Miracle-dz/UniFAR-FTUs huggingface dataset:
The Lazy Sweep Ray Casting Algorithm for Rendering Irregular Grids

Lazy sweep ray casting is a fast algorithm for rendering general irregular grids. It is based on the sweep-plane paradigm, and it is able to accelerate ray casting for rendering irregular grids, including disconnected and nonconvex unstructured irregular grids (even with holes) with a rendering cost that decreases as the "disconnectedness" decreases. The algorithm is carefully tailored to exploit spatial coherence even if the image resolution differs substantially from the object space resolution. Lazy sweep ray casting has several desirable properties, including its generality, (depth-sorting) accuracy, low memory consumption, speed, simplicity of implementation and portability (e.g. no hardware dependencies). We establish the practicality of our method through experimental results based on our implementation, which is shown to be substantially faster (by up to two orders of magnitude) than other algorithms implemented in software. We also provide theoretical results, both lower and upper bounds, on the complexity of ray casting of irregular grids.
Evaluation of Medical Problem Extraction from Electronic Clinical Documents Using MetaMap Transfer (MMTx)

To improve the use and quality of the electronic Problem List, which is at the heart of the problem-oriented medical record in development in our institution (Intermountain Health Care, Utah, U.S.), we developed an Automated Problem List system using Natural Language Processing (NLP) technologies. A key part of this system is a module that automatically extracts potential medical problems from free-text clinical documents. The NLP module uses MMTx, developed at the U.S. National Library of Medicine. Negation detection was added to this application by adapting a negation detection algorithm called NegEx. To evaluate the adequacy of the performance of the NLP module for our Automated Problem List system, we evaluated it with 160 electronic clinical documents of different types. Two different data sets for MMTx were used: the default full UMLS data set and a customised subset adapted to detect the set of 80 medical problems we are interested in. With the default data set, we measured a recall of 0.74 (95% CI 0.68-0.8) and a precision of 0.76 (0.69-0.82). The customised subset had a significantly better recall of 0.9 (0.85-0.94), and a non-significantly different precision of 0.69 (0.63-0.75).
Exposure of T7 RNA Polymerase to the Isolated Binding Region of the Promoter Allows Transcription from a Single-stranded Template*

While the binding region of the T7 promoter must be double-stranded (ds) to function, the non-template strand in the initiation region is dispensable, and a promoter that lacks this element allows efficient initiation. To determine whether the binding region serves merely to recruit the RNA polymerase (RNAP) to the vicinity of a melted initiation region or provides other functions, we utilized a GAL4-T7 RNAP fusion protein to provide an independent binding capacity to the RNAP. When the GAL4-T7 RNAP was recruited to a single-stranded (ss) promoter via a nearby Gal4 recognition sequence, no transcription was observed. However, transcription from the ss promoter could be activated by the addition,in trans, of a ds hairpin loop that contains only the binding region of the promoter. The same results were obtained in the absence of the GAL4 recognition sequence in the template and were also observed with wild type enzyme. Gel-shift experiments indicate that exposure of the RNAP to the isolated binding region facilitates recruitment of the ss template, but that the binding region is displaced from the complex prior to initiation. We conclude that exposure of the RNAP to the isolated binding region reorganizes the enzyme, allowing it to bind to the ss template. These findings have potential implications with regard to mechanisms of promoter binding and melting.
Super-resolution using multiple structured dictionaries based on the gradient operator and bicubic interpolation

In this paper we present an extension to the algorithm of super-resolution via selective sparse representation over a set of coupled low and high resolution cluster dictionary pairs. Patch clustering and sparse model selection are carried out using the magnitude and phase of the patch gradient operator. A compact dictionary pair is learned for each cluster. A low resolution patch is classified into one of the clusters using the two criteria. A high resolution patch is reconstructed using the high resolution cluster dictionary, and the spare representation coefficients of its low resolution counterpart over the low resolution cluster dictionary. This extension aims at super-resolving patches of low sharpness or poor directionality with bicubic interpolation. Accordingly, the computationally expensive sparse representation framework will only be applied on a limited portion of image patches. As a result, the super-resolution reconstruction computational complexity is significantly reduced without sacrificing the performance. Experiments conducted over natural images validate this result.
A framework for wireless LAN monitoring and its applications

Many studies on measurement and characterization of wireless LANs (WLANs) have been performed recently. Most of these measurements have been conducted from the wired portion of the network based on wired monitoring (e.g. sniffer at some wired point) or SNMP statistics. More recently, wireless monitoring, the traffic measurement from a wireless vantage point, is also widely adopted in both wireless research and commercial WLAN management product development. Wireless monitoring technique can provide detailed PHY/MAC information on wireless medium. For the network diagnosis purpose (e.g. anomaly detection and security monitoring) such detailed wireless information is more useful than the information provided by SNMP or wired monitoring. In this paper we have explored various issues in implementing the wireless monitoring system for an IEEE 802.11 based wireless network. We identify the pitfalls that such system needs to be aware of, and then provide feasible solutions to avoid those pitfalls. We implement an actual wireless monitoring system and demonstrate its effectiveness by characterizing a typical computer science department WLAN traffic. Our characterization reveals rich information about the PHY/MAC layers of the IEEE 802.11 protocol such as the typical traffic mix of different frame types, their temporal characteristics and correlation with the user activities. Moreover, we identify various anomalies in protocol and security of the IEEE 802.11 MAC. Regarding the security, we identify malicious usages of WLAN, such as email worm and network scanning. Our results also show excessive retransmissions of some management frame types reducing the useful throughput of the wireless network.
Complete Genome Sequence of Exiguobacterium sp. Strain MH3, Isolated from Rhizosphere of Lemna minor

ABSTRACT We report the complete genome sequence of Exiguobacterium sp. strain MH3, isolated from the rhizosphere of duckweed. The genome assembly is 3.16 Mb, with a G+C content of 47.24%, and it may provide useful information about plant-microbe interactions and the genetic basis for the tolerance of the strain to various environmental stresses.
Rapid Early Triage by Leukocytosis and the Thrombolysis in Myocardial Infarction (TIMI) Risk Score for ST-Elevation Myocardial Infarction Undergoing Primary Percutaneous Coronary Intervention

AbstractThe clinical utility of leukocytosis in risk assessment for ST-elevation myocardial infarction (STEMI) is still unclear. We aim to demonstrate the prognostic value of leukocyte counts independent from traditional risk factors and the TIMI risk score (TRS) for STEMI and to propose a practical model comprising leukocyte count for early triage in STEMI undergoing primary angioplasty.A prospective database (n = 796) of consecutive STEMI cases receiving primary angioplasty at a tertiary medical center was retrospectively analyzed in the period from February 1, 2007 through December 31, 2012. Primary endpoints were 30-day and 1-year mortality. Propensity score-adjusted Cox regression models and subdivision analysis were performed.Leukocytosis group (n = 306) had higher 30-day mortality (5.9% vs 3.1%, P = 0.048) and 1-year mortality (9.2% vs 5.1%, P = 0.022). After adjustment by propensity score and TRS, leukocyte count (per 103/&mgr;L) was an independent predictor of 1-year mortality (HR: 1.086, 95% CI: 1.034–1.140, P = 0.001). Subdivision analysis demonstrated the correlation between leukocytosis and higher 1-year mortality within both high and low TRS strata (divided by 4, the median of TRS). Additionally, 24% (191 out of 796) of patients were characterized by nonleukocytosis and TRS < 4, having 0% of mortality rate at 1-year follow-up.In conclusion, leukocyte count is an independent prognostic factor adding incremental value to TRS for STEMI. Nonleukocytosis in conjunction with TRS < 4 identifies a large patient group at extremely low risk and thus provides rapid early triage for STEMI patients undergoing primary PCI. This finding is worth validation in the future.
Developmental Stage Specificity and the Role of Mitochondrial Metabolism in the Response of Arabidopsis Leaves to Prolonged Mild Osmotic Stress1[C][W][OA]

When subjected to stress, plants reprogram their growth by largely unknown mechanisms. To provide insights into this process, the growth of Arabidopsis (Arabidopsis thaliana) leaves that develop under mild osmotic stress was studied. Early during leaf development, cell number and size were reduced by stress, but growth was remarkably adaptable, as division and expansion rates were identical to controls within a few days of leaf initiation. To investigate the molecular basis of the observed adaptability, leaves with only proliferating, exclusively expanding, and mature cells were analyzed by transcriptomics and targeted metabolomics. The stress response measured in growing and mature leaves was largely distinct; several hundred transcripts and multiple metabolites responded exclusively in the proliferating and/or expanding leaves. Only a few genes were differentially expressed across the three stages. Data analysis showed that proliferation and expansion were regulated by common regulatory circuits, involving ethylene and gibberellins but not abscisic acid. The role of ethylene was supported by the analysis of ethylene-insensitive mutants. Exclusively in proliferating cells, stress induced genes of the so-called “mitochondrial dysfunction regulon,” comprising alternative oxidase. Up-regulation for eight of these genes was confirmed with promoter:β-glucuronidase reporter lines. Furthermore, mitochondria of stress-treated dividing cells were morphologically distinct from control ones, and growth of plants overexpressing the alternative oxidase gene was more tolerant to osmotic and drought stresses. Taken together, our data underline the value of analyzing stress responses in development and demonstrate the importance of mitochondrial respiration for sustaining cell proliferation under osmotic stress conditions.
Branching on Attribute Values in Decision Tree Generation

The problem of deciding which subset of values of a categorical-valued attribute to branch on during decision tree generation is addressed. Algorithms such as ID3 and C4 do not address the issue and simply branch on each value of the selected attribute. The GID3* algorithm is presented and evaluated. The GID3* algorithm is a generalized version of Quinlan's ID3 and C4, and is a non-parametric version of the GID3 algorithm presented in an earlier paper. It branches on a subset of individual values of an attribute, while grouping the rest under a single DEFAULT branch. It is empirically demonstrated that GID3* outperforms ID3 (C4) and GID3 for any parameter setting of the latter. The empirical tests include both controlled synthetic (randomized) domains as well as real-world data sets. The improvement in tree quality as measured by number of leaves and estimated error rate is significant.
The Influence of Exchangeable Ions and Their Concentration in the Pore Fluid on Plastic and Strength Properties of Cohesive Soil

ABD-EL-AZIZ, MAHMOUD H. ; 1933; The Influence of Exchangeable Ions and Their Concentration in the Pore Fluid on Plastic and Strength Properties of Cohesive Soil; Department of Civil Engineering; Dr. A. A. Bishop, major professor. A study was conducted to find out both the effect of different exchangeable cations and the concentration of ions in the soil pore fluid on strength and plastic properties of a sample of cohesive soil taken from the bank of an open drain ditch at the Utah State University Irrigation and Drainage Farm. The experimental results of this study may be sumrp.arized by the following points: 1. A general decrease of liquid limit and an increase -in :}j:oth shear strength and modulus of elasticity, with increasing salt concentration in the pore fluid, were observed for all samples, with the exception of HCI-treated samples for which shear strength was independent of HCI concentration in the pore water. 2. An increase in both shear strength and modulus of elasticity with decreasing exchangeable sodium percentage was definite. 3,\ The increase of soil shear strength caused by different exchangeable cations with distilled water in the soil pores was in the ord~v Na + < Ca ++ < Mg ++ < K + < HCl-treated soil. whereas the modulus of + + ++ . elasticity increased in order Na < K < Ca < HCI-treated solI < ++ Mg 4. A decrease in the liquid lhnit with decreasing exchangeable sodium was found. 5. The influence of the diffe:rent exchangeable cations used on + d 1 M++ soil liquid limit was in the order Na > HCl-treate samp e > g > C ++ K+ a > . From this study it could be concluded that: 1. The strength and plastic properties of cohesive soils are affected greatly by the type and concentration of adsorbed ions as well as by the ions concentration in the pore fluid. 2. The failure of the sloping sides of drain ditches may be attributed at least in part to increasing exchangeable sodium percentage. 3. For satisfactory and economical design of earth structures, a knowledge of chemical as well as physical properties of cohesive soils is essential. The boundary conditions which may change the soil physico . chemical properties with time should be considered. 4. Strength properties of HCl-treated soils are controlled by aluminum rather than hydrogen ions. Exchangeable aluminum ~as liberated as a result of the breakdown of the clay fraction in soils when treated with HC! 5. The experimental results are not completely explained in terms of the Gouy-Chapman theory of double layers. However, the Stern theory which considers the specific adsorption of ions on clay surfaces is a better alternative and does explain the results adequately.
Information systems outsourcing: a Delphi study from Spain

Purpose – The widespread growth of information systems (IS) outsourcing on an international scale contrasts sharply with the somewhat limited development of this practice in Spain. The purpose of this paper is to deal with the situation of IS outsourcing in this country.Design/methodology/approach – For this purpose, the paper has used the opinions and comments of those in charge of IS departments at the largest Spanish firms through a normative Delphi study.Findings – Outsourcing makes it possible to achieve strategic as well as economic advantages and managers propose a number of ways to reduce the risks associated with this practice. Provider specialisation and permanent client‐provider contact are key aspects in order to ensure outsourcing success and development.Research limitations/implications – The paper is basically descriptive and, though it uses quantitative information, the analysis carried out is mainly qualitative. Furthermore, it refers exclusively to the context of large Spanish firms.Orig.
Face photo retrieval by sketch example

Face photo-sketch matching has received great attention in recent years due to its vital role in law enforcement. The major challenge of matching face photo and sketch is difference of visual characteristics between face photo and sketch which is referred as modality gap. Earlier approaches have reduced the modality gap by synthesizing face photos and sketches in a same modality (photo or sketch). However, the effectiveness of these approaches is highly affected by synthesis results. That means a poor synthesis might degrade the performance of matching. Therefore, recent works have focused to directly match face photo and sketch of different modalities. However, the features used by these approaches are not robust against modality gap. In this paper, a modality-invariant face descriptor called Gabor Shape is proposed to retrieve face photos based on a probe sketch. Experiments on CUFS and CUFSF datasets show that the new descriptor outperforms the state-of-the-art approaches.
Development of Linear, Ensemble, and Nonlinear Models for the Prediction and Interpretation of the Biological Activity of a Set of PDGFR Inhibitors

A QSAR modeling study has been done with a set of 79 piperazyinylquinazoline analogues which exhibit PDGFR inhibition. Linear regression and nonlinear computational neural network models were developed. The regression model was developed with a focus on interpretative ability using a PLS technique. However, it also exhibits a good predictive ability after outlier removal. The nonlinear CNN model had superior predictive ability compared to the linear model with a training set error of 0.22 log(IC50) units (R2 = 0.93) and a prediction set error of 0.32 log(IC50) units (R2 = 0.61). A random forest model was also developed to provide an alternate measure of descriptor importance. This approach ranks descriptors, and its results confirm the importance of specific descriptors as characterized by the PLS technique. In addition the neural network model contains the two most important descriptors indicated by the random forest model.
An IR Methodology to Assess the Behavior of Ferrofluidic Transducers—Case of Study: A Contactless Driven Pump

A single drop of ferrofluid can be used as active mass in an innovative pump scheme. The absence of mechanical moving parts and solid-inertial masses provides high reliability and the possibility to implement the pumping mechanism on preexisting channels. The main focus of this paper is to describe the IR-based technique adopted to "observe" the cap movement inside the channel of the developed pump, thus validating the supposed pumping mechanism. Moreover, experiments have been performed on the pump prototype in order to estimate the average amount of pumped liquid, the drop pressure, and the flow rate as functions of frequency and amplitude of the driving signals.
Multicanonical evaluation of joint probability density functions in communication system modeling

Previously, we have adapted multicanonical sampling to the evaluation of general probability distribution functions (pdfs) such as those appearing in communication system modeling. This letter demonstrates that joint pdfs can be computed in an identical manner. To illustrate, we determine the joint distribution function between the first- and second-order polarization-mode dispersion in an optical fiber.
Prediction and Control with Temporal Segment Models

We introduce a method for learning the dynamics of complex nonlinear systems based on deep generative models over temporal segments of states and actions. Unlike dynamics models that operate over individual discrete timesteps, we learn the distribution over future state trajectories conditioned on past state, past action, and planned future action trajectories, as well as a latent prior over action trajectories. Our approach is based on convolutional autoregressive models and variational autoencoders. It makes stable and accurate predictions over long horizons for complex, stochastic systems, effectively expressing uncertainty and modeling the effects of collisions, sensory noise, and action delays. The learned dynamics model and action prior can be used for end-to-end, fully differentiable trajectory optimization and model-based policy optimization, which we use to evaluate the performance and sample-efficiency of our method.
Identification of Genetic Networks from a Small Number of Gene Expression Patterns Under the Boolean Network Model

Liang, Fuhrman and Somogyi (PSB98, 18-29, 1998) have described an algorithm for inferring genetic network architectures from state transition tables which correspond to time series of gene expression patterns, using the Boolean network model. Their results of computational experiments suggested that a small number of state transition (INPUT/OUTPUT) pairs are sufficient in order to infer the original Boolean network correctly. This paper gives a mathematical proof for their observation. Precisely, this paper devises a much simpler algorithm for the same problem and proves that, if the indegree of each node (i.e., the number of input nodes to each node) is bounded by a constant, only O(log n) state transition pairs (from 2n pairs) are necessary and sufficient to identify the original Boolean network of n nodes correctly with high probability. We made computational experiments in order to expose the constant factor involved in O(log n) notation. The computational results show that the Boolean network of size 100,000 can be identified by our algorithm from about 100 INPUT/OUTPUT pairs if the maximum indegree is bounded by 2. It is also a merit of our algorithm that the algorithm is conceptually so simple that it is extensible for more realistic network models.
An overall study of a Dual Active Bridge for bidirectional DC/DC conversion

The increase demand of an intermediate storage of electrical energy in battery systems, in particular due to the use of renewable energy, has resulted in the need of bidirectional DC/DC power converters with galvanic isolation. Uninterruptible Power Supplies (UPS), battery charging systems, photovoltaic equipment and auxiliary power supplies in traction applications are examples of some fields of application of this kind of converters. A Dual Active Bridge (DAB) bidirectional DC/DC converter is a topology with the advantages of decreased number of devices, soft-switching commutations, low cost, and high efficiency. The use of this topology is proposed for applications where the power density, cost, weight, and reliability are critical factors. In the present paper the steady-state analysis of the converter has been carried out, giving some guidelines for the design (considering soft switching limits and the amount of reactive current) and a small-signal model of the topology. Simulations and experimental results are also presented.