gebhart/patrepeval huggingface dataset:
Bioinformatic Analysis of Plasma Apolipoproteins A-I and A-II Revealed Unique Features of A-I/A-II HDL Particles in Human Plasma (2016)

Plasma concentration of apoA-I, apoA-II and apoA-II-unassociated apoA-I was analyzed in 314 Japanese subjects (177 males and 137 females), including one (male) homozygote and 37 (20 males and 17 females) heterozygotes of genetic CETP deficiency. ApoA-I unassociated with apoA-II markedly and linearly increased with HDL-cholesterol, while apoA-II increased only very slightly and the ratio of apoA-II-associated apoA-I to apoA-II stayed constant at 2 in molar ratio throughout the increase of HDL-cholesterol, among the wild type and heterozygous CETP deficiency. Thus, overall HDL concentration almost exclusively depends on HDL with apoA-I without apoA-II (LpAI) while concentration of HDL containing apoA-I and apoA-II (LpAI:AII) is constant having a fixed molar ratio of 2 : 1 regardless of total HDL and apoA-I concentration. Distribution of apoA-I between LpAI and LpAI:AII is consistent with a model of statistical partitioning regardless of sex and CETP genotype. The analysis also indicated that LpA-I accommodates on average 4 apoA-I molecules and has a clearance rate indistinguishable from LpAI:AII. Independent evidence indicated LpAI:A-II has a diameter 20% smaller than LpAI, consistent with a model having two apoA-I and one apoA-II. The functional contribution of these particles is to be investigated.
Structure/Psychophysical Relationships in X-Linked Retinoschisis (2016)

When considered from a single visit, OS thickness within the macula is more closely associated with macular function than TR thickness within the macula in patients with XLRS.
Jamming bacterial communications: new strategies to combat bacterial infections and the development of biofilms (2006)

The growth and activity of microorganisms affect our lives in both positive and negative ways. We have, since early times, tried to combat unwanted microbes and utilize those expressing useful traits. Microorganisms can cause diseases and chronic infections in humans, animals, and plants. In medicine, agriculture and fish farming, treatment scenarios are based on antimicrobial compounds such as antibiotics, with toxic and growth-inhibitory properties. Control of growth by eradication of bacteria is one of the most important scientific achievements. Unfortunately, bacteria have become gradually more and more resistant to antibiotics, and infections caused by resistant bacteria are on a dramatic increase. It has recently become apparent that the bacterial lifestyle also contributes significantly to this problem. The traditional way of culturing bacteria as planktonic, liquid cultures imprinted the view that bacteria live as unicellular organisms. Although it must be emphasized that such test-tube studies have led to fundamental insights into basic life processes and have unraveled complex intracellular regulatory networks, it is now clear that in nature microbial activity is mainly associated with surfaces and we as scientists must therefore turn our attention to this sessile mode of growth (33). It appears that the ability to form surface-associated, structured and cooperative consortia (referred to as biofilms) is one of the most remarkable and ubiquitous characteristics of bacteria (12). In this sessile life form, bacteria can cause various problems in industrial settings, ranging from corrosion and biofouling to food contamination.
A Metagenomic Approach to the Airways Microbiome of Chronic Obstructive Pulmonary Disease (COPD) (2013)

Current research has shown that different sites of the human body house different bacterial communities. There is a strong correlation between an individual's microbial community profile at a given site and the onset of disease. Chronic Obstructive Pulmonary Disease (COPD) is a progressive lung disease resulting in narrowing of the airways and restricted airflow. Despite being the third leading cause of death in the United States, little is known about the differences in the lung microbial community profiles of healthy individuals vs. COPD patients. Metagenomics is the culture-independent study of genetic material obtained directly from samples. A metagenomic analysis of 56 individuals was conducted. Bronchoalveolar lavage (BAL) samples were collected from COPD patients, active or ex-smokers, and never smokers. 454 pyrosequencing of 16S rRNA was performed and analyzed using a newly designed, modular bioinformatic workflow. Substantial colonization of the lungs was found in all subjects and differentially abundant genera in each group were identified (including Tropheryma in COPD and Sneathia in smokers). These discoveries are promising and may further our understanding of how the structure of the lung microbiome is modified as COPD progresses. It is also anticipated that the results will eventually lead to improved treatments for COPD.
Class E high-efficiency tuned power oscillator (1981)

The class E high-efficiency transistor tuned power oscillator, based on the class E power amplifier, is presented. Theoretical conditions for optimum operation of the oscillator are formulated. A new feedback-loop circuit is proposed and a corresponding oscillator design procedure is given. Experimental results show that the collector-voltage and collector-current waveforms and the collector efficiency of the oscillator are the same as in the class E amplifier with the same transistor and operating at the same frequency. The measured collector efficiency was over 95 percent with 3 W output at 2 MHz. The proposed oscillator is especially applicable at high frequencies because it minimizes the power dissipated during the transistor off-to-on transition, even if the switching time is an appreciable fraction of the signal period.
Formaton of Macrozwitterions in the Cationic Polymerization of Propylene Sulfide Initiated with o-Sulfobenzoic Anhydride (1978)

Bulk polymerization of propylene sulfide with o-sulfobenzoic anhydride as initiator was carried out and the polymerization proceeded by a zwitterionic mechanism. Chemical and spectroscopic investigation of the purified polymer revealed that the polymer contained two end groups-thiolester of benzoic acid o-sulfonate anions and acyclic tert-sulfonium ions which were formed by termination of episulfonium ions with sulfide groups in the polymer chains. The concentration of sulfonate anions was nearly the same as the concentration of acyclic tert-sulfonium ions, as expected for macrozwitterions. The cocatalysis mechanism by a trace of water was excluded and the other possible mechanisms were discussed on the basis of end group analysis.
Medical Technology MEMS (2007)

The combination of silicon MEMS technology fabrication techniques and novel low cost materials can be utilized to make disposable low cost devices for biomedical diagnostics and therapies. In the talk a few examples of such devices will be described in detail. The emphasis will be on ultraminiaturized low cost chip-based systems, including a transdermal microneedle patch for drug delivery and an electronic "nose" system for drug detection.
Characterization of iNOS+ Neutrophil-like ring cell in tumor-bearing mice (2012)

In this study, iNOS expression was linked to a homogeneous subset; ring cells with a particular phenotype and immune suppressive function, in a common and well-established murine tumor model; 4T-1. Since the absence of a Gr-1 homolog in humans has made the identification of MDSC much more challenging, use of iNOS as a functional marker of MDSC may also have clinical importance.
Point kernels and superposition methods for scatter dose calculations in brachytherapy (2000)

Point kernels have been generated and applied for calculation of scatter dose distributions around monoenergetic point sources for photon energies ranging from 28 to 662 keV. Three different approaches for dose calculations have been compared: a single-kernel superposition method, a single-kernel superposition method where the point kernels are approximated as isotropic and a novel 'successive-scattering' superposition method for improved modelling of the dose from multiply scattered photons. An extended version of the EGS4 Monte Carlo code was used for generating the kernels and for benchmarking the absorbed dose distributions calculated with the superposition methods. It is shown that dose calculation by superposition at and below 100 keV can be simplified by using isotropic point kernels. Compared to the assumption of full in-scattering made by algorithms currently in clinical use, the single-kernel superposition method improves dose calculations in a half-phantom consisting of air and water. Further improvements are obtained using the successive-scattering superposition method, which reduces the overestimates of dose close to the phantom surface usually associated with kernel superposition methods at brachytherapy photon energies. It is also shown that scatter dose point kernels can be parametrized to biexponential functions, making them suitable for use with an effective implementation of the collapsed cone superposition algorithm.
Objective measurement of motion in the orbit (2001)

The research described in the thesis had two major aims: to find methods for objective measurement of motion in the orbit, and to determine the clinical use of these methods in patients with orbital disorders. This implied that a number of research questions had to be answered in the fields of both image science and of ophthalmology and orbitology.\nThe results have established that measurement of the two- and three-dimensional motion of tissues in the orbit is feasible in humans. It can be imaged in 2-D and 3-D with Magnetic Resonance Imaging (MRI) sequences. It can be calculated objectively from these sequences using optical flow methods. First order techniques were found to be superior for this purpose as they are less sensitive to noise, partial volume effects and aliasing. A new first-order 3-D optical flow algorithm was developed for robust and computationally efficient three-dimensional optical flow estimation. A number of techniques were developed to visualize 2- and 3-D motion combined with the anatomy in 3-D space, using color-coding. \nThe results of two clinical studies have established the clinical use of objective measurement of motion in the orbit in a number of orbital and motion disorders. The studies have resulted in an explanation for the persistent pain that may occur after enucleation of the globe, based on motion measurements in patients after enucleation. They have also shown that orbital tumors can be differentiated using motion studies.\nThe results have also shown that the position of the rectus muscle pulleys is the same in patients with Graves disease and in normals. After surgical decompression of the orbit, the muscles and their pulleys are usually not displaced, except in cases where specific muscle paths and pulleys are displaced in specific patterns, resulting in specific motility disturbances. Thus, a new explanation has been found for the motility disturbances that may occur in some patients after decompression surgery for Graves orbitopathy.\nThese last findings have led to the notion central to this thesis, namely that the orbital tissues are an organ in their own right, the organ of gaze, and do not need their bony orbit to function normally.
Mapping, Planning, and Sample Detection Strategies for Autonomous Exploration (2013)

Abstract This paper presents algorithmic advances and field trial results for autonomous exploration and proposes a solution to perform simultaneous localization and mapping (SLAM), complete coverage, and object detection without relying on GPS or magnetometer data. We demonstrate an integrated approach to the exploration problem, and we make specific contributions in terms of mapping, planning, and sample detection strategies that run in real‐time on our custom platform. Field tests demonstrate reliable performance for each of these three main components of the system individually, and high‐fidelity simulation based on recorded data playback demonstrates the viability of the complete solution as applied to the 2013 NASA Sample Return Robot Challenge.
Total Synthesis of (+)‐Azaspiracid‐1. Part I: Synthesis of the Fully Elaborated ABCD Aldehyde (2007)

Has aspirations: The total synthesis of (+)-azaspiracid-1 has been realized. The ABCD fragment was synthesized in 20 linear steps and 16 % overall yield through the enantioselective syntheses of the AB sulfone and the CD aldehyde, their coupling by a sulfone anion addition, and a thermodynamically controlled bis(spiroketalization) event. The E, FG, and HI ring fragments were synthesized enantioselectively and then coupled by using aldol methodology. Finally, a complex addition of the anion of the anomeric EFGHI sulfone to the ABCD aldehyde completed the synthesis in 26 linear steps and 2.7 % yield. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2007/z701515_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
<title>Semiautomatic construction of 3D medical image-segmentation processes</title> (1994)

We describe a GUI-based system called INTERSEG that can define 3D radiological image-segmentation processes. Using INTERSEG's GUI interface, the user first defines interactively some problem cues, which specify a segmentation task. Then, INTERSEG uses the cues to automatically construct a process for the task. The process consists of automatic image-processing operations, such as image enhancement, image segmentation, shape analysis, and measurement. With other systems the user must resort to trial- and-error experimentation to construct such processes.
Asymptotic properties of Markov decision processes (2009)

In our earlier paper we derived the optimal control policy for a time varying, finite horizon, continuous time Markov processes subject to a quadratic penalty on the amount of the rate adjustment. Some aspects of the time invariant, infinite horizon problem were resolved but questions remained. In this paper we consider a more general class of performance measures and constraints on the controls. After deriving the appropriate Hamilton-Jacobi equation, we discuss asymptotic properties. The central question here relates to the possibility of that non constant (e.g., periodic) steady state policies may have better average performance than the best constant policy.
Three-dimensional modeling of laser-plasma interaction: Benchmarking our predictive modeling tools versus experiments (2008)

New experimental capabilities [Froula et al., Phys. Rev. Lett. 98, 085001 (2007)] have been developed to study laser-plasma interaction (LPI) in ignition-relevant condition at the Omega laser facility (LLE/Rochester). By shooting an interaction beam along the axis of a gas-filled hohlraum heated by up to 17kJ of heater beam energy, a millimeter-scale underdense uniform plasma at electron temperatures above 3keV was created. Extensive Thomson scattering measurements allowed to benchmark hydrodynamic simulations performed with HYDRA [Meezan et al., Phys. Plasmas 14, 056304 (2007)]. As a result of this effort, these simulations can be used with much confidence as input parameters for the LPI simulation code PF3D [Berger et al., Phys. Plasmas 5, 4337 (1998)]. In this paper, it is shown that by using accurate hydrodynamic profiles and full three-dimensional simulations including a realistic modeling of the laser intensity pattern generated by various smoothing options, whole beam three-dimensional linear kinetic modeling of stimulated Brillouin scattering (SBS) reproduces quantitatively the experimental measurements (SBS thresholds, reflectivity values, and the absence of measurable stimulated Raman scattering). This good agreement was made possible by the recent increase in computing power routinely available for such simulations. These simulations accurately predicted the strong reduction of SBS measured when polarization smoothing is used.
Active/passive vibration control systems for tall buildings (1998)

Three examples of vibration control systems are described. The first is a hybrid mass damper system, which is one type of active vibration control system, as installed on the top floor of a complex triangular building of forty-three stories in order to reduce the response of the building to strong winds and moderate earthquakes. The second is an unbonded brace damper, which is a kind of elasto-plastic damper using low-yield-point steel. It has been installed in a fifteen-story building as an energy absorption member to control severe earthquake motion. The last is a rotational variable damper using an electrorheological fluid. The feasibility of applying this type of damper to a real scale structure as a semi-active control device has been investigated.
Delivering directional haptic cues through eyeglasses and a seat (2015)

Navigation systems usually require visual or auditory attention. Providing the user with haptic cues could potentially decrease cognitive demand in navigation. This study is investigating the use of haptic eyeglasses in navigation. We conducted an experiment comparing directional haptic cues to visual cueing in a car navigation task. Participants (N=12) drove the Lane Change Test simulator with visual text cues, haptic cues given by the eyeglasses and haptic cues given by a car seat. The participants were asked to confirm the recognition of a directional cue (left or right) by pressing an arrow on a tablet screen and by navigating to the corresponding lane. Reaction times and errors were measured. The participants filled in the NASA-TLX questionnaire and were also interviewed about the different cues. The results showed that in comparison to the visual text cues the haptic cues were reacted to significantly faster. Haptic cueing was also evaluated as less frustrating than visual cueing. The haptic eyeglasses fared slightly, although not significantly, better than the haptic seat in subjective and objective evaluations. The paper suggests that haptic eyeglasses can decrease cognitive demand in navigation and have many possible applications.
Functionalization of Boron-Doped Nanocrystalline Diamond with N3 Dye Molecules (2014)

N3 dye molecules [cis-bis(isothiocyanato)bis(2,2'-bipyridyl-4,4'-dicarboxylato)ruthenium(II)] are covalently attached to boron-doped nanocrystalline diamond (B:NCD) thin films through a combination of coupling chemistries, i.e., diazonium, Suzuki, and EDC-NHS. X-ray and ultraviolet photoelectron spectroscopy and near-edge X-ray absorption fine structure spectroscopy are used to verify the covalent bonding of the dye on the B:NCD surface (compared to a hydrogen-terminated reference). The spectroscopic results confirm the presence of a dense N3 chromophore layer, and the positions of the frontier orbitals of the dye relative to the band edge of the B:NCD thin film are inferred as well. Proof-of-concept photoelectrochemical measurements show a strong increase in the photocurrent compared to non-dye-functionalized B:NCD films. This study opens up the possibility of applying N3-sensitized B:NCD thin films as hole conductors in dye-sensitized solar cells.
High-Speed Measurement of Mode Shapes and Vibrational Displacement in Piezoelectric Resonators Using Two Lasers with Different Wavelengths (2008)

Our new method solves the limitation, that is, the requirement of two measurements with different device driving levels, of the previous system for measuring the in-plane vibrational displacement, using two lasers with adequately separated wavelengths. Different interference factors γs are determined for each speckle image by using the lasers. The ratio of the two γs is proportional to the reciprocal of the wavelength ratio. The distributions of the absolute vibrational displacement can be mapped based on this relationship and statistical processing of the speckle images. Red-and-violet semiconductor lasers were used in the actual measurement system. A 23-MHz circular AT-cut quartz resonator was used to test the validity of our method, and the results are compared here to the results previously obtained by the two-level burst wave excitation method.
Holographic data storage: science fiction or science fact? (2014)

To compete in the archive and backup industries, holographic data storage must be highly competitive in four critical areas: total cost of ownership (TCO), cost/TB, capacity/footprint, and transfer rate. New holographic technology advancements by Akonia Holographics have enabled the potential for ultra-high capacity holographic storage devices that are capable of world record bit densities of over 2-4Tbit/in<sup>2</sup>, up to 200MB/s transfer rates, and media costs less than $10/TB in the next few years. Additional advantages include more than a 3x lower TCO than LTO, a 3.5x decrease in volumetric footprint, 30ms random access times, and 50 year archive life. At these bit densities, 4.5 Petabytes of uncompressed user data could be stored in a 19” rack system. A demonstration platform based on these new advances has been designed and built by Akonia to progressively demonstrate bit densities of 2Tb/in<sup>2</sup>, 4Tb/in<sup>2</sup>, and 8Tb/in<sup>2</sup> over the next year. Keywords: holographic
Synthesis and biochemical evaluation of 2'-deoxy-lin-benzoadenosine phosphates (1984)

2'-Deoxy-lin-benzoadenosine has been synthesized via reductive deoxygenation of 2-(beta-D-ribofuranosyl)-8-(methylthio)imidazo[4,5-g]quinazoline. The 5'-mono-, 5'-di-, and 5'-triphosphates have been prepared by chemical and/or enzymatic methods. The 5'-diphosphate was found to be a substrate for phosphorylation by pyruvate kinase and was compared with various natural and extended substrates in kinetic assays. When 2'-deoxy-lin-benzoadenosine 5'-triphosphate was tested in a nick-translation experiment with Escherichia coli DNA polymerase I, a very low level of 32P incorporation from [alpha-32P]TTP into poly[d(AT)] was observed. Nearest-neighbor analysis indicated that the analogue was not significantly incorporated into internal positions in the polymer. In DNA-sequencing reactions, the analogue caused chain termination at adensine residues, although termination was less uniform and less efficient than that with 2',3'-dideoxy-ATP. These experiments show that lin-benzoadenine can form a widened Watson-Crick base pair with thymine. They strongly suggest, though they do not prove, that the enzyme is able to attach the analogue to DNA.
Hypothalamic and Cerebral Cortical Inhibition of Melanocyte-Stimulating Hormone Secretion in the Frog,<i>Rana pipiens</i> (1967)

Aqueous extracts of hypothalamic and cerebral cortical tissues of light and dark adapted frogs were assayed in vitro for their ability to inhibit the secretion of melanocyte-stimulating hormone (MSH) from the pars intermedia of the dark adapted frog. The extracts also were assayed for melanocyte-stimulating activity. The pars intermedia secreted large quantities of MSH in vitro. The extracts of the hypothalamus and of cerebral cortex of both light and dark adapted frogs contained a factor(s) that inhibited the secretion of MSH from the pars intermedia. Extracts of the hypothalamus, but not extracts of the cerebral cortex, also contained a melanocytestimulating substance. There was no significant difference between extracts of the hypo hilamus and cerebral cortex of light and dark adapted frogs in their ability to inhibit MSH secretion. The possible chemical nature of the factor(s) was discussed. The ability of the cerebral cortical extracts to inhibit MSH secretion was attributed to the catecholamine content of the brain. The presence of a melanocyte-stimulating substance in the hypoth lamus, but not the cortex, suggests that accumulated ited MSH may be involved in a feedback cortrol loop which regulates the release of the hypothalamic factor that inhibits the secretion of MSH. (Endocrinology80: 399, 1967)