gebhart/patrepeval huggingface dataset:
Photon-sieve lithography (2005)

We present the first lithography results that use high-numerical-aperture photon sieves as focusing elements in a scanning-optical-beam-lithography system [J. Vac. Sci. Technol. B 21, 2810 (2003)]. Photon sieves are novel optical elements that offer the advantages of higher resolution and improved image contrast compared with traditional diffractive optics such as zone plates [Nature 414, 184 (2001)]. We fabricated the highest-numerical-aperture photon sieves reported to date and experimentally verified their focusing characteristics. We propose two new designs of the photon sieve that have the potential to significantly increase focusing efficiency.
TumorNext: A comprehensive tumor profiling assay that incorporates high resolution copy number analysis and germline status to improve testing accuracy (2016)

The development of targeted therapies for both germline and somatic DNA mutations has increased the need for molecular profiling assays to determine the mutational status of specific genes. Moreover, the potential of off-label prescription of targeted therapies favors classifying tumors based on DNA alterations rather than traditional tissue pathology. Here we describe the analytical validation of a custom probe-based NGS tumor panel, TumorNext, which can detect single nucleotide variants, small insertions and deletions in 142 genes that are frequently mutated in somatic and/or germline cancers. TumorNext also detects gene fusions and structural variants, such as tandem duplications and inversions, in 15 frequently disrupted oncogenes and tumor suppressors. The assay uses a matched control and custom bioinformatics pipeline to differentiate between somatic and germline mutations, allowing precise variant classification. We tested 170 previously characterized samples, of which > 95% were formalin-fixed paraffin embedded tissue from 8 different cancer types, and highlight examples where lack of germline status may have led to the inappropriate prescription of therapy. We also describe the validation of the Affymetrix OncoScan platform, an array technology for high resolution copy number variant detection for use in parallel with the NGS panel that can detect single copy amplifications and hemizygous deletions. We analyzed 80 previously characterized formalin-fixed paraffin-embedded specimens and provide examples of hemizygous deletion detection in samples with known pathogenic germline mutations. Thus, the TumorNext combined approach of NGS and OncoScan potentially allows for the identification of the "second hit" in hereditary cancer patients.
Measuring wireless network usage with the Experience Sampling Method (2005)

Abstract — Measuring wireless local area networks has proven useful for characterizing, modeling and provisioning these networks. These measurements are typically taken passively from a vantage point on the network itself. Client devices, or users, are never actively queried. These measurements can indicate what is happening on the network, but it can be difficult to infer why a particular behavior is occurring. In this paper we use the Experience Sampling Method (ESM) to study wireless network users. We monitored 29 users remotely for one week, and signaled them to fill out a questionnaire whenever interesting wireless behavior was observed. We find ESM to be a useful method for collecting data about wireless network usage that cannot be provided by network monitoring, and we present a list of recommendations for network researchers who wish to conduct an ESM study.
Influenza Virus Upregulates CXCR4 Expression in CD4+ Cells (2000)

We examined the effect of prior influenza virus infection on the susceptibility of CD4+ cells to HIV-1 infection. Influenza virus infection of HeLa-CD4 cells resulted in a marked increase in susceptibility to infection by CXCR4-dependent but not CCR5-dependent HIV isolates. Influenza virus infection resulted in an increase in the steady state level of CXCR4 transcripts and an increase in cell surface CXCR4 expression. Our observations suggest that infectious agents such as influenza may contribute to HIV disease progression by modulating coreceptor availability.
Identification of a Novel Set of Genes Regulated by a Unique Liver X Receptor-α-mediated Transcription Mechanism (2003)

We have reported previously that liver X receptor-alpha (LXRalpha) can mediate a novel cAMP-dependent increase in renin and c-myc gene transcription by binding as a monomer to a unique regulatory element termed the cAMP-negative response element (CNRE). To determine whether this novel action of LXRalpha has global implications on gene regulation, we employed expression profiling to identify other genes regulated by this unique mechanism. Here we report the existence of a set of known and unknown transcripts regulated in parallel with renin. Querying the Celera Mouse Genome Assembly revealed that a majority of these genes contained the consensus CNRE. We have confirmed the functionality of these CNREs by competition for LXRalpha binding via electrophoretic mobility shift assays (EMSA) and by the use of CNRE decoy molecules documenting the abolishment of the cAMP-mediated gene induction. Taken together, these results demonstrate that the interaction between cAMP-activated LXRalpha and the CNRE enhancer element is responsible for widespread changes in gene expression and identify a set of LXRalpha/cAMP-regulated genes that may have important biological implications.
Kinetic Study on High-Temperature Solar Thermochemical Energy Conversion using Fe<sub>3</sub>O<sub>4</sub>/Carbon Redox or Boudouard Reaction Process (1998)

Kinetic aspects of highly endothermic Fe30Jcarbon redox and Boudouard reactions were studied for simulation using Xe lamp beam and sunlight concentrated with a Fresne11ens, respectively. CO evolution with oxidation of carbon by Fe304 and C02 was successfully simulated using the energy and material balance equations. The simulation study suggested that several factors affect the CO generation in both systems tested: temperature gradient within the specimen, solar concentration, specimen size, heat capacity of the solar furnace, and radiative heat loss. Further kinetic study will be conducted for better design of the solar receiverlreactor using the stationary bed gasification of carbonaceous materials.
Undertreatment of Osteoporosis in Men With Hip Fracture (2002)

The burden of hip fracture is illustrated by the high incidence of postfracture disability and the high mortality rate in both men and women. Nevertheless, few men receive antiresorptive treatment.
Which of My Assumptions are Unnecessary for Realizability and Why Should I Care? (2023)

Specifications for reactive systems synthesis consist of assumptions and guarantees. However, some specifications may include unnecessary assumptions, i.e., assumptions that are not necessary for realizability. While the controllers that are synthesized from such specifications are correct, they are also inflexible and fragile; their executions will satisfy the specification's guarantees in only very specific environments. In this work we show how to detect unnecessary assumptions, and to transform any realizable specification into a corresponding realizable core specification, one that includes the same guarantees but no unnecessary assumptions. We do this by computing an assumptions core, a locally minimal subset of assumptions that suffices for realizability. Controllers that are synthesized from a core specification are not only correct but, importantly, more general; their executions will satisfy the specification's guarantees in more environments. We implemented our ideas in the Spectra synthesis environment, and evaluated their impact over different benchmarks from the literature. The evaluation provides evidence for the motivation and significance of our work, by showing (1) that unnecessary assumptions are highly prevalent, (2) that in almost all cases the fully-automated removal of unnecessary assumptions pays off in total synthesis time, and (3) that core specifications induce more general controllers whose reachable state space is larger but whose representation more memory efficient.
Conjugation of a Dipicolyl Chelate to Polypeptide Conjugates Increases Binding Affinities for Human Serum Albumin and Survival Times in Human Serum (2017)

The affinity for human serum albumin (HSA) of a series of 2-5 kDa peptides covalently linked to 3,5-bis[[bis(2-pyridylmethyl)amino]methyl]benzoic acid, a dipicolyl chelator with micromolar affinity for Zn<sup>2+</sup> , was found by surface plasmon resonance to increase in the presence of 1 μm ZnCl<sub>2</sub> at physiological pH. The dependence on polypeptide hydrophobicity was found to be minor, thus suggesting that the conjugates bound to the metal-binding site and not to the fatty-acid-binding site. The affinity of the conjugates increased strongly with the positive charge of the polypeptides, thus implicating the negatively charged protein surface surrounding the metal-binding site. The survival times of the peptides in human serum were extended as a consequence of stronger binding to HSA, thus suggesting that Zn<sup>2+</sup> -chelating agents might provide a general route to increased survival time of peptides in serum in therapeutic and diagnostic applications without significantly increasing their molecular weights.
Session 25 overview: Wireless connectivity (2010)

Portable devices of the future are required to integrate an ever-increasing number of wireless functions in a constantly shrinking area and with continually decreasing power consumption budgets. In order to accommodate this goal, wireless communication platforms will be required to support multiple functionalities as well as multiple standards for each function. While advanced CMOS processes allow for higher levels of integration by providing significant area scaling to digital circuits, they impose certain challenges on the radio design. Innovations at the circuit level as well as radio architecture are needed to address these challenges.
Beyond the Lambertian limit: Novel low-symmetry gratings for ultimate light trapping enhancement in next-generation photovoltaics (2016)

This project aims at addressing the efficiency limit and high fabrication cost of current light trapping methods by developing novel low-symmetry gratings (LSG) for next-generation thin c-Si photovoltaic (PV) cells. The LSG design achieves light trapping enhancement exceeding the 4n2 Lambertian limit and can be fabricated over large areas using low-cost, single-step nanoimprint techniques. We further explored the use of deposited high-refractive-index glass materials for low-temperature LSG processing, which enables direct imprint sculpting of even complex grating geometries in glass without requiring an additional pattern transfer step, which minimizes processing cost and surface damage to PV cells. In the project, we have demonstrated fabrication and integration of sub-wavelength LSG with thin c-Si wafers and bifacial solar cells with low defect density. Optical absorption measurements indicate that LSGs demonstrated superior absorption enhancement compared to their traditional symmetric counterparts as predicted by our simulations. Efficiency enhancement was observed in solar cells integrated with LSGs although fabrication yield of the LSG-integrated cells remains a challenge
Fourier‐Transform‐Ferninfrarot(FT‐FIR)‐Spektroskopie an Silberatomen und Silberclustern in Zeolith NaY (1983)

Abstract Das vollständige Manuskript dieser Zuschrift erscheint in: Angew. Chem. Suppl. 1983 , 1075. DOI: 10.1002/ange.198310750
Impact of introducing alien storage proteins on the bread-making quality and agronomic performance of spring wheat (1994)

The relatively narrow genetic base of spring wheat grown in western Canada puts the crop at risk from attack by pests which reduce yield and marketability.Interspecific hybridization is used to introduce new genetic sources of resistance to wheat pests.This study was conducted in order to evaluate the effectiveness of endosperm protein fingerprinting in selecting backcross-derived (BC) lines from the cross Park*3/ T. timopheevi.SDS-PAGE and A-PAGE were used to identify the high molecular weight (HMW) glutenin subunit and gliadin constitution, respectively, of the BC lines.Although no exotic HMW glutenin subunits were present in the BC lines, a high frequency lacked the 'A' genome subunit.This 'null' condition was deleterious to bread-making quality.The BC lines with the null condition were characterized by the transfer of novel omega and ga.mlna gliadin proteins from T. timopheevi and kernel texture normally associated with tetraploid wheat.Despite the level of back-crossing, a large majority of the lines were inferior to the recurrent parent for agronomic performance.Delayed heading, resulting from the putative transfer of a major maturity gene from T. timopheevi, was associated with low grain yield in 1991 but higher yield in 1992.Lines with improved baking quality tended to be low-yielding.Based on this study, protein fingerprinting can be used to select interspecific lines with desirable end-use quality.
Performance of Nondestructive Radioassay Systems for Nuclear Waste (2003)

A statistical analysis of the measurement performance of five mobile nondestructive assay systems currently in use for radioassay of nuclear waste was performed. Actual versus reported isotopic mass composition, reported versus actual measurement uncertainty, detection capability, and low level versus transuranic waste determination were assessed based on measurements of 11 surrogate waste drums. In terms of percent recovery the systems, for the most part, exhibited reasonable capabilities for estimating isotopic quantities in the surrogate waste drums. (By reasonable we mean, for example, that recovery values were in a range of 40% to 160% for most of the configurations tested.) While difference in performance on individual drums was quite large in some cases, nonparametric analysis of variance results for total plutonium and 241Am showed no statistically significant differences in the overall average percent recovery values for the systems evaluated. A similar analysis of the replicate standard deviations indicated significant differences between systems with regard to precision of measurements of total plutonium but not 241Am. The weakest aspect of system performance was the reporting of measurement errors. Reported measurement error values routinely underestimated actual values for certain surrogate waste configurations.
Biomechanical and Microstructural Characteristics of a Collagen Film-Based Corneal Stroma Equivalent (2006)

The growth in refractive surgeries and corneal replacements has fueled interest in the development of a tissue-engineered cornea. This study characterizes the microstructure and biomechanical properties of film-based corneal stroma equivalents over time in culture. The increased collagen density in the films was hypothesized to result in improved mechanical properties both initially and over time. The microstructure of the film-based stromal equivalent was examined using atomic force microscopy and scanning electron microscopy; the mechanical properties, relaxed modulus, and ultimate tensile strength were quantified using uniaxial tensile testing. The dense, film-based stromal equivalent had a lamellae-like microstructure, which was notably different than the porous structure of sponges used previously. Seeded human corneal stromal fibroblasts remained on the surface of the film rather than migrating into the film and produced fibers of extracellular matrix with diameters of 35-75 nm. After an initial decrease during hydration, the relaxed modulus and ultimate tensile strength for fully hydrated collagen films were 0.4 +/- 0.2 MPa and 0.3 +/- 0.1 MPa, respectively. The mechanical properties of cell-seeded films mimicked those of control films. While further studies are needed to quantify the optical properties, the dense, lamellae-like structure of collagen films is a feasible scaffold for the development of tissue-engineered stroma.
Biotin-end-functionalized highly fluorescent water-soluble polymers (2013)

Many biosensing and imaging systems use fluorescence detection. We present the synthesis of biotin-end-functionalized highly fluorescent water-soluble polymers for potential use in biotin–avidin systems. Statistical polymers of N-acryloylmorpholine (NAM) and N-acryloxysuccinimide (NAS) were prepared by RAFT polymerization using a biotinylated chain transfer agent that ensured 95% end-functionalization of the chains. They were further labeled with a lucifer yellow (LY) dye, yielding 7 to 62 LY fluorophores per polymer chain. The resulting polymers exhibited reduced fluorescence self-quenching, with 7- to 43-fold higher brightness than free LY dye. In addition, they featured low pH sensitivity and very good photobleaching resistance. Moreover, we showed that a more extended polymer conformation was beneficial to the binding of the terminal biotin with streptavidin. This work paves the way for the development of polymers for signal amplification in biosensing assays, labeling of biotin-receptors at cell surfaces in some cancer studies, labeling of antibodies and microscopy imaging purposes.
Time-Dependent Attractive Force Between a Silica Particle and a Silica Substrate in Dodecane (2008)

Surface forces in low-dielectric media are much less understood than those in aqueous solutions. In this work, the technique of colloidal-probe atomic force microscopy (AFM) was used to measure the force between a silica sphere and a flat silica plate in dodecane. A transient attractive force was measured, which slowly vanished during the first hour of measurements, following the characteristic dielectric relaxation time of dodecane. Subsequently, equilibrium conditions were reached. Equilibrium forces exhibited a strong dependence on the relative humidity of the environment. An attempt was made to explain the transient attractive force in terms of electrostatic interaction.
Packet Loss Fair Scheduling Scheme for Real-Time Traffic in OFDMA Systems (2004)

In this paper, we propose a packet scheduling discipline called packet loss fair scheduling, in which the packet loss of each user from different real-time traffic is fairly distributed according to the quality of service requirements. We consider an orthogonal frequency division multiple access (OFDMA) system. The basic frame structure of the system is for the downlink in a cellular packet network, where the time axis is divided into a finite number of slots within a frame, and the frequency axis is segmented into subchannels that consist of multiple subcarriers. In addition, to compensate for fast and slow channel variation, we employ a link adaptation technique such as adaptive modulation and coding. From the simulation results, our proposed packet scheduling scheme can support QoS differentiations while guaranteeing short-term fairness as well as long-term fairness for various real-time traffic.
THz Scanner Based on Planar Antenna-Supplied Silicon Field-Effect Transistors (2012)

A scanning device for imaging at THz frequencies was designed and constructed. The device comprised a 335~GHz source of radiation, an x-y-z translation stages, a number of optical elements and a detector. The detector was a silicon field-effect transistor supplied with a resonant antenna and a low-noise preamplifier. With a detector response of 10~V/W and a source power of 10~mW we could generate images in a DC mode with a speed limited only by the velocity of the stages movement. Full Text: PDF References W. Knap et al. "Plasma wave detection of sub-terahertz and terahertz radiation by silicon field-effect transistors", Appl. Phys. Lett. 85, 675 (2004). CrossRef R. Tauk et al. "Plasma wave detection of terahertz radiation by silicon field effects transistors: Responsivity and noise equivalent power", Appl. Phys. Lett. 89, 253511 (2006). CrossRef N. Oda et al. "Development of Terahertz focal plane arrays and handy camera", Proc. SPIE 8012 CrossRef E. Ojefors, U. Pfeiffer, A. Lisauskas, and H. Roskos, "A 0.65 THz Focal-Plane Array in a Quarter-Micron CMOS Process Technology", IEEE J. Solid-state Circuits 44, 1968 (2009). CrossRef M. Dyakonov and M. Shur, "Detection, mixing, and frequency multiplication of terahertz radiation by two-dimensional electronic fluid", IEEE Trans. on Electron Devices 43, 380 (1996). CrossRef P. Kopyt, J. Marczewski, K. Kucharski, J. Łusakowski, and W. Gwarek, "Planar antennas for THz radiation detector based on a MOSFET ", Proc. 36th Conference on Infrared, Millimeter and Terahertz Waves, Huston, CrossRef M. Sakowicz et al. "Terahertz responsivity of field effect transistors versus their static channel conductivity and loading effects", J. Appl. Phys. 110, 054512 (2011). CrossRef
Cold optical design for the Large Aperture Simons Observatory telescope (2018)

The Simons Observatory will consist of a single large (6 m diameter) telescope and a number of smaller (0.5 m diameter) refracting telescopes designed to measure the polarization of the Cosmic Microwave Background to unprecedented accuracy. The large aperture telescope is the same design as the CCAT-prime telescope, a modified Crossed Dragone design with a field-of-view of over 7.8 degrees diameter at 90 GHz. This paper presents an overview of the cold reimaging optics for this telescope and what drove our choice of 350-400 mm diameter silicon lenses in a 2.4 m cryostat over other possibilities. We will also consider the future expandability of this design to CMB Stage-4 and beyond.
NGC 1275 - A burgeoning elliptical galaxy (1983)

Large-aperture spectrophotometry of the peculiar galaxy NGC 1275 is presented. Emission lines from H-beta and the forbidden O II, O III, and Ne III dominate this spectrum, while H-delta, H-epsilon and Na D appear in absorption. A population synthesis model for the absorption-line spectrum suggests that about 20 percent of the optical luminosity is produced by B stars. On the basis of this and the calculated H-beta emission line flux, it is estimated that the current star formation rate in NGC 1275 is about 30 solar masses per yr. This leads to a predicted supernova rate of 1 per yr. The resulting supernova heating rate is approximately one-half the cooling rate predicted by current accretion models and may thus significantly alter the accretion flow. It is proposed that in NGC 1275, the formation of an elliptical galaxy in the cluster potential may be under way.
Diversity-multiplexing tradeoff in multiple-relay network-part I: Proposed scheme and single-antenna networks (2008)

This paper studies the setup of a multiple-relay network in which K half-duplex multiple-antenna relays assist in the transmission between a/several multiple-antenna source(s) and a multiple-antenna destination. Each two nodes are assumed to be either connected through a quasi-static Rayleigh fading channel, or disconnected. This paper is comprised of two parts. In this part of the paper, we propose a new scheme, which we call random sequential (RS), based on the amplify-and-forward relaying. We derive diversity-multiplexing tradeoff (DMT) of the proposed RS scheme for general single-antenna multiple-relay networks. As a result, we show that for single-antenna two-hop multiple-access multiple-relay (K > 1) networks (without direct link between the source(s) and the destination), the proposed RS scheme achieves the optimum DMT. However, for the case of multiple access single relay setup, we show that the RS scheme reduces to the naive amplify-and-forward relaying and is not optimum in terms of DMT, while the dynamic decode-and-forward scheme is shown to be optimum for this scenario.