gebhart/patrepeval huggingface dataset:
Ultrasensitive Label Free Electrical Detection of Insulin in Neat Blood Serum (2013)

Electrical assays potentially offer a highly sensitive, cheap, portable, automated, and multiplexed means of protein biomarker detection, characteristics with an ability to underpin both disease stratification and the development of point of care diagnostics. Most conveniently applied in a reagent free manner, all sensitive assays such as these suffer, however, from profound problems when applied in complex fluids such as blood serum. We report herein, the development, and clinical application, of a highly sensitive and selective electrical insulin biosensor based on a chemisorbed zwittorionic polymer support and a novel reagentless sensing technique based on phase monitoring electrochemical impedance spectroscopy. The polymer adlayer is exceptionally effective in both reducing background response and maintaining receptive antibody binding efficacy, while the non-Faradaic analysis avoids potential interference from background electro-active molecules. Applied to the detection of even a low molecular weight protein (here, insulin), a linear range from 0.1 to 200 pM and an unprecedented femtomolar detection limit are possible in undiluted blood serum.
Quantification of Left Ventricular Function With Premature Ventricular Complexes Reveals Variable Hemodynamics (2016)

Application of real-time cardiovascular magnetic resonance imaging in patients with PVCs revealed differential contribution of PVCs to hemodynamics.
Free‐breathing multislice native myocardial T<sub>1</sub> mapping using the slice‐interleaved T<sub>1</sub> (STONE) sequence (2014)

The STONE sequence allows accurate and precise quantification of native myocardial T<sub>1</sub> times with the additional benefit of covering the entire ventricle. Magn Reson Med 74:115-124, 2015. © 2014 Wiley Periodicals, Inc.
Automatic subspace clustering of high dimensional data for data mining applications (1998)

Data mining applications place special requirements on clustering algorithms including: the ability to find clusters embedded in subspaces of high dimensional data, scalability, end-user comprehensibility of the results, non-presumption of any canonical data distribution, and insensitivity to the order of input records. We present CLIQUE, a clustering algorithm that satisfies each of these requirements. CLIQUE identifies dense clusters in subspaces of maximum dimensionality. It generates cluster descriptions in the form of DNF expressions that are minimized for ease of comprehension. It produces identical results irrespective of the order in which input records are presented and does not presume any specific mathematical form for data distribution. Through experiments, we show that CLIQUE efficiently finds accurate cluster in large high dimensional datasets.
Creating collections with automatic suggestions and example-based refinement (2010)

To create collections, like music playlists from personal media libraries, users today typically do one of two things. They either manually select items one-by-one, which can be time consuming, or they use an example-based recommendation system to automatically generate a collection. While such automatic engines are convenient, they offer the user limited control over how items are selected. Based on prior research and our own observations of existing practices, we propose a semi-automatic interface for creating collections that combines automatic suggestions with manual refinement tools. Our system includes a keyword query interface for specifying high-level collection preferences (e.g., "some rock, no Madonna, lots of U2,") as well as three example-based collection refinement techniques: 1) a suggestion widget for adding new items in-place in the context of the collection; 2) a mechanism for exploring alternatives for one or more collection items; and 3) a two-pane linked interface that helps users browse their libraries based on any selected collection item. We demonstrate our approach with two applications. SongSelect helps users create music playlists, and PhotoSelect helps users select photos for sharing. Initial user feedback is positive and confirms the need for semi-automated tools that give users control over automatically created collections.
High-throughput engineering of infrared plasmonic nanoantenna arrays with nanostencil lithography (2011)

We demonstrate a novel fabrication approach for high-throughput fabrication of engineered infrared plasmonic nanorod antenna arrays with nanostencil lithography (NSL). NSL technique, relying on deposition of materials through a shadow mask, offers the flexibility and the resolution to radiatively engineer nanoantenna arrays for excitation of collective plasmonic resonances. As stencil, we use suspended silicon nitride membrane patterned with nanoapertures and fabricate nanorod antenna arrays. Our spectral measurements and electron microscopy images faithfully confirm the feasibility of NSL technique for large area patterning of nanorod antenna arrays with optical qualities achievable by electron-beam lithography. Furthermore, we show nanostencils can be reused multiple times to fabricate same structures repeatedly and reliably with identical optical responses. This capability is particularly useful when high-throughput replication of the optimized nanoparticle arrays is desired. In addition to its high-throughput capability, NSL permits fabrication of plasmonic devices on surfaces that are difficult to work with electron/ion beam techniques. Nanostencil lithography is a resist free process thus allows the transfer of the nanopatterns to any planar substrate whether it is conductive, insulating or magnetic. As proof of the versatility of the NSL technique, by simply changing the aperture pattern on the silicon nitride membrane, we show fabrication of plasmonic structures in variety of geometries and on different substrates. Nanostencil Lithography enables fabrication of plasmonic substrates supporting spectrally narrow far-field resonances with enhanced near-field intensities. Overlapping these collective plasmonic resonances with molecular specific absorption bands can enable ultrasensitive vibrational spectroscopy.
Quantitative phase-contrast confocal microscope (2014)

We present a quantitative phase-contrast confocal microscope (QPCCM) by combining a line-scanning confocal system with digital holography (DH). This combination can merge the merits of these two different imaging modalities. High-contrast intensity images with low coherent noise, and the optical sectioning capability are made available due to the confocality. Phase profiles of the samples become accessible thanks to DH. QPCCM is able to quantitatively measure the phase variations of optical sections of the opaque samples and has the potential to take high-quality intensity and phase images of non-opaque samples such as many biological samples. Because each line scan is recorded by a hologram that may contain the optical aberrations of the system, it opens avenues for a variety of numerical aberration compensation methods and development of full digital adaptive optics confocal system to emulate current hardware-based adaptive optics system for biomedical imaging, especially ophthalmic imaging. Preliminary experiments with a microscope objective of NA 0.65 and 40 × on opaque samples are presented to demonstrate this idea. The measured lateral and axial resolutions of the intensity images from the current system are ~0.64μm and ~2.70μm respectively. The noise level of the phase profile by QPCCM is ~2.4nm which is better than the result by DH.
Timing synchronization in super-regenerative receivers with a single quench cycle per symbol (2014)

Super-regenerative receivers (SRR) are known for their ultra-low power (ULP) consumption. However, its wide frequency selectivity seriously degrades performance especially in the presence of interference. An attractive approach to address this problem is by lowering the quench rate of the SRR to the modulation rate. However, this brings in uncertainty due to lack of oversamples and leads to the timing synchronization problem in demodulation. This paper proposes a timing synchronization method for SRR with a single quench cycle per modulated symbol. A novel asynchronous preamble structure and an associated timing synchronization algorithm are proposed. Significant performance gains are obtained due to the improved frequency selectivity enabling the SRR system to adhere to the constraints set forth by the IEEE 802.15.4 standard while maintaining the ULP advantage.
RAGE in Diabetic Nephropathy (2007)

As is diabetes itself, diabetic angiopathy is a multi-factorial disease. Advanced glycation endproducts (AGE) cause vascular cell derangement characteristic of diabetes, and this is mainly mediated by their interaction with receptor for AGE (RAGE). When made diabetic, RAGE-overexpressing transgenic mice exhibited exacerbation of the indices of nephropathy, and this was prevented by the inhibition of AGE formation. On the other hand, RAGE-deficient animals showed amelioration of diabetic nephropathy. Accordingly, AGE and RAGE should be regarded as environmental and cellular accounts and as a potential therapeutic target for diabetic nephropathy. In effect, substances that inhibit the formation of AGE, break preformed AGE, change metabolic flows away from glycation, antagonize RAGE, and capture RAGE ligands have been proven as effective remedies against this life-threatening disease.
High temperature ultrasonic sensor for the simultaneous measurement of viscosity and temperature of melts (1999)

An ultrasonic sensor that simultaneously measures temperature and viscosity of molten materials at very high temperature is described. This sensor has applications as a process monitor in melters. The sensor is based on ultrasonic shear reflectance at the solid–melt interface. A delay line probe is constructed using refractory materials. A change in the time of flight within the delay line is used to measure the temperature. The results obtained from this sensor on various calibration glass samples demonstrate a measurement range of 100–20 000 P for the viscosity and 25–1500 °C for the temperature.
Gene cluster controlling conversion to alginate-overproducing phenotype in Pseudomonas aeruginosa: functional analysis in a heterologous host and role in the instability of mucoidy (1994)

Conversion to mucoidy, caused by the overproduction of the exopolysaccharide alginate in laboratory and cystic fibrosis strains of Pseudomonas aeruginosa, can occur via frameshift or nonsense mutations in the second gene of the algU mucA mucB cluster. The first gene of the cluster, algU, encodes a putative alternative sigma factor required for algD transcription. The algD gene encodes a critical alginate biosynthetic enzyme and is invariably activated in mucoid P. aeruginosa cells. To investigate the function of the genes controlling conversion to mucoidy, the wild-type algU mucA mucB cluster from the standard genetic strain PAO1 was used to reconstitute algD transcription in Escherichia coli. Transcription of an algD-lacZ chromosomal fusion in E. coli was detected upon introduction of plasmid-borne algU mucA mucB. Moreover, insertional inactivation of either mucA or mucB resulted in further stimulation of transcriptional activity from the algD promoter. This activation was dependent on algU, since a double algU mucA mutation abrogated transcription of algD. These experiments suggest that the phenotypic manifestations of muc mutations, i.e., increased algD expression and mucoid phenotype, depend on the presence of an active algU gene and that this regulator and the factors encoded by the downstream genes interact. Further support for these conclusions came from the investigations of the mechanism of reversion to nonmucoidy in P. aeruginosa, a phenomenon frequently referred to as the instability of mucoid phenotype. Spontaneous nonmucoid derivatives of the mucoid strain PAO578 carrying the mucA22 mutation were examined for the presence of alterations within the algU mucA mucB locus. Point mutations which inactivated algU were detected in some, but not all, nonmucoid revertants. No reversion of the original mucA22 mutation (a deletion of one C) was observed in any of the investigated strains. This observation suggests that the process of conversion to nonmucoidy ban be explained, at least partially, by second-site suppressor mutations and that a fraction of such mutations occurs in algU.
TU‐H‐BRA‐08: The Design and Characteristics of a Novel Compact Linac‐Based MRI Guided Radiation Therapy (MR‐IGRT) System (2016)

Purpose: To describe the design and characteristics of a novel linac‐based MRI guided radiation therapy system that addresses RF and magnetic field interference and that can be housed in conventional radiotherapy vaults. Methods: The MR‐IGRT system will provide simultaneous MR imaging combined with both simple (3D) and complex (IMRT, SBRT, SRS) techniques. The system is a combination of a) double‐donut split solenoidal superconducting 0.345T MRI; and b) a 90 cm isocenter ring‐gantry mounted 6MV, flattening filter‐free linac coupled with a stacked doubly‐focused multileaf collimator with 4 mm resolution. A novel RF shielding and absorption technology was developed to isolate the beam generating RF emissions from the MR, while a novel magnetic shielding sleeve system was developed to place the magnetic field‐sensitive components in low‐magnetic field regions. The system design produces high spatial resolution radiation beams with state‐of‐the art radiation dose characteristics and simultaneous MR imaging. Results: Prototype testing with a spectrum analyzer has demonstrated complete elimination of linac RF inside the treatment room. The magnetic field inside of the magnetic shielding was well below the specification, allowing the linear accelerator to operate normally. A novel on‐gantry shimming system maintained < 25 ppm magnetic field homogeneity over a 45 cm spherical field of view for all gantry angles. Conclusion: The system design demonstrates the feasibility coupling a state‐of‐the art linac system with a 0.345T MRI, enabling highly conformal radiation therapy with simultaneous MR image guidance. S. Mutic's employer (Washington University) has grant with ViewRay; D. Low is former ViewRay scientific advisory board member (ended October 2015); T. Chmielewski, G. Fought, M. Hernandez, I. Kawrakow, A. Sharma, S. Shvartsman, J. Dempsey are employees of ViewRay with stock options (Dempsey has leadership role and Dempsey/Kawrakow have stock).
Redox-Activated Manganese-Based MR Contrast Agent (2013)

Here we report a simple Mn coordination complex with utility as a redox-sensitive MR probe. The HBET ligand stabilizes both the Mn(2+) and Mn(3+) oxidation states. In the presence of glutathione (GSH), low relaxivity Mn(III)-HBET is converted to high relaxivity Mn(II)-HBET with a 3-fold increase in relaxivity, and concomitant increase in MR signal. Alternately, hydrogen peroxide can convert Mn(II)-HBET to Mn(III)-HBET with a reduction in MR signal.
mTORC1 Promotes Denervation-Induced Muscle Atrophy Through a Mechanism Involving the Activation of FoxO and E3 Ubiquitin Ligases (2014)

Skeletal muscle mass and function are regulated by motor innervation, and denervation results in muscle atrophy. The activity of mammalian target of rapamycin complex 1 (mTORC1) is substantially increased in denervated muscle, but its regulatory role in denervation-induced atrophy remains unclear. At early stages after denervation of skeletal muscle, a pathway involving class II histone deacetylases and the transcription factor myogenin mediates denervation-induced muscle atrophy. We found that at later stages after denervation of fast-twitch muscle, activation of mTORC1 contributed to atrophy and that denervation-induced atrophy was mitigated by inhibition of mTORC1 with rapamycin. Activation of mTORC1 through genetic deletion of its inhibitor TSC1 (tuberous sclerosis complex 1) sensitized mice to denervation-induced muscle atrophy and suppressed the kinase activity of Akt, leading to activation of FoxO transcription factors and increasing the expression of genes encoding E3 ubiquitin ligases atrogin [also known as MAFbx (muscle atrophy F-box protein)] and MuRF1 (muscle-specific ring finger 1). Rapamycin treatment of mice restored Akt activity, suggesting that the denervation-induced increase in mTORC1 activity was producing feedback inhibition of Akt. Genetic deletion of the three FoxO isoforms in skeletal muscle induced muscle hypertrophy and abolished the late-stage induction of E3 ubiquitin ligases after denervation, thereby preventing denervation-induced atrophy. These data revealed that mTORC1, which is generally considered to be an important component of anabolism, is central to muscle catabolism and atrophy after denervation. This mTORC1-FoxO axis represents a potential therapeutic target in neurogenic muscle atrophy.
Recent Advances in the Derivatization of <scp>L</scp>-Ascorbic Acid (1982)

A survey of work since 1975 on the derivatization of ascorbic acid is reviewed from the perspective of the organic chemistry of ascorbic acid. Recent advances in the control of regioselectivity of alkylative derivatization of ascorbic acid have been made possible by the utilization of di- and tri-anions of ascorbic acid. Their use has allowed the facile synthesis of inorganic esters of ascorbic acid. New synthesis of acetal and ketal, side-chain oxidized, and deoxy derivatives are reviewed. The total synthesis of a new side-chain oxidized ascorbic acid denvative, 5-ketoascorbic acid, is reported.
FAIR: a hardware architecture for real-time 3-D image registration (2003)

Mutual information-based image registration, shown to be effective in registering a range of medical images, is a computationally expensive process, with a typical execution time on the order of minutes on a modern single-processor computer. Accelerated execution of this process promises to enhance efficiency and therefore promote routine use of image registration clinically. This paper presents details of a hardware architecture for real-time three-dimensional (3-D) image registration. Real-time performance can be achieved by setting up a network of processing units, each with three independent memory buses: one each for the two image memories and one for the mutual histogram memory. Memory access parallelization and pipelining, by design, allow each processing unit to be 25 times faster than a processor with the same bus speed, when calculating mutual information using partial volume interpolation. Our architecture provides superior per-processor performance at a lower cost compared to a parallel supercomputer.
Use of hydrogen etching to remove existing dislocations in GaN epitaxial layers (2015)

In this paper, based on the anisotropic nature of hydrogen (H2) etching on GaN, we describe a new approach to the removal of threading dislocations in GaN layers. The top surfaces of c-plane (Ga-face) and a-plane GaNs are considered stable in H2; therefore, H2 etches only crystal imperfections such as dislocation and basal plane stacking fault (BSF) sites. We used H2 to etch undoped c-plane GaN, n-type c-plane GaN, a-plane GaN, and an InGaN/GaN multiple quantum well structure. Several examinations were performed, indicating deep cavities on the c-plane GaN samples after H2 etching; furthermore, gorge-like grooves were observed on the a-plane GaN samples. The deep cavities on the c-plane GaN were considered the etched dislocation sites, and the gorge-like grooves on the a-plane GaN were considered the etched BSF sites. Photoluminescence measurements were performed and the results indicated that the H2-etched samples demonstrate superior optoelectronic properties, probably because of the elimination of dislocations.
Design Method for Optimizing Contact Ratio of Hypoid Gears (2013)

Innumerable solutions can be obtained when the pitch surface of a hypoid gear is solved from the requirements of two cones. The pitch angle is determined by the Gleason method based on the idea that the tooth lengthwise curvature corresponds to the cutter radius. This study proposes a new design method that can optimize the contact ratio using the pitch angle, using the new tooth geometry advocated by Honda. The balance of the contact ratios of the convex and concave sides of a gear can be optimized by designing the pitch angle. By optimizing the contact ratio, noise and vibration performance can be improved. In addition, highly efficient gear design can be achieved by decreasing the spiral angle. The effectiveness of this optimized design method is confirmed by measuring transmission errors under load. Design examples of a highly efficient gear by reducing the spiral angle and a gear which ensures high noise and vibration performance are shown. Using this proposed method expands the design freedom of hypoid gears.
Chemical Sensing: All‐in‐Fiber Chemical Sensing (Adv. Mater. 45/2012) (2012)

Photoconductive structures (PCS), embedded directly into the fiber cladding and extending its entire length, capture light emitted by a chemiluminescent material reacting with peroxide vapor flowing through the fiber core, as reported by Yoel Fink and co-workers on page 6005. The PCS directly transform this emissive signal into an electrical signal, thus facilitating a new all-in-fiber platform for remote and distributed photosensing. Image: courtesy of Yan Liang.