gebhart/patrepeval huggingface dataset:
Combining burst wave lithotripsy and ultrasonic propulsion for enhanced kidney stone comminution (2016)

Burst wave lithotripsy (BWL) and ultrasonic propulsion (UP) are two new focused ultrasound technologies for noninvasively treating kidney stones. BWL applies short, focused bursts of ultrasound to fracture stones. UP employs long-duration bursts of ultrasound to reposition stones and has been successfully tested on humans. We hypothesize that application of low-level UP can improve comminution by reorienting the stone and dislodging intervening fragments from the stone surface. Experiments were performed in a degassed water bath with a polyvinyl chloride tissue phantom mimicking a kidney calyx. An artificial calcite stone was placed in the phantom and aligned with the focus of a 330-kHz BWL transducer with a co-axial P4-2 imaging probe used for UP. Fragmentation size was compared between stones treated with a fixed 5-minute BWL exposure using 20-cycle bursts at 40 bursts/sec, with or without interleaved UP. The results showed improved fragmentation with the combined exposure, with 3 UP bursts/minute resulting in 45% of stone debris &lt; 2mm versus 23% without UP (p = 0.011). Stones treated with UP alone did not fragment. These results suggest UP can improve stone fragmentation by BWL. [Work supported by NIH K01 DK104854 and P01 DK043881, and NSBRI through NASA NCC 9-58.]
Optoelectronic Particle-Fallout Sensor (1995)

Portable optoelectronic system monitors fallout of small particles (dust and fibers) onto surface at given location during extended time. Data on accumulated fallout downloaded from system to computer for display and analysis. Typical display is plot of signal proportional to amount of accumulated fallout as function of time and read to determine when contamination occurs. In many cases, possible to establish correlations between accumulations of particles and activities in vicinity. Also capable of signaling alarm in event contamination by fallout exceeds specified level. System made very inexpensively and used to monitor accumulation of dust and fibers associated with motion of air in variety of environments. Phenomena monitored indirectly by use of system might include circulation of air in buildings, and human and animal activity. Also serves as auxiliary intrusion monitor (though probably not real-time alarm) in sealed room because motion of intruder inevitably stirs up some dust.
PR-39 and PR-11 peptides inhibit ischemia-reperfusion injury by blocking proteasome-mediated IκBα degradation (2001)

PR-39 inhibits proteasome-mediated I kappa B alpha degradation and might protect against ischemia-reperfusion injury. We studied PR-39, its truncated form PR-11, and a mutant PR-11AAA, which lacks the ability to prevent I kappa B alpha degradation, in a rat heart ischemia-reperfusion model. After 30 min of ischemia and 24 h of reperfusion, cardiac function, infarct size, neutrophil infiltration, and myeloperoxidase activity were measured. Intramyocardial injection of 10 nmol/kg PR-39 or PR-11 at the time of reperfusion reduced infarct size by 65% and 57%, respectively, which improved blood pressure, left ventricular systolic pressure, and relaxation and contractility (+/-dP/dt) compared with vehicle controls 24 h later. Neutrophil infiltration, myeloperoxidase activity, and the expression of intercellular adhesion molecule-1 and vascular cell adhesion molecule 1 were reduced. Thus PR-39 and PR-11 effectively inhibit myocardial ischemia-reperfusion injury in the rat in vivo. This effect is mediated by inhibition of I kappa B alpha degradation and subsequent inhibition of nuclear factor-kappa B-dependent adhesion molecules. The active sequence is located in the first 11 amino acids, suggesting a potential for oligopeptide therapy as an adjunct to revascularization.
Uncooled pump combiners for fiber laser and amplifier systems (2018)

In this work we demonstrate a high transmission pump combiner that can operate uncooled at a maximum power of 400W for a continuous duration of 100hrs. The 7x1 pump combiner has seven 105/125 μm diameter 0.22 NA input pump fibers and a 247 μm diameter and 0.22 NA glass clad output fiber. The combiner has a high, 99%, pump transmission efficiency. These devices withstand without failure, a series of environmental stress tests, namely Thermal Cycling (-40 to 85ºC) and Damp Humidity (85ºC/85RH). These tests are conducted to uncover any latent defects in the device structure. The combiner’s also survive an elevated temperature of 75ºC at a power of 365W for duration of 5hrs, without any noticeable change in pump transmission.
Specific Inhibition of Syk Is Sufficient to Disrupt Proliferation and Survival of Non-Hodgkin’s Lymphoma Cell Lines without Concomitant Inhibition of JAK. (2008)

Abstract Recent studies indicate that dual inhibition of the spleen tyrosine kinase (Syk) and Janus kinases (JAK) by agents such as R788 (tamatinib fosdium) are clinically efficacious in patients with non-Hodgkin’s lymphoma. Since Syk has been implicated in B cell activation, proliferation, and survival, the present study was designed to determine whether the specific inhibition of Syk alone would suffice to disrupt proliferation and survival of lymphoma cells. To test this, a series of compounds were synthesized and screened to identify those that specifically inhibited Syk in a panel of in vitro multi-kinase assays at 300nM. Of these, three were selected for this study; compounds P459-72, P505-15, and P420-89. All three compounds inhibited purified Syk with IC50’s in the 6-43nM range. P459-72 was highly Syk specific. P505-15 also inhibited purified Lyn with an IC50 of 199nM. P420-89 inhibited multiple kinases in the BCR signaling pathway, in addition to JAK1, 2, and 3; IC50’s of 0.63-6.2nM. Assays using the non-Hodgkin’s lymphoma B cell lines Ramos, SUDHL-4 and -6 showed that each compound also inhibited BCR-induced Syk auto-phosphorylation and BLNK phosphorylation (IC50’s in the 100–400nM range) as well as subsequent Ca2+ flux and ERK phosphorylation (IC50’s in the 50–156nM range). In contrast, the activity of the Src family member Lyn, upstream of Syk in the BCR signaling pathway and responsible for Syk tyrosine phosphorylation at amino acid position 352, was not affected. Cellular proliferation was also attenuated in these lymphomas (IC50’s in the 1–5μM range), and all three compounds induced apoptosis to various extents between 1 and 3μM. Interestingly, while P505-15 did inhibit purified Lyn with an IC50 of 199nM, this did not translate into inhibition of Lyn activity upon BCR cross-linking in cells at concentrations where Syk activity was inhibited. A structurally similar compound with a greater than one hundred fold lower Syk inhibitory activity (P528-85) had no effect on the proliferation and survival of these B cell lines. Finally, the cellular effects of the Syk inhibitors required an active BCR signaling pathway, as the B cell line Toledo which lacks BCR expression was insensitive to these compounds; proliferation was inhibited with IC50’s in the 9-38μM range with no induction of apoptosis below 10μM, the highest concentration tested. Taken together, these data suggest that the specific inhibition of Syk, without concomitant inhibition of JAK, may be sufficient for the treatment of non-Hodgkin’s lymphoma.
Heparinase production by Flavobacterium heparinum (1981)

Heparinase production by Flavobacterium heparinum in complex protein digest medium, with heparin employed as the inducer, has been studied and improved. The maximum productivity of heparinase has been increased 156-fold over that achieved by previously published methods to 375 U/liter per h in the complex medium. Rapid deactivation of heparinase activity, both specific and total, was observed at the onset of the stationary phase. Nutritional studies on growth and heparinase production showed an obligate requirement for L-histidine and no vitamin requirement. L-Methionine partially relieved the L-histidine requirement. A defined medium containing glucose, ammonium sulfate, basal salts, L-methionine, and L-histidine was developed for growth and heparinase production. The growth rate in this medium was 0.21 h-1, which is 40%, higher than that in complex medium. The maximum volumetric productivity of heparinase in the defined medium was increased to 1,475 U/liter per h, providing a 640-fold increase over that achieved by previously published methods. No rapid deactivation was observed. An examination of alternate inducers for heparinase showed that heparin degradation products, hyaluronic acid, heparin monosulfate, N-acetyl-D-glucosamine, and maltose, induce heparinase in complex medium. An Azure A assay was modified and fully developed to measure the heparin concentration during fermentation and the heparinase specific activity of crude extracts of F. heparinum obtained from sonication, thus negating the need for further purification to measure activity."
The precise control of manipulators with joint friction: a base force/torque sensor method (2002)

Joint friction is a major problem in accurately controlling robot position during manipulator tasks involving small and slow motions. Previous research in this field suggests the use of either complex modeling and identification techniques, or expensive and delicate torque sensors that must be integrated into the manipulator. This paper proposes a simple, cost-effective method for compensating the effect of joint friction, which utilizes a six-axis force/torque sensor mounted on the base of the manipulator. From the base wrench measurements, the joint torques are estimated and fed back through a torque controller, that virtually eliminates friction and gravity effects. With such high-quality torque control, a simple PD position controller is sufficient to provide high precision motion control even at very low speed and small motions. Theoretical and practical aspects of the torque estimation are first discussed. Next, the control design and tuning is shown. Experimental results for an industrial Puma manipulator, with high Coulomb friction in its gear trains, show the effectiveness of the method. The achieved precision is substantially greater than for conventional methods and approaches the resolution of the Puma's encoders.
<title>Tunnel near-field optical microscopy (TNOM-2)</title> (1995)

Light emitted from the aperture of a near-field optical probe in the close vicinity of a dielectric object propagates in classically `forbidden' as well as `allowed' directions; the two zones are separated by the critical angle for total internal reflection. The new `tunnel' near-field optical microscopy (TNOM) technique makes use of forbidden and allowed radiation, in contrast to standard scanning near-field optical microscopy (SNOM or NSOM), which records only the allowed light. Scan images obtained with allowed and forbidden light are complementary to some extent; the latter, however, provide high contrast and resolution even in situations in which standard SNOM/NSOM shows little or no contrast. The influence of topography on image formation is analyzed and discussed.
Instrument Development and Gamma Spectroscopy With Strontium Iodide (2013)

Development of the Europium-doped Strontium Iodide scintillator, SrI <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> (Eu), involves advances in crystal growth, optics and readout methodology for prototype detectors. We have demonstrated energy resolution of 3% at 662 keV for a 26 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> SrI <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> (Eu) crystal, which is equivalent to the performance obtained with Cerium-doped Lanthanum Bromide of equivalent size. Compared to standard analog readout, use of a digital readout method allows improved energy resolution to be obtained with large volume SrI <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> (Eu) crystals. Comparative gamma spectra acquired with LaBr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> (Ce) and NaI(Tl) quantitatively depict the value of the high resolution of SrI <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> (Eu) in discriminating closely spaced gamma lines for radioisotope identification applications.
A novel polar format algorithm for SAR images utilizing post azimuth transform interpolation. (2005)

SAR phase history data represents a polar array in the Fourier space of a scene being imaged. Polar Format processing is about reformatting the collected SAR data to a Cartesian data location array for efficient processing and image formation. In a real-time system, this reformatting or ''re-gridding'' operation is the most processing intensive, consuming the majority of the processing time; it also is a source of error in the final image. Therefore, any effort to reduce processing time while not degrading image quality is valued. What is proposed in this document is a new way of implementing real-time polar-format processing through a variation on the traditional interpolation/2-D Fast Fourier Transform (FFT) algorithm. The proposed change is based upon the frequency scaling property of the Fourier Transform, which allows a post azimuth FFT interpolation. A post azimuth processing interpolation provides overall benefits to image quality and potentially more efficient implementation of the polar format image formation process.
Imaging the Nonlinear Ultrasonic Parameter of a Medium (1983)

A technique for imaging the nonlinear ultrasonic parameter B/A has been developed. The nonlinear parameter describes the dependence of ultrasonic velocity on pressure and may well provide a new and powerful tool for characterizing both biological and nonbiological media. Our approach is based on observing the interaction of two ultrasonic waves with different frequencies and power levels. A low frequency pump wave, with power level suitable for medical diagnosis (1 mW/cm2), is used to sinusoidally modulate the sound pressure over the region of interest. A much lower intensity high-frequency probe beam is propagated perpendicularly to the pump beam. The phase of the probe wave is modified in proportion to the integral of the product of the nonlinear parameter B/A and the pressure of the pump wave, which varies sinusoidally along the probe beam. This phase change provides a Fourier component of the distribution of the nonlinear parameter B/A for the spatial frequency corresponding to the inverse of the pump wavelength. By changing the frequency of the pump waves, the spatial frequency is changed and a set of spatial Fourier coefficients of the distribution of the nonlinear parameter B/A is obtained. An inverse operation then gives the one-dimensional image along the probe beam. If the probe beam is scanned mechanically, the entire cross-sectional image is obtained. Several images of the nonlinear parameter of biological objects were generated with our system. To our knowledge, these represent the first images of the nonlinear parameter to be reported in the literature. The nonlinear parameter of water was also measured and agreed well with values obtained by other techniques.
In vivo human assessment of bladder elasticity and compliance using Ultrasound Bladder Vibrometry (UBV) and comparison with urodynamic studies (2013)

The bladder stiffens with age and various pathological processes. We have previously proposed the use of Ultrasound Bladder Vibrometry (UBV) to measure mechanical properties of the bladder wall. In UBV, ultrasound radiation force is focused at the bladder wall to excite impulsive anti-symmetric Lamb waves, and pulse-echo ultrasound is used to track tissue motion. Fourier-space analysis of tissue motion is used to calculate Lamb wave velocity dispersion, i.e. the change of Lamb wave velocity as a function of frequency. The Lamb wave velocity dispersion equation is fit to the dispersion data to estimate bladder viscoelastic parameters. Ex vivo formalin studies aimed at demonstrating the ability of UBV to detect bladder stiffening are demonstrated. UBV measurements of compliant and incompliant neurogenic patient bladders were compared with concomitant Urodynamic Cystometry Studies (UDS), which are the clinical gold standard for evaluation of bladder compliance. Results of UBV and UDS measurements in neurogenic patients were in good agreement. Healthy bladders were more compliant than the neurogenic bladders as their bladder elasticity does not increase significantly over the full range of bladder capacity. The results presented in this study demonstrate the potential of UBV serving as a surrogate to UDS studies.
Efficient Software Implementations of Modular Exponentiation. (2011)

Abstract. RSA computations have a significant effect on the workloads of SSL/TLS servers, and therefore their software implementations on general purpose processors are an important target for optimization. We concentrate here on 512-bit modular exponentiation, used for 1024-bit RSA. We propose optimizations in two directions. At the primitives ’ level, we study and improve the performance of an “Almost ” Montgomery Multiplication. At the exponentiation level, we propose a method to reduce the cost of protecting the w-ary exponentiation algorithm against cache/timing side channel attacks. Together, these lead to an efficient software implementation of 512-bit modular exponentiation, which outperforms the currently fastest publicly available alternative. When measured on the latest x86-64 architecture, the 2 nd Generation Intel ® Core ™ processor, our implementation is 43 % faster than that of the current version of OpenSSL (1.0.0d).
[C7GC4]4 Association into supra molecular i-motif structures (2010)

The self-associative properties of cytidine-rich oligonucleotides into symmetrical i-motif tetramers give to these oligonucleotides the capacity of forming supramolecular structures (sms) that have potential applications in the nanotechnology domain. In order to facilitate sms formation, oligonucleotides containing two cytidine stretches of unequal length (C(n)XC(m)) separated by a non-cytidine spacer were synthesized. They were designed to associate into a tetramer including an i-motif core built by intercalation of the C.C(+) pairs of the longer C stretch with the two dangling non-intercalated strands of the shorter C stretch at each end. Gel filtration chromatography shows that the non-intercalated C-rich ends give to this structure the capacity of forming extremely stable sms. Using C(7)GC(4) as a model, we find that the sms formation rate varies as the oligonucleotide concentration and increases at high temperature. Competitively with the tetramer involved in sms elongation, C(n)XC(m) oligonucleotides form i-motif dimers that compete with sms elongation. The dimer stability is strongly reduced when the pH is moved away from the cytidine pK. This results in an equilibrium shift towards the tetramer and in the acceleration of the sms formation rate. The chromatograms of the sms formed by C(7)GC(4) indicate a broad distribution. In a 1.5 mM solution incubated at 37 degrees C, the equilibrium distribution is centered on a molecular weight corresponding to the assembly of nine tetramers and the upper limit corresponds to 80 tetramers. The lifetime of this structure is about 4 days at 40 degrees C, pH 4.6.
Training and validation of a novel 4-miRNA ratio model (MiCaP) for prediction of postoperative outcome in prostate cancer patients (2018)

We identified a novel 4-miRNA ratio model (MiCaP) with significant independent prognostic value in three RP cohorts, indicating promising potential to improve PC risk stratification.
Improved Methods for Immunoassay of Mycothiol (1999)

Improved enzyme-linked immunosorbent assay (ELISA) methods have been developed for the determination of femtomole amounts of mycothiol (MSH), the main low-molecular-weight thiol in mycobacteria. The immunoassays utilize an affinity-purified rabbit polyclonal antibody that is highly specific for the pseudodisaccharide moiety of MSH. MSH was first biotinylated by the thiol-specific reagent 3-(N-maleimidopropionyl)biocytin. The MSH-biotin adduct was then captured with immobilized avidin and detected with anti-MSH antibody (biotin-capture ELISA) or was captured with immobilized anti-MSH antibody and detected with alkaline phosphatase-labelled avidin (MSH-capture ELISA). The MSH-capture ELISA was the most sensitive method, measuring as little as 0.3 fmol of MSH. Methods for biotinylating MSH directly from Mycobacterium spp. are described. The MSH-capture ELISA was tested for the detection of M. avium seeded in human urine or cerebrospinal fluid samples and for screening mutant M. smegmatis strains to detect MSH production.
Kramers–Kronig relationships applied to shear wave propagation in soft tissues. (2010)

Multiple methods have been proposed to characterize the viscoelastic material properties of soft tissues to differentiate normal from pathological tissue. Shearwave dispersion ultrasound vibrometry is a method that uses the dispersion of the shear wave velocity to characterize tissue shear elasticity and viscosity. It has recently been shown [M. W. Urban and J. F. Greenleaf, Phys. Med. Biol. 54, 5919–5933 (2009)] that the Kramers–Kronig relationships can be applied to shear wave measurements in ex vivo skeletal muscle over a frequency bandwidth of 100–600 Hz. We will describe this process where shear wave attenuation is modeled using a power law, and the shear wave velocity dispersion is predicted by applying the Kramers–Kronig relationships. In this study, we apply this method to shear wave propagation measurements made in different soft tissues such as ex vivo porcine skeletal muscle and kidney and in vivo porcine liver. The shear wave velocity predictions using the Kramers–Kronig relationships agree with the velocity measurements. The mean square error for these tissues ranged from 0.0024–0.0625 m2/s2. The Kramers–Kronig relationships can be used in shear wave propagation measurements in different types of soft tissues. [This work was supported in part by NIH Grants Nos. EB002167 and DK082408.]
Enzyme inhibitory homogeneous immunoassay for high molecular weight antigen (I) (1988)

Abstract A highly sensitive homogeneous enzyme immunoassay has been developed for the determination of antigens with high molecular weight. The method presented is based on steric hindrance of the enzyme against an insoluble substrate by antigen binding to antibody: enzyme, conjugate, and consists of α‐amylase from Bacillus subtilis as label with antibody, human α‐fetoprotein (AFP) or human ferritin as ligands, and insoluble substrate. The assay procedure is as follows: sample is mixed and incubated with the conjugate at 37° C for 20 min. Thereafter, the mixture is incubated at 37° C for 20 min following addition of substrate, and the enzyme reaction is terminated by adding the stopper. Then the mixture is centrifuged at 3,000 rpm for 1 minute, and the absorbance of the supernatant is measured at 620 nm. The measurable range for AFP was 5‐200 ng/ml for ferritin, it was 10‐800 ng/ml. In addition, the method was well correlated with radioimmunoassay; i.e., for AFP r = 0.892 and for ferritin r = 0.951. Furthermore, there was no interference during the assay of endogenous a‐amylase in human serum as a result of the use of the inhibitor specific to mammalian amylase which was purified from bacteria.