Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying Patients for Clinical Studies from Electronic Health Records: TREC 2012 Medical Records Track at OHSU

Abstract : The goal of the TREC 2012 Medical Records Track was to search medical record documents to identify patients as possible candidates for clinical studies based on diagnosis, age, and other attributes. For TREC 2012, the Oregon Health & Science University (OHSU) group experimented with both manual and automated techniques. We used a derivative of Lucene to build an interactive retrieval system that can process queries in one of two ways. Users can manually specify Boolean queries whose terms may include words as well as ICD-9 codes. Alternatively, the system features an automated query parser that transforms free-text queries into structured Boolean queries. The query parser is built on top of MetaMap and the UMLS Metathesaurus. We submitted both automatic runs (which relied solely on the automated query parser) as well as manual runs consisting of queries built by an expert clinician. Overall, our automated query parser performed below the mean of other groups, although there were individual topics for which it performed very well. This irregular performance was in part due to our parser's tendency to over-specify queries, leading to reduced recall. There were, however, several topics for which our parser performed very well, suggesting that our fundamental approach has merit. In contrast, our manual runs performed very well, scoring second-best among official manual runs. With further modification of the manual queries, we were able to achieve even better performance. Query of electronic health records for the use case of identifying patients as candidates for clinical studies still requires manual query development, at least until better automated methods can be developed that outperform them.
FCA-based approach for mining contextualized folksonomy

We present a novel approach to build the contextualized folksonomy and concept hieracrhies from tags of blogosphere based on Formal Concept Analysis. Our approach is based on the assumption that if a blog has the relationships with others, they would use the similar set of tags. We collect the sample data from blogosphere randomly and then build the concept hierarchies on the basis of the inclusion relations(tags) between the extensions(bloggers). We propose the formalization of the contextualized folksonomy in terms of Formal Concept Analysis and show how our approach can be used to create the contextualized folksonmy for blogosphere. We evaluate our approach by considering an already existing tags of blogosphere.
On describing multivariate skewed distributions: A directional approach

Most multivariate measures of skewness in the literature measure the overall skewness of a distribution. These measures were designed for testing the hypothesis of distributional symmetry; their relevance for describing skewed distributions is less obvious. In this article, the authors consider the problem of characterizing the skewness of multivariate distributions. They define directional skewness as the skewness along a direction and analyze two parametric classes of skewed distributions using measures based on directional skewness. The analysis brings further insight into the classes, allowing for a more informed selection of classes of distributions for particular applications. The authors use the concept of directional skewness twice in the context of Bayesian linear regression under skewed error: first in the elicitation of a prior on the parameters of the error distribution, and then in the analysis of the skewness of the posterior distribution of the regression residuals.
Mixed Copula Model with Random Recovery Rate for CDO Pricing

This paper presents a new factor copula model for pricing CDO tranches, where the involved distributions are mixtures of Gaussian distribution and VG distribution. Besides, random recovery rate is introduced into the mixed copula framework to effectively model "correlation smile" in CDO pricing. Numerical analysis shows that the new model may better simulate the loss distribution of the reference assets pool and the fairy credit spread of the CDO tranche.
Evidence of spatial embedding in the IPv4 router-level Internet network

Much interest has been taken in understanding the global routing structure of the Internet, both to model and protect the current structures and to modify the structure to improve resilience. These studies rely on trace-routes and algorithmic inference to resolve individual IP addresses into connected routers, yielding a network of routers. Using WHOIS registries, parsing of DNS registries, as well as simple latency-based triangulation, these routers can often be geolocated to at least their country of origin, if not specific regions. In this work, we use node subgraph summary statistics to present evidence that the router-level (IPv4) network is spatially embedded, with the similarity (or dissimilarity) of a node from it's neighbor strongly correlating with the attributes of other routers residing in the same country or region. We discuss these results in context of the recently proposed gravity models of the Internet, as well as the potential application to geolocation inferrence.
Bridging Spatial Modulation With Spatial Multiplexing: Frequency-Domain ESM

Spatial modulation (SM) is a multi-input multi-output (MIMO) technique, which was originally introduced to reduce the number of radio frequency (RF) chains in a MIMO transmitter and thereby reduce cost and power consumption. Although it is very appealing in theory, this concept actually has two main problems: The first is that SM involves antenna switching, which degrades the spectral shaping and the Nyquist property of the transmitted signal. The second is the limited spectral efficiency due to the presence of silent antennas. In order to remedy the second problem, enhanced spatial modulation (ESM) was introduced in which multiple signal constellations are used, and information bits are conveyed not only by the transmitted symbols and the indices of the active antennas, but also by the constellation types activated. As for the problem of antenna switching, it actually disappears when SM is combined with OFDM, because the switching operation in frequency-domain SM (FD-SM) occurs at baseband. But the number of RF chains required becomes equal to the number of transmit antennas and the property of reduced number of RF chains, which was the original motivation for SM also disappears. FD-SM turns out to be a particular type of underloaded MIMO-OFDM system, which reduces the power requirements of the transmit power amplifiers rather than their number. In this paper, we introduce frequency-domain ESM (FD-ESM), which avoids both the spectral efficiency limitations and the antenna switching issues of the original SM. Exploiting the property that switching occurs at baseband and no savings in terms of the number of RF chains can be achieved in frequency-domain implementation, we design FD-ESM schemes in which the transmitted codewords do not include any zero-valued components. These designs bridge the concept of SM with spatial multiplexing, and they provide spectacular gains with respect to multi-stream SM (MSM) and also some significant gains compared to conventional spatial multiplexing.
A Cys2/His2 zinc finger protein acts as a repressor of gibberellins biosynthesis by regulating SD1/OsGA20ox2 in rice (Oryza sativa L.)

Gibberellins (GAs) play important roles in the regulation of plant growth and development. The green evolution gene SD1 encoding gibberellin 20-oxidase 2 (GA20ox2) has been widely used in modern rice breeding. However, the molecular mechanism of how SD1/OsGA20ox2 expression is regulated remains unclear. Here we report a Cys2/His2 zinc finger protein ZFP207 acting as a transcriptional repressor of OsGA20ox2. ZFP207 was mainly accumulated in young tissues and more specifically in culm nodes. ZFP207-overexpression (ZFP207OE) plants displayed semi-dwarfism phenotype and small grains by modulating cell length. RNA interference of ZFP207 caused higher plant and longer grains. The endogenous bioactive GA levels were significantly reduced in ZFP207OE plants and application of exogenous GA3 rescued the semi-dwarf phenotype. The in vivo and in vitro studies showed that ZFP207 repressed the expression of OsGA20ox2 via binding to its promoter region. Together, ZFP207 acts as a transcriptional repressor of gibberellins biosynthesis and it may play a critical role in plant growth and development through fine-tuning GA biosynthesis in rice.
Parallel GPU Processing for Fast Radio Signal Propagation Computation in GRASS-RaPlaT

Radio propagation simulation tools are important for prediction and verification of the radio signal coverage by individual transmitters or transmitter networks such as mobile phone cellular networks. In the case of a large geographic area with a relative high resolution, the simulation can become computationally demanding, taking a considerable amount of time to accomplish. Parallel processing can be used to speed up the computation and shorten the response time. We used the GPGPU (General-Purpose Computing on Graphics Processing Units) approach for the open source GRASS-RaPlaT radio propagation tool. By using OpenCL, we modified the existing radio propagation model modules for GPU (Graphics Processing Unit) execution, achieving multiple times processing speedup for computationally intensive modules. In the article, we present our GPU parallelization approach and analyze the results and conditions that must be fulfilled to successfully employ GPU computation and achieve a considerable computation speedup. Key-Words: Radio propagation simulation, GRASS, RaPlaT, parallel processing, GPU computing, OpenCL
The scoring function based on amino acid network

With the contact energy between residues as the weight, we constructed a weighted amino acid network. Two parameters are introduced. Based on this network model, we proposed a new docking scoring function Sn. For 42 systems' bound docking results, we do the scoring sort with this scorning function. Comparing the results got from this new scorning function with that from the RP scorning function, we find that the Sn scorning function has a better performance than the RP on some items.
DIRECT CAMERA CALIBRATION USING TWO CONCENTRIC CIRCLES FROM A SINGLE VIEW

This paper describes a new camera calibration method based on ellipses properties. We demonstrate that the calibration is possible using one view of two concentric circles of known radii. Based on the estimation of the projected circle centers and on the ellipses properties as the perspective projection of circles, our algorithm estimates both the focal length and the pose and orientation of the camera. We validate the performances of our algorithm using both synthetic and real images. The use of circles greatly simplifies the calibration problem. A noise analysis is also made to compare the accuracy of the results with another well-known calibration method. This calibration method is also well-suited to the 3Dreconstruction problem from an image sequence of an object placed on a turn-table.
ACADO toolkit—An open‐source framework for automatic control and dynamic optimization

In this paper the software environment and algorithm collection ACADO Toolkit is presented, which implements tools for automatic control and dynamic optimization. It provides a general framework for using a great variety of algorithms for direct optimal control, including model predictive control as well as state and parameter estimation. The ACADO Toolkit is implemented as a self‐contained C++ code, while the object‐oriented design allows for convenient coupling of existing optimization packages and for extending it with user‐written optimization routines. We discuss details of the software design of the ACADO Toolkit 1.0 and describe its main software modules. Along with that we highlight a couple of algorithmic features, in particular its functionality to handle symbolic expressions. The user‐friendly syntax of the ACADO Toolkit to set up optimization problems is illustrated with two tutorial examples: an optimal control and a parameter estimation problem. Copyright © 2010 John Wiley & Sons, Ltd.
Fast alignment of 3D geometrical models and 2D color images using 2D distance maps

This paper presents a fast pose estimation algorithm of a 3D free form object in 2D images using 2D distance maps. One of the popular techniques of the pose estimation of 3D object in 2D image is the point-based method such as the ICP algorithm. However, the calculation cost for determining point correspondences is expensive. To overcome this problem, the proposed method utilizes a distance map on the 2D image plane, which is constructed quite rapidly by the fast marching method. For pose estimation of the object, contour lines of the 2D image and the projection of the 3D object are aligned using the distance map iteratively by the robust m-estimator. Some experimental results with simulated models and actual images of the endoscopic operation are successfully carried out.
Estimating 3D Finger Angle on Commodity Touchscreens

We describe a novel approach for estimating the pitch and yaw of fingers relative to a touchscreen's surface, offering two additional, analog degrees of freedom for interactive functions. Further, we show that our approach can be achieved on off-the-shelf consumer touchscreen devices: a smartphone and smartwatch. We validate our technique though a user study on both devices and conclude with several demo applications that illustrate the value and immediate feasibility of our approach.
Ganglion Identifiable Cells in the Crustacean Stomatogastric

Physiol. Soc. ESSN: 1548-9221. Visit our website at http://www.the-aps.org/. American Physiological Society, 9650 Rockville Pike, Bethesda MD 20814-3991. ©2010 Int. Union Physiol. Sci./Am. the physiological developments. It is published bimonthly in February, April, June, August, October, and December by (formerly published as News in Physiological Science) publishes brief review articles on major Physiology by gest on O cber 9, 2016 http://physioline.physiology. org/ D ow nladed fom
Performance, ingestive behavior and carcass traits of lambs fed rations containing soybean cake

The aim of this study was to evaluate the performance, ingestive behavior and carcass traits of crossbred Dorper x Santa Ines lambs fed rations containing soybean cake. Twenty-four lambs (4 months of age and 24.3 ± 3.1 kg BW) were used in a completely randomized design with four treatments and six replicates. Treatments were the inclusion of 50, 100 or 150 g kg -1 of soybean cake in the ration, on a DM basis, and a control diet without this ingredient. Rations were offered ad libitum for 75 days and the lambs were slaughtered at 35 to 40 kg BW. Dry matter intake reduced linearly and the average daily gain had a quadratic response to the soybean cake levels, also decreasing with the addition of this ingredient. The time spent feeding increased and the idle time decreased linearly with the soybean cake levels, whereas the time spent in rumination was not affected. Hot and cold carcass weights decreased linearly with the addition of this ingredient. The addition of 50 to 150 g kg DM -1 of soybean cake to the ration for lambs is not recommended due to reduced animal performance, which may compromise the profitability of sheep farmers.
Wavelet Based 3D Compression for Very Large Volume Data Supporting Fast Random Access

We propose a wavelet based method for compressing volumetric data with little loss in quality. The method supports fast random access to individual voxels within the compressed volume. Such a method is important since storing and visualising very large volumes impose heavy demands on internal memory and external storage facilities making it accessible only to users with huge and expensive computers. This problem is not likely to become less in the future. Experimental results on the CT dataset of the Visible Human have shown that our method provides very high compression rates with fairly fast random access.
Phase-correction Data Assimilation and Application to Storm-scale Numerical Weather Prediction. Part I: Method Description and Simulation Testing

An objective method of determining and correcting phase or position errors in numerical weather prediction is described and tested in a radar data observing system simulation experiment (OSSE) addressing the forecasting of ongoing thunderstorms. Such phase or position errors are common in numerical forecasts at grid resolutions of 1-to-20 km (meso-γ scale). It is proposed that the process of correcting a numerical forecast field can be simplified if such errors are addressed directly. An objective method of determining the phase error in the forecast by searching for a field of shift vectors that minimizes a squared-error difference from high-resolution observations is described. Three methods of applying a phase error correction to a forecast model are detailed. The first applies the entire correction at the initial time, the second in discrete steps during an assimilation window, and the third applies the correction continuously through the model's horizontal advection process. It is shown that the phase correction method is effective in producing an analysis field that agrees with the data yet preserves the structure developed by the model. The three methods of assimilating the correction in the forecast are successful, and a long-term positive effect on the thunderstorm simulation is achieved in the simulations, even as the modeled storms go through a cycle of decline and regeneration.
Interstellar Deuterium, Nitrogen, and Oxygen Abundances toward BD +28°4211: Results from the FUSE Mission

High-resolution far-UV spectra of the O-type subdwarf BD +28°4211 were obtained with the Far Ultraviolet Spectroscopic Explorer (FUSE) to measure the interstellar deuterium, nitrogen, and oxygen abundances in this direction. The interstellar D I transitions are analyzed down to Lyι at 920.7 Å. The star was observed several times at different target offsets in the direction of spectral dispersion. The aligned and co-added spectra have high signal-to-noise ratios (S/N = 50-100). D I, N I, and O I transitions were analyzed with curve-of-growth and profile fitting techniques. A model of interstellar molecular hydrogen on the line of sight was derived from H2 lines in the FUSE spectra and used to help analyze some features where blending with H2 was significant. The H I column density was determined from high-resolution Hubble Space Telescope Space Telescope Imaging Spectrograph spectra of Lyα to be log N(H ) = 19.846 ± 0.035 (2 σ), which is higher than is typical for sight lines in the local interstellar medium (ISM) studied for D/H. We found that D/H = (1.39 ± 0.21) × 10-5 (2 σ) and O/H = (2.37 ± 0.55) × 10-4 (2 σ). O/H toward BD +28°4211 appears to be significantly below the mean O/H ratio for the ISM and the Local Bubble.
Main-sequence stars of 10 and 30M : approaching the steady-state rotation

The evolution of the angular velocity profile in 10 and30 M main-sequence (MS) stars has been calculated from the initial uniform rotation to the asymptotic steady-state rota- tion. Following Zahn (1992) we assume that both transport of angular momentum and mixing of chemical elements are pro- duced by rotationally induced meridional circulation and tur- bulent diffusion. It is shown that for a sufficiently large surface rotational velocity, whose value can be estimated a priori, the relaxation time for star's achieving the steady-state rotation is much shorter than the star's MS life-time. In this case the as- sumption that a star is in a state of stationary rotation from the very beginning of its MS evolution is quite reasonable. On the other hand, for a star rotating slowly one has to solve the nonsta- tionary angular momentum transport equation simultaneously with the stellar evolution calculations. Despite the fact that the rate of mixing of chemical elements by meridional circulation is strongly reduced by horizontal erosion, diffusion-like abun- dance profiles of C and N are built up in the radiative envelope by the end of the star's MS life. The surface N abundance begins to increase after some delay time required for the diffusion wave to reach the atmosphere. If mixing penetrates the convective core the abundance of He is expected to behave like that of N. In- ternal gravity waves generated near the convective core border are shown to probably play an important role as another angular momentum transport mechanism, especially in the inner part of the envelope.
A search based approach to non maximum suppression in face detection

Face detectors typically produce a large number of false positives and this leads to the need to have a further non maximum suppression stage to eliminate multiple and spurious responses. This stage is based on considering spatial heuristics: true positive responses are selected by implicitly considering several restrictions on the spatial distribution of detector responses in natural images. In this paper we analyze the limitations of this approach and propose an efficient search method to overcome them. Results show how the application of this new non-maximum suppression approach to a simple face detector boosts its performance to state of the art results.
Compressed Bitmaps Based Frequent Itemsets Mining on Hadoop

Frequent itemsets mining is one of the interesting applications of data mining. Recently data mining has got a great deal of attention due to the explosive growth in data and the economic and scientific need for turning such data into useful information. However, the traditional frequent itemsets mining algorithms have become inefficient to work with large datasets effectively on a single machine due to computational power and memory limits. Current methods prefer to control the execution time and output by using higher minimum support thresholds, which lead to less candidates and frequent itemsets. In this paper, an improved-version of Apriori like HFDM-EB algorithm that can deal with lower minimum support thresholds is proposed for mining frequent itemsets over big transactional data on Hadoop framework and by utilizing compressed bitmaps. The experimental results show that the improved algorithm is efficient and scalable for mining frequent itemsets in big data.
A type directed translation of MLF to system F

The MLF type system by Le Botlan and Rémy is a natural extension of Hindley-Milner type inference that supports full first-class polymorphism, where types can be of higher-rank and impredicatively instantiated. Even though MLF is theoretically very attractive, it has not seen widespread adoption. We believe that this partly because it is unclear how the rich language of MLF types relate to standard System F types. In this article we give the first type directed translation of MLF terms to System F terms. Based on insight gained from this translation, we also define "Rigid MLF" (MLF=), a restriction of MLF where all bound values have a System F type. The expressiveness of MLF= is the same as that of boxy types, but MLF= needs fewer annotations and we give a detailed comparison between them.