gebhart/patrepeval huggingface dataset:
Spam detection in voice-over-IP calls through semi-supervised clustering (2009)

In this paper, we present an approach for detection of spam calls over IP telephony called SPIT in VoIP systems. SPIT detection is different from spam detection in email in that the process has to be soft real-time, fewer features are available for examination due to the difficulty of mining voice traffic at runtime, and similarity in signaling traffic between legitimate and malicious callers. Our approach differs from existing work in its adaptability to new environments without the need for laborious and error-prone manual parameter configuration. We use clustering based on the call parameters, using optional user feedback for some calls, which they mark as SPIT or non-SPIT. We improve on a popular algorithm for semi-supervised learning, called MPCK-Means, to make it scalable to a large number of calls and operate at runtime. Our evaluation on captured call traces shows a fifteen fold reduction in computation time, with improvement in detection accuracy.
Discovery of Imidazo[1,2-<i>b</i>]pyridazine Derivatives: Selective and Orally Available Mps1 (TTK) Kinase Inhibitors Exhibiting Remarkable Antiproliferative Activity (2015)

Monopolar spindle 1 (Mps1) is an attractive oncology target due to its high expression level in cancer cells as well as the correlation of its expression levels with histological grades of cancers. An imidazo[1,2-a]pyrazine 10a was identified during an HTS campaign. Although 10a exhibited good biochemical activity, its moderate cellular as well as antiproliferative activities needed to be improved. The cocrystal structure of an analogue of 10a guided our lead optimization to introduce substituents at the 6-position of the scaffold, giving the 6-aryl substituted 21b which had improved cellular activity but no oral bioavailability in rat. Property-based optimization at the 6-position and a scaffold change led to the discovery of the imidazo[1,2-b]pyridazine-based 27f, an extremely potent (cellular Mps1 IC50 = 0.70 nM, A549 IC50 = 6.0 nM), selective Mps1 inhibitor over 192 kinases, which could be orally administered and was active in vivo. This 27f demonstrated remarkable antiproliferative activity in the nanomolar range against various tissue cancer cell lines.
Structural Characterization of the Interaction between a Pleckstrin Homology Domain and Phosphatidylinositol 4,5-Bisphosphate (1995)

The pleckstrin homology (PH) domain is a protein module of approximately 100 amino acids that is found in several proteins involved in signal transduction [for a recent review, see Gibson et al. (1994) Trends Biochem. Sci. 19, 349-353]. Although the specific function of the PH domain has not yet been elucidated, many of the proteins which contain this domain associate with phospholipid membranes, and PH domains have been shown to bind to phosphatidylinositol 4,5-bisphosphate (PIP2) [Harlan et al. (1994) Nature 371, 168-170] and the beta gamma subunits of G-proteins [Touhara et al. (1994) J. Biol. Chem. 269, 10217-10220]. We have postulated that pleckstrin homology domains may be important for the translocation of proteins to the membrane by an interaction with the negatively charged head group of phospholipids. Here we show the importance of three conserved lysine residues for binding to PIP2 by site-directed mutagenesis. These results should aid future site-directed mutagenesis studies in probing the function of PIP2-PH domain interactions in the various proteins containing this module. In addition, we examine the specificity of this binding and illustrate the importance of charge--charge interactions in PIP2-PH domain complex formation from binding experiments involving PIP2 analogs.
Synthesis: an efficient implementation of fundamental operating system services (1992)

This dissertation shows that operating systems can provide fundamental services an order of magnitude more efficiently than traditional implementations. It describes the implementation of a new operating system kernel, Synthesis, that achieves this level of performance. The Synthesis kernel combines several new techniques to provide high performance without sacrificing the expressive power or security of the system. The new ideas include: ffl Run-time code synthesis --- a systematic way of creating executable machine code at runtime to optimize frequently-used kernel routines --- queues, buffers, context switchers, interrupt handlers, and system call dispatchers --- for specific situations, greatly reducing their execution time. ffl Fine-grain scheduling --- a new process-scheduling technique based on the idea of feedback that performs frequent scheduling actions and policy adjustments (at submillisecond intervals) resulting in an adaptive, self-tuning system that can support real-ti...
Determination of optimal PTV margin for patients receiving CBCT‐guided prostate IMRT: comparative analysis based on CBCT dose calculation with four different margins (2015)

Variations in daily setup and rectum/bladder filling lead to uncertainties in the delivery of prostate IMRT. The purpose of this study is to determine the optimal PTV margin for CBCT-guided prostate IMRT based on daily CBCT dose calculations using four different margins. Five patients diagnosed with low-risk prostate cancer were treated with prostate IMRT to 70 Gy in 28 fractions using daily CBCT for image guidance. The prostate CTV and OARs were contoured on all CBCTs. IMRT plans were created using 1 mm, 3 mm, 5 mm, and 7 mm CTV to PTV expansions. For each delivered fraction, dose calculations were generated utilizing the pretreatment CBCT translational shifts performed and dosimetric analysis was performed. One hundred and forty total treatment fractions (CBCT sessions) were evaluated. The planned prostate CTV V100% was 100% for all PTV margins. Based on CBCT analysis, the actual cumulative CTVs V100% were 96.55% ± 2.94%, 99.49% ± 1.36%, 99.98% ± 0.26%, and 99.99% ± 0.05% for 1, 3, 5, and 7 mm uniform PTV margins, respectively. Delivered rectum and bladder doses were different as compared to expected planned doses, with the magnitude of differences increasing with PTV margin. Daily setup variation during prostate IMRT yields differences in the actual vs. expected doses received by the prostate CTV, rectum, and bladder. The magnitude of these differences is significantly affected by the PTV margin utilized. It was found that when daily CBCT was used for soft-tissue alignment of the prostate, a 3 mm PTV margin allowed for CTV to be covered for 99% of cases.
Mice lacking the adenosine A<sub>1</sub> receptor are anxious and aggressive, but are normal learners with reduced muscle strength and survival rate (2002)

Behavioural assessment of mice lacking adenosine A1 receptors (A1Rs) showed reduced activity in some phases of the light-dark cycle, reduced exploratory behaviour in the open-field and in the hole-board, increased anxiety in the plus maze and dark-light box and increased aggressiveness in the resident-intruder test. No differences were found in spatial reference and working memory in several Morris water maze tasks. Both mutant mice had reduced muscle strength and survival rate. These results confirm the involvement of adenosine in motor activity, exploratory behaviour, anxiety and aggressiveness. A1Rs also appear to play a critical role in ageing-related deterioration.
Inverse Kinematics – Cyclic Coordinate Descent (CCD) (2012)

This article examines the popular inverse kinematic (IK) method known as cyclic coordinate descent (CCD) and its viability for creating and controlling highly articulated characters (e.g., humans and insects). The reason CCD is so popular is that it is a computationally fast, algorithmically simple, and straight-forward technique for generating IK solutions that can run at interactive frame rates. Whereas it can be relatively clear-cut to construct an IK system using CCD, we address a number of engineering solutions necessary to make the CCD technique a viable and practical method for character-based environments, such as games. We discuss implementation details, limitations (e.g., angle limits, performance tips, convergence problems, oscillation issues, and comfort factors), and their applicability to articulated configurations. Whereas a plain implementation may focus only on a single-linked chained IK problem and disregard multiple connected hierarchical goals (e.g., articulated characters), we examine both cases. We also examine why naïve constructions of the CCD algorithm can be incorrect even, though they converge on a solution. Furthermore, we discuss how the CCD algorithm can be fine-tuned to produce more natural lifelike character poses that can be used to generate realistic motions. Hence, after reading this article, the reader should have the knowledge to design and create an effective and flexible CCD implementation for real-time environments, such as games, while understanding and appreciating the limitations and hazards in a practical situation.
Formulation studies on cysteamine for the treatment of nephropathic cystinosis (2011)

Nephropathic cystinosis is a rare autosomal recessive disease characterised by raised lysosomal levels of cystine in the cells of almost all organs. It is treated by regular oral and topical administration of the aminothiol, cysteamine(Cystagon™), which possesses an offensive taste and smell. The oral form frequently causes emesis,and should be administered every\nsix hours to be maximally effective. The topical eye drop treatment requires hourly application to be most effective.In an attempt to reduce this frequency and improve the treatment, the preparation and evaluation of three alternative cysteamine containing formulations (suppositories, long-acting ophthalmic gels and an inhaler) was undertaken.\nThe physiochemical properties, stability and release profiles of the active (cysteamine or phe conjugate) from the formulations were evaluated. The suppositories released cysteamine over a 20-40 minute period with a T75=\n10-13minutes. They were most stable at 4°C. The analysis of the ophthalmic gels demonstrated that a weak gel network was formed at low shear stress, the bioadhesion of the gel was increased with inclusion of a cysteamine derivative (e.g.mean force of 0.067N compared to 0.107N with compound included) and eight-hour, first order release from the gel was observed. There was significant adhesion observed between the ophthalmic gels and bovine corneal tissue. The pulmonary microspheres were spherical and within the optimum size range for deep lung delivery (1-5μm). However, Andersen Cascade Impactor analysis revealed poor deep lung penetration.\nIn conclusion, these results demonstrated that more development work was required to produce a useful pulmonary formulation of cysteamine, however, formulation of an ocular applicable gel or suppository was readily achievable. The suppository preparations may be particularly beneficial for the treatment of infants, whilst the ophthalmic gel preparations could be developed for daily or overnight use. With respect to pulmonary delivery, microspheres in the optimum size range were produced. However, deep lung targeting was prevented by static agglomeration, which requires further investigation.
Cooperative forest fire surveillance using a team of small unmanned air vehicles (2006)

This research was supported by NASA under STTR contract No. NNA04AA19C to Scientific Systems Company, Inc (SSCI) and Brigham Young University (BYU), and by AFOSR grants F49620-01-1-0091 and F49620-02-C- 0094. The objective of this paper is to explore the feasibility of using multiple low-altitude, short endurance (LASE) unmanned air vehicles (UAVs) to cooperatively monitor and track the propagation of large forest fires. A real-time algorithm for tracking the perimeter of a fire with an on-board infrared sensor is developed. Using this algorithm, we develop a decentralized multiple-UAV approach to monitoring the perimeter of the fire. The UAVs are assumed to have limited communication and sensing range. The effectiveness of the approach is demonstrated in simulation using a 6 DOF dynamic model for the UAV and numerical propagation model for the forest fire. Salient features of the approach include the ability to monitor a changing fire perimeter, the ability to systematically add and remove UAVs from the team, and the ability to supply time-critical information to forest fire fighters.
A new technique for fabrication of a Gas Electron Multiplier (2002)

The Gas Electron Multiplier (GEM) represents one of the most promising micro-pattern detectors for providing stable, charge multiplication over a wide range of active areas, and with genuinely affordable and reproducible fabrication methods. Several important characteristics of the GEM remain to be investigated and optimized. One key feature is the charging-up of the dielectric insulating layer of GEMs and its dependence on hole geometry. Using an epoxy-based photoresist, we are developing a fabrication technique that naturally generates purely cylindrical holes in the GEM electrode, a geometry that has been found by previous researchers to minimize or eliminate this effect. This report describes the principle of the fabrication technique and presents experimental results of energy resolution, gain, rate capability and potential for large area applications. These compare favorably with the attributes of existing techniques.
Experimental verification of dose calculation using the simplified Monte Carlo method with an improved initial beam model for a beam-wobbling system (2013)

A beam delivery system using a single-radius-beam-wobbling method has been used to form a conformal irradiation field for proton radiotherapy in Japan. A proton beam broadened by the beam-wobbling system provides a non-Gaussian distribution of projection angle different in two mutually orthogonal planes with a common beam central axis, at a certain position. However, the conventional initial beam model for dose calculations has been using an approximation of symmetric Gaussian angular distribution with the same variance in both planes (called here a Gaussian model with symmetric variance (GMSV)), instead of the accurate one. We have developed a more accurate initial beam model defined as a non-Gaussian model with asymmetric variance (NonGMAV), and applied it to dose calculations using the simplified Monte Carlo (SMC) method. The initial beam model takes into account the different distances of two beam-wobbling magnets from the iso-center and also the different amplitudes of kick angle given by each magnet. We have confirmed that the calculation using the SMC with NonGMAV reproduced the measured dose distribution formed in air by a mono-energetic proton beam passing through a square aperture collimator better than with the GMSV and with a Gaussian model with asymmetric variance (GMAV) in which different variances of angular distributions are used in the two mutually orthogonal planes. Measured dose distributions in a homogeneous phantom formed by a modulated proton beam passing through a range shifter and an L-shaped range compensator, were consistent with calculations using the SMC with GMAV and NonGMAV, but in disagreement with calculations using the SMC with GMSV. Measured lateral penumbrae in a lateral direction were reproduced better by calculations using the SMC with NonGMAV than by those with GMAV, when an aperture collimator with a smaller opening was used. We found that such a difference can be attributed to the non-Gaussian angular distribution of the initial beam at a lateral position for the beam-wobbling system. Calculations using the SMC with NonGMAV are effective to reproduce dose distributions formed by a beam-wobbling system more accurately than that with GMSV or that with GMAV.
Flicker reduction in intraframe codecs (2004)

Videos coded with intraframe codecs show flicker. For wavelet codecs this flicker impairs the visual quality significantly which is a major problem. It is said to be intrinsic to intraframe wavelet codecs. This paper analyses why flicker artifacts happen. We will illustrate our findings refering to motion JPEG2000. We will present some statistics on the flicker location in the wavelet domain. Depending on the frequency-band flicker will be more or less significant. Based on our analysis a flicker filter is developed which employs interframe information. The amount of this interframe information is minimal: 2 bits per pixel often produce compelling results. The interframe information does not have to be stored. We have developed an encoder which makes use of this filter. Our encoder produces a fully compliant motion JPEG2000 codestream.
A binary algorithm for the Jacobi symbol (1993)

We present a new algorithm to compute the Jacobi symbol, based on Stein's binary algorithm for the greatest common divisor, and we determine the worst-case behavior of this algorithm. Our implementation of the algorithm runs approximately 7--25% faster than traditional methods on inputs of size 100--1000 decimal digits.
Extracting lay paraphrases of specialized expressions from monolingual comparable medical corpora (2009)

Whereas multilingual comparable corpora have been used to identify translations of words or terms, monolingual corpora can help identify paraphrases. The present work addresses paraphrases found between two different discourse types: specialized and lay texts. We therefore built comparable corpora of specialized and lay texts in order to detect equivalent lay and specialized expressions. We identified two devices used in such paraphrases: nominalizations and neo-classical compounds. The results showed that the paraphrases had a good precision and that nominalizations were indeed relevant in the context of studying the differences between specialized and lay language. Neo-classical compounds were less conclusive. This study also demonstrates that simple paraphrase acquisition methods can also work on texts with a rather small degree of similarity, once similar text segments are detected.
Efficacy and tolerance of adapalene cream 0.1% compared with its cream vehicle for the treatment of acne vulgaris. (2001)

Adapalene gel 0.1% is approved for use in the treatment of acne vulgaris. A new cream formulation, adapalene cream 0.1%, has been developed. Our objective was to evaluate the efficacy and tolerability of adapalene cream 0.1% in comparison with its cream vehicle, applied once daily for 12 weeks to patients with facial acne vulgaris. We used a 12-week, multicenter, randomized, double-blind, vehicle-controlled, comparative phase 3 study of adapalene cream 0.1% and cream vehicle. The study enrolled 237 patients (125 males and 112 females), aged 12 through 30 years, with mild-to-moderate acne vulgaris. Adapalene cream 0.1% demonstrated superior efficacy compared with its cream vehicle. Significantly lower numbers of total inflammatory and noninflammatory lesion counts were observed at the end of the study period in patients using adapalene cream 0.1% as opposed to those using cream vehicle (P<.05 compared with baseline, for all 3 parameters). Adapalene cream 0.1% caused more cutaneous side effects than the cream vehicle, but these were tolerated in most patients. In summary, the results of this study indicate that adapalene cream 0.1% demonstrates superior efficacy over cream vehicle for the treatment of acne vulgaris. Adapalene cream 0.1% also has excellent tolerability and is associated with a low incidence of cutaneous adverse events.
Influence of nonlinear electrostatics on transfer energies between liquid phases: Charge burial is far less expensive than Born model (2008)

The widely used Born model describes the electrostatic response of continuous media using static dielectric constants. However, when applied to a liquid environment, a comparison of Born model predictions with experimental values (e.g., transfer free energies and pK(a) shifts) found that agreement is only achieved by using physically unrealistic dielectric constants for proteins, lipids, etc., and/or equally unrealistic atomic radii. This leads to questions concerning the physical origins for this failure of the Born model. We partially resolve this question by applying the Langevin-Debye (LD) model of a continuous distribution of point, polarizable dipoles, a model that contains an added dependence of the electrostatic response on the solvent's optical dielectric constant and both gas- and liquid-phase dipole moments, features absent in the Born model to which the LD model reduces for weak fields. The LD model is applied to simple representations of three biologically relevant systems: (i) globular proteins, (ii) lipid bilayers, and (iii) membrane proteins. The linear Born treatment greatly overestimates both the self-energy and the transfer free energy from water to hydrophobic environments (e.g., a protein interior). By using the experimental dielectric constant, the energy cost of charge burial in either globular or membrane proteins of the Born model is reduced by almost 50% with the nonlinear theory as is the pK(a) shift, and the shifts agree well with experimental trends.
Impact of Genetic Features on Treatment Decisions in AML (2011)

In recent years, research in molecular genetics has been instrumental in deciphering the molecular pathogenesis of acute myeloid leukemia (AML). With the advent of the novel genomics technologies such as next-generation sequencing, it is expected that virtually all genetic lesions in AML will soon be identified. Gene mutations or deregulated expression of genes or sets of genes now allow us to explore the enormous diversity among cytogenetically defined subsets of AML, in particular the large subset of cytogenetically normal AML. Nonetheless, there are several challenges, such as discriminating driver from passenger mutations, evaluating the prognostic and predictive value of a specific mutation in the concert of the various concurrent mutations, or translating findings from molecular disease pathogenesis into novel therapies. Progress is unlikely to be fast in developing molecular targeted therapies. Contrary to the initial assumption, the development of molecular targeted therapies is slow and the various reports of promising new compounds will need to be put into perspective because many of these drugs did not show the expected effects.