Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptional and Proteomic Analysis of a Ferric Uptake Regulator (Fur) Mutant of Shewanella oneidensis: Possible Involvement of Fur in Energy Metabolism, Transcriptional Regulation, and Oxidative Stress

ABSTRACT The iron-directed, coordinate regulation of genes depends on the fur (ferric uptake regulator) gene product, which acts as an iron-responsive, transcriptional repressor protein. To investigate the biological function of a fur homolog in the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1, a fur knockout strain (FUR1) was generated by suicide plasmid integration into this gene and characterized using phenotype assays, DNA microarrays containing 691 arrayed genes, and two-dimensional polyacrylamide gel electrophoresis. Physiological studies indicated that FUR1 was similar to the wild-type strain when they were compared for anaerobic growth and reduction of various electron acceptors. Transcription profiling, however, revealed that genes with predicted functions in electron transport, energy metabolism, transcriptional regulation, and oxidative stress protection were either repressed (ccoNQ, etrA, cytochrome b and c maturation-encoding genes, qor, yiaY, sodB, rpoH, phoB, and chvI) or induced (yggW, pdhC, prpC, aceE, fdhD, and ppc) in the fur mutant. Disruption of fur also resulted in derepression of genes (hxuC, alcC, fhuA, hemR, irgA, and ompW) putatively involved in iron uptake. This agreed with the finding that the fur mutant produced threefold-higher levels of siderophore than the wild-type strain under conditions of sufficient iron. Analysis of a subset of the FUR1 proteome (i.e., primarily soluble cytoplasmic and periplasmic proteins) indicated that 11 major protein species reproducibly showed significant (P < 0.05) differences in abundance relative to the wild type. Protein identification using mass spectrometry indicated that the expression of two of these proteins (SodB and AlcC) correlated with the microarray data. These results suggest a possible regulatory role of S. oneidensis MR-1 Fur in energy metabolism that extends the traditional model of Fur as a negative regulator of iron acquisition systems.
Blocking PirB up-regulates spines and functional synapses to unlock visual cortical plasticity and facilitate recovery from amblyopia

Inhibition of a cell surface, Ig-like receptor in the adult mouse visual cortex increases neural plasticity and facilitates recovery from amblyopia. In Search of a Young and Supple Brain It is easy to learn a language as a small child, but not so easy as an adult. Similarly, children who are born with certain defects in one eye can recover vision in that eye if it’s corrected early in childhood, but not if it’s corrected too late. Bochner et al. now report a way to unlock youthful brain plasticity in adult mice. Blocking a cell surface receptor called PirB (initially characterized as an innate immune receptor) found on neurons in the cortex, either genetically or biochemically, allowed the animals to rapidly adjust to the loss of sight in one eye—just as if it were a young pup. A closer look revealed new, functional synapses and extra synapse-containing spines on the neurons. Even mice that were blind in one eye for a long time, mimicking human amblyopia, could adapt and compensate after inhibition of PirB. This ability to enhance neural plasticity could be harnessed for recovery after brain injury or for correction of developmental disorders. During critical periods of development, the brain easily changes in response to environmental stimuli, but this neural plasticity declines by adulthood. By acutely disrupting paired immunoglobulin-like receptor B (PirB) function at specific ages, we show that PirB actively represses neural plasticity throughout life. We disrupted PirB function either by genetically introducing a conditional PirB allele into mice or by minipump infusion of a soluble PirB ectodomain (sPirB) into mouse visual cortex. We found that neural plasticity, as measured by depriving mice of vision in one eye and testing ocular dominance, was enhanced by this treatment both during the critical period and when PirB function was disrupted in adulthood. Acute blockade of PirB triggered the formation of new functional synapses, as indicated by increases in miniature excitatory postsynaptic current (mEPSC) frequency and spine density on dendrites of layer 5 pyramidal neurons. In addition, recovery from amblyopia—the decline in visual acuity and spine density resulting from long-term monocular deprivation—was possible after a 1-week infusion of sPirB after the deprivation period. Thus, neural plasticity in adult visual cortex is actively repressed and can be enhanced by blocking PirB function.
One-step purification of assembly-competent tubulin from diverse eukaryotic sources

A method is presented that allows rapid and efficient purification of native, active tubulin from a variety of species and tissue sources by affinity chromatography. It eliminates the need to use heterologous systems for the study of microtubule-associated proteins and motor proteins, which has been a major issue in microtubule-related research.
A Differential QAM Detection in Uplink Massive MIMO Systems

In this paper, we address differential non-coherence detections in uplink massive multiple input multiple output (MIMO) systems. Utilizing the channel statistics information, a special 16 quadrature amplitude modulation (QAM) can be adopted to achieve differential detection in uplink massive MIMO systems, which avoids costs of pilots or channel estimation. In addition, a higher-order extension of this differential 16-QAM is also presented in this paper. Moreover, it is found that users in different cells can transmit symbols simultaneously without causing interference to each other by jointly processing signals from all base stations if the number of receive antennas goes to infinity. For comparison, we also provide the performances of the differential amplitude phase shift keying (DAPSK) and coherence detection with pilot contamination in uplink massive MIMO systems, respectively. Simulation results show that the proposed differential 16-QAM scheme exhibits significant advantage over 16-DAPSK, and exhibits a large performance gain compared with the coherence detection with pilot contamination.
Mutual information maximization for optimal spatial modulation MIMO system

Combining Spatial Modulation (SM) with multiple-input multiple-output (MIMO) systems constitutes a promising technique for exploiting full spatial multiplexing. To further maximize its capacity, we propose to optimize the activation probability with an iternative optimization method. Moreover, we propose to incorporate the newly-proposed distribution matcher encoder for probability shaping. Numerical results are provided to substantiate the proposed system's improvement in terms of mutual information lower bound, and to validate the efficiency of the proposed encoding scheme.
Parenting Behavior, Adolescent Depression, Alcohol Use, Tobacco Use, and Academic Performance: A Path Model

ii INDEX OF TABLES AND FIGURES iv CHAPTER I: INTRODUCTION 1 Statement of Problem 1 Rationale 3 Purpose 4 Research Hypotheses 7 Theoretical Framework 8 Parenting 9 CHAPTER II: LITERATURE REVIEW 13 Parenting and Depression 13 Parenting and Academic Performance 15 Depression and Academic Performance 17 Parenting and Alcohol/Tobacco Use 17 Depression and Alcohol/Tobacco Use 19 CHAPTER III: METHODS . 21 Study Participants and Procedures 21 Demographics 21 Data Collection Instrument 22 Authoritative Parenting 22 Parental Monitoring 23 Parental Care 23 Depression 23 Alcohol and Tobacco Use 24 Academic Performance 24 CHAPTER IV: RESULTS 25 CHAPTER V: DISCUSSION 38 Clinical Implications 40 Limitations and Future Direction . 42 REFERENCES . 45
Risk-aware trajectory generation with application to safe quadrotor landing

In navigation tasks, mobile robots often have to deal with substantial uncertainty due to imperfect actuators and noisy sensor measurements. In this paper, we consider the problem of online trajectory generation for safe navigation in the presence of state uncertainty and the resulting deviations from the desired trajectory. Our approach combines probabilistic estimation of the a priori collision risk with efficient trajectory generation, exploiting the differential flatness of many robotic systems in an explicitly constrained polynomial trajectory representation. Through trajectory optimization, our approach allows to flexibly trade off risk against, for example, the duration of the trajectory. It is computationally efficient because each optimization step has polynomial complexity. In contrast to other approaches, our method can also optimize the trajectory duration and supports cost functions that facilitate higher-order smoothness of the trajectory. Our experiments demonstrate the performance of the approach and show that our trajectories result in substantially lower collisions probabilities compared to minimum-snap trajectories in a quadrotor landing task.
Comprehensive Energy Balance Measurements in Mice

In mice with altered body composition, establishing whether it is food intake or energy expenditure, or both, that is the major determinant resulting in changed energy balance is important. In order to ascertain where the imbalance is, the acquisition of reproducible data is critical. Therefore, here we provide detailed descriptions of how to determine energy balance in mice. This encompasses protocols for establishing energy intake from home cage measurement of food intake, determining energy lost in feces using bomb calorimetry, and using equations to calculate parameters such as energy intake (EI), digested energy intake (DEI), and metabolisable energy intake (MEI) to determine overall energy balance. We also discuss considerations that should be taken into account when planning these experiments, including diet and sample sizes. © 2016 by John Wiley & Sons, Inc.
In situ depth maps based feature extraction and tracking

Parallel numerical simulation is a powerful tool used by scientists to study complex problems. It has been a common practice to save the simulation output to disk and then conduct post-hoc in-depth analyses of the saved data. System I/O capabilities have not kept pace as simulations have scaled up over time, so a common approach has been to output only subsets of the data to reduce I/O. However, as we are entering the era of peta- and exa-scale computing, this sub-sampling approach is no longer acceptable because too much valuable information is lost. In situ visualization has been shown a promising approach to the data problem at extreme-scale. We present a novel in situ solution using depth maps to enable post-hoc image-based visualization and feature extraction and tracking. An interactive interface is provided to allow for fine-tuning the generation of depth maps during the course of a simulation run to better capture the features of interest. We use several applications including one actual simulation run on a Cray XE6 supercomputer to demonstrate the effectiveness of our approach.
Accessing DNA damage in chromatin: Insights from transcription

Recently, there has been a convergence of fields studying the processing of DNA, such as transcription, replication, and repair. This convergence has been centered around the packaging of DNA in chromatin. Chromatin structure affects all aspects of DNA processing because it modulates access of proteins to DNA. Therefore, a central theme has become the mechanism(s) for accessing DNA in chromatin. It seems likely that mechanisms involved in one of these processes may also be used in others. For example, the discovery of transcriptional coactivators with histone acetyltransferase activity and chromatin remodeling complexes has provided possible mechanisms required for efficient repair of DNA in chromatin. BioEssays 21:596–603, 1999. © 1999 John Wiley & Sons, Inc.
Argumentation over ontology correspondences in MAS

In order to support semantic interoperation in open environments, where agents can dynamically join or leave and no prior assumption can be made on the ontologies to align, the different agents involved need to agree on the semantics of the terms used during the interoperation. Reaching this agreement can only come through some sort of negotiation process. Indeed, agents will differ in the domain ontologies they commit to; and their perception of the world, and hence the choice of vocabulary used to represent concepts. We propose an approach for supporting the creation and exchange of different arguments, that support or reject possible correspondences. Each agent can decide, according to its preferences, whether to accept or refuse a candidate correspondence. The proposed framework considers arguments and propositions that are specific to the matching task and are based on the ontology semantics. This argumentation framework relies on a formal argument manipulation schema and on an encoding of the agents' preferences between particular kinds of arguments.
High-level authoring of illustrated documents

This paper starts by introducing a class of future document authoring systems that will allow authors to specify the content and form of a text+pictures document at a high level of abstraction, while leaving responsibility for linguistic and graphical details to the system. Next, we describe two working prototypes that implement parts of this functionality, based on semantic modeling of the pictures and the text of the document; one of these two, the ILLUSTRATE prototype, is a multimedia extension of previous text authoring systems in the What You See Is What You Meant (WYSIWYM) tradition. The paper concludes with an exploration of the ways in which Multimedia WYSIWYM can be further enhanced, allowing it to approximate the ‘ideal’ systems that were sketched earlier in the paper. Applications of Multimedia WYSIWYM to general-purpose picture retrieval (in the context of the Semantic Web, for example) are also discussed.
Non-parametric Estimation of Probability Distributions from Sampled Signals Timor

This paper is concerned with the non-parametric estimation of probability distributions from band-limited and at least critically sampled signals such as images. Conventional approaches employing histograms or Parzen windows often perform unsatisfactorily since they ignore two important properties of such signals, namely that they are ordered and contain sufficient information to reconstruct the original continuous band-limited signal exactly. Based on these observations we propose a method to estimate the density and distribution of such signals. The technique has a number of interesting and useful properties. First, that domain resolution of the estimate is independent of the number of sample points. Second, the estimate is continuous and consequently no arbitrary bin widths or smoothing kernel parameters have to be set. Third, if a suitable analytic form of the band-limited signal or equivalently the sampling pre-filter is available then the resulting density is exact (aside from signal quantisation).
Study of scalable declustering algorithms for parallel grid files

The efficient storage and retrieval of large multidimensional datasets is an important concern for large-scale scientific computations, such as long-running time-dependent simulations which periodically generate snapshots of the state. The main challenge for efficiently handling such datasets is to minimize response time for multidimensional range queries. The grid file is one of the well known access methods for multidimensional and spatial data. We investigate effective and scalable declustering techniques for grid files with the primary goal of minimizing response time and the secondary goal of maximizing the fairness of data distribution. The main contributions of this paper are (1) the analytic and experimental evaluation of existing index-based declustering techniques and their extensions for grid files; and (2) the development of a proximity-based declustering algorithm called 'minimax', which is experimentally shown to scale and to consistently achieve better response time compared to available algorithms while maintaining perfect disk distribution.
AGING SUSCEPTIBILITY AND PERFORMANCE OF OIL MODIFIED ASPHALT BINDERS

As oils are becoming more popular additives in asphalt binders as low temperature modifiers, there has been interest in the performance, especially the long-term aging, of oil modified asphalts. Research studies have reported widely varying effects of different types of oils on asphalt binders in terms of rheological and aging properties. This thesis is focused on characterizing the aging susceptibility or oxidation potential of commonly used oils to determine if the susceptibility is related to observed aging susceptibility of asphalt binders modified with oil and polymers. To accomplish this, two common oils, bio-oil and re-recycled engine oil bottoms (REOB), were aged in the PAV for several different intervals and then tested in a dynamic shear rheometer to detect changes in complex shear modulus and phase angle. Aging indices were calculated to normalize the magnitudes of change. Then 6 blends were prepared using bio-oil and REOB with combinations of polymers including SBS, Elvaloy, and PPA. Each oil was combined with each polymer combination to meet similar low-temperature performance grades. Two control blends, one containing SBS, the other a refinery produced PG 58-34 using an unknown quantity of Elvaloy, were prepared and obtained, respectively. Extended PAV aging was performed for 20-, 40-, and 60-hour cycles. Blends were then tested using frequency sweeps, elastic recovery tests, bending beam rheometer testing, and bitumen bond strength testing to evaluate the aging susceptibility on various performance metrics at different temperature levels. Results show that bio-oil exhibits nonlinear and high aging susceptibility while the REOB exhibits no appreciable susceptibility to aging in terms of its complex shear modulus aging index and phase angle aging index. Testing of the modified asphalt blends yielded performance results that varied based on not only the aging susceptibility of the oil itself, but also of the polymer additives, as well as the interaction of the oil with the polymer. Blends containing the bio-oil performed better in the
University of Glasgow at TREC 2012: Experiments with Terrier in Medical Records, Microblog, and Web Tracks

Abstract : In TREC 2012, we focus on tackling the new challenges posed by the Medical, Microblog and Web tracks, using our Terrier Information Retrieval Platform. In particular, for the Medical track, we investigate how to exploit implicit knowledge within medical records, with the aim of better identifying those records from patients with specific medical conditions. For the Microblog track adhoc task, we investigate novel techniques to leverage documents hyperlinked from tweets to better estimate relevance of those tweets and increase recall. Meanwhile, for the Microblog track filtering task, we developed a new stream processing infrastructure for real-time adaptive filtering on top of the Storm framework. For the TREC Web track, we continue to build upon our learning-to-rank approaches and novel xQuAD framework within Terrier, increasing both effectiveness and efficiency when ranking.
Study on Hardware-In-the-Loop Simulation System During Design and Testing of Intermittent Track-to-Train Data Transmission Equipment: BTM

Balise has been immigrated and widely used for passenger dedicated lines and high speed lines in China. This paper gave a deep insight into the principle of on-board BTM as it passes the wayside balise at high speed and proposed a real-time hardware-in-the-loop simulation (HILS) system for testing and evaluating the major performance of BTM. The real-time HILS system architecture, the up-link simulator design, the hardware realization were explained in brief. Test cases were also designed and verified finally.
An introduction to multivariate adaptive regression splines

Multivariate Adaptive Regression Splines (MARS) is a method for flexible modelling of high dimensional data. The model takes the form of an expansion in product spline basis functions, where the number of basis functions as well as the parameters associated with each one (product degree and knot locations) are automatically determined by the data. This procedure is motivated by recursive partitioning (e.g. CART) and shares its ability to capture high order interactions. However, it has more power and flexibility to model relationships that are nearly additive or involve interactions in at most a few variables, and produces continuous models with continuous derivatives. In addition, the model can be represented in a form that separately identifies the additive contributions and those associated with different multivariable interactions. This paper summarizes the basic MARS algorithm, as well as extensions for binary response, categorical predictors, nested variables and missing values. It presents tips on interpreting the output of the standard FORTRAN implementation of MARS, and provides an example of MARS applied to a set of clinical data.
The Experience of Realizing a Semantic Web Urban Computing Application

Urban Computing is a branch of Pervasive Computing that investigates urban settings and everyday lifestyles. A large quantity of information to develop pervasive applications for urban environments is often already available, even if scattered and not integrated: maps, points of interest, user locations, traffic, pollution, and events are just a few examples of the digitalized information which we can access on the Web. Applications for mobile users that leverage such information are rapidly growing. In this article, we report our experience in addressing practical computational issues influencing the use of Geographic Information Systems and geospatial data from the standpoint of semantics and pervasive computing. We refer to the early achievements of the LarKC project, in which we developed an Urban Computing demonstrator. We highlight the positive sides of our experience and we discuss open issues and possible advances.
Effect of the racket mass and the rate of strokes on kinematics and kinetics in the table tennis topspin backhand

Abstract The purpose of this study was to investigate the effect of the racket mass and the rate of strokes on the kinematics and kinetics of the trunk and the racket arm in the table tennis topspin backhand. Eight male Division I collegiate table tennis players hit topspin backhands against topspin balls projected at 75 balls · min−1 and 35 balls · min−1 using three rackets varying in mass of 153.5, 176 and 201.5 g. A motion capture system was used to obtain trunk and racket arm motion data. The joint torques of the racket arm were determined using inverse dynamics. The racket mass did not significantly affect all the trunk and racket arm kinematics and kinetics examined except for the wrist dorsiflexion torque, which was significantly larger for the large mass racket than for the small mass racket. The racket speed at impact was significantly lower for the high ball frequency than for the low ball frequency. This was probably because pelvis and upper trunk axial rotations tended to be more restricted for the high ball frequency. The result highlights one of the advantages of playing close to the table and making the rally speed fast.
The Real Time Endoscopic Image Analysis Algorithm

New algorithm for the real time processing of narrow--band endoscopic images with a highly productive distributed intellectual analytic decision--making system for multiscale endoscopic diagnostics is presented. The algorithm uses scale--invariant feature transform detector, computing skeletons of gastric mucosa pit-patterns, "Bag of visual words" ("Bag of features") method, and K--means method for key points. Resulting algorithm is completely automated, performs real time analysis, and does not require preliminary selection of interest area. Image classification accuracy exceeds 78%. The use of neural network recognition improves image classification accuracy up to 93%.