Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcription Profiling of Bacillus subtilis Cells Infected with AR9, a Giant Phage Encoding Two Multisubunit RNA Polymerases

ABSTRACT Bacteriophage AR9 is a recently sequenced jumbo phage that encodes two multisubunit RNA polymerases. Here we investigated the AR9 transcription strategy and the effect of AR9 infection on the transcription of its host, Bacillus subtilis. Analysis of whole-genome transcription revealed early, late, and continuously expressed AR9 genes. Alignment of sequences upstream of the 5′ ends of AR9 transcripts revealed consensus sequences that define early and late phage promoters. Continuously expressed AR9 genes have both early and late promoters in front of them. Early AR9 transcription is independent of protein synthesis and must be determined by virion RNA polymerase injected together with viral DNA. During infection, the overall amount of host mRNAs is significantly decreased. Analysis of relative amounts of host transcripts revealed notable differences in the levels of some mRNAs. The physiological significance of up- or downregulation of host genes for AR9 phage infection remains to be established. AR9 infection is significantly affected by rifampin, an inhibitor of host RNA polymerase transcription. The effect is likely caused by the antibiotic-induced killing of host cells, while phage genome transcription is solely performed by viral RNA polymerases. IMPORTANCE Phages regulate the timing of the expression of their own genes to coordinate processes in the infected cell and maximize the release of viral progeny. Phages also alter the levels of host transcripts. Here we present the results of a temporal analysis of the host and viral transcriptomes of Bacillus subtilis infected with a giant phage, AR9. We identify viral promoters recognized by two virus-encoded RNA polymerases that are a unique feature of the phiKZ-related group of phages to which AR9 belongs. Our results set the stage for future analyses of highly unusual RNA polymerases encoded by AR9 and other phiKZ-related phages. Phages regulate the timing of the expression of their own genes to coordinate processes in the infected cell and maximize the release of viral progeny. Phages also alter the levels of host transcripts. Here we present the results of a temporal analysis of the host and viral transcriptomes of Bacillus subtilis infected with a giant phage, AR9. We identify viral promoters recognized by two virus-encoded RNA polymerases that are a unique feature of the phiKZ-related group of phages to which AR9 belongs. Our results set the stage for future analyses of highly unusual RNA polymerases encoded by AR9 and other phiKZ-related phages.
Hazardous Waste Lawsuits, Financial Disclosure, and Investors' Interests

Under the semi-strong form of the efficient capital market hypothesis, the stock price reaction to the public announcement of a new loss contingency provides the market’s assessment of the impact of the contingency. The financial statemcnt treatment of the loss contingency, guided by Statement of Financial Accounting Standards (SFAS) No. 5, provides a second assessment of the materiality of the contingency. In the absence of management holding private information, the two assessments should be the same, with the financial statement disclosure confirming the markct’s rcaction. However, high proprietary costs of disclosure, management deception, and the ambiguitics of SFAS No. 5 may affect disclosure decisions and contribute to differences between thc markct reaction and the financial statement treatment. This papers tests whether there is a systematic relationship between stock price reactions to publicly announced hazardous waste mismanagement lawsuits and the financial statement treatment of those suits. ’ In the simplest form, thc research question is: will two firms facing hazardous waste lawsuits that produced similar market reactions be equally likely to disclose the suits? Hazardous waste lawsuits were selected as the loss contingency for the current study for two reasons. First, hazardous waste lawsuits have a large variation in both the size of the damages being sought and the size of firms being sued. Given the variation in both attributes, we expect both significant and insignificant market reactions across the sample. Second, evaluating hazardous waste lawsuits is a complex task that occurs infrequently (Rigsby, Lambert, and Alexander [ 1989]), mak-
Meteorological Data Analysis and Prediction by Means of Genetic Programming

Weather systems use extremely complex combinations of mathematical tools for analysis and forecasting. Unfortunately, due to phenomena in the world climate, such as the greenhouse effect, classical models may become inadequate mostly because they lack adaptation. Therefore, the weather prediction problem is suited for heuristic approaches, such as Evolutionary Algorithms. Experimentation with heuristic methods like Genetic Programming (GP) can lead to the development of new insights or promising models that can be fine tuned with more focused techniques. This paper describes a GP approach for analysis and prediction of data and provides experimental results of the afore mentioned method on real-world meteorological time series.
TypeInBraille: a braille-based typing application for touchscreen devices

Smartphones provide new exciting opportunities to visually impaired users because these devices can support new assistive technologies that cannot be deployed on desktops or laptops. Some devices, like the iPhone, are rapidly gaining popularity among the visually impaired since the use of pre-installed screenreader applications renders these devices accessible. However, there are still some operations that require a longer time or higher mental workload to be completed by a visually impaired user. In this contribution we present a novel application for text entry, called TypeInBraille, that is based on the Braille code and hence is specifically designed for blind users.
Semantic Web Service Research: Current Challenges and Proximate Achievements

Semantic Web services pledge the automation of core Web service tasks such as discovery, selection, composition, and execution. They are supposed to enable seamless interoperation between systems, whereby human intervention is kept at a minimum. Nevertheless, Semantic Web services have not yet been adopted by the industry. Within the scope of this work, we discuss the correspondence of the viewpoints of experts from academia and industry with respect to current challenges and proximate achievements in the field of Semantic Web service research. Our primary objective is to identify technology locks between industrial needs and academic research activities. Additionally, we take a first step toward the production of a Semantic Web service technology roadmap. The discourse is based on the findings of a comprehensive Delphi study which was conducted in 2007.
Charging in Dielectricless Capacitive RF-MEMS Switches

This paper presents results on high lifetime RF microelectromechanical (RF-MEMS) dielectricless capacitive switches. Using air gap variation only, these RF MEMS capacitive switches achieve a capacitance ratio of 9, associated with small residual charging. The reliability of the switch has been studied, pull-in and pull-out voltages shifts have been observed, modeled and validated with good agreement between model and measurements for a switch held for one month in the down state. The dependence of charging mechanism to the biasing signal is also presented by applying unipolar and bipolar waveforms with different duty cycles. Charging can be modeled using a simple Curie-Von Schweidler equation. It is shown that the duty cycle of the bias signal is strongly accelerating switch failure, and that using bipolar signals improves the lifetime of these switches by several orders of magnitude. The projected lifetime of current RF-MEMS dielectricless switches held in the down state using bipolar signals is several tens of years.
Source number estimation for minimum redundancy arrays with Gerschgorin disk estimator

Source number estimation for minimum redundancy arrays (MRAs) is considered in this paper. When the manifold ambiguity is present, the dimension of signal subspace of conventional covariance matrix will be reduced. Therefore Akaike's information criterion (AIC) and minimum description length (MDL) approaches based on the conventional covariance matrix can not provide the correct estimation. In conventional MRA configuration, manifold ambiguities can be eliminated by augmenting the covariance matrix. However, the conventional AIC and MDL based on the augmented covariance matrix are still not able to estimate the source number correctly, due to the fluctuation of the noise eigenvalues of the augmented covariance matrix. The Gerschgorin disk estimator (GDE) based on the augmented covariance matrix is proposed in this paper. Because the noise eigenvectors of augmented covariance matrix are orthogonal to the signal subspace spanned by steering vectors, GDE can give a correct estimation. By numerical simulation we can see that GDE based on the augmented covariance matrix has a good performance.
Content-Based Image Retrieval via Subspace-Projected Salient Features

In this paper we present a novel image representation method which treats images as frequency histograms of salient features. The histograms are computed making use of linear discriminant analysis (LDA). The method employs saliency feature extraction and image binarisation. Then subspace-projected features are extracted. Using the saliency maps as the positive and negative labels, the image features are mapped onto a lower-dimensional space using LDA. This enables us to construct a 3D-histogram by direct binning on the feature space. This gives rise to a "cube" of image features which have been projected onto a ower-dimensional space so as to maximise the separability of the salient regions with respect to the background. Image retrieval can be performed by computing the distances between the histograms for the query image and the images in the database. We demonstrate our algorithm on a real world database and compare our results to those yielded by codebook representation.
Post-transcriptional nucleotide modification and alternative folding of RNA

Alternative foldings are an inherent property of RNA and a ubiquitous problem in scientific investigations. To a living organism, alternative foldings can be a blessing or a problem, and so nature has found both, ways to harness this property and ways to avoid the drawbacks. A simple and effective method employed by nature to avoid unwanted folding is the modulation of conformation space through post-transcriptional base modification. Modified nucleotides occur in almost all classes of natural RNAs in great chemical diversity. There are about 100 different base modifications known, which may perform a plethora of functions. The presumably most ancient and simple nucleotide modifications, such as methylations and uridine isomerization, are able to perform structural tasks on the most basic level, namely by blocking or reinforcing single base-pairs or even single hydrogen bonds in RNA. In this paper, functional, genomic and structural evidence on cases of folding space alteration by post-transcriptional modifications in native RNA are reviewed.
Validity of Fitbit Charge 2 in Controlled College Physical Education Settings.

Purpose: The study aimed to determine the validity of the Fitbit Charge 2 (FC2) for measuring PA steps in college physical education settings using the Yamax SW-200 (YX) as the criterion device. Methods: Undergraduate students (n = 17) worn both FC2 and YX in two conditions (i.e., controlled and college physical education settings). The absolute value of average percent error (APE) was calculated to evaluate the agreement between FC2 and YX in both conditions. Results: FC2 estimates of total steps in walking, jogging, and running in the controlled condition were within acceptable range (i.e., APE < 5%) without gender difference. However, FC2 tended to overestimate total steps per class in physical education teaching football and baseball units, and gender difference was significant while no difference in sport units were shown. Conclusions: FC2 revealed promising validity evidence measuring total steps in a controlled setting and its validity may be questionable in college physical education settings where student physical activity patters are irregular.
Simulated nonparametric estimation of continuous time models of asset prices and returns

This paper introduces a new parameter estimator of dynamic models in which the state is a multidimensional, continuous-time, partially observed Markov process. The estimator minimizes appropriate distances between nonparametric joint (and/or conditional) densities of sample data and nonparametric joint (and/or conditional) densities estimated from data simulated out of the model of interest. Sample data and model-simulated data are smoothed with the same kernel. This makes the estimator: 1) consistent independently of the amount of smoothing; and 2) asymptotically root-T normal when the smoothing parameter goes to zero at a reasonably mild rate. When the underlying state is observable, the estimator displays the same asymptotic efficiency properties as the maximum-likelihood estimator. In the partially observed case, we derive conditions under which efficient estimators can be implemented with the help of auxiliary prediction functions suggested by standard asset pricing theories. The method is flexible, fast to implement and possesses finite sample properties that are well approximated by the asymptotic theory.
Strategy-proof allocation mechanisms for public good economies ∗

We study the properties of mechanisms for deciding upon the provision of public goods when the feasible set is exogenously given (by financial and/or technological constraints), and individuals’ preferences are represented by continuous, increasing and concave utility functions. We establish a result analog to the Gibbard-Satterthwaite Theorem: strategy-proof mechanisms are dictatorial. Further, efficient and strategy-proof mechanisms are strongly dictatorial (i.e., maximize the dictator’s welfare on the entire feasible set).
Intelligent Information Retrieval in a Digital Library Service

We present the Private Digital Library (PDL) project that represents a service of the Corporate Digital Library (CDL) prototype. The main ideas underlying this project are the following. When a user is looking for documents that he already retrieved in the past, he has to repeat the search procedure and solve the same problems he encountered in the past access. On the contrary, consider the possibility for the user to store documents in a private library. In this case, he will have the chance to retrieve the documents of interest more easily and quickly. It may also be the case that the user has not a clear understanding of what he is looking for. Moreover, he might not know exactly the library content and organization. Thus, he needs for assistance to suggest him what to look for and how to query the system. A method to store and catalogue documents according to personal criteria might help to overcome these problems.
SAMUELSON'S FALLACY OF LARGE NUMBERS AND OPTIONAL STOPPING

Accepting a sequence of independent positive mean bets that are individually unacceptable is what Samuelson called a fallacy of large numbers. Recently, utility functions were characterized where this occurs rationally, and examples were given of utility functions where any finite number of good bets should never be accepted.1 Here the author shows how things change if you are allowed the option to quit early: Subject to some mild conditions, you should essentially always accept a sufficiently long finite sequence of good bets. Interestingly, the strategy of quitting when you get ahead does not perform well, but quitting when you get behind does. This sheds some light on more possible behavioral reasons for Samuelson's fallacy, as well as strategies for handling a series of sequentially observed good investments.
A comparison of the diagnostic utility of the sFlt-1/PlGF ratio versus PlGF alone for the detection of preeclampsia/HELLP syndrome

Abstract Objective: The Elecsys® immunoassay sFlt-1/PlGF ratio and the Triage® PlGF assay were compared (in a prospective, multicenter, case-control study) for diagnosis of preeclampsia/hemolysis, elevated liver enzymes, low platelets (HELLP) syndrome. Methods: Women in European perinatal care centers with singleton pregnancies were enrolled: 178 cases had confirmed preeclampsia and 391 controls had normal outcome. Patients in the preeclampsia/HELLP syndrome group were matched pairwise by gestational week to healthy controls (1:2). Maternal blood samples were analyzed using (a) fully automated Elecsys PlGF and Elecsys sFlt-1 immunoassays with two cutoffs (early-onset [<34 weeks] ≤33, ≥85; late-onset [≥34 weeks] ≤33, ≥110), and (b) Triage PlGF immunoassay (single cutoff). Diagnostic performance and utility were assessed. Results: Respectively, 83 and 95 women had early-onset or late-onset preeclampsia/HELLP syndrome. The overall diagnostic performance of the Elecsys immunoassay sFlt-1/PlGF ratio (area under the curve [AUC] 0.941) was higher than for Triage PlGF (AUC 0.917). The Elecsys immunoassay sFlt-1/PlGF ratio sensitivity and specificity was: 94.0% (95% confidence interval [CI] 86.5–98.0) and 99.4% (95% CI: 96.8–99.9) for early-onset preeclampsia; and 89.5% (95% CI: 81.5–94.8) and 95.4% (95% CI: 91.7–97.8) for late-onset preeclampsia. The Triage assay sensitivity and specificity was: 96.4% (95% CI: 89.8–99.3) and 88.5% (95% CI: 82.8–92.8) (early-onset); and 90.5% (95% CI: 83–96) and 64.5% (95% CI: 57.8–70.9) (late onset). Conclusions: The fully automated Elecsys immunoassay sFlt-1/PlGF ratio provides improved diagnostic utility over the Triage PlGF assay with improved specificity for the clinical management of pregnant women with suspected preeclampsia/HELLP syndrome.
Low Power Adder Based Digital Filter for QRS Detector

Most of the Biomedical applications use dedicated processors for the implementation of complex signal processing. Among them, sensor network is also a type, which has the constraint of low power consumption. Since the processing elements are the most copiously used operations in the signal processors, the power consumption of this has the major impact on the system level application. In this paper, we introduce low power concept of transistor stacking to reduce leakage power; and new architectures based on stacking to implement the full adder and its significance at the digital filter level for QRS detector are implemented. The proposed concept has lesser leakage power at the adder as well as filter level with trade-off in other quality metrics of the design. This enabled the design to be dealt with as the low-power corner and can be made adaptable to any level of hierarchical abstractions as per the requirement of the application. The proposed architectures are designed, modeled at RTL level using the Verilog-HDL, and synthesized in Synopsys Design Compiler by mapping the design to 65 nm technology library standard cells.
Singularity structure of the two point function of the free Dirac field on a globally hyperbolic spacetime

We give an introduction to the techniques from microlocal analysis that have successfully been applied in the investigation of Hadamard states of free quantum field theories on curved spacetimes. The calculation of the wave front set of the two point function of the free Klein‐Gordon field in a Hadamard state is reviewed, and the polarization set of a Hadamard two point function of the free Dirac field on a curved spacetime is calculated.
A Study of Code Design Skills in Novice Programmers using the SOLO taxonomy

There is a wealth of literature dealing with the difficulties of novice programmers with basic programming constructs such as variables, assignment and conditionals. In this paper we extend the study to two other core CS1 topics: loops and vectors (represented as single dimensional arrays). By the end of their first semester of instruction, students are expected to have acquired both the ability to reproduce given syntactic structure and basic design skills that allow them to write small pieces of code that extend, modify or combine in new ways the basic programming constructs. This work presents an evaluation framework that uses the SOLO taxonomy to assess programming questions' complexity. Our framework extends SOLO by using the term "building block" as an adaptable parameter that explicitly defines the student's ability to increasingly write more complex pieces of code. The granularity of a "building block" is determined by the amount of programming practice students have carried out up to that point. The analysis of final exam answers using this framework allows us to quantify the progress made by one cohort of novice programmers in the mastery of basic design skills and to study correlations between mastery of these skills and overall course performance. Furthermore, we identify common errors that illustrate the challenges students face when trying to combine programming constructs in non-trivial ways.
A modified particle swarm optimizer based on cloud model

In this paper, we introduce cloud model theory to the particle swarm optimization algorithm to improve the global search ability and make a faster convergence speed of the algorithm. Some modifications are presented. First, we adopt cloud model to initialize the positions and velocities for entire population in the initialization range. Second, inertia weight is dynamically, nonlinearly decreased as the search progresses by using the data set, which can be obtained by cloud model. Third, two random variants in the velocity rule are assigned with cloud model. Four, inertia weight and the two random variants are correlated by cloud model. The modified particle swarm optimization is tested on some benchmark functions and the results are compared with the result of the standard particle swarm optimization. Experimental results indicate that the modified particle swarm optimization outperforms the standard particle swarm optimization in the global search ability with a quicker convergent speed.
Counting and exploring sizes of Markov equivalence classes of directed acyclic graphs

When learning a directed acyclic graph (DAG) model via observational data, one generally cannot identify the underlying DAG, but can potentially obtain a Markov equivalence class. The size (the number of DAGs) of a Markov equivalence class is crucial to infer causal effects or to learn the exact causal DAG via further interventions. Given a set of Markov equivalence classes, the distribution of their sizes is a key consideration in developing learning methods. However, counting the size of an equivalence class with many vertices is usually computationally infeasible, and the existing literature reports the size distributions only for equivalence classes with ten or fewer vertices. In this paper, we develop a method to compute the size of a Markov equivalence class. We first show that there are five types of Markov equivalence classes whose sizes can be formulated as five functions of the number of vertices respectively. Then we introduce a new concept of a rooted sub-class. The graph representations of rooted subclasses of a Markov equivalence class are used to partition this class recursively until the sizes of all rooted subclasses can be computed via the five functions. The proposed size counting is efficient for Markov equivalence classes of sparse DAGs with hundreds of vertices. Finally, we explore the size and edge distributions of Markov equivalence classes and find experimentally that, in general, (1) most Markov equivalence classes are half completed and their average sizes are small, and (2) the sizes of sparse classes grow approximately exponentially with the numbers of vertices.