Miracle-dz/UniFAR-FTUs huggingface dataset:
Network Analysis of Plasmidomes: The Azospirillum brasilense Sp245 Case

Azospirillum brasilense is a nitrogen-fixing bacterium living in association with plant roots. The genome of the strain Sp245, isolated in Brazil from wheat roots, consists of one chromosome and six plasmids. In this work, the A. brasilense Sp245 plasmids were analyzed in order to shed some light on the evolutionary pathways they followed over time. To this purpose, a similarity network approach was applied in order to identify the evolutionary relationships among all the A. brasilense plasmids encoded proteins; in this context a computational pipeline specifically devoted to the analysis and the visualization of the network-like evolutionary relationships among different plasmids molecules was developed. This information was supplemented with a detailed (in silico) functional characterization of both the connected (i.e., sharing homology with other sequences in the dataset) and the unconnected (i.e., not sharing homology) components of the network. Furthermore, the most likely source organism for each of the genes encoded by A. brasilense plasmids was checked, allowing the identification of possible trends of gene loss/gain in this microorganism. Data obtained provided a detailed description of the evolutionary landscape of the plasmids of A. brasilense Sp245, suggesting some of the molecular mechanisms responsible for the present-day structure of these molecules.
Monte Carlo simulations of dusty spiral galaxies: extinction and polarization properties

We present Monte Carlo simulations of dusty spiral galaxies, modelled as bulge + disk systems, aimed to study their extinction and polarization properties. The extinction parameters (absorption and scattering) of dust grains are calculated from Mie's theory for a full distribution of sizes and materials; the radiation transfer is carried on for the four Stokes parameters. Photometric and polarimetric maps of galaxies of different optical depths, inclinations and bulge-to-total ratios have been produced in the B and I bandpasses. As expected, the effect of scattering is to reduce substantially the extinction for a given optical depth, in particular for what concerns the obscuration of bright bulge cores. For the same reason, scattering reduces also the reddening, as evaluated from B-I maps. On the other hand the bluing directly due to forward scattering is hardly appreciable. Radial color gradients are often found. A comparison with ``sandwich'' models shows that they fail dramatically to reproduce the extinction - optical depth relation. The degree of linear polarization produced by scattering is usually of the order of a few percent; it increases with optical depth, and with inclination (less than 80 degrees). The polarization pattern is always perpendicular to the major axis, unless the dust distribution is drastically modified. There is little local correlation between extinction and polarization degree and there is a trend of increasing polarization from the B to the I band. We discuss implications and relevance of the results for studies of the structure and morphology of spiral galaxies and of their interstellar medium.
Design and Control of the MINDWALKER Exoskeleton

Powered exoskeletons can empower paraplegics to stand and walk. Actively controlled hip ab/adduction (HAA) is needed for weight shift and for lateral foot placement to support dynamic balance control and to counteract disturbances in the frontal plane. Here, we describe the design, control, and preliminary evaluation of a novel exoskeleton, MINDWALKER. Besides powered hip flexion/extension and knee flexion/extension, it also has powered HAA. Each of the powered joints has a series elastic actuator, which can deliver 100 Nm torque and 1 kW power. A finite-state machine based controller provides gait assistance in both the sagittal and frontal planes. State transitions, such as stepping, can be triggered by the displacement of the Center of Mass (CoM). A novel step-width adaptation algorithm was proposed to stabilize lateral balance. We tested this exoskeleton on both healthy subjects and paraplegics. Experimental results showed that all users could successfully trigger steps by CoM displacement. The step-width adaptation algorithm could actively counteract disturbances, such as pushes. With the current implementations, stable walking without crutches has been achieved for healthy subjects but not yet for SCI paraplegics. More research and development is needed to improve the gait stability.
Essays on GMO effects on crop yields, the effects of pricing errors on implied volatilities and smoothing for seasonal time series with a long cycle

Yields improvements are critical to ensuring food security for a growing world population, especially in view of the increasing use of land for bio-fuel production. Efforts to sustain the impressive rate of past productivity gains, epitomized by such successes as the green revolution, are bound to rely on biotechnology innovations such as those responsible for the development of genetically modified (GM) crops. Some argue that the use of biotechnology can substantially improve yields relative to the trajectory established by traditional breeding in the 20th century. Because U.S. adoption of GM varieties has been very strong since their introduction in the late 1990s, we propose to investigate empirically whether and to what extent the GM technology has improved realized yields. We study this question for non-irrigated U.S. maize and soybean yields over 1964-2010, having controlled for local effects, weather, fertilization and the pre-existing (non-GM) crop improvement trend. For maize we find that GM varieties have increased realized yields, with a stronger gain in the Central Corn Belt. For soybeans, GM varieties appear to have slightly reduced yields. For both crops we find a strong trend in yield growth, which may have accelerated in recent years Departments of Economics and Statistics, Iowa State University, Ames, IA, 50011, USA Department of Economics, Iowa State University, Ames, IA, 50011, USA Department of Policy Studies, TERI University, New Delhi, 110070, India Department of Economics, Iowa State University, Ames, IA, 50011, USA
An Empirical Study on Inflation and Economic Growth in Bangladesh

In this study, the relationship between the inflation and the economic growth in Bangladesh has been examined in the framework of data covering 1988:2008 periods. The existence of the long term relationship between these two variables has been examined using Bound Test developed by Pesaran et al. (2001), and the existence of a cointegration relationship between the two series has been detected following the test result. Whereas no statistically significant long term relationship has been found with the formed ARDL models, a negative and statistically significant short term relationship has been found. The Causality relationship between the two series has been examined in the framework of the causality test developed by Toda Yamamoto (1995) but no Causality relationship has been found from economic growth to inflation, a Causality relationship has been found from inflation to economic growth.
The O(n) ϕ4 model with free surfaces in the large-n limit: some exact results for boundary critical behaviour, fluctuation-induced forces and distant-wall corrections

The O(n) ϕ4 model on a slab Rd−1×[0,L]? > bounded by free surfaces is studied for 2 < d < 4 in the limit n → ∞. The self-consistent potential V(z) which the exact n → ∞ solution of the model involves is analysed by means of boundary operator expansions. Building on the known exact n → ∞ solution for V(z) in the semi-infinite case L = ∞ at the bulk critical point, we exactly determine two types of corrections to this potential: (i) those linear in the temperature scaling field t at L = ∞, and (ii) the leading L-dependent (distant-wall) corrections at the critical point. From (i) exact analytical results at d = 3 are obtained for the leading temperature singularity of the excess surface free energy and the implied asymptotic behaviours of the scaling functions Θ3(x) and ϑ3(x) of the residual free energy fres = L1 − d Θd(tL) and the critical Casimir force βFC(T,L)=L−dϑd(tL)? > in the limit x → 0 ±. The second derivative ϑ3′′(0)? > is computed exactly.
On the electrodynamics of moving bodies at low velocities

We discuss an article by Le Bellac and Lévy-Leblond in which they have identified two Galilean limits of electromagnetism (1973 Nuovo Cimento B 14 217–33). We use their results to point out some confusion in the literature, and in the teaching of special relativity and electromagnetism. For instance, it is not widely recognized that there exist two well-defined non-relativistic limits, so that researchers and teachers are likely to utilize an incoherent mixture of both. Recent works have shed new light on the choice of gauge conditions in classical electromagnetism. We retrieve the results of Le Bellac and Lévy-Leblond first by examining orders of magnitudes and then with a Lorentz-like manifestly covariant approach to Galilean covariance based on a five-dimensional Minkowski manifold. We emphasize the Riemann–Lorenz approach based on the vector and scalar potentials as opposed to the Heaviside–Hertz formulation in terms of electromagnetic fields.
Connections Between Network Topology and Network Security

This paper is the project proposal for a Ph.D thesis at Gjøvik Universtity College. Based on the resent advanced in graph theory and studies of complex networks we want to emphasise the connection between network topology and risks in the network. Today network security focuses on single machine single session security. We hope to show that this approach is missing the crucial fact that all machines are part of a large, dynamic, complex network. This might imply that many measures taken today are ineffective. The theory of heavy tailed distribution eliminates to some extent the finite size cut-off effect from the models and includes observations that by previous models has been considered as extremal observations or outliers. Possible paths for our project, depending on our findings are: Network dependability, epidemiology in networks, redundancy strategies in networks and risk management in networks.
Reversible Cerebral Vasoconstriction Syndrome: An Important Cause of Acute Severe Headache

Reversible cerebral vasoconstriction syndrome (RCVS) is an increasingly recognized and important cause of acute headache. The majority of these patients develop potentially serious neurological complications. Rigorous investigation is required to exclude other significant differential diagnoses. Differentiating RCVS from subarachnoid haemorrhage (SAH) and primary angiitis of the central nervous system (PACNS) may be difficult but has important therapeutic implications. This paper describes what is currently known about the epidemiology, pathophysiology, clinical, and diagnostic features of the syndrome, an approach to investigation, a summary of treatments, and what is known of prognosis.
FMR1 CGG expansions: Prevalence and sex ratios

We have estimated the prevalence of FMR1 premutation and gray zone CGG repeat expansions in a population‐based sample of 19,996 male and female adults in Wisconsin and compared the observed sex ratios of the prevalence of FMR1 CGG premutation and gray zone expansions to theoretical sex ratios. The female premutation prevalence was 1 in 148 and comparable to past research, but the male premutation prevalence of 1 in 290 is somewhat higher than most previous estimates. The female:male premutation prevalence ratio is in line with the theoretically predicted sex ratio. The prevalence of CGG repeats in the gray zone (45–54 repeats) was 1 in 33 females and 1 in 62 males. The prevalence of the “expanded” gray zone (defined here as 41–54 CGG repeats) was 1 in 14 females and 1 in 22 males, leading to a female:male ratio of 1.62 (95% confidence interval 1.39–1.90). This female:male ratio was significantly lower than the expected ratio of 2.0. We examined results from three previously published FMR1 prevalence studies and found similar female:male ratios for CGG repeats in this “expanded” gray zone range (pooled female:male ratio across all four studies 1.66, 95% confidence interval 1.51–1.82). Further research is needed to understand the apparent excess prevalence of males with CGG repeats in this range. © 2013 Wiley Periodicals, Inc.
Smoothing a probablistic lexicon via syntactic transformations

Probabilistic parsing requires a lexicon that specifies each word's syntactic preferences in terms of probabilities. To estimate these probabilities for words that were poorly observed during training, this thesis assumes the existence of arbitrarily powerful transformations (also known to linguists as lexical redundancy rules or metarules) that can add, delete, retype or reorder the argument and adjunct positions specified by a lexical entry. In a given language, some transformations apply frequently and others rarely. We describe how to estimate the rates of the transformations from a sample of lexical entries. More deeply, we learn which properties of a transformation increase or decrease its rate in the language. As a result, we can smooth the probabilities of lexical entries. Given enough direct evidence about a lexical entry's probability, our Bayesian approach trusts the evidence; but when less evidence or no evidence is available, it relies more on the transformations' rates to guess how often the entry will be derived from related entries. Abstractly, the proposed “transformation models” are probability distributions that arise from graph random walks with a log-linear parameterization. A domain expert constructs the parameterized graph, and a vertex is likely according to whether random walks tend to halt at it. Transformation models are suited to any domain where “related” events (as defined by the graph) may have positively covarying probabilities. Such models admit a natural prior that favors simple regular relationships over stipulative exceptions. The model parameters can be locally optimized by gradient-based methods or by Expectation-Maximization. Exact algorithms (matrix inversion) and approximate ones (relaxation) are provided, with optimizations. Variations on the idea are also discussed. We compare the new technique empirically to previous techniques from the probabilistic parsing literature, using comparable features, and obtain a 20% perplexity reduction (similar to doubling the amount of training data). Some of this reduction is shown to stem from the transformation model's ability to match observed probabilities, and some from its ability to generalize. Model averaging yields a final 24% perplexity reduction.
Phonological decoding involves left posterior fusiform gyrus

Aloud reading of novel words is achieved by phonological decoding, a process in which grapheme‐to‐phoneme conversion rules are applied to “sound out” a word's spoken representation. Numerous brain imaging studies have examined the neural bases of phonological decoding by contrasting pseudoword (pronounceable nonwords) to real word reading. However, only a few investigations have examined pseudoword reading under both aloud and silent conditions, task parameters that are likely to significantly alter the functional anatomy of phonological decoding. Subjects participated in an fMRI study of aloud pseudoword, aloud real word, silent pseudoword, and silent real word reading. Using this two‐by‐two design, we examined effects of word‐type (real words vs. pseudowords) and response‐modality (silent vs. aloud) and their interactions. We found 1) four regions to be invariantly active across the four reading conditions: the anterior aspect of the left precentral gyrus (Brodmann's Area (BA) 6), and three areas within the left ventral occipitotemporal cortex; 2) a main effect of word‐type (pseudowords > words) in left inferior frontal gyrus and left intraparietal sulcus; 3) a main effect of response‐modality (aloud > silent) that included bilateral motor, auditory, and extrastriate cortex; and 4) a single left hemisphere extrastriate region showing a word‐type by response‐modality interaction effect. This region, within the posterior fusiform cortex at BA 19, was uniquely modulated by varying phonological processing demands. This result suggests that when reading, word forms are subject to phonological analysis at the point they are first recognized as alphabetic stimuli and BA 19 is involved in processing the phonological properties of words. Hum Brain Mapp, 2005. © 2005 Wiley‐Liss, Inc.
Transhydrogenase and Growth Substrate Influence Lipid Hydrogen Isotope Ratios in Desulfovibrio alaskensis G20

Microbial fatty acids preserve metabolic and environmental information in their hydrogen isotope ratios (2H/1H). This ratio is influenced by parameters that include the 2H/1H of water in the microbial growth environment, and biosynthetic fractionations between water and lipid. In some microbes, this biosynthetic fractionation has been shown to vary systematically with central energy metabolism, and controls on fatty acid 2H/1H may be linked to the intracellular production of NADPH. We examined the apparent fractionation between media water and the fatty acids produced by Desulfovibrio alaskensis G20. Growth was in batch culture with malate as an electron donor for sulfate respiration, and with pyruvate and fumarate as substrates for fermentation and for sulfate respiration. A larger fractionation was observed as a consequence of respiratory or fermentative growth on pyruvate than growth on fumarate or malate. This difference correlates with opposite apparent flows of electrons through the electron bifurcating/confurcating transhydrogenase NfnAB. When grown on malate or fumarate, mutant strains of D. alaskensis G20 containing transposon disruptions in a copy of nfnAB show different fractionations than the wild type strain. This phenotype is muted during fermentative growth on pyruvate, and it is absent when pyruvate is a substrate for sulfate reduction. All strains and conditions produced similar fatty acid profiles, and the 2H/1H of individual lipids changed in concert with the mass-weighted average. Unsaturated fatty acids were generally depleted in 2H relative to their saturated homologues, and anteiso-branched fatty acids were generally depleted in 2H relative to straight-chain fatty acids. Fractionation correlated with growth rate, a pattern that has also been observed in the fractionation of sulfur isotopes during dissimilatory sulfate reduction by sulfate reducing bacteria. Abbreviations CNIH Cornichon
Theory II: Landscape of the Empirical Risk in Deep Learning

Previous theoretical work on deep learning and neural network optimization tend to focus on avoiding saddle points and local minima. However, the practical observation is that, at least in the case of the most successful Deep Convolutional Neural Networks (DCNNs), practitioners can always increase the network size to fit the training data (an extreme example would be [1]). The most successful DCNNs such as VGG and ResNets are best used with a degree of "overparametrization". In this work, we characterize with a mix of theory and experiments, the landscape of the empirical risk of overparametrized DCNNs. We first prove in the regression framework the existence of a large number of degenerate global minimizers with zero empirical error (modulo inconsistent equations). The argument that relies on the use of Bezout theorem is rigorous when the RELUs are replaced by a polynomial nonlinearity (which empirically works as well). As described in our Theory III [2] paper, the same minimizers are degenerate and thus very likely to be found by SGD that will furthermore select with higher probability the most robust zero-minimizer. We further experimentally explored and visualized the landscape of empirical risk of a DCNN on CIFAR-10 during the entire training process and especially the global minima. Finally, based on our theoretical and experimental results, we propose an intuitive model of the landscape of DCNN's empirical loss surface, which might not be as complicated as people commonly believe.
Orientation of spindle axis and distribution of plasma membrane proteins during cell division in polarized MDCKII cells

MDCKII cells differentiate into a simple columnar epithelium when grown on a permeable support; the monolayer is polarized for transport and secretion. Individual cells within the monolayer continue to divide at a low rate without disturbing the function of the epithelium as a barrier to solutes. This presents an interesting model for the study of mitosis in a differentiated epithelium which we have investigated by confocal immunofluorescence microscopy. We monitored the distribution of microtubules, centrioles, nucleus, tight junctions, and plasma membrane proteins that are specifically targeted to the apical and basolateral domains. The stable interphase microtubule cytoskeleton was rapidly disassembled at prophase onset and reassembled at cytokinesis. As the interphase microtubules disassembled at prophase, the centrioles moved from their interphase position at the apical membrane to the nucleus and acquired the ability to organize microtubule asters. Orientation of the spindle parallel to the plane of the monolayer occurred between late prophase and metaphase and persisted through cytokinesis. The cleavage furrow formed asymmetrically perpendicular to the plane of the monolayer initiating at the basolateral side and proceeding to the apical domain. The interphase microtubule network reformed after the centrioles migrated from the spindle poles to resume their interphase apical position. Tight junctions (ZO-1), which separate the apical from the basolateral domains, remained assembled throughout all phases of mitosis. E-cadherin and a 58-kD antigen maintained their basolateral plasma membrane distributions, and a 114- kD antigen remained polarized to the apical domain. These proteins were useful for monitoring the changes in shape of the mitotic cells relative to neighboring cells, especially during telophase when the cell shape changes dramatically. We discuss the changes in centriole position during the cell cycle, mechanisms of spindle orientation, and how the maintenance of polarized plasma membrane domains through mitosis may facilitate the rapid reformation of the polarized interphase cytoplasm.
Static and dynamic tactile directional cues experiments with VTPlayer mouse

Braille cells have good potential to provide information. Users don't have to know the braille alphabet to be able to use them. In this study we show that it is possible to create 4 × 4 patterns to give the users some directional information. Two kinds of icons have been designed: static patterns and dynamic ones (animations). It appears that users rather like, and recognize better static icons.