gebhart/patrepeval huggingface dataset:
Inference of Security-Sensitive Entities in Libraries (2017)

Programming languages such as Java and C# execute code with different levels of trust in the same process, and rely on an access control model with fine-grained permissions to protect program code. Permissions are checked programmatically, and rely on programmer discipline. This can lead to subtle errors. To enable automatic security analysis about unauthorised access or information flow, it is necessary to reason about security-sensitive entities in libraries that must be protected by appropriate sanitisation/declassification via permission checks. Unfortunately, security-sensitive entities are not clearly identified. In this paper, we investigate security-sensitive entities used in Java-like languages, and develop a static program analysis technique to identify them in large codebases by analysing the patterns of permission checks. Although the technique is generic, our focus is on Java where checkPermission calls are used to guard potential security-sensitive entities. Our inference analysis uses two parameters called proximity and coverage to reduce false-positive and false-negative reports. The usefulness of the analysis is illustrated by the results obtained while checking the OpenJDK7-b147 for conformance to Java Secure Coding Guidelines that relate to the confidentiality and integrity requirements.
An A Posteriori Probability Calculation Method for Analytic Word Recognition Applicable to Address Recognition (2009)

In this paper, we propose a novel calculation method of an ldquoa posteriorirdquo probability for analytic word recognition.The method is suitable for address recognition tasks. Our previous method needs calculation over all words in a lexicon,while the proposed method only needs calculation on the concerned word. In the address recognition task, lexicon size becomes very large and only a part of it can be handled. Hence, the previous method cannot be used, and the proposed method is convenient. Experimental results show that the proposed method guarantees high precision of probability calculation.
Improved modeling of audio signals by modifying transient locations (2002)

We propose a method for obtaining an improved representation of transients in audio signals. The representation is based on a damped sinusoidal model. To improve the representation, transient locations are modified in such a way that a transient can start only at the beginning of a sinusoidal segment. The introduced modifications facilitate a reduction of the number of damped sinusoids needed to model a transient well and eliminate pre-echo artifacts. We verify with a listening test that the modifications do not result in a perceptual difference between the original and modified audio signals.
Multi Impairment Monitoring for Optical Networks (2009)

As optical networks become more complex, the need for in-line monitoring of more than just channel wavelength, power and OSNR becomes compelling. In this paper we describe an asynchronous delay tap sampling technique coupled with statistical machine learning that enables a single monitor to measure multiple simultaneous impairments on multiple formats. We demonstrate the technique for simultaneous measures of CD and 1st order PMD on a 40 Gbit/s NRZ-DPSK signal.
Fermat Photons: Paths Propagation and Imaging in Turbid Media (1996)

Photon diffusion on the velocity sphere describes photon migration in highly forward scattering media. The non-Euclidean diffusion leads to the concept of the most favorable photon paths described by Generalized Fermat Principle for turbid media. Experimental results are compared to theoretical predictions. Application of Fermat photons to imaging will be discussed.
Link Adaptation Control in LTE Uplink (2012)

Long Term Evolution (LTE) technology aims at addressing the increasing demand for mobile multimedia services in high user density areas. Channel aware scheduling across wide system bandwidth is one of the key techniques enabling this goal. To this end, the LTE scheduler heavily relies on an accurate and robust Link Adaptation (LA) function for predicting the best modulation and coding scheme (MCS) of a user. In this paper, we complement the popular block error rate (BLER) based LA with a scheme maximizing the throughput without BLER constraint and show that it indeed optimizes the spectral efficiency performance. We also describe a sub-optimal UL scheduler providing a good performance/complexity trade-off between a low-complexity basic scheduler and the optimal, but impractical complexity-wise.
ChemInform Abstract: AROMATIC RETINOIC ACID ANALOGS. SYNTHESIS AND PHARMACOLOGICAL ACTIVITY (1981)

Abstract Das aus (Ia) zugängliche Phosphonat (Ib) kondensiert mit β‐Ionon (II) zu einem Gemisch der isomeren Triene (III) und (IV), von denen (III) zum Epoxid (V) oxidiert wird.
Surface energy gradient driven convection for generating nanoscale and microscale patterned polymer films using photosensitizers (2014)

The Marangoni effect describes how fluid flows in response to gradients in surface energy. This phenomenon could be broadly harnessed to pattern the surface topography of polymer films if generalizable techniques for programming surface energy gradients existed. Here, a near UV–visible light (NUV–vis) photosensitizer, 9,10-dibromo-anthracene (DBA), was doped into thin films of a model polymer, poly(isobutyl methacrylate). After exposure to light through a photomask and heating above the glass transition, thermolysis of photo-oxidized DBA and grafting to the polymer promoted flow of the film material into the exposed regions. This mechanism did not significantly alter the molecular weight of PiBMA or the film's glass transition temperature, but resulted in an increase in film surface energy as indicated by a decrease in water contact angle. Film height variations of 580 nm were produced using a mask with 12.5 μm features; a mask with 800 nm features was also employed to generate topographic features of corresponding width without expensive contacting equipment. Due to the broad absorbance spectra of DBA, highly accessible and/or unconventional light sources may be employed in this process; this advantage was demonstrated by patterning with sunlight. The nonspecific radical-mediated nature of the DBA grafting reaction makes this a promising approach for many classes of polymers. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2014, 52, 1195–1202
Real-time wide-field-of-view passive millimeter-wave imaging (2002)

Passive millimeter wave imaging has been shown to be a useful for enhanced vision and concealed weapons detection applications. Trex Enterprises is developing a second generation passive millimeter wave imaging system which operates in real time with a 20 X 30 degree field of view and a 2K temperature sensitivity. This system is based on a pupil-plane aperture architecture used in a first generation system, but also includes advances in technology which improve system performance and utility. These include a flat panel dielectric antenna and W-band amplifiers, detectors, and processors. This second generation system will serve as the basis for a production millimeter-wave imager.
Prolaris: A novel genetic test for prostate cancer prognosis. (2013)

5005 Background: The natural history of prostate cancer is highly variable and difficult to predict. Improved tools are needed to match treatment more appropriately to a patient’s risk of progression. Therefore, we developed an expression signature composed of genes involved in cell cycle progression (Prolaris) and tested its utility in prostate cancer. Methods: We developed an expression signature composed of 31 cell cycle progression and 15 housekeeper genes. An expression score (Prolaris score) was derived as the mean of all cell cycle progression genes. The signature was tested at disease diagnosis in two conservatively managed cohorts from the UK (N=337 and 349), after radical prostatectomy in two cohorts from the U.S. (N=366 Scott & White Hospital, TX and 413 USCF, CA), and after external beam radiation therapy (N=141) in a cohort from Durham VA Medical Center. All studies were retrospective. Results: The cell cycle progression signature was a highly significant predictor of outcome in all five studies. In conservatively managed patients, the Prolaris score was the dominant variable for predicting death from prostate cancer in univariate analysis (p = 6.1 x 10 -22 after diagnosis by TURP, and p = 8.6 x 10 -10 after diagnosis by needle biopsy). In both studies, the Prolaris score remained highly significant in multivariate analysis making it a stronger predictor of disease-specific mortality than other prognostic variables. After prostatectomy, Prolaris predicted biochemical recurrence (BCR) in univariate analysis (S&W p = 5.6 x 10 -9 ; UCSF p= 2.23 x 10 -6 ) and provided additional prognostic information in multivariate analysis (S&W p = 3.3 x10 -6 ; UCSF 9.5 x10 -5 ). After radiation therapy, Prolaris predicted BCR (Phoenix) in univariate (p=0.0017) and multivariate analysis (p=0.034). In all five studies the HR per unit change in the Prolaris score was remarkably similar, ranging from 1.89 to 2.92, indicating that the effect size for the Prolaris score is robust to clinical setting and patient composition. Conclusions: The Prolaris test predicts prostate cancer outcome in multiple patient cohorts and diverse clinical settings. In all cases, it provides information beyond clinicopathologic variables to help differentiate aggressive from indolent disease.
Retrospective Case—Control Study of the Effects of Long-Term Dosing with Meloxicam on Renal Function in Aged Cats with Degenerative Joint Disease (2011)

Medical records (2005-2009) of a feline-only practice were searched for cats with degenerative joint disease (DJD) treated using meloxicam. DJD was diagnosed by the presence of at least two of the following: (i) altered mobility (observed by the owner), (ii) abnormal physical findings, (iii) characteristic radiographic changes. The primary study cohort consisted of cats older than 7 years that had received meloxicam for variable intervals in excess of 6 months, and for which complete records were available. These cats were subdivided according to whether detectable chronic kidney disease (CKD) was present ('renal group'), or not ('non-renal group'), and, for the 'renal group', according to the cat's IRIS category. Serum biochemistry, urinalysis (including urine specific gravity [USG]), body mass and condition score were monitored regularly. Progression of CKD in the 'renal group' and 'non-renal group' of cats was compared to two groups of age- and IRIS-matched control cats not receiving meloxicam (from the same clinic, over the same time period). The study was thus a case-control design, with two study groups. Thirty-eight cats with DJD receiving long-term meloxicam therapy met the inclusion criteria. Of these, 22 cats had stable CKD at the start of treatment (stage 1, eight cats; stage 2, 13 cats; stage 3, one cat). No cats initially had an elevated urinary protein to creatinine ratio. The remaining 16 cats initially had normal renal analytes and adequately concentrated urine. The median age of the 'renal' and 'non-renal' meloxicam groups was 15.5 and 13.4 years, respectively. The median treatment duration was 467 days in the 'renal group' and 327 days in the 'non-renal group'. After titration (to the lowest effective dose), the median maintenance dose was 0.02 mg/kg/day in both groups (range 0.015-0.033 mg/kg/day). There was no difference in sequential serum creatinine concentration or USG measurements between the 'non-renal group' treated with meloxicam compared to control cats not treated with meloxicam. There was less progression of renal disease in the 'renal group' treated with meloxicam compared to the age- and IRIS-matched cats with CKD not given meloxicam. These results suggest that a long-term maintenance dose of 0.02 mg/kg of meloxicam can be safely administered to cats older than 7 years even if they have CKD, provided their overall clinical status is stable. Long-term meloxicam therapy may slow the progression of renal disease in some cats suffering from both CKD and DJD. Prospective studies are required to confirm these findings.
Plastic Anisotropy and Formability of Aluminum Alloy Sheets. Numerical simulation of formability for Al-Mg alloys with plastic anisotropy. (1998)

Crystallographic texture is an important material characteristic for the formability of Aluminum alloys. The r-value is well known as a good index of formability for steel. However, there is no such index for aluminum alloys. In this paper, we discuss forming limit strains at the bi-axial region as the formability. We will discuss such an index for aluminum alloys by using numerical simulation and data analysis, in the following steps: Experimentally, we determined a yield function. Such functions can predict the yield surfaces and r-value distributions. Examining the experimental data, we confirmed the reliability of prediction of forming limit strains to predict forming limit strains by using the M–K model. Finally, we will propose a simple linear equation by using mean r-value, Δr-value and work hardening parameters. This equation can separate texture effect and work hardening effect on the forming limit strains. This equation well predicts the formability for 11 examined Al–Mg alloys.
Subunit Structure of Islets-Activating Protein (IAP), a New Protein Isolated from the Culture Media of Bordetella pertussis (1978)

The subunit structure was studied of islets-activating protein (IAP), a new protein recently isolated from the culture media of Bordetella pertussis and possessing a unique action, i.e., potentiating insulin secretory responses of animals, IAP dissociated into three subunits, F-1, F-2, and F-3, when incubated in 8M urea. Three subunits isolated by chromatography on CM-Sepharose and DEAE-Sepharose columns showed different molecular weights (F-1: 44,000, F-2: 20,000, F-3: 11,000) and different isoelectric points, but similar amino acid compositions. The F-1 subunit consisted of two polypeptide chains linked by S-S bonding(s), while the F-2 and F-3 subunits were single-chain peptides. These subunits, none of which was biologically active alone, associated upon incubation for 2 h at 37 degrees C and regained biological activities after association only when the F-3 subunit was present in the association product. Thus, the F-3 subunit was essential, and the F-1 and F-2 subunits were permissive, for the development of IAP activity in animals.
Dynamic gamma knife radiosurgery (2009)

Gamma knife has been the treatment of choice for various brain tumors and functional disorders. Current gamma knife radiosurgery is planned in a 'ball-packing' approach and delivered in a 'step-and-shoot' manner, i.e. it aims to 'pack' the different sized spherical high-dose volumes (called 'shots') into a tumor volume. We have developed a dynamic scheme for gamma knife radiosurgery based on the concept of 'dose-painting' to take advantage of the new robotic patient positioning system on the latest Gamma Knife C and Perfexion units. In our scheme, the spherical high dose volume created by the gamma knife unit will be viewed as a 3D spherical 'paintbrush', and treatment planning reduces to finding the best route of this 'paintbrush' to 'paint' a 3D tumor volume. Under our dose-painting concept, gamma knife radiosurgery becomes dynamic, where the patient moves continuously under the robotic positioning system. We have implemented a fully automatic dynamic gamma knife radiosurgery treatment planning system, where the inverse planning problem is solved as a traveling salesman problem combined with constrained least-square optimizations. We have also carried out experimental studies of dynamic gamma knife radiosurgery and showed the following. (1) Dynamic gamma knife radiosurgery is ideally suited for fully automatic inverse planning, where high quality radiosurgery plans can be obtained in minutes of computation. (2) Dynamic radiosurgery plans are more conformal than step-and-shoot plans and can maintain a steep dose gradient (around 13% per mm) between the target tumor volume and the surrounding critical structures. (3) It is possible to prescribe multiple isodose lines with dynamic gamma knife radiosurgery, so that the treatment can cover the periphery of the target volume while escalating the dose for high tumor burden regions. (4) With dynamic gamma knife radiosurgery, one can obtain a family of plans representing a tradeoff between the delivery time and the dose distributions, thus giving the clinician one more dimension of flexibility of choosing a plan based on the clinical situations.
Identification of Potent Soluble Epoxide Hydrolase Inhibitors for Veterinarian Usage (2018)

The veterinary pharmacopeia to treat pain and inflammation in companion animals is very limited. Currently, cyclooxygenase inhibitors (both NSAIDs and COXIBs) are the main class of drugs available to reduce pain and inflammation in cats, dogs and horses. However, these drugs often have insufficient efficacy and a great number of known adverse effects, underlying the need for novel pain medication for companion animals. Soluble epoxide hydrolase (sEH) inhibitors are a new class of anti‐inflammatory and analgesic drugs being tested in humans. They block the hydrolysis, and thus increase endogenous concentrations, of signaling molecules called epoxy‐fatty acids (EpFAs) that modulate inflammation and nociception. In addition to their use in human, sEH inhibitors may be a suitable alternative to cyclooxygenase inhibitors in companion animals. However, the compounds optimized for usage in primates and rodents are typically not sufficiently potent inhibitors of other animals' sEH for in vivo usage. Here, we screened a library of 2,300 inhibitors developed for the human enzyme with partially purified feline, canine and equine hepatic sEH to identify inhibitors that are broadly potent among species. Six candidate sEH inhibitors that are very potent across species (IC 50 < 1nM for each enzyme tested) were identified. Their microsomal stability was then measured in hepatic extracts from cat, dog and horse, as well as their solubility in drug‐able solvents. Based on this work, trans ‐4‐{4‐[3‐(4‐trifluoromethoxy‐phenyl)‐ureido]‐cyclohexyloxy}‐benzoic acid was selected for further testing in veterinary clinical trials of pain and inflammation in companion animals. Support or Funding Information This work was supported by the National Institute of Environmental Health Sciences grant numbers ES002710 and ES004699. This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
Abstract A045: Cadherin-11, a common therapeutic target in poor prognosis malignancies and rheumatoid arthritis (2013)

Abstract Rational: Poor prognosis epithelial-derived cancers often exhibit morphologic and molecular changes characteristic of an epithelial to mesenchymal transition (EMT). EMT markers are predominantly found in tumors with a basal-like phenotype. Increased expression of the mesenchymal cadherins N-cadherin and/or Cadherin-11 (CDH11) and decreased E-cadherin, have been associated with both EMT and tumor progression. Importantly, CDH11 is a therapeutic target in rheumatoid arthritis (RA), an inflammatory disease with properties often compared with cancer. As CDH11 antibody based therapeutics are in clinical trials for RA and we recently showed that the arthritis drug celecoxib has the structural potential to bind CDH11, there is a strong possibility that, if CDH11can be shown to drive malignant progression rather than simply be associated with it, therapeutic options may be rapidly developed. Results: We show that CDH11 is increased early in breast cancer and ductal carcinoma in-situ. CDH11 knockdown and antibodies effective in RA slowed the growth of basal-like breast tumors. CDH11 attenuation decreased proliferation and colony formation of breast, glioblastoma and prostate cancer cells. The arthritis drug celecoxib, which has characteristics consistent with CDH11 binding, an analogue without COX-2 inhibitory activity and other molecules that target CDH11, preferentially affect CDH11 positive cancer cells. Conclusion: Our work demonstrates that cadherin-11 is important for malignant progression, is a therapeutic target in several aggressive tumors and introduces an antibody, novel small molecules and an approved arthritis drug that inhibit its function with potential for rapid clinical translation. Citation Format: Shahin Assefnia, Sivanesan Dakshanamurthy, Jaime M. Guidry Auvil, Constanze Hampel, Panos Anastasiadis, Bhaskar Kallakury, Aykut Uren, David W. Foley, Milton Brown, Lawrence Shapiro, Michael Brenner, David Haigh, Stephen W. Byers. Cadherin-11, a common therapeutic target in poor prognosis malignancies and rheumatoid arthritis. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research: Genetics, Biology, and Clinical Applications; Oct 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2013;11(10 Suppl):Abstract nr A045.
Architecture design of a multiaxis cellular actuator array using segmented binary control of shape memory alloy (2006)

A new approach to artificial muscle actuator design is presented, and is implemented using shape memory alloys (SMA). An array of SMA actuators is segmented into many independently controlled, spatially discrete volumes, each contributing a small displacement to create a large motion. The segmented cellular architecture of SMA wires is extended to a multiaxis actuator array by arranging the segments in a two-dimensional (2-D) array. The multiaxis control is streamlined and coordinated using a 2-D segmentation method in order to activate multiple links of a robot mechanism in a coordinated manner. The basic principle of segmented binary control (SBC) is first presented, followed by multiaxis segmentation theory and a design procedure. The method is applied to a five-fingered robotic hand capable of taking a variety of postures. A 10-axis SMA actuator array is built, and SBC is implemented using Peltier-effect thermoelectric devices for selective local heating and cooling. Experiments demonstrate the feasibility and effectiveness of the new method.
Diffusional kurtosis imaging: The quantification of non‐gaussian water diffusion by means of magnetic resonance imaging (2005)

A magnetic resonance imaging method is presented for quantifying the degree to which water diffusion in biologic tissues is non-Gaussian. Since tissue structure is responsible for the deviation of water diffusion from the Gaussian behavior typically observed in homogeneous solutions, this method provides a specific measure of tissue structure, such as cellular compartments and membranes. The method is an extension of conventional diffusion-weighted imaging that requires the use of somewhat higher b values and a modified image postprocessing procedure. In addition to the diffusion coefficient, the method provides an estimate for the excess kurtosis of the diffusion displacement probability distribution, which is a dimensionless metric of the departure from a Gaussian form. From the study of six healthy adult subjects, the excess diffusional kurtosis is found to be significantly higher in white matter than in gray matter, reflecting the structural differences between these two types of cerebral tissues. Diffusional kurtosis imaging is related to q-space imaging methods, but is less demanding in terms of imaging time, hardware requirements, and postprocessing effort. It may be useful for assessing tissue structure abnormalities associated with a variety of neuropathologies.