atrial adipose tissue mass contributes to structural and electric remodeling leading to AF.
Characterisation and Comparison of Lactating Mouse and Bovine Mammary Gland miRNomes

Background The mammary gland is a dynamic organ that undergoes important physiological changes during reproductive cycles. Until now, data regarding the characterisation of miRNA in the mammary gland have been scarce and mainly focused on their abnormal expression in breast cancer. Our goal was to characterise the microRNA (miRNA) involved in mechanisms regulating the mammary function, with particular focus on the lactation stage. Methodology/principal findings Using high-throughput sequencing technology, the exhaustive repertoires of miRNA expressed (miRNome) in mouse and bovine mammary glands during established lactation were identified, characterized and compared. Furthermore, in order to obtain more information on miRNA loading in the RNA-induced silencing complex (RISC), the miRNome was compared with that obtained from RNA associated with the AGO2 protein (AGO2-miRNome) in mouse lactating mammary gland. This study enabled the identification of 164 and 167 miRNA in mouse and bovine, respectively. Among the 30 miRNA most highly expressed in each species, 24 were common to both species and six of them were preferentially highly expressed in lactating than non-lactating mammary gland. The potential functional roles of these 24 miRNA were deduced using DIANA-miRPath software, based on miRNA/mRNA interactions. Moreover, seven putative novel miRNA were identified. Using DAVID analysis, it was concluded that the predicted targets of two of these putative novel miRNA are involved in mammary gland morphogenesis. Conclusion/significance Our study provides an overview of the characteristics of lactating mouse and bovine mammary gland miRNA expression profiles. Moreover, species-conserved miRNA involved in this fundamental biological function were identified. These miRNomes will now be used as references for further studies during which the impact of animal breeding on the miRNA expression will be analysed.