gebhart/patrepeval huggingface dataset:
Method of Fabricating Multiple-Frequency Film Bulk Acoustic Resonators in a Single Chip (2006)

We report experimental results of a novel approach to integrate multiple-frequency film bulk acoustic resonators (FBAR) in a single chip. An additional tuning layer was deposited and patterned on a conventional Metal/AlN/Metal FBAR film stack. By controlling in-plane dimensions of the periodic tuning patterns, resonance frequencies are modulated according to the corresponding loading percentages. To obtain a desirable frequency response of the modulated resonance peaks (a pure frequency shift), the pitch of the tuning patterns needs to be smaller than the membrane thickness. Three thicknesses of the tuning layers are fabricated to demonstrate different tuning ranges and sensitivities. This approach provides a potential solution to integrate multiple-frequency FBAR filters of adjacent bands by only one additional lithographic patterning step
Hepatitis B and Hepatitis C Virus Replication Upregulates Serine Protease Inhibitor Kazal, Resulting in Cellular Resistance to Serine Protease-Dependent Apoptosis (2009)

Hepatitis B and C viruses (HBV and HCV, respectively) are different and distinct viruses, but there are striking similarities in their disease potential. Infection by either virus can cause chronic hepatitis, liver cirrhosis, and ultimately, liver cancer, despite the fact that no pathogenetic mechanisms are known which are shared by the two viruses. Our recent studies have suggested that replication of either of these viruses upregulates a cellular protein called serine protease inhibitor Kazal (SPIK). Furthermore, the data have shown that cells containing HBV and HCV are more resistant to serine protease-dependent apoptotic death. Since our previous studies have shown that SPIK is an inhibitor of serine protease-dependent apoptosis, it is hypothesized that the upregulation of SPIK caused by HBV and HCV replication leads to cell resistance to apoptosis. The evasion of apoptotic death by infected cells results in persistent viral replication and constant liver inflammation, which leads to gradual accumulation of genetic changes and eventual development of cancer. These findings suggest a possibility by which HBV and HCV, two very different viruses, can share a common mechanism in provoking liver disease and cancer.
Diffractive optic fluid shear stress sensor (2000)

Light scattering off particles flowing through a two-slit interference pattern can be used to measure the shear stress of the fluid. We have designed and fabricated a miniature diffractive optic sensor based on this principle.
Surface microscopy with laserless MEMS based AFM probes (2010)

We report here on results of AFM microscopy using laserless MEMS based probes. This new concept of atomic force microscope (AFM) probes using bulk-mode silicon resonators was previously presented [1]. They consist on silicon ring resonators with capacitive transducers and integrated sensing nanotip. We have also demonstrated that these probes are sensitive to nanoscale tip-surface interactions [2], paving the way for AFM imaging. We describe here probes fabrication and their implementation on a Veeco commercial AFM microscope. Force curve measurements are realized in order to set the experimental conditions for AFM operation. For the first time, AFM microscopy images using these laserless MEMS based AFM probes are presented.
A recombination hotspot delimits a wild-species quantitative trait locus for tomato sugar content to 484 bp within an invertase gene (2000)

In nature, genetic variation usually takes the form of a continuous phenotypic range rather than discrete classes. The genetic variation underlying quantitative traits results from the segregation of numerous interacting quantitative trait loci (QTLs), whose expression is modified by the environment. To uncover the molecular basis of this variation, we characterized a QTL (Brix9-2-5) derived from the green-fruited tomato species Lycopersicon pennellii. The wild-species allele increased glucose and fructose contents in cultivated tomato fruits in various genetic backgrounds and environments. Using nearly isogenic lines for the QTL, high-resolution mapping analysis delimited Brix9-2-5 to a single nucleotide polymorphism-defined recombination hotspot of 484 bp spanning an exon and intron of a fruit-specific apoplastic invertase. We suggest that the differences between the Brix9-2-5 alleles of the two species are associated with a polymorphic intronic element that modulates sink strength of tomato fruits. Our results demonstrate a link between naturally occurring DNA variation and a Mendelian determinant of a complex phenotype for a yield-associated trait.
Self-Assembled Magnetic Surface Swimmers (2009)

We report studies of novel self-assembled magnetic surface swimmers (magnetic snakes) formed from a dispersion of magnetic microparticles at a liquid-air interface and energized by an alternating magnetic field. We show that under certain conditions the snakes spontaneously break the symmetry of surface flows and turn into self-propelled objects. Parameters of the driving magnetic field tune the propulsion velocity of these snakelike swimmers. We find that the symmetry of the surface flows can also be broken in a controlled fashion by attaching a large bead to a magnetic snake (bead-snake hybrid), transforming it into a self-locomoting entity. The observed phenomena have been successfully described by a phenomenological model based on the amplitude equation for surface waves coupled to a large-scale hydrodynamic mean flow equation.
Effect of drive-axis displacement on MEMS Birdbath Resonator Gyroscope performance (2017)

We report the latest experimental results from a fused-silica Birdbath Resonator Gyroscope (BRG) with a quality factor of 419k and a resonant frequency of 9030 Hz. The BRG and its readout/control system achieve an angle random walk (ARW) of 0.00126 deg/√hr and a bias stability of 0.0391 deg/hr. These results were obtained using a force-rebalanced control architecture without temperature control or additional compensation. The ARW and bias stability are further improved by driving the resonator at displacements near 10% of the nominal electrostatic gap. The low gyroscope noise is attributed to a relatively large measured scale factor of 100 mV/deg/s.
Robust estimators for frequency offset of OFDM in non-Gaussian noise (2011)

This paper addresses robust estimation for the frequency offset of orthogonal frequency division multiplexing in non-Gaussian noise channels. We first propose a maximum-likelihood (ML) estimator in non-Gaussian noise modeled as a complex isotropic Cauchy process, and then present a simpler, yet still robust, estimator based on the ML estimator. From numerical results, it is confirmed that the proposed estimators offer a substantial performance improvement over the conventional estimators in non-Gaussian noise channels.
A SYSTEMS APPROACH TO ROBOTIC BULK HARVESTING OF APPLES (1999)

A unique robotic bulk harvester was conceived and developed to remove apples grown on narrow inclinedtrellises. The system combined mechanical harvesting technology with sensors and intelligent adaptive technology toidentify an individual branch, determine fruit locations, position a Rapid Displacement Actuator (RDA) and a catchingsurface under the apples, and execute the RDA. Detachment was effected by rapidly displacing the limb away from thefruit. Requirements for a compatible tree training system were developed. Field testing demonstrated feasibility of thecomplete system. Fruit removal averaged 95% and detached fruit graded 99% U.S. Extra Fancy. Factors were identifiedto improve all aspects of the system and will require additional research.
Stabilizing Liquid Drops in Nonequilibrium Shapes by the Interfacial Jamming of Nanoparticles (2014)

Nanoparticles assemble at the interface between two fluids into disordered, liquid-like arrays where the nanoparticles can diffuse laterally at the interface. Using nanoparticles dispersed in water and amine end-capped polymers in oil, nanoparticle surfactants are generated in situ at the interface overcoming the inherent weak forces governing the interfacial adsorption of nanoparticles. When the shape of the liquid domain is deformed by an external field, the surface area increases and more nanoparticles adsorb to the interface. Upon releasing the field, the interfacial area decreases, jamming the nanoparticle surfactants and arresting further shape change. The jammed nanoparticles remain disordered and liquid-like, enabling multiple, consecutive deformation and jamming events. Further stabilization is realized by replacing monofunctional ligands with difunctional versions that cross-link the assemblies. The ability to generate and stabilize liquids with a prescribed shape poses opportunities for reactive liquid systems, packaging, delivery, and storage.
Abstract 2774: High levels of 5-hydroxymethylcytosine (5hmC) predict biochemical recurrence after prostatectomy in ERG negative prostate cancer (2016)

Abstract Background: Prostate cancer (PC) can be stratified into distinct molecular subtypes based on TMPRSS2-ERG gene fusion status, but its potential prognostic value remains controversial. Likewise, routine clinicopathological features cannot clearly distinguish aggressive from indolent tumors at the time of diagnosis, thus new prognostic biomarkers are urgently needed. The DNA methylation variant 5-hydroxymethylcytosine (5hmC, an oxidized derivative of 5-methylcytosine) has recently emerged as a new diagnostic and/or prognostic biomarker candidate for several human malignancies. However, this remains to be systematically investigated for PC. In this study, we determined 5hmC levels in 311 PC (stratified by ERG status) and 228 adjacent non-malignant (NM) prostate tissue specimens by immunohistochemical analysis of a tissue microarray, representing a large radical prostatectomy (RP) cohort with long clinical follow-up. We investigated possible correlations between 5hmC and routine clinicopathological variables and assessed the prognostic potential of 5hmC by Kaplan-Meier, uni- and multivariate Cox regression analyses in ERG+ (n = 178) vs. ERG- (n = 133) PCs using biochemical recurrence (BCR) as endpoint. Results: We observed a borderline significant (p = 0.06) reduction in 5hmC levels in PC compared to NM tissue samples, which was explained by a highly significant (p&lt;0.001) loss of 5hmC in ERG- PCs. ERG status was not predictive of BCR in this cohort (p = 0.73) and no significant association was found between BCR and 5hmC levels in ERG+ PCs (p = 0.98). In contrast, high 5hmC immunoreactivity was a significant adverse predictor of BCR after RP in ERG- PCs, independent of Gleason score, pathological tumor stage, surgical margin status, and pre-operative PSA level (HR (95% CI): 1.62 (1.15-2.28), p = 0.006). Conclusions: This is the first study to demonstrate a prognostic potential for 5hmC in PC. Our findings highlight the importance of ERG stratification in PC biomarker studies, and suggest that epigenetic mechanisms involving 5hmC are important for the development and/or progression of ERG- PC. Citation Format: Siri H. Strand, Soren Hoyer, Anne-Sofie Lynnerup, Christa Haldrup, Tine M. Storebjerg, Michael Borre, Torben F. Orntoft, Karina D. Sorensen. High levels of 5-hydroxymethylcytosine (5hmC) predict biochemical recurrence after prostatectomy in ERG negative prostate cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2774.
Highly Porous, Rigid-Rod Polyamide Aerogels with Superior Mechanical Properties and Unusually High Thermal Conductivity (2017)

We report here the fabrication of polyamide aerogels composed of poly-p-phenylene-terephthalamide, the same backbone chemistry as DuPont's Kevlar. The all-para-substituted polymers gel without the use of cross-linker and maintain their shape during processing-an improvement over the meta-substituted cross-linked polyamide aerogels reported previously. Solutions containing calcium chloride (CaCl<sub>2</sub>) and para-phenylenediamine (pPDA) in N-methylpyrrolidinone (NMP) at low temperature are reacted with terephthaloyl chloride (TPC). Polymerization proceeds over the course of 5 min resulting in gelation. Removal of the reaction solvent via solvent exchange followed by extraction with supercritical carbon dioxide provides aerogels with densities ranging from 0.1 to 0.3 g/cm<sup>3</sup>, depending on the concentration of calcium chloride, the formulated number of repeat units, n, and the concentration of polymer in the reaction mixture. These variables were assessed in a statistical experimental study to understand their effects on the properties of the aerogels. Aerogels made using at least 30 wt % CaCl<sub>2</sub> had the best strength when compared to aerogels of similar density. Furthermore, aerogels made using 30 wt % CaCl<sub>2</sub> exhibited the lowest shrinkage when aged at elevated temperatures. Notably, whereas most aerogel materials are highly insulating (thermal conductivities of 10-30 mW/m K), the polyamide aerogels produced here exhibit remarkably high thermal conductivities (50-80 mW/(m K)) at the same densities as other inorganic and polymer aerogels. These high thermal conductivities are attributed to efficient phonon transport by the rigid-rod polymer backbone. In conjunction with their low cost, ease of fabrication with respect to other polymer aerogels, low densities, and high mass-normalized strength and stiffness properties, these aerogels are uniquely valuable for applications such as lightweighting in consumer electronics, automobiles, and aerospace where weight reduction is desirable but trapping of heat may be undesirable-applications where other polymer aerogels have to date otherwise been unsuitable-creating new opportunities for commercialization of aerogels.
Design and production of 3D printed bolus for electron radiation therapy (2014)

This is a proof-of-concept study demonstrating the capacity for modulated electron radiation therapy (MERT) dose distributions using 3D printed bolus. Previous reports have involved bolus design using an electron pencil beam model and fabrication using a milling machine. In this study, an in-house algorithm is presented that optimizes the dose distribution with regard to dose coverage, conformity, and homogeneity within the planning target volume (PTV). The algorithm takes advantage of a commercial electron Monte Carlo dose calculation and uses the calculated result as input. Distances along ray lines from the distal side of 90% isodose line to distal surface of the PTV are used to estimate the bolus thickness. Inhomogeneities within the calculation volume are accounted for using the coefficient of equivalent thickness method. Several regional modulation operators are applied to improve the dose coverage and uniformity. The process is iterated (usually twice) until an acceptable MERT plan is realized, and the final bolus is printed using solid polylactic acid. The method is evaluated with regular geometric phantoms, anthropomorphic phantoms, and a clinical rhabdomyosarcoma pediatric case. In all cases the dose conformity are improved compared to that with uniform bolus. For geometric phantoms with air or bone inhomogeneities, the dose homogeneity is markedly improved. The actual printed boluses conform well to the surface of complex anthropomorphic phantoms. The correspondence of the dose distribution between the calculated synthetic bolus and the actual manufactured bolus is shown. For the rhabdomyosarcoma patient, the MERT plan yields a reduction of mean dose by 38.2% in left kidney relative to uniform bolus. MERT using 3D printed bolus appears to be a practical, low-cost approach to generating optimized bolus for electron therapy. The method is effective in improving conformity of the prescription isodose surface and in sparing immediately adjacent normal tissues.
Application of loudness models to sound processing for cochlear implants (2003)

A new paradigm for processing sound signals for multiple-electrode cochlear implants is introduced, and results are presented from an initial psychophysical evaluation of its effect on the perceived loudness of complex sounds. A real-time processing scheme based on this paradigm, called SpeL, has been developed primarily to improve control of loudness for implant users. SpeL differs from previous schemes in several ways. Most importantly, it incorporates a published numerical model which predicts the loudness perceived by implant users for complex patterns of pulsatile electric stimulation as a function of the pulses' physical parameters. This model is controlled by the output of a corresponding model that estimates the loudness perceived by normally hearing listeners for complex sounds. The latter model produces an estimate of the specific loudness arising from an acoustic signal. In SpeL, the specific loudness function, which describes the contribution to total loudness of each of a number of frequency bands (or cochlear positions), is converted to a pattern of electric stimulation on an appropriate set of electrodes. By application of the loudness model for electric stimulation, this pattern is designed to produce a specific loudness function for the implant user which approximates that produced by the normal-hearing model for the same input signal. The results of loudness magnitude estimation experiments with five users of the SpeL scheme confirmed that the psychophysical functions relating overall loudness perceived to input sound level for five complex acoustic signals were, on average, very similar to those for normal hearing.
Kinetoplastid Membrane Protein-11 DNA Vaccination Induces Complete Protection against Both Pentavalent Antimonial-Sensitive and -Resistant Strains of <i>Leishmania donovani</i> That Correlates with Inducible Nitric Oxide Synthase Activity and IL-4 Generation: Evidence for Mixed Th1- and Th2-Like Responses in Visceral Leishmaniasis (2005)

The emergence of an increasing number of Leishmania donovani strains resistant to pentavalent antimonials (SbV), the first line of treatment for visceral leishmaniasis worldwide, accounts for decreasing efficacy of chemotherapeutic interventions. A kinetoplastid membrane protein-11 (KMP-11)-encoding construct protected extremely susceptible golden hamsters from both pentavalent antimony responsive (AG83) and antimony resistant (GE1F8R) virulent L. donovani challenge. All the KMP-11 DNA vaccinated hamsters continued to survive beyond 8 mo postinfection, with the majority showing sterile protection. Vaccinated hamsters showed reversal of T cell anergy with functional IL-2 generation along with vigorous specific anti-KMP-11 CTL-like response. Cytokines known to influence Th1- and Th2-like immune responses hinted toward a complex immune modulation in the presence of a mixed Th1/Th2 response in conferring protection against visceral leishmaniasis. KMP-11 DNA vaccinated hamsters were protected by a surge in IFN-gamma, TNF-alpha, and IL-12 levels along with extreme down-regulation of IL-10. Surprisingly the prototype candidature of IL-4, known as a disease exacerbating cytokine, was found to have a positive correlation to protection. Contrary to some previous reports, inducible NO synthase was actively synthesized by macrophages of the protected hamsters with concomitant high levels of NO production. This is the first report of a vaccine conferring protection to both antimony responsive and resistant Leishmania strains reflecting several aspects of clinical visceral leishmaniasis.
Generation of Urethanes and Isocyanates from Amines and Carbon Dioxide (1994)

Use of carbon dioxide as a reagent in place of phosgene offers the potential for an inexpensive, safer, and more selective route to polyurethanes. Traditionally, isocyanates, which are used for the production of polyurethanes, are generated from the reaction of a primary amine with the highly toxic agent phosgene. The reaction of CO2 with either primary or secondary amines generates the carbamate anion. By understanding those factors which control the nucleophilicity of the carbamate anion, we have been able to generate urethanes quantitatively even with secondary amine-derived carbamate anions. We have also found that isocyanates can be generated quantitatively by the "dehydration" of carbamate anions derived from primary amines and carbon dioxide using a variety of dehydrating reagents. These processes are accomplished under very mild conditions; e. g., 1 atm CO2 at 50-80°C. The factors which favor production of urethane or carbamate are discussed and examples of the utility of these new chemistries are presented.
Atlas-Based Neuroinformatics via MRI: Harnessing Information from Past Clinical Cases and Quantitative Image Analysis for Patient Care (2013)

With the ever-increasing amount of anatomical information radiologists have to evaluate for routine diagnoses, computational support that facilitates more efficient education and clinical decision making is highly desired. Despite the rapid progress of image analysis technologies for magnetic resonance imaging of the human brain, these methods have not been widely adopted for clinical diagnoses. To bring computational support into the clinical arena, we need to understand the decision-making process employed by well-trained clinicians and develop tools to simulate that process. In this review, we discuss the potential of atlas-based clinical neuroinformatics, which consists of annotated databases of anatomical measurements grouped according to their morphometric phenotypes and coupled with the clinical informatics upon which their diagnostic groupings are based. As these are indexed via parametric representations, we can use image retrieval tools to search for phenotypes along with their clinical metadata. The review covers the current technology, preliminary data, and future directions of this field.
Large area deposition of 〈100〉-textured diamond films by a 60-kW microwave plasma CVD reactor (2002)

Diamond films were deposited on silicon wafers of 25–152 mm in diameter by a 60-kW 915-MHz plasma CVD system with a input power of 15–60 kW at a gas pressure of 11.3–17.7 kPa using H2CH4 or H2CH4CO2 gas mixtures. Growth orientation of the diamond films and α parameters for the different growth conditions have been investigated in order to control the morphology of the diamond films of 152 mm in diameter. It was clearly seen that the α parameters for the 60-kW system were greater than those for conventional microwave plasma CVD systems in the substrate temperature–CH4 concentration plane. This means that the contour of the α parameter shifts to the higher substrate temperature and the lower CH4 concentration, as compared with the results of the conventional CVD systems. It was also found that the parameter range of diamond growth by the 60-kW reactor is broader than that of the conventional CVD systems. Based on the present study, 〈100〉-textured diamond films were successfully grown almost uniformly on the entire surface of a 152-mmφ Si substrate by choosing appropriate process conditions.