gebhart/patrepeval huggingface dataset:
Flat RF body coil design for open MRI (2002)

A flat disc shaped RF body coil design, for application in open vertical field high field strength MRI scanners, is presented. The homogeneity is better than 3 dB inside a 40 cm imaging sphere. Multi response optimization resulted in a 6 Sigma design.
Learning to generalize for complex selection tasks (2009)

Selection tasks are common in modern computer interfaces: we are often required to select a set of files, emails, data entries, and the like. File and data browsers have sorting and block selection facilities to make these tasks easier, but for complex selections there is little to aid the user without writing complex search queries. We propose an interactive machine learning solution to this problem called "smart selection," in which the user selects and deselects items as inputs to a selection classifier which attempts at each step to correctly generalize to the user's target state. Furthermore, we take advantage of our data on how users perform selection tasks over many sessions, and use it to train a label regressor that models their generalization behavior: we call this process learning to generalize. We then combine the user's explicit labels as well the label regressor outputs in the selection classifier to predict the user's desired selections. We show that the selection classifier alone takes dramatically fewer mouse clicks than the standard file browser, and when used in conjunction with the label regressor, the predictions of the classifier are significantly more accurate with respect to the target selection state.
Streptococcal antitumor protein: Expression in Escherichia coli cells and properties of the recombinant protein. (1991)

Streptococcal antitumor protein (SAGP) was produced by transformed E. coli JM103 carrying the SAGP gene downstream from the tac promoter. The purified recombinant SAGP had the same N-terminal amino acid sequence as that of the native SAGP isolated from Streptococcus pyogenes Su cells. Gel filtration analysis showed that the recombinant SAGP was a dimer, while the native SAGP was a tetramer. When the antitumor activity was tested against sarcoma 180 cells, the IC50 of the recombinant SAGP was 0.3 microgram/ml, about a quarter as active as the native SAGP. These results suggest that the quaternary structure of SAGP is important for the antitumor activity.
Introduction of a distance cut-off into structural alignment by the double dynamic programming algorithm (1997)

Two approximations were introduced into the double dynamic programming algorithm, in order to reduce the computational time for structural alignment. One of them was the so-called distance cut-off, which approximately describes the structural environment of each residue by its local environment. In the approximation, a sphere with a given radius is placed at the center of the side chain of each residue. The local environment of a residue is constituted only by the residues with side chain centers that are present within the sphere, which is expressed by a set of center-to-center distances from the side chain of the residue to those of all the other constituent residues. The residues outside the sphere are neglected from the local environment. Another approximation is associated with the distance cut-off, which is referred to here as the delta N cut-off. If two local environments are similar to each other, the numbers of residues constituting the environments are expected to be similar. The delta N cut-off was introduced based on the idea. If the difference between the numbers of the constituent residues of two local environments is greater than a given threshold value, delta N, the evaluation of the similarity between the local environments is skipped. The introduction of the two approximations dramatically reduced the computational time for structural alignment by the double dynamic programming algorithm. However, the approximations also decreased the accuracy of the alignment. To improve the accuracy with the approximations, a program with a two-step alignment algorithm was constructed. At first, an alignment was roughly constructed with the approximations. Then, the epsilon-suboptimal region for the alignment was determined. Finally, the double dynamic programming algorithm with full structural environments was applied to the residue pairs within the epsilon-suboptimal region to produce an improved alignment.
Trace Detection of Dissolved Hydrogen Gas in Oil Using a Palladium Nanowire Array (2011)

The electrical resistance, R, of an array of 30 palladium nanowires is used to detect the concentration of dissolved hydrogen gas (H(2)) in transformer oil over the temperature range from 21 to 70 °C. The palladium nanowire array (PdNWA), consisting of Pd nanowires ∼100 nm (width), ∼20 nm (height), and 100 μm (length), was prepared using the lithographically patterned nanowire electrodeposition (LPNE) method. The R of the PdNWA increased by up to 8% upon exposure to dissolved H(2) at concentrations above 1.0 ppm and up to 2940 ppm at 21 °C. The measured limit-of-detection for dissolved H(2) was 1.0 ppm at 21 °C and 1.6 ppm at 70 °C. The increase in resistance induced by exposure to H(2) was linear with [H(2)](oil)(1/2) across this concentration range. A PdNWA sensor operating in flowing transformer oil has functioned continuously for 150 days.
Synthesis, Anticancer Activity, and Preliminary Pharmacokinetic Evaluation of 4,4-Disubstituted Curcuminoid 2,2-bis(Hydroxymethyl)Propionate Derivatives (2020)

Compound <b>1</b> is a curcumin di-<i>O</i>-2,2-bis(hydroxymethyl)propionate that shows significant in vitro and in vivo inhibitory activity against MDA-MB-231 cells with eight to ten-fold higher potency than curcumin. Here, we modified the α-position (C-4 position) of the central 1,3-diketone moiety of <b>1</b> with polar or nonpolar functional groups to afford a series of 4,4-disubstituted curcuminoid 2,2-bis(hydroxymethyl)propionate derivatives and evaluated their anticancer activities. A clear structure-activity relationship of compound 1 derivatives focusing on the functional groups at the C-4 position was established based on their anti-proliferative effects against the MDA-MB-231 and HCT-116 cell lines. Compounds <b>2</b>-<b>6</b> are 4,4-dimethylated, 4,4-diethylated, 4,4-dibenzylated, 4,4-dipropargylated and 4,4-diallylated compound <b>1</b>, respectively. Compounds 2m-6m, the ester hydrolysis products of compounds <b>2</b>-<b>6</b>, respectively, were synthesized and assessed for anticancer activity. Among all compound <b>1</b> derivatives, compound <b>2</b> emerged as a potential chemotherapeutic agent for colon cancer due to the promising in vivo anti-proliferative activities of <b>2</b> (IC<sub>50</sub> = 3.10 ± 0.29 μM) and its ester hydrolysis product <b>2m</b> (IC<sub>50</sub> = 2.17 ± 0.16 μM) against HCT-116. The preliminary pharmacokinetic evaluation of <b>2</b> implied that <b>2</b> and <b>2m</b> are main contributors to the in vivo efficacy. Compound 2 was further evaluated in an animal study using HCT-116 colon tumor xenograft bearing nude mice. The results revealed a dose-dependent efficacy that led to tumor volume reductions of 27%, 45%, and 60% at 50, 100, and 150 mg/kg doses, respectively. The established structure-activity relationship and pharmacokinetic outcomes of <b>2</b> is the guidance for future development of 4,4-disubstituted curcuminoid 2,2-bis(hydroxymethyl)- propionate derivatives as anticancer drug candidates.
MicroRNA genes are frequently located near mouse cancer susceptibility loci (2007)

MicroRNAs (miRNAs) are short 19- to 24-nt RNA molecules that have been shown to regulate the expression of other genes in a variety of eukaryotic systems. Abnormal expression of miRNAs has been observed in several human cancers, and furthermore, germ-line and somatic mutations in human miRNAs were recently identified in patients with chronic lymphocytic leukemia. Thus, human miRNAs can act as tumor suppressor genes or oncogenes, where mutations, deletions, or amplifications can underlie the development of certain types of leukemia. In addition, previous studies have shown that miRNA expression profiles can distinguish among human solid tumors from different organs. Because a single miRNA can simultaneously influence the expression of two or more protein-coding genes, we hypothesized that miRNAs could be candidate genes for cancer risk. Research in complex trait genetics has demonstrated that genetic background determines cancer susceptibility or resistance in various tissues, such as colon and lung, of different inbred mouse strains. We compared the genome positions of mouse tumor susceptibility loci with those of mouse miRNAs. Here, we report a statistically significant association between the chromosomal location of miRNAs and those of mouse cancer susceptibility loci that influence the development of solid tumors. Furthermore, we identified distinct patterns of flanking DNA sequences for several miRNAs located at or near susceptibility loci in inbred strains with different tumor susceptibilities. These data provide a catalog of miRNA genes in inbred strains that could represent genes involved in the development and penetrance of solid tumors.
Top-Gated Chemical Vapor Deposition Grown Graphene Transistors with Current Saturation (2011)

Graphene transistors are of considerable interest for radio frequency (rf) applications. In general, transistors with large transconductance and drain current saturation are desirable for rf performance, which is however nontrivial to achieve in graphene transistors. Here we report high-performance top-gated graphene transistors based on chemical vapor deposition (CVD) grown graphene with large transconductance and drain current saturation. The graphene transistors were fabricated with evaporated high dielectric constant material (HfO(2)) as the top-gate dielectrics. Length scaling studies of the transistors with channel length from 5.6 μm to 100 nm show that complete current saturation can be achieved in 5.6 μm devices and the saturation characteristics degrade as the channel length shrinks down to the 100-300 nm regime. The drain current saturation was primarily attributed to drain bias induced shift of the Dirac points. With the selective deposition of HfO(2) gate dielectrics, we have further demonstrated a simple scheme to realize a 300 nm channel length graphene transistors with self-aligned source-drain electrodes to achieve the highest transconductance of 250 μS/μm reported in CVD graphene to date.
Ferroelectric Generators (2012)

Ferroelectric Generators (FEGs) are compact single shot high voltage generators. They consist of a small explosive charge, ferroelectric ceramic, and an output circuit. There has been and continues to be active Small Business Innovative Research (SBIR), University, and Government programs to develop FEGs as very compact power supplies for a variety of loads including antennas, microwave sources, and detonator arrays. In this paper, we will report on some of our recent efforts to improve the performance of FEGs and to use them to drive various loads.
Fusion of angiography and intravascular ultrasound in vivo: establishing the absolute 3-D frame orientation (1999)

Data fusion of biplane angiography and intravascular ultrasound (IVUS) facilitates geometrically correct reconstruction of coronary vessels. The locations of IVUS frames along the catheter pullback trajectory can be identified, however the IVUS image orientations remain ambiguous. An automated approach to determination of correct IVUS image orientation in three-dimensional space is reported. Analytical calculation of the catheter twist is followed by statistical optimization determining the absolute IVUS image orientation. The fusion method was applied to data acquired in patients undergoing routine coronary intervention, demonstrating the feasibility and good performance of our approach.
Optical Spatial integration methods for ambiguity function generation (1981)

A coherent optical spatial integration approach to ambiguity function generation is described. It uses one dimensional acousto-optic Bragg cells as input tranducers in conjunction with a space variant linear phase shifter, a passive optical element, to generate the two dimensional ambiguity function in one exposure. Results of a real time implementation of this system are shown.
Nanotechnology Strategies for Antibacterial and Remineralizing Composites and Adhesives to Tackle Dental Caries (2015)

Dental caries is the most widespread disease and an economic burden. Nanotechnology is promising to inhibit caries by controlling biofilm acids and enhancing remineralization. Nanoparticles of silver were incorporated into composites/adhesives, along with quaternary ammonium methacrylates (QAMs), to combat biofilms. Nanoparticles of amorphous calcium phosphate (NACP) released calcium/phosphate ions, remineralized tooth-lesions and neutralized acids. By combining nanoparticles of silver/QAM/NACP, a new class of composites and adhesives with antibacterial and remineralization double benefits was developed. Various other nanoparticles including metal and oxide nanoparticles such as ZnO and TiO2, as well as polyethylenimine nanoparticles and their antibacterial capabilities in dental resins were also reviewed. These nanoparticles are promising for incorporation into dental composites/cements/sealants/bases/liners/adhesives. Therefore, nanotechnology has potential to significantly improve restorative and preventive dentistry.
An Analytical Method to Generate Walking Pattern of Humanoid Robot (2006)

An analytic method to generate the real-time trajectory of the center of mass (CoM) is proposed for given zero moment point (ZMP) pattern. The whole walking process is divided into transient and periodic walking phases. For each phase of walking, we compute the analytic solution of the center of mass for given ZMP based on the inverted pendulum model. Specially, for the transient walking phase, we actively utilize the non-minimum phase solution to extract the center of mass trajectory. The proposed pattern generation method were implemented to a real humanoid robot system called by MAHRUII. Those are verified by the experiments.
Hand-held optical imager (Gen-2): improved instrumentation and target detectability (2012)

Hand-held optical imagers are developed by various researchers towards reflectance-based spectroscopic imaging of breast cancer. Recently, a Gen-1 handheld optical imager was developed with capabilities to perform two-dimensional (2-D) spectroscopic as well as three-dimensional (3-D) tomographic imaging studies. However, the imager was bulky with poor surface contact (~30%) along curved tissues, and limited sensitivity to detect targets consistently. Herein, a Gen-2 hand-held optical imager that overcame the above limitations of the Gen-1 imager has been developed and the instrumentation described. The Gen-2 hand-held imager is less bulky, portable, and has improved surface contact (~86%) on curved tissues. Additionally, the forked probe head design is capable of simultaneous bilateral reflectance imaging of both breast tissues, and also transillumination imaging of a single breast tissue. Experimental studies were performed on tissue phantoms to demonstrate the improved sensitivity in detecting targets using the Gen-2 imager. The improved instrumentation of the Gen-2 imager allowed detection of targets independent of their location with respect to the illumination points, unlike in Gen-1 imager. The developed imager has potential for future clinical breast imaging with enhanced sensitivity, via both reflectance and transillumination imaging.
Method and apparatus to stablize an offshore platform (1990)

This patent describes a column-stabilized floating platform for utilization in deep water, offshore hydrocarbon exploration and production, above a selected portion of a seafloor. It comprises: a floating platform having at least one column which is at least partially hollow to provide positive buoyancy, the column supporting at least one above-surface deck; a stabilizer connected to and suspended a substantial distance beneath the floating platform by a plurality of suspension tendons. The stabilizer has sufficient submerged weight to maintain the suspension tendons in tension and a sufficient added mass, produced by the submerged weight plus resistance to motion of a portion of the water surrounding the stabilizer, to satisfactorily control first order wave-induced heave, pitch, roll, surge and sway motions of the floating platform without the need for anchoring the platform to sid seafloor.
Improved Method for In-situ Elastic Constants of Isotropic and Orthotropic Composite Materials Using Plate Modal Data With Trimodal and Hexamodal Rayleigh Formulations (1995)

This paper relates a further development of an earlier work by the authors, in which they presented a method for deriving the four independent elastic constants (longitudinal and transverse Young’s moduli, in-plane shear modulus and major Poisson’s ratio) of an orthotropic material from resonance data obtained in a modal analysis of a freely-supported plate made out of the material. In the present work, simple averaging, as opposed to the weighted averaging employed in the earlier version, is utilized. The use of three modes and six modes is compared on the basis of results of both the forward and the inverse problems. Results are obtained for materials spanning orthotropy ratios from unity (i.e., isotropic) to about 13. The results suggest that, in comparison with our earlier method, the improved method is easier to use and is just as accurate. The adaptability of the basic method developed by the authors to various levels and types of refinement is also demonstrated, as is the potential of the method for fast characterization of elastic properties of advanced composites.
Sustained TL1A<i>(TNFSF15)</i>expression on both lymphoid and myeloid cells leads to mild spontaneous intestinal inflammation and fibrosis (2013)

TL1A is a member of the TNF superfamily, and its expression is increased in the mucosa of inflammatory bowel disease patients. Moreover, patients with certain <i>TNFSF15</i> variants over-express TL1A and have a higher risk of developing strictures in the small intestine. Consistently, mice with sustained Tl1a expression in either lymphoid or myeloid cells develop spontaneous ileitis and increased intestinal collagen deposition. Transgenic <i>(Tg)</i> mice with constitutive Tl1a expression in both lymphoid and myeloid cells were generated to assess their <i>in vivo</i> consequence. Constitutive expression of Tl1a in both lymphoid and myeloid cells showed increased spontaneous ileitis and collagen deposition than WT mice. T cells with constitutive expression of Tl1a in both lymphoid and myeloid cells were found to have a more activated phenotype, increased gut homing marker CCR9 expression, and enhanced Th1 and Th17 cytokine activity than WT mice. Although no differences in T cell activation marker, Th1 or Th17 cytokine activity, ileitis, or collagen deposition were found between constitutive Tl1a expression in lymphoid only, myeloid only, or combined lymphoid and myeloid cells. Double hemizygous Tl1a-Tg mice appeared to have worsened ileitis and intestinal fibrosis. Our findings confirm that TL1A-DR3 interaction is involved in T cell-dependent ileitis and fibrosis.
Non-contact probe calibration for THz-frequency device characterization (2013)

We present a non-contact, on-wafer, broadband device and component testing methodology scalable to the THz band. The “contactless” probe setup is based on radiative coupling of vector network analyzer test ports onto the coplanar waveguide environment of monolithic devices and integrated circuits. Efficient power coupling is achieved via planar, broadband, antennas that act as the “virtual” probe-tips on the chip under test. For accurate S-parameter measurements, repeatable errors in the setup are calibrated. In this paper, we demonstrate for the first time experimental validation of the calibration of the new non-contact probes for the 325-500 GHz band (using WR 2.2 frequency extenders and a standard vector network analyzer as the backend). This non-contact probe setup is accurate, low-cost and is readily scalable down to the mmW band and up to the THz band (60GHz-3THz).
Microbubbles as a contrast agent in grating interferometry mammography: an ex vivo proof-of-mechanism study (2019)

Grating interferometry mammography (GIM) is an experimental breast imaging method at the edge of being clinically implemented. Besides attenuation, GIM can measure the refraction and scattering of x-rays resulting in differential phase contrast (DPC) and dark-field (DF) images. In this exploratory study, we assessed the feasibility of using microbubbles as a contrast agent in GIM. Two millilitres of microbubbles and iodine were respectively injected into ex vivo breast phantoms, consisting of fresh chicken breasts. Native and postcontrast images were acquired with a clinically compatible GIM setup, operated at 38 kVp, 14-s acquisition time, and with a dose of 1.3 mGy. The visibility of the contrast agents was analysed in a side-by-side comparison by three radiologists. The contrast-to-noise-ratio (CNR) was calculated for each contrast agent. We found that both contrast agents were judged to be visible by the readers. The mean CNR was 3.1 ± 1.9 for microbubbles in DF and 24.2 ± 6.5 for iodine in attenuation. In conclusion, this is a first proof-of-mechanism study that microbubbles could be used as a contrast agent in clinically compatible GIM, due to their scattering properties, which implies the potential use of a contrast agent with a high safety profile in x-ray-based breast imaging.
Cell free biosynthesis of isoprenoids from isopentenol (2019)

Cell-free systems are growing in importance for the biosynthesis of complex molecules. These systems combine the precision of traditional chemistry with the versatility of biology in creating superior overall processes. Recently, a new synthetic pathway for the biosynthesis of isoprenoids using the substrate isopentenol, dubbed the isopentenol utilization pathway (IUP), was demonstrated to be a promising alternative to the native 2C-methyl-d-erythritol-4-phosphate (MEP) and mevalonate (MVA) pathways. This simplified pathway, which contains a minimum of four enzymes to produce basic monoterpenes and only depends on ATP and isopentenol as substrates, allows for a highly flexible approach to the commercial synthesis of isoprenoid products. In this work, we use metabolic reconstitution to characterize this new pathway in vitro and demonstrate its use for the cell-free synthesis of mono-, sesquit-, and diterpenoids. Kinetic modeling and sensitivity analysis were also used to identify the most significant parameters for taxadiene productivity, and metabolic control analysis was employed to elucidate protein-level interactions within this pathway, which demonstrated that the IUP enzymatic system is primarily controlled by the concentration and kinetics of choline kinase (CK) and not regulated by any pathway intermediates. This is a significant advantage over the natural MEP or MVA pathways as it greatly simplifies future metabolic engineering efforts, both in vitro and in vivo, aiming at improving the kinetics of CK. Finally, we used the insights gathered to demonstrate an in vitro IUP system that can produce 220 mg/L of the diterpene taxadiene, in 9 hr, almost 3-fold faster than any system reported thus far.
Efficacy and Safety of MEDI2070, an Antibody Against Interleukin 23, in Patients With Moderate to Severe Crohn’s Disease: A Phase 2a Study (2017)

In a phase 2a trial of patients with moderate to severe Crohn's disease who had failed treatment with tumor necrosis factor antagonists, 8 and 24 weeks of treatment with MEDI2070 were associated with clinical improvement. ClinicalTrials.gov ID: NCT01714726.
Intraocular Camera for Retinal Prostheses: Optical Design (2007)

Optical system design considerations are presented for an intraocular camera that is intended for use in conjunction with an epiretinal microstimulator array to form an intraocular retinal prosthesis for restoring functional vision to the blind.