gebhart/patrepeval huggingface dataset:
SU‐DD‐A3‐02: Real‐Time Tracking of Implanted Fiducial Markers Using Combined KV and MV Imaging (2008)

Purpose: In the presence of organ motion, geometric target uncertainty can hamper the benefits of highly conformal dose techniques such as IMRT. A critical step in dealing with intra‐fraction tumor motion is the real‐time monitoring of the tumor position. The aim of this study is the first time demonstration of a real‐time 3D internal fiducial tracking system based on onboard kV diagnostic imaging together with a MV electronic portal‐imaging device (EPID). Method and Materials: A Varian Trilogy radiotherapy system equipped with both kV and MV imaging systems was used in this work. A hardware frame grabber was used to capture both kV and MV video streams simultaneously at 30 fps. An in house built support vector machine (SVM) classifier tool using prior CT based knowledge was used to locate gold cylindrical markers in the kV/MV frames. Controlled kV beam switching, synced with the ‘step’ part of a step‐and‐shoot IMRT delivery, was investigated in allowing continuous 3D tracking in the presence of beam interruption. A correlation/prediction algorithm was used to buffer lost geometric marker information during kV/MV synchronization. The geometric tracking capabilities of the system were evaluated using a pelvic phantom with embedded fiducials placed on a 3D moveable stage. Results: The maximum 3D tracking speed of the kV‐MV system is approximately 9 Hz. The geometric accuracy of the system is found to be on the order of less than 1 mm in all three spatial dimensions. Synchronized kV/MV switching is found to reduce MV scatter interference on kV imaging and to reduce the overall kV diagnostic dose needed for continuous tracking. Conclusion: A real‐time 3D fiducial tracking system using combined kV and MV imaging has been successfully demonstrated for the first time. The technique is especially suitable for RT systems already equipped with on board kV and EPID imaging devices.
Fast‐marching segmentation of three‐dimensional intravascular ultrasound images: A pre‐ and post‐intervention study (2010)

This new IVUS segmentation method provides accurate results that correspond well to the experts' manually traced contours, but requires much less manual interactions and is faster.
Melt/solution processable conducting polyaniline: Elastomeric blends with EVA (2002)

Abstract Polyaniline (PANI) protonated with dopant, the sulfonic acid of 3‐pentadecylphenoxyacetic acid (SPDPAA; synthesized from an inexpensive naturally existing biomonomer, cardanol), was blended with an elastomeric polymer, the ethylene vinyl acetate (EVA) copolymer. Blending was performed either by emulsion polymerization of aniline into the EVA matrix or by the solution‐mixing method. Thin films were prepared by the conventional melt‐processing technique for an emulsion‐polymerized system and by the solution‐casting method for a solution‐mixed system. In the case of the emulsion‐polymerized system, the percolation threshold occurs at a very low weight percentage of PANI, and a maximum conductivity value of 0.85 S cm −1 was obtained for 28.5 wt % of PANI. These elastomeric conducting blends were characterized by elemental analysis, FTIR and UV‐visible spectral analysis, conductivity measurements, SEM, XRD, tensile properties, TGA, and DSC. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 84: 1438–1447, 2002; DOI 10.1002/app.10408
Code relatives: detecting similarly behaving software (2016)

Detecting “similar code” is useful for many software engineering tasks. Current tools can help detect code with statically similar syntactic and–or semantic features (code clones) and with dynamically similar functional input/output (simions). Unfortunately, some code fragments that behave similarly at the finer granularity of their execution traces may be ignored. In this paper, we propose the term “code relatives” to refer to code with similar execution behavior. We define code relatives and then present DyCLINK, our approach to detecting code relatives within and across codebases. DyCLINK records instruction-level traces from sample executions, organizes the traces into instruction-level dynamic dependence graphs, and employs our specialized subgraph matching algorithm to efficiently compare the executions of candidate code relatives. In our experiments, DyCLINK analyzed 422+ million prospective subgraph matches in only 43 minutes. We compared DyCLINK to one static code clone detector from the community and to our implementation of a dynamic simion detector. The results show that DyCLINK effectively detects code relatives with a reasonable analysis time.
A novel high-viscosity, two-solution acrylic bone cement: Effect of chemical composition on properties (1999)

Solutions of poly(methyl methacrylate) (PMMA) powder predissolved in methyl methacrylate (MMA) have been developed as an alternative to current powder/liquid bone cements. They utilize the same addition polymerization chemistry as commercial cements, but in mixing and delivering via a closed system, porosity is eliminated and the dependence of material properties on the surgical technique is decreased. Twelve different sets of compositions were prepared, with two solutions of constant polymer-to-monomer ratio (80 g of PMMA/100 mL of MMA) and all combinations of four benzoyl peroxide (BPO) initiator levels added to the first solution and three N, N-dimethyl-p-toluidine (DMPT) activator levels added to the second. These compositions were tested, along with Simplex-P bone cement, for effects of BPO and DMPT concentrations on polymerization exotherm, setting time, flexural strength, modulus, and maximum strain. The results show that each of these dependent variables was affected significantly by the individual concentrations of BPO and DMPT and their interactions. The flexural strength, modulus, and polymerization exotherm reached their maximums at about a 1:1 molar ratio of BPO to DMPT. Most compositions had exotherms, setting times, and maximum strains within the range of commercial cements and flexural strengths and moduli up to 54 and 43% higher than Simplex-P, respectively.
Nanoceria-Supported Single-Atom Platinum Catalysts for Direct Methane Conversion (2018)

Nanoceria-supported atomic Pt catalysts (denoted as Pt<sub>1</sub>@CeO<sub>2</sub>) have been synthesized and demonstrated with advanced catalytic performance for the non-oxidative, direct conversion of methane. These catalysts were synthesized by calcination of Pt-impregnated porous ceria nanoparticles at high temperature (ca. 1,000 °C), with the atomic dispersion of Pt characterized by combining aberra-tion-corrected high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM), X-ray photoelectron spectroscopy (XPS), X-ray absorption spec-troscopy (XAS) and diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) analyses. The Pt<sub>1</sub>@CeO<sub>2</sub> catalysts exhibited much superior catalytic performance to its nanoparticulated counterpart, achieving 14.4% of methane conversion at 975 °C and 74.6% selectivity toward C<sub>2</sub> products (ethane, ethylene and acetylene). Comparative studies of the Pt1@CeO<sub>2</sub> catalysts with different loadings as well as the nanoparticulated counterpart reveal the single-atom Pt to be the active sites for selective conversion of methane into C<sub>2</sub> hydrocarbons.
MUC1 expression by human airway epithelial cells mediates pseudomonas aeruginosa adhesion (2010)

Human MUC1 (Muc1 in animals) is an extensively O-glycosylated membrane-tethered mucin expressed on the surface of epithelial cells and some cells of the hematopoietic system. Recently, we showed that the hamster Muc1 on Chinese hamster ovary (CHO) cells served as a binding site for Pseudomonas aeruginosa (PA) through interaction between bacterial flagellin and the Muc1 ectodomain. Because CHO cells are known to produce an atypical pattern of protein glycosylation, we determined whether or not PA interacted with MUC1 endogenously expressed on human airway epithelial cells. Knock down of MUC1 expression in bronchial (NuLi-1) or alveolar (A549) epithelial cells by RNA interference significantly reduced PA binding to the cells. Conversely, over-expression of MUC1 in HEK293 cells increased bacterial adherence. By confocal microscopy, PA and MUC1 were colocalized on the surface of NuLi-1 cells. Taken together, these results confirm our previous observations in CHO cells and suggest that MUC1 serves as a binding site for PA on the surface of airway epithelial cells, which may have important consequences in the pathogenesis of PA lung infections.
Axially illuminated fluorescence imaging detection for capillary isoelectric focusing on Teflon capillary (2000)

An axially illuminated laser induced fluorescence (LIF) whole column imaging detection (WCID) method was developed for capillary isoelectric focusing (CIEF). In this method, an argon ion laser was used as the excitation source and the isoelectric focusing process was monitored dynamically by a thermoelectrically (TE) cooled (charge coupled device) CCD camera. Low refractive index PTFE capillary was used in the experiment, and electroosmotic flow (EOF) and protein adsorption were minimized by dynamic conditioning of the capillary with methyl cellulose (MC). With the addition of a small amount of high refractive index organic solvent such as glycerol in the sample mixture, the laser beam was axially propagated with total internal reflection. Stray light and scattering light originating from the wall of the capillary were minimized. The instrumentation is simple and the method is sensitive. Two naturally fluorescent proteins (R-phycoerythrin and green fluorescent protein) were separated, and a concentration detection limit (LOD) of 10−13 M or mass LOD of 10−19 mol for R-phycoerythrin was obtained.
Boron neutron capture enhancement of fast neutron radiotherapy (1997)

Clinical trials have revealed a therapeutic advantage for fast neutron radiation over conventional photon radiation for salivary gland cancer, prostate cancer, sarcoma, and a subgroup of lung cancer. Conversely, fast neutron treatment of high grade astrocytic brain tumors [glioblastoma multiforme (GBM)] resulted in tumor sterilization, but also caused significant brain injury such that no therapeutic gain was attained. This effect was important, however, in that photon radiation and other conventional treatments have not demonstrated sterilization of GBM at any dose. Recent laboratory studies demonstrated that the hospital-based fast neutron beam from the University of Washington cyclotron has a thermal neutron component that may be used in a boron-10 neutron capture (BNC) reaction to enhance cell kill. The degree of enhancement was approximately 10 fold, and was dependent upon the boron-10 concentration, the boron-10 carrier agent, and the fast neutron dose per fraction. The results of these experiments will be discussed in the context of creating a therapeutic window for treatment of glioblastoma using BNC-enhanced fast neutron radiation in a clinically tolerable regimen.
Development of topical treatment for cutaneous leishmaniasis caused by Leishmania major in experimental animals (1984)

Topical treatment, with drug-containing ointments, of cutaneous leishmaniasis caused by Leishmania major in BALB/c mice was studied. Twenty chemotherapeutic agents having potential or established antileishmanial activity were formulated in different ointment and cream bases. Only 15% paromomycin sulfate with 12% methylbenzethonium chloride, 12% benzethonium chloride, 12% cetalkonium chloride, or 12% dimethyl sulfoxide, all incorporated in white soft paraffin (United Kingdom patent application no. 2117237A), were completely effective. Topical treatment twice daily for 6 or more days caused total elimination of the parasites and healing of the lesion in all treated mice. All the other antileishmanial compounds, including sodium stibogluconate, pentamidine, amphotericin B, emetine hydrochloride, metronidazole, co-trimoxazole, allopurinol, and rifampin, either showed a slight effect on the parasites or were highly toxic to the animal host at the concentrations tested.
Structures and Biosynthesis of Aflastatins: Novel Inhibitors of Aflatoxin Production by Aspergillus parasiticus. (1998)

Two novel inhibitors of aflatoxin production by Aspergillus parasiticus were isolated from the mycelial extracts of Streptomyces sp. MRI142 and termed aflastatin A and B. The structures of aflastatin A (1) and B (5) were elucidated by NMR and chemical degradation experiments. These compounds have a novel skeleton of a tetramic acid derivative with a highly oxygenated long alkyl chain. The incorporation experiments using 13C-labeled acetates, propionate, glucose and glycolate suggested that most of the C2 and C3 units involved in the alkyl chain moiety of aflastatin A were biosynthesized from acetic and propionic acids, but five C2 units in the alkyl chain originated from glycolic acid.
Fluorine-enhanced plasma growth of native layers on silicon (1980)

Fluorine-enhanced low-temperature (⩽600 °C) plasma growth of oxides and nitrides from Si has been studied. It is shown that the growth rates are greatly increased by incorporation of less than 1/2 atomic percent fluorine into the films. Auger profiles of fluorine-enhanced-plasma-grown SiO2 films show that they are nearly indistinguishable from those grown thermally. Uniform silicon oxynitride films (with N/O concentration ratios near 2) of thicknesses over 1000 Å can be grown in about four hours.
Automated Detection of Ventricular Fibrillation to Guide Cardiopulmonary Resuscitation (2007)

Sudden death due to ventricular fibrillation (VF) is a catastrophic event, especially in out-of-hospital settings. Prompt detection of VF and preparedness to intervene with cardiopulmonary resuscitation (CPR) and especially the delivery of an electrical shock is potentially lifesaving. The reliability and accuracy of automated VF detection by current versions of automated external defibrillators (AEDs) require interruption of CPR because the ECG signal, which is the source of rhythm detection, is corrupted by chest compressions. Significantly better outcomes have been reported if effective chest compression precedes electrical defibrillation and especially if interruptions are minimized. We therefore sought a method by which VF detection could proceed without interrupting chest compressions. A VF detection algorithm was therefore derived based on a method by which continuous wavelet transform is used, together with measurement of morphologic consistency. This method was intended to distinguish between disorganized and organized rhythms. The Fourier-transform-based amplitude spectrum analysis was then used to detect the likelihood that VF was the rhythm prompting the delivery of an electrical shock. The algorithm was validated on 33,095 electrocardiographic segments, including 8840 segments corrupted by compression artifacts from 232 patients after out-of-hospital cardiac arrest. Nine thousand one hundred eighty-seven of 10,042 VF segments and 20,884 of 23,053 non-VF segments were correctly classified, with a sensitivity of 91.5% and a specificity of 90.6%. Although the proposed algorithm has a lesser predictive value for VF detection than the uncorrupted ECGs in clinical settings, it has the major potential for automated rhythm identification to guide defibrillation without repetitive interruptions of CPR.
Maximum likelihood approach to “informed” Sound Source Localization for Hearing Aid applications (2015)

Most state-of-the-art Sound Source Localization (SSL) algorithms have been proposed for applications which are “uninformed” about the target sound content; however, utilizing a wireless microphone worn by a target talker, enables recent Hearing Aid Systems (HASs) to access to an almost noise-free sound signal of the target talker at the HAS via the wireless connection. Therefore, in this paper, we propose a maximum likelihood (ML) approach, which we call MLSSL, to estimate the Direction of Arrival (DoA) of the target signal given access to the target signal content. Compared with other “informed” SSL algorithms which use binaural microphones for localization, MLSSL performs better using signals of one or more microphones placed on just one ear, thereby reducing the wireless transmission overhead of binaural hearing aids. More specifically, when the target location confined to the front-horizontal plane, MLSSL shows an average absolute DoA estimation error of 5 degrees at SNR of -5 dB in a large-crowd noise and non-reverberant situation. Moreover, MLSSL suffers less from front-back confusions compared with the recent approaches.
The Multileveled Regulation of the Human Cholinesterase Genes and Their Protein Products (1993)

The human ACHE and BCHE genes encoding the acetylcholine hydrolyzing enzymes acetyl- and butyrylcholinesterase (AChE, BuChE) were molecularly cloned and their chromosomal positions determined to be 7q22 and 3q26, respectively. Several point mutations were found in these two genes and their frequency determined within ethnically distinct populations of Israeli residents. Xenopus oocyte expression studies revealed the BuChE mutations variably alter sensitivity to inhibitors, including organophosphorous poisons. The promoter controlling ACHE gene expression was characterized and shown to direct the expression of human AChE in developing myotomes from transiently transgenic Xenopus laevis embryos, where the transgenic enzyme faithfully accumulated in neuromuscular junctions. Alternative splicing in ACHEmRNA transcripts was found to lead to 3 distinct enzyme forms, 2 of which are abundant in tumors. Antisense phosphorothioate oligodeoxynucleotide-targetted destruction of ACHEmRNA in mice was found to cause transient hematopoietic alterations, notably reduced erythrocyte counts. Acetylcholinesterase, Butyrylcholinesterase, DNA sequencing, Alternative splicing, Natural variants, Xenopus expression, Site-directed mutagenesis
Synthesis and Biological Evaluation of Amidine, Guanidine, and Thiourea Derivatives of 2-Amino(6-trifluoromethoxy)benzothiazole as Neuroprotective Agents Potentially Useful in Brain Diseases (2009)

A series of amidine, thiourea, and guanidine derivatives of 2-amino-6-(trifluoromethoxy)benzothiazole termed 2, 3, and 4, respectively, and structurally related to riluzole, a neuroprotective drug in many animal models of brain disease, have been synthesized. The biological activity of compounds 2a-e, 3a-f, and 4a,b was preliminarily tested by means of an in vitro protocol of ischemia/reperfusion injury. The results demonstrated that 2c and 3a-d significantly attenuated neuronal injury. Selected for testing of their antioxidant properties, compounds 3a-d were shown to be endowed with a direct ROS scavenging activity. Compounds 3b and 3d were also evaluated for their activity on voltage-dependent Na(+) and Ca(2+) currents in neurons from rat piriform cortex. At 50 microM, compound 3b inhibited the transient Na(+) current to a much smaller extent than riluzole, whereas 3d was almost completely ineffective.
Efficient insertion mutagenesis of <i>Arabidopsis</i> by tissue culture‐induced activation of the tobacco retrotransposon <i>Tto1</i> (2000)

The tobacco retrotransposon Tto1 is one of a few active retrotransposons in plants. Its transposition is activated by tissue culture and is primarily regulated at the transcriptional level. Here we demonstrate that Tto1 introduced in Arabidopsis is also activated by tissue culture. Transcription of Tto1 was induced by tissue culture and driven by its LTR promoter. Transposed copies of Tto1 were observed in almost all of the plants regenerated from the explants cultured for only 1 week. A total of 255 independent regenerated lines have been produced, and the average copy number of transposed Tto1 in these lines is estimated to be 3.2. Sequences flanking Tto1 were amplified by thermal asymmetric interlaced (TAIL)-PCR. Of 165 independent amplified products, 123 showed significant homology to known genes or hypothetical protein genes. The insertion sites of Tto1 are spread over all chromosomes and the target site sequence shows moderate consensus. Taken together, these results indicate that Tto1 can be used as a tool for efficient insertion mutagenesis of Arabidopsis which is especially suitable as a reverse genetics system.
Correlation-Based Motion Vector Processing With Adaptive Interpolation Scheme for Motion-Compensated Frame Interpolation (2009)

In this paper, we address the problems of unreliable motion vectors that cause visual artifacts but cannot be detected by high residual energy or bidirectional prediction difference in motion-compensated frame interpolation. A correlation-based motion vector processing method is proposed to detect and correct those unreliable motion vectors by explicitly considering motion vector correlation in the motion vector reliability classification, motion vector correction, and frame interpolation stages. Since our method gradually corrects unreliable motion vectors based on their reliability, we can effectively discover the areas where no motion is reliable to be used, such as occlusions and deformed structures. We also propose an adaptive frame interpolation scheme for the occlusion areas based on the analysis of their surrounding motion distribution. As a result, the interpolated frames using the proposed scheme have clearer structure edges and ghost artifacts are also greatly reduced. Experimental results show that our interpolated results have better visual quality than other methods. In addition, the proposed scheme is robust even for those video sequences that contain multiple and fast motions.
Development of two novel nontoxic mutants of Escherichia coli heat-labile enterotoxin (1999)

Escherichia coli heat-labile enterotoxin (LT) is composed of catalytic A and non-catalytic homo-pentameric B subunits and causes diarrheal disease in human and animals. In order to produce a nontoxic LT for vaccine and adjuvant development, two novel derivatives of LT were constructed by a site-directed mutagenesis of A subunit; Ser63 to Tyr63 in LTS63Y and Glu110, Glu112 were deleted in LT Δ 110/112. The purified mutant LTs (mLTs) showed a similar molecular structural complex as AB5 to that of wild LT. In contrast to wild-type LT, mLTs failed to induce either elongation activity, ADP-ribosyltransferase activity, cAMP synthesis in CHO cells or fluid accumulation in mouse small intestine in vivo. Mice immunized with mLTs either intragastrically or intranasally elicited high titers of LT-specific serum and mucosal antibodies comparable to those induced by wild-type LT. These results indicate that substitution of Ser63 to Tyr63 or deletion of Glu110 and Glu112 eliminate the toxicity of LT without a change of AB5 conformation, and both mutants are immunogenic to LT itself. Therefore, both mLTs may be used to develop novel anti-diarrheal vaccines against enterotoxigenic E. coli.
The open circuit nitrogen washout technique for measuring the lung volume in infants: methodological aspects (1999)

This technique increases the accuracy in vitro and the precision in vivo of volume measurement by nitrogen washout. Sources of potential errors including baseline drifting and inadequate equipment warming times were identified. The breathing bag acted as a buffer reservoir, preventing large swings in flows within the nitrogen mixing chamber during washouts, and should be an integral component of the nitrogen washout circuit.