gebhart/patrepeval huggingface dataset:
Cloning, sequencing, and expression of the P-protein gene (pheA) of Pseudomonas stutzeri in Escherichia coli: implications for evolutionary relationships in phenylalanine biosynthesis (1991)

Summary: The pheA gene encoding the bifunctional P-protein (chorismate mutase: prephenate dehydratase) was cloned from Pseudomonas stutzeri and sequenced. This is the first gene of phenylalanine biosynthesis to be cloned and sequenced from Pseudomonas. The pheA gene was expressed in Escherichia coli, allowing complementation of an E. coli pheA auxotroph. The enzymic and physical properties of the P-protein from a recombinant E. coli auxotroph expressing the pheA gene were identical to those of the native enzyme from P. stutzeri. The nucleotide sequence of the P. stutzeri pheA gene was 1095 base pairs in length, predicting a 365-residue protein product with an M r of 40844. Codon usage in the P. stutzeri pheA gene was similar to that of Pseudomonas aeruginosa but unusual in that cytosine and guanine were used at nearly equal frequencies in the third codon position. The deduced P-protein product showed sequence homology with peptide sequences of the E. coli P-protein, the N-terminal portion of the E. coli T-protein (chorismate mutase: prephenate dehydrogenase), and the monofunctional prephenate dehydratases of Bacillus subtilis and Corynebacterium glutamicum. A narrow range of values (26-35%) for amino acid matches revealed by pairwise alignments of monofunctional and bifunctional proteins possessing activity for prephenate dehydratase suggests that extensive divergence has occurred between even the nearest phylogenetic lineages.
Velocity measurement of particulate flow in microfluidic channels using single point confocal fluorescence detection. (2001)

This article presents a non-invasive, optical technique for measuring particulate flow within microfluidic channels. Confocal fluorescence detection is used to probe single fluorescently labeled microspheres (0.93 microm diameter) passing through a focused laser beam at a variety of flow rates (50 nL min(-1)-8 microL min(-1)). Simple statistical methods are subsequently used to investigate the resulting fluorescence bursts and generate velocity data for the flowing particles. Fluid manipulation is achieved by hydrodynamically pumping fluid through microchannels (150 microm wide and 50 microm deep) structured in a polydimethylsiloxane (PDMS) substrate. The mean fluorescence burst frequency is shown to be directly proportional to flow speed. Furthermore, the Poisson recurrence time and width of recovered autocorrelation curves is demonstrated to be inversely proportional to flow speed. The component-based confocal fluorescence detection system is simple and can be applied to a diversity of planar chip systems. In addition, velocity measurement only involves interrogation of the fluidic system at a single point along the flow stream, as opposed to more normal multiple-point measurements.
Serum .ALPHA.1-acid glycoprotein in cattle with inflammatory disease and that after operation. (1990)

[in Japanese]
Free volume quantities and viscoelasticity of polymer glasses (1996)

We have investigated, in terms of the Cohen-Turnbull theory, a relationship for polycarbonate (PC) glasses between average stress relaxation times, , and average free volume sizes, , obtained from positron annihilation lifetime spectroscopy. This examination suggests that the minimum free volume required for stress relaxation, υ*, decreases with decreasing temperature and that, near the glass transition temperature, only a subset of extremely large free volume elements contributes to the stress relaxation of PC glasses. This suggestion is consistent with the idea that near the glass transition temperature, the viscoelastic response is dominated by large-scale, main-chain motion, whereas at lower temperature it is controlled by local motion. Moreover, comparison with the υ* value estimated from gas diffusivity through various PC species at room temperature shows that the required free volume size for stress relaxation in the glass transition region is much larger than that for gas diffusion. Previously we showed that the Doolittle equation fails to correlate viscoelastic relaxation times of polymer glasses with changing temperature ; determining the free volume fraction, h, from theoretical analysis of volume recovery data and theory, the Doolittle equation is shown to be valid in PC above 135°C (T g - 14°C) irrespective of temperature and physical aging times. This result supports the idea suggested in the previous article that, as glassy polymers approach the transition region, viscoelastic properties increasingly tend to be controlled by free volume.
Algorithms for Chordal Analysis (2002)

June 01 2002 Algorithms for Chordal Analysis Bryan Pardo, Bryan Pardo Artificial Intelligence Laboratory, Electrical Engineering and Computer Science Department, The University of Michigan, 110 ATL Building, 1101 Beal Ave., Ann Arbor, MI 48109-2110, USA, bryanp@umich.eduwpb@eecs.umich.edu Search for other works by this author on: This Site Google Scholar William P. Birmingham William P. Birmingham Artificial Intelligence Laboratory, Electrical Engineering and Computer Science Department, The University of Michigan, 110 ATL Building, 1101 Beal Ave., Ann Arbor, MI 48109-2110, USA, wpb@eecs.umich.edu Search for other works by this author on: This Site Google Scholar Author and Article Information Bryan Pardo Artificial Intelligence Laboratory, Electrical Engineering and Computer Science Department, The University of Michigan, 110 ATL Building, 1101 Beal Ave., Ann Arbor, MI 48109-2110, USA, bryanp@umich.eduwpb@eecs.umich.edu William P. Birmingham Artificial Intelligence Laboratory, Electrical Engineering and Computer Science Department, The University of Michigan, 110 ATL Building, 1101 Beal Ave., Ann Arbor, MI 48109-2110, USA, wpb@eecs.umich.edu Online Issn: 1531-5169 Print Issn: 0148-9267 © 2002 Massachusetts Institute of Technology2002 Computer Music Journal (2002) 26 (2): 27–49. https://doi.org/10.1162/014892602760137167 Cite Icon Cite Permissions Share Icon Share Facebook Twitter LinkedIn MailTo Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Search Site Citation Bryan Pardo, William P. Birmingham; Algorithms for Chordal Analysis. Computer Music Journal 2002; 26 (2): 27–49. doi: https://doi.org/10.1162/014892602760137167 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsComputer Music Journal Search Advanced Search This content is only available as a PDF. © 2002 Massachusetts Institute of Technology2002 Article PDF first page preview Close Modal You do not currently have access to this content.
Complete characterization of utilization-voltage power system impedance using wideband measurement (2002)

Inexpensive portable instrumentation is used to measure the impedance of an example utilization-voltage power system. With the power system in normal operation, line-to-neutral, line-to-ground, and neutral-to-ground impedances are measured over a bandwidth of 20 Hz to 24 kHz. The measured impedance is presented as resistance and inductance which vary with frequency. Based on the measurements, additional calculations are performed to find the resistance and inductance of every conductor in the system. This complete wideband characterization of power system impedance provides valuable data for power quality calculations.
Bone Tissue Engineering: Current Strategies and Techniques—Part I: Scaffolds (2011)

Bone repair and regeneration is a dynamic process that involves a complex interplay between the (1) ground substance, (2) cells, and (3) milieu. While each constituent is integral to the final product, it is often helpful to consider each component individually. Therefore, we created a two-part review to examine scaffolds and cells' roles in bone tissue engineering. In Part I, we review the myriad of materials use for in vivo bone engineering. In Part II, we discuss the variety cell types (e.g., osteocytes, osteoblasts, osteoclasts, chondrocytes, mesenchymal stem cells, and vasculogenic cells) that are seeded upon or recruited to these scaffolds. In Part III, we discuss the optimization of the microenvironment. The biochemical processes and sequence of events that guide matrix production, cellular activation, and ossification are vital to developing successful bone tissue engineering strategies and are thus succinctly reviewed herein.
On-line ringing characterization as a PHM technique for power drives and electrical machinery (2007)

Embeddable features easily incorporated in traditional power drive systems are identified for prognostic health management (PHM) systems. This novel technique utilizes the original PWM waveform produced by the inverter to evaluate the power electronic circuit and electric machine against transistor degradation. Evaluation of the primary feature, ringing characterization, with experimental data demonstrates its viability as a practical real-time power device health-state indicator.
High-gain In <sub>0.53</sub> Ga <sub>0.47</sub> As:Fe photoconductive detectors (1984)

Photoconductive detectors were fabricated on semi-insulating liquid phase epitaxial In0.53Ga0.47As/InP doped with Fe for the first time. Their performance characteristics have been compared with identical devices made from Zn-doped p-In0.53Ga0.47As/InP. Internal optical gains up to 10 were measured in the Fe-doped devices. The bias and intensity-dependent gain characteristics of these devices are discussed.
Maximum Likelihood from Incomplete Data Via the <i>EM</i> Algorithm (1977)

Summary A broadly applicable algorithm for computing maximum likelihood estimates from incomplete data is presented at various levels of generality. Theory showing the monotone behaviour of the likelihood and convergence of the algorithm is derived. Many examples are sketched, including missing value situations, applications to grouped, censored or truncated data, finite mixture models, variance component estimation, hyperparameter estimation, iteratively reweighted least squares and factor analysis.
Novel pathogenic LRRK2 p.Asn1437His substitution in familial Parkinson's disease (2010)

Genealogical investigation of a large Norwegian family (F04) with autosomal dominant parkinsonism has identified 18 affected family members over four generations. Genetic studies have revealed a novel pathogenic LRRK2 mutation c.4309 A>C (p.Asn1437His) that co-segregates with disease manifestation (LOD = 3.15, θ = 0). Affected carriers have an early age at onset (48 ± 7.7 SD years) and are clinically asymmetric and levodopa responsive. The variant was absent in 623 Norwegian control subjects. Further screening of patients from the same population identified one additional affected carrier (1 of 692) with familial parkinsonism who shares the same haplotype. The mutation is located within the Roc domain of the protein and enhances GTP-binding and kinase activity, further implicating these activities as the mechanisms that underlie LRRK2-linked parkinsonism.
Prediction of Properties from Simulations:  Free Energies of Solvation in Hexadecane, Octanol, and Water (2000)

Monte Carlo (MC) statistical mechanics simulations have been carried out for more than 200 organic solutes, including 125 drugs and related heterocycles, in aqueous solution. The calculations were highly automated and used the OPLS-AA force field augmented with CM1P partial charges. Configurationally averaged results were obtained for a variety of physically significant quantities including the solute−water Coulomb and Lennard-Jones interaction energies, solvent-accessible surface area (SASA), and numbers of donor and acceptor hydrogen bonds. Correlations were then obtained between these descriptors and gas to liquid free energies of solvation in hexadecane, octanol, and water and octanol/water partition coefficients. Linear regressions with three or four descriptors yielded fits with correlation coefficients, r2, of 0.9 in all cases. The regression equation for log P(octanol/water) only needs four descriptors to provide an rms error of 0.55 for 200 diverse compounds, which is competitive with the best fragment methods. For water, the expanded data set of 85 solutes and improved statistical analyses bring into question the significance of the Lennard-Jones and surface area terms that have been featured in prior linear-response treatments. The results are sensitive to the choice of partial charges for the solute atoms; poor representation of some functional groups can lead to the need for specific corrections in the regression equations. This is expected to also be true for force-field-based scoring functions for protein−ligand binding. In all cases, the present descriptors that emerge as most significant sensibly reveal the key physical factors that control solvation, especially solute size in organic solvents and electrostatic interactions in water. Furthermore, additional MC simulations for solutes in both water and ethanol clearly demonstrate that the key differential between water and alcohols is the greater hydrogen-bond-donating ability of water, which explains the significance of a solute's hydrogen-bond-accepting ability for log P(octanol/water).
A Software Framework For Musical Data Augmentation. (2015)

[TODO] Add abstract here.
Three-Dimensional Object Detection and Layout Prediction Using Clouds of Oriented Gradients (2016)

We develop new representations and algorithms for three-dimensional (3D) object detection and spatial layout prediction in cluttered indoor scenes. RGB-D images are traditionally described by local geometric features of the 3D point cloud. We propose a cloud of oriented gradient (COG) descriptor that links the 2D appearance and 3D pose of object categories, and thus accurately models how perspective projection affects perceived image boundaries. We also propose a "Manhattan voxel" representation which better captures the 3D room layout geometry of common indoor environments. Effective classification rules are learned via a structured prediction framework that accounts for the intersection-over-union overlap of hypothesized 3D cuboids with human annotations, as well as orientation estimation errors. Contextual relationships among categories and layout are captured via a cascade of classifiers, leading to holistic scene hypotheses with improved accuracy. Our model is learned solely from annotated RGB-D images, without the benefit of CAD models, but nevertheless its performance substantially exceeds the state-of-the-art on the SUN RGB-D database. Avoiding CAD models allows easier learning of detectors for many object categories.
Evaluation of dual-front active contour segmentation and metal shadow filling methods on metal artifact reduction in multi-slice helical CT (2010)

A novel metal artifact reduction strategy including projection reformation, metal region segmentation, and metal shadow filling was proposed. Both metal region segmentation and shadow filling are critical steps to assure good artifact suppression results. This preliminary study evaluated the performance of two segmentation methods and three region filling methods on metal artifact reduction of clinical cases. Gradient-based threshold method (GBT) and dual-front active contour model-based method (DFAC) were utilized to segment metal implants from reformatted projections, Delaunay triangulation-based (DTB), anisotropic diffusion-based, and exemplar-based, interpolation methods were utilized to fill the metal shadows, respectively. The image quality was evaluated by a radiologist in terms of visual conspicuity of the bladder base, prostate, and rectum. Overall, the image quality and the conspicuity in some critical organs were significantly improved for all corrections. Compared to the GBT method, the DFAC method had more accurate segmentation, which resulted in better artifact suppression. The interpolation process does not guarantee the data consistency among projection views, which can introduce additional artifacts, especially for large metal objects. Although the DTB method produced the smoothest metal shadow interpolation results, which is considered the worst scenario according to the criterion of image restoration, it induced the least additional artifacts to the reconstructed images compared to the other two structure-saving methods. As such, region interpolation methods should follow the criterion to generate metal shadow data consistent with the CT acquisition geometry, which might be quite different from the general standard of image restoration in computer vision and image processing.
Vascular Targeting and Antiangiogenesis Agents Induce Drug Resistance Effector GRP78 within the Tumor Microenvironment (2005)

Therapeutic targeting of the tumor vasculature that destroys preexisting blood vessels of the tumor and antiangiogenesis therapy capitalize on the requirement of tumor cells on an intact vascular supply for oxygen and nutrients for growth, expansion and metastasis to the distal organs. Whereas these classes of agents show promise in delaying tumor progression, they also create glucose and oxygen deprivation conditions within the tumor that could trigger unintended prosurvival responses. The glucose-regulated protein GRP78, a major endoplasmic reticulum chaperone, is inducible by severe glucose depletion, anoxia, and acidosis. Here we report that in a xenograft model of human breast cancer, treatment with the vascular targeting agent, combretastatin A4P, or the antiangiogenic agent, contortrostatin, promotes transcriptional activation of the Grp78 promoter and elevation of GRP78 protein in surviving tumor cells. We further show that GRP78 is overexpressed in a panel of human breast cancer cells that has developed resistance to a variety of drug treatment regimens. Suppression of GRP78 through the use of lentiviral vector expressing small interfering RNA sensitizes human breast cancer cells to etoposide-mediated cell death. Our studies imply that antivascular and antiangiogenesis therapy that results in severe glucose and oxygen deprivation will induce GRP78 expression that could lead to drug resistance.
A new electronic mobility aid for the blind – A field evaluation (1987)

International Journal of Rehabilitation Research: December 1987 - Volume 10 - Issue - p 298-300
Helium (42He,32He) within Deuterated Pd-black. (1997)

Authors have clearly proven for the first time that deuterium nuclear reaction was continuously generated inside a highly deuterated solid by showing both of the excess energy and corresponding amount of helium as the reaction product generated simultaneously. Whenever there is a nuclear fusion reaction inside a metal, helium generated is unable to escape to the surroundings and is trapped in a frozen state inside that metal. The concentration of the helium within the metal will rise with increasing rate of reactions. Pd-black is under such state as the sample used and sealed within the“closed QMS”developed by the authors (closed vessel including the Getter pump and the QMS). It is completely separated from the surroundings and the internal gases are removed to create super-vacuum. The reaction product released by the“Sample-Heating”process (room temp._??_ 1500[°C]) is thus the only matter which occupies the interior of the closed vessel and its detection by the QMS is assured. When the“closed QMS”works under the above mentioned-state, it was clarified that the“ash”or the reaction product of this fusion reaction within a solid is 42He and 32He and their ratio is 42He/32He≈4. It can be concluded from the result that the main reaction product is 42He and it is created directly as an inherent feature of the solid-state nuclear fusion. Authors think that the reaction process responsible for the creation of 32He may be a different one from that creates 42He. One of which is the Rutherford reaction process and the other occurs based on the specific properties of solid, similar to the case of 42He. The existence of 31T will be required that the process is responsible for the generation of 32He as the Rutherford reaction. The proof for the existence of 31T within the“closed QMS”, however, was not obtained in this experiments.
The Effect of Mechanical Treatment on the Crystal Structure and Thermal Behavior of Kaolinite (1993)

Abstract The destruction of the crystal structure of kaolinite caused by mechanical forces was investigated by X-ray diffraction, thermal analysis, infrared spectroscopy, and specific surface area determination. Attention was also directed to the change of thermal reactions of milled kaolinite. Grinding experiments for 5 min, 10 min, and 1, 2, 4, 6, and 10 h were carried out in an AGO I planetary mill. After 1 h of grinding, the crystalline order of kaolin is destroyed; but the amorphization continues in the course of prolonged grinding. Grinding for 1 h produces a favorable state for forming mullite-type crystals after heating even at 1000°C.
SUPERPAVE SUPPORT AND PERFORMANCE MODELS MANAGEMENT: EVALUATION OF THE SHRP PERFORMANCE MODELS SYSTEM (1997)

A principal result of the Strategic Highway Research Program (SHRP) was a set of pavement performance models for predicting low temperature thermal cracking, fatigue cracking, and permanent deformation in asphalt pavements under environmental and traffic loadings. The Federal Highway Administration, as part of its Superpave implementation plan, awarded a contract to the University of Maryland and a team of subcontractors to provide a comprehensive and unbiased evaluation of the original SHRP pavement performance models. The principal conclusions from this evaluation are: (a) the SHRP Superpave system provides an excellent framework for future modifications and enhancements to the models; (b) the existing non-load related thermal fracture model predicts field behavior reasonably well, although some minor modifications and enhancements to the model are necessary; (c) the performance prediction models for load related fatigue fracture and permanent deformation perform poorly, and substantial corrections and enhancements to these models are imperative if they are to be sufficiently reliable for acceptance and use by industry; (d) although some of the problems in the load related distress models are the consequence of technical and other constraints during the original SHRP research effort, many are the direct result of problems in the asphalt material characterization models and associated test procedures; and (e) the necessary corrections, modifications, and enhancements to the models will mandate new field calibration and validation. Detailed evaluation findings supporting these conclusions are presented in the paper. Future plans for the enhancement and implementation of the Superpave performance models are also briefly described.
Leukemia treatment in severe combined immunodeficiency mice by antisense oligodeoxynucleotides targeting cooperating oncogenes. (1995)

Transformation of hematopoietic cells by the p210bcr/abl tyrosine kinase appears to require the expression of a functional MYC protein, suggesting that simultaneous targeting of BCR-ABL and c-myc might be a rational strategy for attempting treatment of Phil-adelphia leukemia. To test this hypothesis, severe combined immunodeficiency mice injected with Philadelphia leukemic cells were treated systemically with equal doses of bcr-abl or c-myc antisense oligodeoxynucleotides (ODNs) or with both ODNs in combination. Compared with the mice treated with individual agents, the disease process was much slower in the group treated with both ODNs, as revealed by flow cytometry, clonogenic assay, and reverse transcriptase-polymerase chain reaction analysis to detect leukemic cells in mouse tissue cell suspensions, and by enumeration of liver metastases. The retardation of the disease process was positively correlated with a markedly increased survival of leukemic mice treated with both ODNs. These data demonstrate the therapeutic potential of targeting multiple cooperating oncogenes.