gebhart/patrepeval huggingface dataset:
A parallelizable real-time motion tracking algorithm with applications to ultrasonic strain imaging (2007)

Ultrasound-based mechanical strain imaging systems utilize signals from conventional diagnostic ultrasound systems to image tissue elasticity contrast that provides new diagnostically valuable information. Previous works (Hall et al 2003 Ultrasound Med. Biol. 29 427, Zhu and Hall 2002 Ultrason. Imaging 24 161) demonstrated that uniaxial deformation with minimal elevation motion is preferred for breast strain imaging and real-time strain image feedback to operators is important to accomplish this goal. The work reported here enhances the real-time speckle tracking algorithm with two significant modifications. One fundamental change is that the proposed algorithm is a column-based algorithm (a column is defined by a line of data parallel to the ultrasound beam direction, i.e. an A-line), as opposed to a row-based algorithm (a row is defined by a line of data perpendicular to the ultrasound beam direction). Then, displacement estimates from its adjacent columns provide good guidance for motion tracking in a significantly reduced search region to reduce computational cost. Consequently, the process of displacement estimation can be naturally split into at least two separated tasks, computed in parallel, propagating outward from the center of the region of interest (ROI). The proposed algorithm has been implemented and optimized in a Windows system as a stand-alone ANSI C++ program. Results of preliminary tests, using numerical and tissue-mimicking phantoms, and in vivo tissue data, suggest that high contrast strain images can be consistently obtained with frame rates (10 frames s(-1)) that exceed our previous methods.
Characterization of a coherent optical RF channelizer based on a diffraction grating (2001)

A coherent optical RF channelizer has been constructed and characterized. The optical channelizer is based on a free-space optical diffraction grating, and utilizes coherent optical heterodyne detection to translate all of the frequency channels to a common intermediate frequency (IF). The designed optical channelizer has a 1-GHz channel spacing, and a nominal 5-GHz IF and can offer an instantaneous bandwidth greater than 100 GHz. The channelizing receiver has been characterized for its frequency response, crosstalk, and spur-free dynamic range, and the results are in a good agreement with the theoretical values.
Use of alkali nitrate molten salts as electrolytes in intermediate temperature lithium batteries (1981)

Advanced lithium batteries presently under development operate either at the high temperatures associated with the LiCl-KCl molten salt (350-450/degree/C), or at ambient temperatures employing organic solvent based electrolytes. An intermediate temperature lithium battery is proposed as an alternative if it reduces corrosion problems present at high temperatures and improved kinetic performance with respect to ambient temperature cells. 17 refs.
Properties of diode laser pumps for high-power solid-state lasers (2005)

Diode lasers used to pump high average power solid-state lasers typically have broad spectral width so that most of the pump light is not at the peak of the gain medium's absorption feature. However, the long absorption length in these lasers enables even weakly absorbed light to pump efficiently. The result is that high absorption efficiency and improved pump distribution uniformity are possible when using realistic pump diodes. In addition, both quantities are nearly independent of the pump center wavelength.
Manufacturability Feedback and Model Correction for Additive Manufacturing (2014)

Additive manufacturing, or 3D printing, is the process of building three-dimensional solid shapes by accumulating material laid out in sectional layers. Additive manufacturing has been recognized for enabling production of complex custom parts that are difficult to manufacture otherwise. However, the dependence on build orientation and physical limitations of printing processes invariably lead to geometric deviations between manufactured and designed shapes that are usually evaluated after manufacture. In this paper, we formalize the measurement of such deviations in terms of a printability map that simulates the printing process and partitions each printed layer into disjoint regions with distinct local measures of size. We show that manufacturing capabilities, such as printing resolution, and material specific design recommendations, such as minimal feature sizes, may be coupled in the printability map to evaluate expected deviations before manufacture. Furthermore, we demonstrate how partitions with size measures below required resolutions may be modified using properties of the medial axis transform and use the corrected printability map to construct a representation of the manufactured model. We conclude by discussing several applications of the printability map for additive manufacturing.
Automated scoring of liver fibrosis through combined features from different collagen groups (2011)

Liver biopsy remains the gold standard in monitoring progression of liver fibrosis associated with an abnormal increase in collagen. Descriptive scoring systems are still being widely used to grade biopsy samples. In this study, we propose a new set of features by clustering collagen fibers into three groups first based on their localization and connectivity properties, and then by extracting morphological features of collagen fibers. The new feature set is compared to the earlier features used in classification of liver fibrosis, which were based on the total amount of collagen fibers. Our results show that new features lead to more accurate grading of liver fibrosis.
A Single Flexible Coldplate Cools Multiple Devices (2019)

For high-speed computer systems, the high-power devices such as Central Processor Units (CPUs) and Graphics Processing Units (GPUs) generally must be arranged close together to reduce electrical channel routing distances. In such cases water cooling enables greater device density than that achievable with air cooling. In contrast to typical implementations that utilize a separate coldplate for each high-power device, we use a single flexible coldplate to cool multiple devices. The flexibility allows the single coldplate to adapt to varying device heights and/or tilts. We solder or braze the perimeters of two thin, concave metal sheets to form a coldplate chamber. Cooling fin packs inside the chamber are soldered or brazed to internal chamber walls. Careful control of this metal-to-metal interface is required to minimize voiding and achieve good thermal contact. Under the fin packs the external chamber wall contacts the heat generating devices through a thermal interface material (TIM). In the regions between devices, the thin walls of the empty cavity provide mechanical flexibility. This allows for device height variation while maintaining full contact through a thin TIM. Having a single coldplate reduces both cost and potential water leakage at attachment junctions.
Preparation of Nuclear Spin Singlet States Using Spin-Lock Induced Crossing (2013)

We introduce a broadly applicable technique to create nuclear spin singlet states in organic molecules and other many-atom systems. We employ a novel pulse sequence to produce a spin-lock induced crossing (SLIC) of the spin singlet and triplet energy levels, which enables triplet-singlet polarization transfer and singlet-state preparation. We demonstrate the utility of the SLIC method by producing a long-lived nuclear spin singlet state on two strongly coupled proton pairs in the tripeptide molecule phenylalanine-glycine-glycine dissolved in D(2)O and by using SLIC to measure the J couplings, chemical shift differences, and singlet lifetimes of the proton pairs. We show that SLIC is more efficient at creating nearly equivalent nuclear spin singlet states than previous pulse sequence techniques, especially when triplet-singlet polarization transfer occurs on the same time scale as spin-lattice relaxation.
Crystal Structure of the West Nile Virus Envelope Glycoprotein (2006)

The envelope glycoprotein (E) of West Nile virus (WNV) undergoes a conformational rearrangement triggered by low pH that results in a class II fusion event required for viral entry. Herein we present the 3.0-A crystal structure of the ectodomain of WNV E, which reveals insights into the flavivirus life cycle. We found that WNV E adopts a three-domain architecture that is shared by the E proteins from dengue and tick-borne encephalitis viruses and forms a rod-shaped configuration similar to that observed in immature flavivirus particles. Interestingly, the single N-linked glycosylation site on WNV E is displaced by a novel alpha-helix, which could potentially alter lectin-mediated attachment. The localization of histidines within the hinge regions of E implicates these residues in pH-induced conformational transitions. Most strikingly, the WNV E ectodomain crystallized as a monomer, in contrast to other flavivirus E proteins, which have crystallized as antiparallel dimers. WNV E assembles in a crystalline lattice of perpendicular molecules, with the fusion loop of one E protein buried in a hydrophobic pocket at the DI-DIII interface of another. Dimeric E proteins pack their fusion loops into analogous pockets at the dimer interface. We speculate that E proteins could pivot around the fusion loop-pocket junction, allowing virion conformational transitions while minimizing fusion loop exposure.
A Novel Synthetic TLR-4 Agonist Adjuvant Increases the Protective Response to a Clinical-Stage West Nile Virus Vaccine Antigen in Multiple Formulations (2016)

West Nile virus (WNV) is a mosquito-transmitted member of the Flaviviridae family that has emerged in recent years to become a serious public health threat. Given the sporadic nature of WNV epidemics both temporally and geographically, there is an urgent need for a vaccine that can rapidly provide effective immunity. Protection from WNV infection is correlated with antibodies to the viral envelope (E) protein, which encodes receptor binding and fusion functions. Despite many promising E-protein vaccine candidates, there are currently none licensed for use in humans. This study investigates the ability to improve the immunogenicity and protective capacity of a promising clinical-stage WNV recombinant E-protein vaccine (WN-80E) by combining it with a novel synthetic TLR-4 agonist adjuvant. Using the murine model of WNV disease, we find that inclusion of a TLR-4 agonist in either a stable oil-in-water emulsion (SE) or aluminum hydroxide (Alum) formulation provides both dose and dosage sparing functions, whereby protection can be induced after a single immunization containing only 100 ng of WN-80E. Additionally, we find that inclusion of adjuvant with a single immunization reduced viral titers in sera to levels undetectable by viral plaque assay. The enhanced protection provided by adjuvanted immunization correlated with induction of a Th1 T-cell response and the resultant shaping of the IgG response. These findings suggest that inclusion of a next generation adjuvant may greatly enhance the protective capacity of WNV recombinant subunit vaccines, and establish a baseline for future development.
Cloning and expression of the bovine intestinal alkaline phosphatase gene: biochemical characterization of the recombinant enzyme (1993)

A complete genomic clone and a full-length cDNA coding for bovine intestinal alkaline phosphatase have been isolated and sequenced. The gene (5.4 kb) contains 11 exons separated by ten small introns at positions identical to those other members of the eukaryotic tissue-specific alkaline phosphatase family. In addition, 1.5 kb of upstream sequences contain putative regulatory elements showing sequence similarity to human and mouse intestinal alkaline phosphatase promoter sequences. To achieve recombinant bovine intestinal alkaline phosphatase expression, the coding region of the gene was subcloned into the pcDNA I eukaryotic expression vector and transfected into Chinese hamster ovary cells. Recombinant bovine intestinal alkaline phosphatase displays enzymatic properties comparable with those of purified native bovine intestinal alkaline phosphatase, a slightly increased thermal stability and, upon desialylation, it shows a homogeneous behaviour in agarose gel electrophoresis and isoelectric focusing. The availability of the recombinant bovine intestinal alkaline phosphatase and the elucidation of its primary sequence will help to accelerate our efforts to obtain the first crystallographic model of a eukaryotic alkaline phosphatase molecule.
ENHANCED CLEARANCE USING NOVEL MID-DILUTION HEMODIAFILTRATION TECHNIQUE (2001)

Urea & β2, clearances were measured in vitro with bovine blood to evaluate a mid-dilution diafiltration (MD-HDF) technique. Two HF polysulfone dialyzers (F60's) “1” and “2” were connected in series with substitution fluid infused in a mid-dilution mode (i.e. between “1” and “2”). An inter-device dialysate pump was used to set the UF rate in “1” to 25% of Qb. Total fluid filtration rate (Qf) was set to 70–75% of Qb such that TMP(2) = TMP(1). Clearance data was also collected in a) double high flux hemodiafiltration (DHF-HDF) mode in the same configuration without external replacement fluid (i.e. forward filtration in “1” and backfiltration in “2”), and b) parallel dialysis mode. Clearances reported at Qd = 800 ml/min are the average of whole blood clearance and dialysate side clearance, with mass balance errors <10% (urea) and <20% (β2m).TableFor urea, DHF-HDF and MD-HDF showed a 6% (10%) increase over parallel dialysis at Qb=400 (500) ml/min. For β2m, DHF-HDF resulted in a 38% (55%) increase, whereas for MD-HDF, increases were 109% (139%). The dramatic increase in β2m clearance observed with MD-HDF is attributed to the high filtration rate (Qf) achievable with the mid-dilution technique.
Effect of Charge-transporting Molecules on Electrophosphorescence in a Device Fabricated Using Third-generation Dendrimer Encapsulated Tris[2-benzo[<i>b</i>]thiophen-2-ylpyridyl]iridium Complex (2009)

Abstract We have synthesized a new deep-red light-emitting phosphorescent third-generation dendrimer with hole-transporting carbazole dendrons. The new dendrimer is highly efficient when used as a solution-processable emitting material and when used in an electrophosphorescent light-emitting diode system. We selected 4,4′-bis(9-carbazolyl)-1,1′-biphenyl (CBP) and 2-(1,1′-biphenyl-4-yl)-5-(4-tert-butylphenyl)-1,3,4-oxadiazole (PBD) as guest molecules in order to manipulate the carrier transport and carrier confinement in the emissive layer. We fabricated a dendrimer light-emitting diode (DLED) whose configuration is represented as ITO/PEDOT:PSS (40 nm)/dendrimer containing guest molecules (55 nm)/BCP (2,9-dimethyl-4,7-diphenylphenanthroline) (10 nm)/Alq3 (40 nm)/LiF (1 nm)/Al (100 nm) and investigated the device performance. The luminance of the multilayered devices fabricated using the PBD-containing dendrimer was 381 cd/m2 at 52.42 mA/cm2 (20 V) for the dendrimer bearing PBD, which was slightly better than that of a device fabricated using dendrimer alone.
Occlusion handling based on support and decision (2010)

This paper proposes a novel method for handling occluded pixels in stereo images based on a probabilistic voting framework that utilizes a novel support-and-decision process. Occlusion handling aims to assign a reasonable disparity value to occluded pixels in the disparity maps. In an initial step, disparities and their corresponding supports at the occluded pixels are calculated using a probabilistic voting method using the disparities at visible pixels. In this way, the visible pixel information is propagated when the disparities and supports at the occluded pixels are computed. The final disparities for occluded pixels are then computed through an iterative support-and-decision process to propagate the information inside the occluded pixel region. An acceleration technique is also proposed to improve the performance of the iterative support-and-decision process. Experimental results show that the proposed occlusion handling method works well for several challenging stereo images.
Programmed assembly of nanoscale structures using peptoids. (2011)

Sequence-specific polymers are the basis of the most promising approaches to bottom-up programmed assembly of nanoscale materials. Examples include artificial peptides and nucleic acids. Another class is oligo(N-functional glycine)s, also known as peptoids, which permit greater sidegroup diversity and conformational control, and can be easier to synthesize and purify. We have developed a set of peptoids that can be used to make inorganic nanoparticles more compatible with biological sequence-specific polymers so that they can be incorporated into nucleic acid or other biologically based nanostructures. Peptoids offer degrees of modularity, versatility, and predictability that equal or exceed other sequence-specific polymers, allowing for rational design of oligomers for a specific purpose. This degree of control will be essential to the development of arbitrarily designed nanoscale structures.
Host Immunity to Ticks (1996)

The tick-host-pathogen interface is characterized by complex immunological interactions. Tick feeding induces host immune regulatory and effector pathways involving antibodies, complement, antigen-presenting cells, T lymphocytes, and other bioactive molecules. Acquired resistance impairs tick engorgement, ova production, and viability. Tick countermeasures to host defenses reduce T-lymphocyte proliferation, elaboration of the TH1 cytokines interleukin-2 and interferon-gamma, production of macrophage cytokines interleukin-1 and tumor necrosis factor, and antibody responses. The dynamic balance between acquired resistance and tick modulation of host immunity affects engorgement and pathogen transmission. A thorough understanding of acquired immunity to ticks is essential for rational development of antitick vaccines.
Incorporating SIMS Structures in Product Wafers in Order to Perform SIMS and other Material Analysis and Achieve Wafer Level Information about the Front-End Processing (2006)

In this paper, we summarize how the introduction of SIMS structures near the global alignment marks of product wafers serve as an additional way to acquire detailed analytical information about front-end processing and can minimize product yield loss without waiting for metal 1 processing when electrical testing (ET) becomes possible
A multidimensional slit-scan flow system. (1979)

A new slit-scan type flow system is described which provides three (X, Y, and Z) orthogonal one-dimensional projections of cell fluorescence. A photomultiplier tube and two semiconductor array detectors are used to obtain the three slit-scan contours from cells traversing a single fluorescence excitation beam. A high speed, dedicated preprocessor analyzes the three contours in parallel, extracting certain features useful for rejecting cells from which an accurate measurement of nuclear fluorescence cannot be obtain. Contour data is buffered and transferred to a PDP-11/40 computer where nuclear fluorescence is measured and cells are classified. It is anticipated that this new instrument will provide a significant reduction in false alarm rate when applied to prescreening of gynecologic cytology specimens.
Monitoring the performance of a semiconductor optical amplifier (1990)

Measurements of optical gain and spontaneous emission of optical amplifiers show that the latter is a good measure of the former. A device structure is fabricated where a photodetector is integrated next to the amplifier. A fraction of the spontaneous emission from the amplifier impinges on the photodetector in this device producing a photocurrent. The photodetector current is found to be a monotonic function of the amplifier gain. Hence, the photodetector output can be used to monitor the performance of the amplifier.
Differentiation of mouse and human embryonic stem cells into hepatic lineages (2008)

We recently reported a novel method to induce embryonic stem (ES) cells differentiate into an endodermal fate, especially pancreatic, using a supporting cell line. Here we describe the modified culture condition with the addition and withdrawal of secreted growth factors could induce ES cells to selectively differentiate into a hepatic fate efficiently. The signaling of BMP and FGF that have been implicated in hepatic differentiation during normal embryonic development are shown to play pivotal roles in generating hepatic cells from the definitive endoderm derived from ES cells. Moreover, the expression of AFP, Albumin or a biliary molecular marker appeared sequentially thus suggested the differentiation of ES cells recapitulated normal developmental processes of liver. The ES cell-derived differentiated cells showed evidence of glycogen storage, secreted Albumin, exhibited drug metabolism activities and expressed a set of cytochrome or drug conjugate enzymes, drug transporters specifically expressed in mature hepatocytes. With the same procedure, human ES cells also gave rise to cells with mature hepatocytes' characteristics. In conclusion, this novel procedure for hepatic differentiation will be useful for elucidation of molecular mechanisms of hepatic fate decision at gut regionalization, and could represent an attractive approach for a surrogate cell source for pharmaceutical studies such as toxicology.
An application of the monopulse principle to determining elevation angles in SAR images (1994)

In mapping nonflat regions of the Earth using airborne synthetic aperture radar, (SAR), terrain height variations cause two problems in radiometric calibration: the first being that the local incidence angle for any pixel may vary from that given by the flat (or curved) Earth assumption, the second, being that the wrong elevation angle may be used in correcting for the radiometric variation of the antenna pattern. In tracking radars, simultaneous amplitude or phase measurements made by the same radar antenna, but modulated differently, are compared to determine the angular position of targets. This is known as the monopulse principle. In the present paper, the authors show how polarimetric SAR data can be used in a novel application of the monopulse principle to determine the elevation angle and thus, the height at the different parts of the image. The authors' approach begins with the observation that, provided like- and cross-polarized backscatter are uncorrelated, then the algorithm described in van Zyl (1990) for calculating antenna crosstalk yields a measurable quantity whose amplitude (and phase) depends only on elevation angle (or off-boresight angle). Thus, if one determines the crosstalk for a given point in the image, one can relate that measurement to the elevation angle appropriate to that point. Knowledge of the slant range to the point then allows determination of the height of the platform above it. This operation, repeated at many locations throughout the image, allows a topographic map of the height of the aircraft above each location to be built up. The approach described in this paper gives sufficient resolution in elevation to allow the antenna pattern radiometric correction to be done properly, since it allows the determination of elevation angles at a grid of points in the image. Knowledge of the slant range to each point and the height of the aircraft then allows a grid of height estimates for the imaged area to be built up. Unfortunately, the spatial resolution of the grid was not sufficient to turn the height maps into usable maps of local incidence angle. The approach may be improved upon, using an active, phased array antenna.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>