Miracle-dz/UniFAR-FTUs huggingface dataset:
Susceptibility testing of multidrug-resistant Staphylococcus aureus with the Sceptor microdilution system

The antimicrobial susceptibilities of Staphylococcus aureus isolates were concurrently determined by the Sceptor system (BBL Microbiology Systems, Cockeysville, Md.) and by the standard disk diffusion method. For the methicillin-resistant isolates, there was greater than 98% agreement between the two test results with penicillin G, erythromycin, clindamycin, tetracycline, gentamicin, and tobramycin. Major disagreements (susceptible by one method and resistant by the other) were 7% for methicillin, 13.5% for cephalothin, 3.5% for cefamandole, and 27% for amikacin. The major discrepancies for methicillin were eliminated by supplementing the inoculum broth with salt. For methicillin-susceptible isolates, agreement between the two methods was 96 to 100% for all antibiotics except amikacin.
A Cdc28 Mutant Uncouples G1 Cyclin Phosphorylation and Ubiquitination from G1 Cyclin Proteolysis*

Proteolysis of the yeast G1cyclins is triggered by their Cdc28-dependent phosphorylation. Phosphorylated Cln1 and Cln2 are ubiquitinated by the SCF-Grr1 complex and then degraded by the 26 S proteasome. In this study, we identified a cak1 allele in a genetic screen for mutants that stabilize the yeast G1 cyclins. Further characterization showed that Cln2HA was hypophosphorylated, unable to bind Cdc28, and stabilized in cak1 mutants at the restrictive temperature. Hypophosphorylation of Cln2HA could thus explain its stabilization. To test this possibility, we expressed a Cak1-independent mutant of Cdc28 (Cdc28-43244) in cak1mutants and found that Cln2HA phosphorylation was restored, but surprisingly, the phospho-Cln2HA was stabilized. When bound to Cdc28-43244, Cln2HA was recognized and polyubiquitinated by SCF-Grr1. The Cdc28-43244 mutant thus reveals an unexpected complexity in the degradation of polyubiquitinated Cln2HA by the proteasome.
Template Requirements for RNA Synthesis by a Recombinant Hepatitis C Virus RNA-Dependent RNA Polymerase

ABSTRACT The RNA-dependent RNA polymerase (RdRp) from hepatitis C virus (HCV), nonstructural protein 5B (NS5B), has recently been shown to direct de novo initiation using a number of complex RNA templates. In this study, we analyzed the features in simple RNA templates that are required to direct de novo initiation of RNA synthesis by HCV NS5B. NS5B was found to protect RNA fragments of 8 to 10 nucleotides (nt) from RNase digestion. However, NS5B could not direct RNA synthesis unless the template contained a stable secondary structure and a single-stranded sequence that contained at least one 3′ cytidylate. The structure of a 25-nt template, named SLD3, was determined by nuclear magnetic resonance spectroscopy to contain an 8-bp stem and a 6-nt single-stranded sequence. Systematic analysis of changes in SLD3 revealed which features in the stem, loop, and 3′ single-stranded sequence were required for efficient RNA synthesis. Also, chimeric molecules composed of DNA and RNA demonstrated that a DNA molecule containing a 3′-terminal ribocytidylate was able to direct RNA synthesis as efficiently as a sequence composed entirely of RNA. These results define the template sequence and structure sufficient to direct the de novo initiation of RNA synthesis by HCV RdRp.
Does Biomedicine Entail the Successful Reduction of Pathology to Biology?

The idea of reducing pathology to biology has an extensive history, and the initial forms of the enterprise were unsuccessful. This article discusses the philosophical literature surrounding the notion of reduction in the sciences in general and of biology in particular; reviews several 19th-century programs that promoted the reduction of medicine to other biological disciplines; and examines the post-war origins of the notion of biomedicine. It shows how biology and medicine tend to interact in the constitution of new biomedical knowledge and how the notion of a pathological process resulting in a lesion remains central to the understanding of disease. The article proposes that while strict reduction has yet to be realized, one can speak of a continuing and successful realignment of biology and pathology since the Second World War.
Measurement of infrared absorption spectra by absorption on Japanese hand-made paper and its application to paper chromatography.

Minimization of samples for infrared spectral measurement was attempted by the use of a Japanese folkcraft, hand-made paper, impregnated with liquid paraffin. By this method, it is possible to measure 0.1 mg. of a sample. This hand-made paper was also used for paper chromatography and the developed paper was submitted directly to infrared spectral measurement. Component of Penicillium islandicun and inorganic sulfate ion were determined by spectral measurement of their chromatogram.
Tangible mixed reality desktop for digital media management

This paper presents a tangible mixed reality desktop that supports gesture-oriented interactions in 3D space. The system is based on computer vision techniques for hand and finger detection, without the need for attaching any devices to the user. The system consists of a pair of stereo cameras that point to a planar surface as the work bench. Using stereo triangulation, the 3D locations and directions of the user's fingers are detected and tracked in the space on and above the surface. Based on our 3D finger tracking technique, we design a few simple multi-finger gestural interactions for digital media management. The system provides a convenient and user-friendly way of manipulating virtual objects in 3D space and supports seamless interactions with physical objects.
silages by mixed ruminal microorganisms in vitro Influence of supplementary fibrolytic enzymes on the fermentation of corn and grass 2001

This study was done to determine the effectiveness of supplementary enzymes at increasing the fiber digestion by ruminal microorganisms and to assess whether enzyme activity limits the rate of fiber digestion in ruminal digesta. In vitro comparisons of enzyme activities in two feed enzyme preparations (A and B) with enzyme activities extracted from ruminal fluid indicated that the addition of fibrolytic enzymes at the application rates recommended by the manufacturers would not be expected to increase significantly glycanase and polysaccharidase activities in ruminal fluid. Preparations A and B both increased (P < 0.001) the rate of gas production from freeze-dried corn and grass silages in in vitro incubations with ruminal fluid, but only at concentrations much higher than recommended application rates. Autoclaved controls had little or no effect. Ultrafiltration of enzyme B indicated that most stimulation was due to components >100 kDa, which is consistent with the cause of the stimulation being enzyme activity. Fibrolytic enzymes from other sources were also able to stimulate gas production: increased rates of gas production were observed in seven
Manipulator motion planning with unconstrained end-effector under obstacle environment

This paper proposes a novel way of carrying out manipulator motion planning with unconstrained end-effector (MMP-UE) under an obstacle environment, where an unconstrained end-effector implies that the end-effector can be displaced from the target object. We introduce two kinds of manipulator motion planning methods: the -based MMP-UE method and the -based MMP-UE method. The former finds a solution path for manipulator motion planning in the configuration space iteratively by extending the terminal trees in the constraint-satisfying subspace and a messenger tree in the configuration space and by connecting the terminal trees and the messenger tree to each other. The latter finds a solution path for manipulator motion planning in the task space by incrementally and randomly generating an extended point that can be added to the current master tree, finding the nearest point in the current master tree from the generated extended point, generating a set of reachable configurations that corresponds to the generated extended point, checking whether two consecutive sets of reachable configurations and are connectable, and finally extending the current slave and master tree if the consecutive sets of reachable configurations are connectable. We evaluated the performance of the two proposed methods in terms of the number of iterations, number of samples, number of generated nodes, and the total computation time through three different experiments: a toy train tunnel passing simulation, a wheel turning simulation, and a basket tunnel passing experiment using a real robot. The experimental results indicate that the two proposed methods succeed in finding the solution paths in all the experiments and that the -based MMP-UE method is faster and requires less storage than the -based MMP-UE method. Graphical Abstract
Intermittent behavior in slow drainage.

The water pressure measured during slow, constant rate drainage in a two-dimensional porous model exhibits sudden jumps as bursts of air quickly displace water from a region. The measured size distribution of the pressure jumps is exponential. Invasion percolation (IP) simulations give a power-law size distribution of the connected regions invaded in bursts. In the experiments the meniscii of the fluid-fluid front adjust during a burst, causing the capillary pressure to decrease. Including this effect in a modified invasion percolation algorithm causes potentially large bursts to split up into smaller bursts that are exponentially distributed. From the experimental pressure curve it is possible to identify groups of bursts that would become a single, ``composite'' burst in a larger system. These composite bursts are power-law distributed, consistent with simulations and percolation theory. Different versions of the IP model result in different structures and power-law exponents. The best choice of model for the present experiment is discussed. \textcopyright{} 1996 The American Physical Society.
Style Congruency and Persuasion: A Cross-cultural Study Into the Influence of Differences in Style Dimensions on the Persuasiveness of Business Newsletters in Great Britain and the Netherlands

Research problem: The purpose of the present study was to investigate whether style congruency on the dimensions succinct-elaborate and instrumental-affective influenced the persuasiveness of business newsletters in the Netherlands and Great Britain. Research question: Is a writing style more persuasive in a country with cultural preferences that are congruent with this writing style? Literature review: The purpose of the literature review was to present two theoretical frameworks for investigating cross-cultural differences in style preferences. Theories about cross-cultural differences in value orientations show that value orientations can be linked to cross-cultural differences in persuasion. Theories about cross-cultural differences in communication styles show that preferences for particular communication styles can be linked to cultural value orientations. Methodology: Two quantitative experimental studies were conducted among 344 business-to-business customers of a company in the Netherlands and Great Britain. Using seven-point scales, participants evaluated different versions of a newsletter on comprehensibility, attractiveness, and intention to order goods. Statistical analyses included general linear model (GLM) repeated measures and two-way ANOVAs. Results and discussion: Findings reveal limited differences between the Dutch and British participants in preferences for communication styles. Consequently, it may not be worthwhile for organizations to adjust the style of their documents to preferences in different cultures. A limitation of the current study was that it only investigated style preferences for one particular business genre (i.e., newsletters). Future research should investigate stylistic preferences in other business genres and in other cultures.
Extraction des zones urbaines fondée sur une analyse de la texture par modélisation markovienne

Pour delimiter un masque urbain precis a partir d'une image satellitaire la seule information du niveau de gris est insuffisante. Laplupart des methodes font donc appel a une analyse de la texture de l'image. Nous nous sommes places dans ce cadre. Dans une premiere etape, nous avons defini un nouveau parametre de texture a partir d'un modele markovien gaussien. Nous obtenons ce nouveau parametre en calculant la variance conditionnelle de l'image dans huit directions. Ainsi, nous eliminons la mauvaise classification d'objets ayant une orientation privilegiee tels que les vignes et les serres par exemple. Dans une seconde etape, nous proposons un algorithme de \emph{fuzzy Cmeans} modifie incluant un terme d'entropie et pour lequel le nombre de classes n'est pas fixe a priori. Cet algorithme nous permet d'obtenir une premiere classification de l'image. Enfin, nous regularisons l'image ainsi obtenue grâce a une modelisation par champs de Markov. Des resultats obtenus sur des simulations d'images SPOT5 fournies par le CNES sont presentes.
Quantification method in [18F]fluorodeoxyglucose brain positron emission tomography using independent component analysis

ObjectiveTo extract accurate image-derived input functions from dynamic brain positron emission tomography images (DBPIs) using independent component analysis (ICA). MethodsA modified linear model with haematocrit correction was used to improve the accuracy of input functions estimated by independent component analysis and to reduce the error of quantitative analysis. Two types of material were examined: (1) a simulated dynamic phantom with a three-compartment, four-parameter model; (2) clinical 2-h DBPIs with a standard plasma sampling procedure. The input function was extracted from DBPIs using independent component analysis. The modified linear model with haematocrit correction was used to obtain the independent component analysis-estimated input function (Iica). For comparison, the input function derived from the last three blood samples (Iest) was used. The image-derived input functions (Iica and Iest) were compared with the input function from blood sampling (Itp). The mean percentage error of the metabolic rate of [18F]-2-fluoro-2-deoxy-D-glucose (MRFDG) was calculated for both Iica and Iest against that of Itp. ResultsIn simulated studies, the mean percentage errors of MRFDG between true simulated and estimated values of Iest and Iica were 8.2% and 4.2%, respectively. In clinical studies, six clinical cases were collected. The mean percentage errors and standard deviations of MRFDG with Iest and Iica were 12.6±7.5% and 7.7±3.3%, respectively. ConclusionsWe have proposed a technique for estimating image-derived input functions using independent component analysis without blood sampling. The results of our method were highly correlated with those from standard blood sampling, and more accurate than those of other methods proposed previously.
Microcomputer system for ion microscopy digital imaging and processing

Analytical ion microscopy is a powerful tool for biological tissue analysis as it allows direct chemical distribution imaging, even at low element concentrations. A microcomputer based digital imaging system achieving acquisition at low light level is presented. It includes a high sensitivity video camera connected to a specialized image processor subsystem. Acquired images consist of 512 times 512 pixels with 8 bits accuracy. Real‐time image processing software has been implemented so that image processing may be performed on‐line. Image processing software allows off‐line image manipulation and correlation for biological interpretation of elemental mapping images. System capabilities are illustrated by a study of stable and radio iodine mapping in rat thyroid tissue.
NarE: a novel ADP‐ribosyltransferase from Neisseria meningitidis

Mono ADP‐ribosyltransferases (ADPRTs) are a class of functionally conserved enzymes present in prokaryotic and eukaryotic organisms. In bacteria, these enzymes often act as potent toxins and play an important role in pathogenesis. Here we report a profile‐based computational approach that, assisted by secondary structure predictions, has allowed the identification of a previously undiscovered ADP‐ribosyltransferase in Neisseria meningitidis (NarE). NarE shows structural homologies with E. coli heat‐labile enterotoxin (LT) and cholera toxin (CT) and possesses ADP‐ribosylating and NAD‐glycohydrolase activities. As in the case of LT and CT, NarE catalyses the transfer of the ADP‐ribose moiety to arginine residues. Despite the absence of a signal peptide, the protein is efficiently exported into the periplasm of Neisseria. The narE gene is present in 25 out of 43 strains analysed, is always present in ET‐5 and Lineage 3 but absent in ET‐37 and Cluster A4 hypervirulent lineages. When present, the gene is 100% conserved in sequence and is inserted upstream of and co‐transcribed with the lipoamide dehydrogenase E3 gene. Possible roles in the pathogenesis of N. meningitidis are discussed.
ECONOMICAL MEMORY MANAGEMENT FOR AVIONICS SYSTEMS

Unlike old-fashioned aircrafts that almost did not have avionics systems, up to date aircrafts have numerous avionics systems. Nearly all new aircrafts have devices for navigation, automatic flight control, collision avoidance systems, flight data recorder, weather radar system in addition to communication and monitoring systems. All of these devices employ embedded computer systems with growing memory requirements. To facilitate reduction of the electricity power required for these devices, detecting the portions of the computer memory that are currently not in use is suggested. The unused portions can be temporarily shut down and after that turn them on when they are required again. Such a power cut can greatly lower the electricity consumption of the aircraft's avionics devices.
Minimum energy point tracking using combined dynamic voltage scaling and adaptive body biasing

Scaling the supply voltage (VDD) and threshold voltage (VTH) for minimizing the energy consumption of processors dynamically is highly desired for applications such as wireless sensor network and Internet of Things (IoT). In this paper, we refer to the pair of VDD and VTH, which minimizes the energy consumption of the processor under a given operating condition, as a minimum energy point (MEP). Since the MEP is heavily dependent on an operating condition determined by a chip temperature, an activity factor, and a performance required for the processor, it is not very easy to closely track the MEP at run-time. In this paper, a simple but effective algorithm for dynamically tracking the MEP of a processor under a situation that the operating condition of the processor dynamically varies is proposed. Gate-level simulation of a 32-bit RISC processor in a 65nm process demonstrates that the proposed algorithm tracks the MEP under a wide variety of dynamically changing operating conditions.
Otimização de biscoito tipo cookie à base de quinoa (Chenopodium quinoa Willd.) utilizando planejamento experimental de mistura

A quinoa (Chenopodium quinoa Willd) e um pseudocereal de origem andina, designado como alimento funcional. A adicao de quinoa como ingrediente de produtos de panificacao afeta positivamente as caracteristicas reologicas das massas devido a propriedades tecnologicas de suas sementes como solubilidade, capacidade de retencao de agua, de geleificacao e de emulsificacao. O presente estudo foi desenvolvido com o objetivo de formular um bicoito tipo cookie a base de quinoa isento de gluten, com valor nutricional agregado e boa aceitacao sensorial. A partir de um planejamento experimental de misturas completo, foram desenvolvidas 14 formulacoes com diferentes proporcoes da mistura ternaria, composta por farinha de quinoa (FI), flocos de quinoa (FL) e amido de milho (CS), a qual correspondeu a 55,7% do total em cada formulacao. A receita base (acucar, sal, agua, fermento, oleo e ovo desidratado) foi mantida constante em todos os ensaios. As formulacoes foram caracterizadas quanto aos parâmetros fisicos de cor, dureza e volume especifico (variaveis dependentes) e a partir das analises dos efeitos de cada ingrediente da mistura, foram geradas equacoes de modelos cubicos completos que se ajustaram aos dados experimentais (R2≥0,94). O CS apresentou efeito positivo na luminosidade dos biscoitos, porem proporcoes aumentadas de FQ e FLQ resultaram em cookies mais escuros. FQ apresentou efeito negativo no volume especifico dos biscoitos a medida que suas concentracoes aumentaram na mistura, em relacao FLQ e CS. No entanto, FQ e FLQ tiveram efeito sinergico positivo na dureza dos cookies. Com base nos modelos gerados e no perfil de desejabilidade, foi desenhada uma formulacao otimizada para os parâmetros analisados,composta por 30% de FQ, 25% de FLQ e 45% de CS. As analises da formulacao otimizada caracterizaram o cookie de quinoa como um produto rico em fibra alimentar (11%), fonte de aminoacidos essenciais, acido linolenico e minerais. O cookie a base de quinoa isento de gluten formulado foi bem aceito pelos provadores com aceitacao (7,0) revelando seu potencial de consumo. Considerando as caracteristicas nutricionais do biscoito de quinoa otimizado, com destaque na sua composicao de acidos graxos, teor de fibras, minerais e perfil aminoacidico, os resultados deste estudo indicam a quinoa como um importante ingrediente promissor para enriquecimento nutricional de produtos de panificacao, em especial biscoitos do tipo cookies.
A FAST AND EFFICIENT HEURISTIC NUCLEAR-NORM ALGORITHM FOR AFFINE RANKMINIMIZATION

The problem of affine rank minimization seeks to find the minimum rank matrix that satisfies a set of linear equality constraints. Generally, since affine rank minimization is NP-hard, a popular heuristic method is to minimize the nuclear norm that is a sum of singular values of the matrix variable [1]. A recent intriguing paper [2] shows that if the linear transform that defines the set of equality constraints is nearly isometrically distributed and the number of constraints is at least O(r(m + n) log mn), where r and m × n are the rank and size of the minimum rank matrix, minimizing the nuclear norm yields exactly the minimum rank matrix solution. Unfortunately, it takes a large amount of computational complexity and memory buffering to solve the nuclear norm minimization problem with known nearly isometric transforms. This paper presents a fast and efficient algorithm for nuclear norm minimization that employs structurally random matrices [3] for its linear transform and a projected subgradient method that exploits the unique features of structurally random matrices to substantially speed up the optimization process. Theoretically, we show that nuclear norm minimization using structurally random linear constraints guarantees the minimum rank matrix solution if the number of linear constraints is at least O(r(m+n) log mn). Extensive simulations verify that structurally random transforms still retain optimal performance while their implementation complexity is just a fraction of that of completely random transforms, making them promising candidates for large scale applications.