Miracle-dz/UniFAR-FTUs huggingface dataset:
An Escherichia coli Nissle 1917 Missense Mutant Colonizes the Streptomycin-Treated Mouse Intestine Better than the Wild Type but Is Not a Better Probiotic

ABSTRACT Previously we reported that the streptomycin-treated mouse intestine selected for two different Escherichia coli MG1655 mutants with improved colonizing ability: nonmotile E. coli MG1655 flhDC deletion mutants that grew 15% faster in vitro in mouse cecal mucus and motile E. coli MG1655 envZ missense mutants that grew slower in vitro in mouse cecal mucus yet were able to cocolonize with the faster-growing flhDC mutants. The E. coli MG1655 envZ gene encodes a histidine kinase that is a member of the envZ-ompR two-component signal transduction system, which regulates outer membrane protein profiles. In the present investigation, the envZ P41L gene was transferred from the intestinally selected E. coli MG1655 mutant to E. coli Nissle 1917, a human probiotic strain used to treat gastrointestinal infections. Both the E. coli MG1655 and E. coli Nissle 1917 strains containing envZ P41L produced more phosphorylated OmpR than their parents. The E. coli Nissle 1917 strain containing envZ P41L also became more resistant to bile salts and colicin V and grew 50% slower in vitro in mucus and 15% to 30% slower on several sugars present in mucus, yet it was a 10-fold better colonizer than E. coli Nissle 1917. However, E. coli Nissle 1917 envZ P41L was not better at preventing colonization by enterohemorrhagic E. coli EDL933. The data can be explained according to our “restaurant” hypothesis for commensal E. coli strains, i.e., that they colonize the intestine as sessile members of mixed biofilms, obtaining the sugars they need for growth locally, but compete for sugars with invading E. coli pathogens planktonically.
Efficient construction of metadata-enhanced web corpora

Metadata extraction is known to be a problem in general-purpose Web corpora, and so is extensive crawling with little yield. The contributions of this paper are threefold: a method to find and download large numbers of WordPress pages; a targeted extraction of content featuring much needed metadata; and an analysis of the documents in the corpus with insights of actual blog uses. The study focuses on a publishing software (WordPress), which allows for reliable extraction of structural elements such as metadata, posts, and comments. The download of about 9 million documents in the course of two experiments leads after processing to 2.7 billion tokens with usable metadata. This comparatively high yield is a step towards more efficiency with respect to machine power and " Hi-Fi " web corpora. The resulting corpus complies with formal requirements on metadata-enhanced corpora and on weblogs considered as a series of dated entries. However, existing typologies on Web texts have to be revised in the light of this hybrid genre.
Measure and conquer: a simple O(20.288n) independent set algorithm

For more than 30 years Davis-Putnam-style exponential-time backtracking algorithms have been the most common tools used for finding exact solutions of NP-hard problems. Despite of that, the way to analyze such recursive algorithms is still far from producing tight worst case running time bounds.The "Measure and Conquer" approach is one of the recent attempts to step beyond such limitations. The approach is based on the choice of the measure of the subproblems recursively generated by the algorithm considered; this measure is used to lower bound the progress made by the algorithm at each branching step. A good choice of the measure can lead to a significantly better worst case time analysis.In this paper we apply "Measure and Conquer" to the analysis of a very simple backtracking algorithm solving the well-studied maximum independent set problem. The result of the analysis is striking: the running time of the algorithm is O(20.288n), which is competitive with the current best time bounds obtained with far more complicated algorithms (and naive analysis). Our example shows that a good choice of the measure, made in the very first stages of exact algorithms design, can have a tremendous impact on the running time bounds achievable.
Structure-activity Relationships in Flexible Protein Domains : Regulation of rho GTPases by RhoGDI and D 4 GDI

0022-2836/01/010121±15 $35.00/0 The guanine dissociation inhibitors RhoGDI and D4GDI inhibit guanosine 50-diphosphate dissociation from Rho GTPases, keeping these small GTPases in an inactive state. The GDIs are made up of two domains: a ̄exible N-terminal domain of about 70 amino acid residues and a folded 134-residue C-terminal domain. Here, we characterize the conformation of the N-terminal regions of both RhoGDI and D4GDI using a series of NMR experiments which include N relaxation and amide solvent accessibility measurements. In each protein, two regions with tendencies to form helices are identi®ed: residues 36 to 58 and 9 to 20 in RhoGDI, and residues 36 to 57 and 20 to 25 in D4GDI. To examine the functional roles of the N-terminal domain of RhoGDI, in vitro and in vivo functional assays have been carried out with N-terminally truncated proteins. These studies show that the ®rst 30 amino acid residues are not required for inhibition of GDP dissociation but appear to be important for GTP hydrolysis, whilst removal of the ®rst 41 residues completely abolish the ability of RhoGDI to inhibit GDP dissociation. The combination of structural and functional studies allows us to explain why RhoGDI and D4GDI are able to interact in similar ways with the guanosine 50-diphosphate-bound GTPase, but differ in their ability to regulate GTP-bound forms; these functional differences are attributed to the conformational differences of the N-terminal domains of the guanosine 50-diphosphate dissociation inhibitors. Therefore, the two transient helices, appear to be associated with different biological effects of RhoGDI, providing a clear example of structure-activity relationships in a ̄exible protein domain. # 2001 Academic Press
Estimation of Non-Normalized Statistical Models by Score Matching

One often wants to estimate statistical models where the probability density function is known only up to a multiplicative normalization constant. Typically, one then has to resort to Markov Chain Monte Carlo methods, or approximations of the normalization constant. Here, we propose that such models can be estimated by minimizing the expected squared distance between the gradient of the log-density given by the model and the gradient of the log-density of the observed data. While the estimation of the gradient of log-density function is, in principle, a very difficult non-parametric problem, we prove a surprising result that gives a simple formula for this objective function. The density function of the observed data does not appear in this formula, which simplifies to a sample average of a sum of some derivatives of the log-density given by the model. The validity of the method is demonstrated on multivariate Gaussian and independent component analysis models, and by estimating an overcomplete filter set for natural image data.
Bipolar OxRRAM memory array reliability evaluation based on fault injection

In this paper, a fault injection and simulation approach is used to study effects of resistive and capacitive defects on the faulty behavior of Oxide-based Resistive Memory RAM devices (OxRRAM). During the memory operations, logical and electrical characteristics of each memory cell of an elementary array are evaluated by using a bipolar OxRRAM compact model calibrated on actual devices. Simulation results are analyzed in terms of OxRRAM electrical characteristic variations to evaluate the robustness of the memory array against injected defects, inherent to the routing circuitry.
A unified framework and algorithm for (T/F/C)DMA channel assignment in wireless networks

Channel assignment problems in the time, frequency and code domains have thus far been studied separately. Exploiting the similarity of "constraints" that characterize assignments within and across these domains, we introduce the first unified framework for the study of assignment problems. Our framework identifies eleven atomic constraints underlying most current and potential assignment problems, and characterizes a problem as a combination of these constraints. Based on this framework, we present a unified algorithm for efficient (T/F/C)DMA channel assignments to nodes or to inter-nodal links in a (multihop) wireless network. The algorithm is parametrized to allow for tradeoff-selectable use as three different variants called random (RAND) ordering, minimum neighbors first (MNF), and progressive minimum neighbors first (PMNF). Using theoretical analysis, we show that the worst-case performance guarantee of PMNF is an order of magnitude better than that of the traditional RAND and MNF for most networks. We also experimentally study the relative performance for one node and one link assignment problem. We observe that PMNF performs the best, and that a larger fraction of unidirectional links degrades the performance in general.
Modelling stand basal area growth for radiata pine plantations in Northwestern Spain using the GADA

A stand basal area growth system for radiata pine (Pinus radiata D. Don) plantations in Galicia (Northwestern Spain) was developed from data corresponding to 247 plots measured between one and five times. Six dynamic equations were considered for analysis and both numerical and graphical methods were used to compare alternative models. The equation that best described the data was a dynamic equation derived from the Korf growth function by the generalized algebraic difference approach (GADA) and by considering two parameters as site-specific. This equation was fitted in one stage by the base-age-invariant dummy variables method. The system also incorporated an equation for predicting initial stand basal area, expressed as a function of stand age, site index, and the number of trees per hectare. This information can be used to establish the starting point for the projection equation when no inventory data are available. The effect of thinning on stand basal area growth was also analyzed and the results showed that the same projection equation can be used to obtain reliable predictions of unit-area basal area development in thinned and unthinned stands. RésuméUn système d’équations modélisant la croissance en surface terrière a été développé pour des plantations de Pinus radiata D. Don en Galice (Nord-ouest de l’Espagne) à partir des données recueillies dans 247 placettes mesurées entre une et cinq fois. Six équations dynamiques ont été analysées et des méthodes graphiques et numériques ont été employées pour comparer des modèles alternatifs. Une équation dynamique dérivée de la fonction de croissance de Korf, dont les deux paramètres spécifiques à la station sont estimés par l’approche de la différence algébrique généralisée (GADA), décrit le mieux les données. L’équation a été ajustée en une seule étape en utilisant la méthode des variables indicatives indépendantes de l’âge. En outre, pour prédire la surface terrière initiale, le système incorpore aussi une fonction de l’âge du peuplement, de l’indice de fertilité de station et du nombre d’arbres à l’hectare. Cette information peut être utilisée pour fixer l’état initial de l’équation de projection quand les données d’inventaire ne sont pas disponibles. L’effet de l’éclaircie sur la croissance en surface terrière a également été analysé et les résultats montrent que la même équation de projection peut être utilisée pour prédire de façon fiable l’évolution de la surface terrière dans les peuplements non éclaircis et les peuplements éclaircis.
Green Revolution

It led to him winning the Nobel Peace Prize in 1970 for his work in developing High Yielding Varieties (HYVs) of wheat. In India, the Green Revolution was mainly led by M.S. Swaminathan. The Green Revolution resulted in a great increase in production of food grains (especially wheat and rice) due to the introduction into developing countries of new, high-yielding variety seeds, beginning in the mid-20th century.
Genome-wide Views of Aging Gene Networks

AGING IS A COMPLEX PROCESS INVOLVING THE ADDITIVE EFFECTS of many genetic pathways (Kirkwood and Austad 2000). To embrace the complexity of aging, an attractive approach is to use DNA microarrays to scan the entire genome for genes that change expression as a function of age or under conditions when longevity is extended. The list of age-regulated genes provides clues about genetic pathways and mechanisms that underlie the aging process. In addition to single-gene analysis, the combined transcriptional profile of aging can act as a molecular phenotype of old age. Over the last 20 years, there has been a great deal of effort to search for biomarkers of aging, and recent studies have shown that expression profiles of aging derived from DNA microarray experiments may provide this long-desired goal. A gene expression signature for aging is a quantitative phenotype that gives a high-resolution view of the aging process, much like using transcriptional profiles of cancer to inform about their severity or malignancy. Previously, one could recognize old versus young individuals in a photograph, or old versus young tissue on a microscope slide. Now it is possible to recognize old versus young genetic networks by analyzing expression levels of the entire set of age-regulated genes (Fig. 1). Unlike photographs or micrographs, expression data from DNA microarrays are quantitative, and thus it is possible to compare age-related transcriptional profiles between different tissues, between different conditions that affect
Estimating the Affine Transformation between Textures

A method is presented that solves the affine transformation between two images of the same texture. This problem is encountered in many areas of Computer Vision such as object retexturing and it is an essential part of many Shape-from-Texture algorithms. The new method is based on transforming each image such that the texture is isotropic, then solving the similarity transformation between the isotropic versions. We point out the difficulties in using other methods such as feature point methods. Quantitative results are given for images created with the Brodatz textures, followed by results for real images. This is followed by an application of the method: placing an object on the textured surface.
Control of underactuated manipulators with uncertain static friction

In this paper the control of 2R underactuated planar manipulator with uncertain static friction is considered. The control process is divided into two phases. In the first phase, terminal sliding mode control is used to stabilize the passive joint to the desired position in finite time; during this phase the motion of the active joint is regarded as mechanical disturbance. In the second phase, the dynamic equation of the active joint becomes a linear equation with a limited control input and a parameter containing the uncertain static friction of the passive joint. A two-dimension fuzzy controller, the domain of which is dynamically adjusted, is applied to stabilize the active joint to the desired position, while the passive joint remains at its desired position all the time. The simulation results indicate that the control scheme proposed in this paper is valid.
Dynamics of multi-scalar-field cosmological models and assisted inflation

We investigate the dynamical properties of a class of spatially homogeneous and isotropic cosmological models containing a barotropic perfect fluid and multiple scalar fields with independent exponential potentials. We show that the assisted inflationary scaling solution is the global late-time attractor for the parameter values for which the model is inflationary, even when curvature and barotropic matter are included. For all other parameter values the multi-field curvature scaling solution is the global late-time attractor (in these solutions asymptotically the curvature is not dynamically negligible). Consequently, we find that in general all of the scalar fields in multi-field models with exponential potentials are non-negligible in late-time behaviour, contrary to what is commonly believed. The early-time and intermediate behaviour of the models is also studied. In particular, n-scalar field models are investigated and the structure of the saddle equilibrium points corresponding to inflationary m-field scaling solutions and non-inflationary m-field matter scaling solutions are also studied (where m
Dynamic hand gesture recognition based on SURF tracking

A novel method of dynamic hand gesture recognition based on Speeded Up Robust Features (SURF) tracking is proposed. The main characteristic is that the dominant movement direction of matched SURF points in adjacent frames is used to help describing a hand trajectory without detecting and segmenting the hand region. The dynamic hand gesture is then modeled by a series of trajectory direction data streams after time warping. Accordingly, the data stream clustering method based on correlation analysis is developed to recognize a dynamic hand gesture and to speed up calculation. The proposed algorithm is tested on 26 alphabetical hand gestures and yields a satisfactory recognition rate which is 87.1% on the training set and 84.6% on the testing set.
Towards a framework to perform DPA attack on GALS pipeline architectures

Differential power analysis (DPA) is a low cost method to extract secret information from supposedly secure cryptographic systems. DPA correlates the data processed with power consumption of the device through statistical analyses to unveil the secret key of the system. A common approach to counteract DPA is randomizing the data processing in order to misalign power consumption traces in time and amplitude domains using strategies such as random delay insertion and random clock frequency. The combination of strategies requires more computational effort for a successful DPA attack. This paper introduces the first steps toward a framework to compromise cryptographic systems that combine misalignment strategies to hide leakage information. The steps of the proposed framework are discussed in terms of computational efforts and successful attacks rate. The results obtained in an architecture prototyped on FPGA show that noise filtering can significantly improve the DPA success rate. Furthermore, clustering traces by frequency allow the improvement of the alignment step, thus increasing about 40 times the efficiency of the DPA attack to the cost of an increase of the computational efforts.
Mortality experience of Tsimane Amerindians of Bolivia: Regional variation and temporal trends

This paper examines regional and temporal trends in mortality patterns among the Tsimane, a population of small‐scale forager‐horticulturalists in lowland Bolivia. We compare age‐specific mortality in remote forest and riverine regions with that in more acculturated villages and examine mortality changes among all age groups over the past 50 years. Discrete‐time logistic regression is used to examine impacts of region, period, sex, and age on mortality hazard. Villages in the remote forest and riverine regions show 2–4 times higher mortality rates from infancy until middle adulthood than in the acculturated region. While there was little change in mortality for most of the life course over the period 1950–1989, overall life expectancy at birth improved by 10 years from 45 to 53 after 1990. In both periods, over half of all deaths were due to infectious disease, especially respiratory and gastrointestinal infections. Accidents and violence accounted for a quarter of all deaths. Unlike typical patterns described by epidemiologic transition theory, we find a much larger period reduction of death rates during middle and late adulthood than during infancy or childhood. In the remote villages, infant death rates changed little, whereas death rates among older adults decreased sharply. We hypothesize that this pattern is due to a combination of differential access to medical interventions, a continued lack of public health infrastructure and Tsimane cultural beliefs concerning sickness and dying.Am. J. Hum. Biol. 19:376–398, 2007. © 2007 Wiley‐Liss, Inc.
Bidirectionalization transformation based on automatic derivation of view complement functions

Bidirectional transformation is a pair of transformations: a view function and a backward transformation. A view function maps one data structure called source onto another called view. The corresponding backward transformation reflects changes in the view to the source. Its practically useful applications include replicated data synchronization, presentation-oriented editor development, tracing software development, and view updating in the database community. However, developing a bidirectional transformation is hard, because one has to give two mappings that satisfy the bidirectional properties for system consistency. In this paper, we propose a new framework for bidirectionalization that can automatically generate a useful backward transformation from a view function while guaranteeing that the two transformations satisfy the bidirectional properties. Our framework is based on two known approaches to bidirectionalization, namely the constant complement approach from the database community and the combinator approach from the programming language community, but it has three new features: (1) unlike the constant complement approach, it can deal with transformations between algebraic data structures rather than just tables; (2) unlike the combinator approach, in which primitive bidirectional transformations have to be explicitly given, it can derive them automatically; (3) it generates a view update checker to validate updates on views, which has not been well addressed so far. The new framework has been implemented and the experimental results show that our framework has promise.
ASSESSING THE ACCURACY OF SATELLITE IMAGE CLASSIFICATIONS FOR POLLUTANT LOADINGS ESTIMATION

We examined the accuracy measures to evaluate maps created from knowledge-based classifications of remotely sensed data. The automated classifications involved categories that showed different levels of annual loadings of six pollutants. From the classification error matrices that used spectral information and ancillary data, we computed the overall accuracy and the kappa coefficients. These common measures, however, assume that misclassification errors are equally serious. We propose a procedure, directly related to the pollutant loadings, to calculate weights for the cells in the error matrix to reflect the severity of the misclassification errors. With the weights we were able to calculate the weighted overall accuracy and the weighted kappa coefficient. By using the weighted equivalents of the usual measures of accuracy, we find that there is more specificity in the measures of quality of the classifications for the individual pollutants. * Corresponding author