Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of RuvABC and RecG Involvement in the Escherichia coli Response to the Covalent Topoisomerase-DNA Complex

ABSTRACT Topoisomerases form a covalent enzyme-DNA intermediate after initial DNA cleavage. Trapping of the cleavage complex formed by type IIA topoisomerases initiates the bactericidal action of fluoroquinolones. It should be possible also to identify novel antibacterial lead compounds that act with a similar mechanism on type IA bacterial topoisomerases. The cellular response and repair pathways for trapped topoisomerase complexes remain to be fully elucidated. The RuvAB and RecG proteins could play a role in the conversion of the initial protein-DNA complex to double-strand breaks and also in the resolution of the Holliday junction during homologous recombination. Escherichia coli strains with ruvA and recG mutations are found to have increased sensitivity to low levels of norfloxacin treatment, but the mutations had more pronounced effects on survival following the accumulation of covalent complexes formed by mutant topoisomerase I defective in DNA religation. Covalent topoisomerase I and DNA gyrase complexes are converted into double-strand breaks for SOS induction by the RecBCD pathway. SOS induction following topoisomerase I complex accumulation is significantly lower in the ruvA and recG mutants than in the wild-type background, suggesting that RuvAB and RecG may play a role in converting the initial single-strand DNA-protein cleavage complex into a double-strand break prior to repair by homologous recombination. The use of a ruvB mutant proficient in homologous recombination but not in replication fork reversal demonstrated that the replication fork reversal function of RuvAB is required for SOS induction by the covalent complex formed by topoisomerase I.
A Linear-Time Kernel Goodness-of-Fit Test

We propose a novel adaptive test of goodness-of-fit, with computational cost linear in the number of samples. We learn the test features that best indicate the differences between observed samples and a reference model, by minimizing the false negative rate. These features are constructed via Stein's method, meaning that it is not necessary to compute the normalising constant of the model. We analyse the asymptotic Bahadur efficiency of the new test, and prove that under a mean-shift alternative, our test always has greater relative efficiency than a previous linear-time kernel test, regardless of the choice of parameters for that test. In experiments, the performance of our method exceeds that of the earlier linear-time test, and matches or exceeds the power of a quadratic-time kernel test. In high dimensions and where model structure may be exploited, our goodness of fit test performs far better than a quadratic-time two-sample test based on the Maximum Mean Discrepancy, with samples drawn from the model.
Accelerating gate matching in the mapping step using don ' t cares

At the end of the logic synthesis, the technology mapping maps the Boolean function on physical cells. This step is based on a matching check, which complexity depends on the number of library cell inputs, and increases if don't cares are considered. We present a method based on fault analysis techniques, which uses a structural equivalent of the cell. This method allows to prune dramatically the design space, and directly derives the input phase. The experimental results show a gain of 2 to 3 orders of magnitude relative to the conventional ones, and behaves almost linearly with the complexity.
From Query-By-Keyword to Query-By-Example: LinkedIn Talent Search Approach

One key challenge in talent search is to translate complex criteria of a hiring position into a search query, while it is relatively easy for a searcher to list examples of suitable candidates for a given position. To improve search e ciency, we propose the next generation of talent search at LinkedIn, also referred to as Search By Ideal Candidates. In this system, a searcher provides one or several ideal candidates as the input to hire for a given position. The system then generates a query based on the ideal candidates and uses it to retrieve and rank results. Shifting from the traditional Query-By-Keyword to this new Query-By-Example system poses a number of challenges: How to generate a query that best describes the candidates? When moving to a completely di erent paradigm, how does one leverage previous product logs to learn ranking models and/or evaluate the new system with no existing usage logs? Finally, given the di erent nature between the two search paradigms, the ranking features typically used for Query-By-Keyword systems might not be optimal for Query- By-Example. This paper describes our approach to solving these challenges. We present experimental results con rming the e ectiveness of the proposed solution, particularly on query building and search ranking tasks. As of writing this paper, the new system has been available to all LinkedIn members.
Bmc Musculoskeletal Disorders Biomechanical Comparison of a New Stand-alone Anterior Lumbar Interbody Fusion Cage with Established Fixation Techniques – a Three-dimensional Finite Element Analysis

Background: Initial promise of a stand-alone interbody fusion cage to treat chronic back pain and restore disc height has not been realized. In some instances, a posterior spinal fixation has been used to enhance stability and increase fusion rate. In this manuscript, a new stand-alone cage is compared with conventional fixation methods based on the finite element analysis, with a focus on investigating cage-bone interface mechanics and stress distribution on the adjacent tissues.
Distribution of the Fittest Individuals and the Rate of Muller's Ratchet in a Model with Overlapping Generations

Muller's ratchet is a paradigmatic model for the accumulation of deleterious mutations in a population of finite size. A click of the ratchet occurs when all individuals with the least number of deleterious mutations are lost irreversibly due to a stochastic fluctuation. In spite of the simplicity of the model, a quantitative understanding of the process remains an open challenge. In contrast to previous works, we here study a Moran model of the ratchet with overlapping generations. Employing an approximation which describes the fittest individuals as one class and the rest as a second class, we obtain closed analytical expressions of the ratchet rate in the rare clicking regime. As a click in this regime is caused by a rare, large fluctuation from a metastable state, we do not resort to a diffusion approximation but apply an approximation scheme which is especially well suited to describe extinction events from metastable states. This method also allows for a derivation of expressions for the quasi-stationary distribution of the fittest class. Additionally, we confirm numerically that the formulation with overlapping generations leads to the same results as the diffusion approximation and the corresponding Wright-Fisher model with non-overlapping generations.
Frustration in Infancy: Implications for Emotion Regulation, Physiological Processes, and Temperament.

A study sample of 162 six-month-old children was selected from a larger sample of 346 infants on the basis of parents' report of their infants' temperament and a laboratory assessment of temperament. Infants were classified as easily frustrated and less easily frustrated and compared on a number of emotion regulation, physiology, and temperament measures. Results indicated that male and female infants were equally likely to be classified as frustrated and less easily frustrated; however, male infants were less able to regulate physiologically. Easily frustrated infants used different emotion regulation strategies and were observed to be less attentive and more active than less easily frustrated infants when observed in the laboratory. These infants were also characterized by their parents as more active, less attentive, and more distressed to novelty. Infants classified as easily frustrated were more reactive physiologically and less able to regulate physiological reactivity than their less easily frustrated counterparts. It is hypothesized that this cluster of characteristics may constitute a unique temperamental type that may have implications for other types of behavioral functioning. Limitations of the study are that observations are based on a single brief assessment of the infant, modest effect sizes were found, and the study is cross-sectional.
Micro/nano scale mechanical tests based on the probe platform

Instrumentation for testing of mechanical properties on the micro and nano scales has developed enormously in recent years. This has enabled the mechanical behavior of surfaces, thin films, and micro/nano components to be studied with unprecedentedly small scale and high accuracy. In this paper, several testing systems and techniques for studying micromechanical properties are reviewed with particular emphasis on the probe based platform and its applications. Topics include the principles and performances of the integrated systems between the probe and the micromanipulator, the piezo-stage, the optical and high resolution scanning microscopes, the single and dual probe testing systems and the related method of micro force test. Researches on the capillary interaction between the probe tip and air-water surface, the motion of graphite microflakes, and accurate measurement of the mechanical parameter of nanowire are provided.
A numerical toolbox for homoclinic bifurcation analysis

This paper presents extensions and improvements of recently developed algorithms for the numerical analysis of orbits homoclinic to equilibria in ODEs and describes the implementation of these algorithms within the standard continuation package AUTO86. This leads to a kind of toolbox, called HOMCONT, for analysing homoclinic bifurcations either as an aid to producing new theoretical results, or to understand dynamics arising from applications. This toolbox allows the continuation of codimension-one homoclinic orbits to hyperbolic or non-hyperbolic equilibria as well as detection and continuation of higher-order homoclinic singularities in more parameters. All known codimension-two cases that involve a unique homoclinic orbit are supported. Two specific example systems from ecology and chemical kinetics are analysed in some detail, allowing the reader to understand how to use the the toolbox for themselves. In the process, new results are also derived on these two particular models.
Open Source WFST Tools for LVCSR Cascade Development

This paper introduces the Transducersaurus toolkit which provides a set of classes for generating each of the fundamental components of a typical WFST-based ASR cascade, including HMM, Context-dependency, Lexicon, and Grammar transducers, as well as an optional silence class WFST. The toolkit further implements a small scripting language in order to facilitate the construction of cascades via a variety of popular combination and optimization methods and provides integrated support for the T3 and Juicer WFST decoders, and both Sphinx and HTK format acoustic models. New results for two standard WSJ tasks are also provided, and the toolkit is used to compare a variety of construction and optimization algorithms. These results illustrate the flexibility of the toolkit as well as the tradeoffs of various build algorithms.
Colonial multi-swarm: A modular approach to administration of particle swarm optimization in large scale problems

In this paper we have introduced the colonial multi-swarm, an algorithm with modular characteristics that can be augmented on several existing variants of Particle Swarm Optimization to alleviate the premature convergence problem. Colonial multi-swarm ensures a decent degree of exploration by administrating a number of parallel swarms. It uses a meta-level decision system that allows the particles to switch their swarms when they are not successful in their own. This migration strategy helps preserve the local exploitation of thriving swarms as well as providing diversity and ground for emerge of other swarms. The module has been implemented on conventional PSO. The method is tested on 28 benchmark problems and has exhibited significant improvement over the original algorithm and also notable merits compared to the latest version of Standard PSO (SPSO 2011), presented by the particle swarm central, in large scale problems. It is shown that application of colonial multi swarm exhibits bolder improvement over the mentioned algorithms as the problem dimensionality rises.
Long-term effects of gastrectomy in patients with spirometry-defined COPD and patients at risk of COPD: a case-control study

Objective Comorbidities are characteristic of COPD. However, little is known about the secondary manifestations of COPD in the gastrointestinal tract. Therefore, we aimed to explore the long-term effects of gastrectomy in patients with spirometry-defined COPD or those at risk of COPD. Participants Subjects included 87 patients either with COPD or at risk of COPD (symptomatic) who underwent gastrectomy between December 2003 and October 2013 (group A), and 174 patients either with COPD or at risk of COPD, matched by age (±5 years), sex, and forced expiratory volume in 1 second (FEV1) as percentage of predicted (FEV1% predicted) (±5%) (group B). Methods All patients underwent routine blood chemistry and pulmonary function tests, arterial blood gas analysis, 6-minute walk test (6MWT), high-resolution chest computed tomography scans, and nutritional assessments. Results The mean duration postgastrectomy was 18.3±15.4 years. The mean FEV1 and FEV1% predicted were 2.07±0.76 L and 74.6±24.5%, respectively. Univariate analysis indicated that group A patients had significantly lower body mass index, fat-free mass index, and serum hemoglobin and albumin concentration (all P=0.00), and walked a significantly shorter distance in the 6MWT (P<0.05). Multivariate linear regression analysis for the distance in the 6MWT indicated that increased residual volume (RV) to total lung capacity (TLC) as percentage of predicted (%RV/TLC) alone was an independent and significant predictor of reduced distances in the 6MWT. Conclusion We concluded that nutritional insufficiency in patients with COPD (or those at risk of COPD) who previously underwent gastrectomy might lead to hyperinflation and consequently, decreased exercise capacity.
A Paper Currency Recognition System Using Negatively Correlated Neural Network Ensemble

This paper presents a currency recognition system using ensemble neural network (ENN). The individual neural networks (NNs) in an ENN are trained via negative correlation learning. The objective of using negative correlation learning (NCL) is to expertise the individuals on different parts or portion of input patterns in an ensemble. The available currencies in the market consist of new, old and noisy ones. It is often difficult for machine to recognize these currencies; therefore we propose a system that uses ENN to identify them efficiently. We performed our experiment for seven different types of TAKA (Bangladeshi currency) which are 2, 5, 10, 20, 50, 100 and 500 TAKA. The image of different types note is converted in gray scale and compressed in the desired range. Each pixel of the compressed image is given as an input to the network. This system is able to recognize highly noisy or old image of TAKA. Ensemble network is very useful for the classification of different types of currencies. It reduces the chances of misclassification than a single network and ensemble network with independent training. In experimental results we have shown this with artificially added noise in the test set. We also find good result for similar pattern available in market.
Change-point detection method on 100Gb/s Ethernet interface

This paper deals with hardware acceleration of statistical methods for detection of anomalies on 100Gb/s Ethernet. The approach is demonstrated by implementing a sequential Non-Parametric Cumulative Sum (NP-CUSUM) procedure. We use high-level synthesis in combination with emerging software defined monitoring (SDM) methodology for rapid development of FPGA-based hardware-accelerated network monitoring applications. The implemented method offloads detection of network attacks and anomalies directly into an FPGA chip. The parallel nature of FPGA allows for simultaneous detection of various kinds of anomalies. Our results show that hardware acceleration of statistical methods using the SDM concept with high-level synthesis from C/C++ is possible and very promising for traffic analysis and anomaly detection in high-speed 100Gb/s networks.
Knowledge Acquisition by Demonstration

Traditional knowledge acquisition tools rely either on conversational textual interfaces or on graphical editing of rule and description structures. Both these methods divorce the user from the actual concrete problem-solving situations where the knowledge is created and applied. We show how a programming by demonstration system can be used as a knowledge acquisition tool by allowing a user to demonstrate procedures interactively on images taken from a video of the procedure being performed in the real world. Graphical annotation and speech input and output are used to provide declarative information that informs the system about objects in the scene, and how to interpret the user’s actions.
A methodology for the design of robust rollover prevention controllers for automotive vehicles: Part 2-Active steering

In this paper we apply recent results from robust control to the problem of rollover prevention in automotive vehicles. Specifically, we exploit the results of Pancake, Corless and Brockman, which provide controllers to robustly guarantee that the peak magnitudes of the performance outputs of an uncertain system do not exceed certain values. We use the dynamic Load Transfer Ratio LTRd as a performance output for rollover prevention, and design active-steering based rollover controllers to keep the magnitude of this quantity below a certain level, while we use control input u as an additional performance output to limit the maximum amount of control effort. We present numerical simulations to demonstrate the efficacy of our controllers.
Instabilities in Close Neutron Star Binaries.

We report on a new analysis of instabilities in close neutron star binaries based upon (3+1) dimensional general relativistic numerical hydrodynamics calculations. When a realistic equation of state is employed, orbit calculations for two 1.45{ital M}{sub {circle_dot}} neutron stars reveal surprising evidence that general relativistic effects may cause otherwise stable stars to individually collapse prior to merging. Also, the strong fields cause the last stable orbit to occur at a larger separation distance and lower frequency than post-Newtonian estimates. {copyright} {ital 1995} {ital The} {ital American} {ital Physical} {ital Society}.
Super Iterator A design pattern for Algorithm and Data structure collections

The Super Iterator pattern, like the standard Iterator pattern, traverses an unknown data structure without exposing that structure. With the standard Iterator pattern, clients must create a different iterator for each new structure, and the object returned must be of the specific type stored in the structure, even when they share a common super class. With the Super Iterator pattern, the object returned is of the common super class, and the iterator itself need not be altered when adding a new subtype with custom data structures. The client, however, must change two lines of code to load and instantiate the new subclass
A dynamical systems framework for stochastic iterative optimization

Stochastic optimization typically are solved via stochastic iterative algorithms. Examples are stochastic gradient descent, and other first-order methods for stochastic optimization. In such algorithms, exact computation of the gradient of the objective function is generally not possible. Hence, empirical estimates are used instead. We view such algorithms as a linear dynamical system but with noisy non-linear feedback. We give a general framework for probabilistic stability analysis of such dynamical systems. This is done via a novel stochastic dominance argument that was developed for convergence analysis of iterated random operators. We are also able to give a non-asymptotic rate of convergence within this framework.
Hybrid Multiple Channels-Based Recommendations for Mobile Commerce

Mobile data communications have evolved as the number of third generation (3G) subscribers has increased to conduct mobile commerce. Multichannel companies would like to develop mobile commerce but meet difficulties because of lack of knowledge about users' consumption behaviors on the new mobile channel. Typical collaborative filtering (CF) recommendations may suffer from the so-called sparsity problem because few products are browsed on the mobile Web. In this study, we propose a hybrid multiple channels method to resolve the lack of knowledge about users' consumption behaviors on the new channel and the difficulty of finding similar users due to the sparsity problem of the typical CF. Products are recommended to the new mobile channel users based on their browsing behaviors on the new mobile channel as well as consumption behaviors on the existing multiple channels according to different weights. Our experimental results show that the proposed method performs well compared to the other recommendation methods.
Preparation and Characterization of Cu-Doped Zno Sol-Gel Derived Optical Thin Films

In this work, we report the preparation of Cu-doped ZnOthin films by sol-gel method based on zinc acetate dihydrate (CH3COO)2Zn·2H2O, Copper acetate dihydrate Cu3(CH3COO)2·H2O) and diethanolamine (HN(CH2OH)2, DEA). The precursor solution was prepared at various Cu composition ranging from 2-20 wt%. All films were spin-coated on borosilicate substrates for several coating repetition followed by annealing process at 550 °C for 4 h in an ambient air. The structural properties of the films were characterized by X-ray diffraction (XRD) and scanning electron microscope (SEM). The XRD results indicate the domination of hexagonal wurtzite structure of ZnO with noticeable alternation in the XRD peak intensity upon Cu doping content. SEM results revealed the grain size shape and surface morphologies of as-prepared samples. Crucial optical properties of as-prepared films were scrutinized from their UV-Vis transmission spectra. The films are highly transparent in the visible region with more than 90 % transparency within 380 nm to 800 nm. Their corresponding band gaps indicate significant red shift with increasing Cu doping content. Overall results suggest that Cu additive play a vital role on relevant optical properties of ZnO that can be adjusted to meet the requirement for practical optoelectronics applications.