gebhart/patrepeval huggingface dataset:
From mice to men: A novel serum signature for prostate cancer diagnosis (2008)

11015 Background: Sensitivity and specificity of prostate specific antigen (PSA) for prostate cancer (CaP) detection are limited. Hence, discovery and validation of new biomarkers is important. We hypothesized that a comprehensive knowledge of the glycoproteome of CaP will allow a targeted search for serum glycopeptides and thus be a novel approach to uncover new biomarkers. Methods: We have established a new platform for human biomarker discovery that is based on the initial identification of the glycoproteome of the PTEN conditional knockout (cKO) mouse CaP model and the subsequent search of shed glycopeptides in the sera of mice and men. N- glycopeptides from murine prostate tissue and serum are enriched using a hydrazide chemistry-based approach. Label-free quantitation is performed to compare the differentially expressed glycoproteins in tumorigenic vs. normal prostate. Interesting proteins are monitored in the corresponding murine sera by targeted mass spectrometry. Potential biomarkers are then validated in human sera using standard ELISA techniques and targeted mass spectrometry. Fisher discriminance analysis is used as a multivariate statistical model to detect a signature for best discrimination between benign prostatic hyperplasia (BPH) and CaP. Results: We identified 153 proteins with interesting properties, among which 6 have now been validated in human sera. All 6 showed a significant differential expression in sera from patients with CaP compared to BPH. A multivariate model was created to distinguish between sera collected from 37 patients with BPH (n=19) or CaP (n=18). Using leave one-out cross-validation, the 6-biomarker signature had an accuracy of 78% (sens. 56%; spec. 100%), in comparison to PSA with an accuracy of 62% (sens. 28%; spec. 95%). By combining PSA with the 6-biomarker signature accuracy was further improved to 84% (sens. 72%; spec. 95%). Conclusions: By establishing a PTEN-dependent CaP glycoproteome catalogue, we were able to develop a new targeted approach to serum biomarker discovery. Specifically, we identified a novel 6-biomarker signature that can in addition to PSA potentially be used for improved diagnosis of human CaP. We propose that the glycoproteome of a tumor may be a good starting point for an unbiased sensitive search for cancer signatures in human serum. No significant financial relationships to disclose.
The Ligand Binding Region of the Sigma-1 Receptor: Studies Utilizing Photoaffinity Probes, Sphingosine and N-Alkylamines (2012)

The sigma-1 receptor is a 26 kDa endoplasmic reticulum resident membrane protein that has been shown to have chaperone activity in addition to its promiscuous binding to pharmacological agents. Ligand binding domain(s) of the sigma-1 receptor have been identified using the E. coli expressed and purified receptor protein and novel radioiodinated azido photoaffinity probes followed by proteolytic and chemical cleavage strategies. The outcome of these experiments indicates that the sigma-1 receptor ligand binding regions are formed primarily by juxtaposition of its second and third hydrophobic domains, regions where the protein shares considerable homology with the fungal enzyme, sterol isomerase that is essential for the biosynthesis of ergosterol. Data indicate that these hydrophobic steroid binding domain like (SBDL) regions on the sigma-1 receptor are likely to interact selectively with N-alkyl amines such as the endogenous sphingolipids and with synthetic N-alkylamines and N-aralkylamines derivatives. A proposed model for the sigma-1 receptor is presented.
A Unified Approach to Generating Sound Zones Using Variable Span Linear Filters (2018)

Sound zones are typically created using Acoustic Contrast Control (ACC), Pressure Matching (PM), or variations of the two. ACC maximizes the acoustic potential energy contrast between a listening zone and a quiet zone. Although the contrast is maximized, the phase is not controlled. To control both the amplitude and the phase, PM instead minimizes the difference between the reproduced sound field and the desired sound field in all zones. On the surface, ACC and PM seem to control sound fields differently, but we here demonstrate they are actually extreme special cases of a much more general framework. The framework is inspired by the variable span linear filtering framework for speech enhancement. Using this framework, we demonstrate that 1) ACC gives the best contrast, but the highest signal distortion in the bright zone, and 2) PM gives the smallest signal distortion in the bright zone, but the worst contrast. Aside from showing this mathematically, we also demonstrate this via a small toy example.
Solution‐Based Evolution and Enhanced Methanol Oxidation Activity of Monodisperse Platinum–Copper Nanocubes (2009)

Shape-controlled catalysis: High-quality Pt-Cu nanocubes with an average size of about 8 nm (see picture, scale bar = 20 nm) were synthesized from a high-temperature organic solution system in the presence of various capping ligands. These cubic Pt-Cu nanocrystals terminated with {100} facets demonstrated a superior catalytic activity towards methanol oxidation compared to similar sized Pt-Cu and Pt nanospheres.
Shape measurement of discontinuous objects using projected fringes and temporal phase unwrapping (1996)

Shape measurement of discontinuous objects using projected fringes and temporal phase unwrapping
Theory and Design of Low-Noise Multipath Amplifiers (2011)

<?Pub Dtl=""?> The theoretical minimum noise measure of a multipath amplifier (an amplifier that has multiple parallel amplifiers) is achieved by using the optimum source impedance and optimum gain for each amplification path. This optimum source impedance and gain can be calculated by replacing each amplifier with its optimum source impedance. The resulting noise measure is the same as the minimum noise measure of the amplifiers used.
The Actifier (1996)

A new device for the stimulation of intraoral tissues in human neonates is described. This instrument, known as an actifier, features a wide frequency range for mechanical stimulation, integrated multichannel electomyographic electrode pairs, and the capacity for transducing law compression during non-nutritive sucking behavior. The stimulus/recording interface consists of a modified pacifier. The actifier has been used to investigate the responsiveness of the sucking central pattern generator in human infants to mechanical perturbation.
Development and characterization of highly efficient new cerium doped rare earth halide scintillator materials (2006)

Inorganic scintillators for γ-ray detection are used in many fields from medical-diagnostic imaging to industrial measuring systems. Accordingly they face various demands with respect to e.g. response time, light yield, and energy resolution. The development of the new family of rare-earth halide scintillators LaCl3 ∶ Ce3+, LaBr3 ∶ Ce3+, and LuI3 ∶ Ce3+ is reviewed and their properties are compared to those of the established materials NaI ∶ Tl+ and Lu2SiO5 ∶ Ce3+. Extraordinary properties such as the short lifetime of 15 ns and the narrow energy resolution of 2.6% in LaBr3 ∶ 5% Ce3+, or the high light yield of 95000 photons per MeV in LuI3 ∶ 5% Ce3+ improve the performance of scintillators in existing applications and open the way to novel ones. The development of these new materials was empowered by the close interdisciplinary collaboration between scientists in the fields of inorganic chemistry, optical spectroscopy, and applied physics.
The Commons: A Toolkit for the Quantitative Analysis of Trust and Cooperation in Online Environments (1999)

A toolkit for performing social dilemma tests has been built which allows for the measurement of the development of trust and cooperation within an online group. This is especially important for online environments since many of the cues that we rely on in face to face communication are missing from online interaction.
Terahertz Synthetic Aperture and Interferometric Imaging (2007)

Experimental results of terahertz 2-D synthetic aperture/ interferometric imaging are presented. The performance of an N element detector array is imitated by only one detector placed at N positions. The reconstructed images of small objects are in a good agreement with theoretical predictions. The imaging method can be used to detect objects behind a barrier and spectroscopically identify materials that exhibit a characteristic THz reflection spectra.
Evaluation of carborane-containing porphyrins as tumour targeting agents for boron neutron capture therapy. (1998)

A number of carborane-containing porphyrins were administered to mice bearing subcutaneously transplanted mammary carcinomas. Administration was via serial intraperitoneal (i.p.) injections to assess their relative toxicities and tumour affinities. Three analogues of the natural porphyrin heme and four tetraphenylporphyrins (TPPs) were given at total doses of 78-245 micrograms g-1 body weight. The water-insoluble TPPs were less toxic to mice, and delivered greater amounts of boron to tumour than did the water-soluble TPPS and the heme analogues. One such compound, NiTCP-H, delivered more than 100 micrograms B g-1 to tumour tissue with a tumour:blood boron concentration ratio greater than 500:1 and a tumour: brain boron concentration ratio greater than 50:1, 4 days after the last of six i.p. injections given over 2 days. Another TPP analogue, NiTCP, delivered approximately 50 micrograms B g-1 to tumour with similar boron concentrations in normal tissues. Neither compound was toxic to mice at total doses of approximately 200 micrograms g-1 body weight. In contrast, the heme analogues were toxic and, with the exception of VCDP, delivered less boron to tumour than NiTCP and NiTCP-H. The two porphyrins with the greatest potential for application to boron neutron capture therapy (BNCT), NiTCP and NiTCP-H, yielded higher tumour:blood and tumour:brain boron concentration ratios in mice than could be achieved with p-boronophenylalanine (BPA) and sodium mercaptoundecahydrododecaborate (BSH), the compounds which are currently being used in clinical trials of BNCT in the treatment of glioblastoma. The boron delivered by each of the porphyrins tested remained in tumour tissue longer than did boron delivered by either BPA or BSH. The copper and nickel chelates of these porphyrins behave identically in vivo. The former offer the potential for imaging by 67Cu-mediated single photon emission computed tomography (SPECT) to aid BNCT treatment planning.
Bonding Elastomers To Metal Substrates (1990)

Improved, economical method for bonding elastomers to metals prevents failures caused by debonding. In new technique, vulcanization and curing occur simultaneously in specially designed mold that acts as form for desired shape of elastomer and as container that positions and supports metal parts. Increases interface adhesion between metal, adhesive, and elastomer.
Spermatogonial transplantation and reconstitution of donor cell spermatogenesis in recipient mice (1998)

Recently, we described a method to transplant testicular cells from a fertile donor mouse to the seminiferous tubules of an infertile recipient male, where the donor cells generate spermatogenesis. Spermatozoa produced by the transplanted cells in the recipient testis will fertilize eggs and transmit the donor haplotype to the resulting animals. In the most successful transplantations, up to 80 per cent of progeny sired by the recipient male arise from donor cell-derived spermatozoa. The cell responsible for generation of spermatogenesis following transplantation clearly is a spermatogonial stem cell, since the repopulation of recipient testes extends for periods exceeding 12 months. In the past year, experiments have shown that rat testicular cells transplanted to the seminiferous tubules of immunodeficient mice will generate rat spermatogenesis and produce normal appearing rat spermatozoa, opening the possibility of xenogeneic testicular cell transplantation for other species. In addition, it has proved possible to cryopreserve spermatogonial stem cells for long periods, following which they will produce normal spermatogenesis when transplanted to a recipient. The ability to cryopreserve testicular stem cells makes individual male germ lines immortal. In current work, we are focusing on techniques to increase the efficiency of spermatogonial transplantation and methods to culture the stem cells.
Preparation of azetidinotriazole compounds as gamma secretase modulators useful for treatment of Aβ-related diseases. (2014)

The invention relates to azetidinotriazole compds. of formula I and pharmaceutically acceptable salts and pharmaceutical compns. thereof, as well as processes for making these compds. for use in th ...
Fast discrete function evaluation using decision diagrams (1995)

Abstract: An approach for fast discrete function evaluation based on multi-valued decision diagrams (MDD) is proposed. The MDD for a logic function is translated into a table on, which function evaluation is performed by a sequence of address lookups. The value of a function for a given input assignment is obtained with at most one lookup per input. The main application is to cycle-based logic simulation of digital circuits, where the principal difference from other logic simulators is that only values of the output and latch ports are computed. Theoretically, decision-diagram based function evaluation offers orders-of-magnitude potential speedup over traditional logic simulation methods. In practice, memory bandwidth becomes the dominant consideration on large designs. We describe techniques to optimize usage of the memory hierarchy.
Reagentless optical biosensor (2004)

Critical to our ability to respond effectively to a biothreat attack is the development of sensitive and specific sensor systems that can easily be used for rapid screening of potential victims for infection due to biothreat agents and detection of pathogens in the environment. To help address these needs, we have developed a Reagentless Optical Biosensor (ROB) based on protein specific assays and waveguide-based evanescent fluorescence excitation. Modeled on host pathogen interactions, the sensor's membrane based assay provides rapid, sensitive detection without the addition of reagents. We report here the development of two waveguide based detection systems: a laboratory sensor test-bed system and a handheld, battery operated, prototype. Evanescent fluorescence excitation using planar optical waveguides provides spatial filtering of background auto-fluorescence found in many natural samples, thereby permitting direct analysis of complex environmental and medical samples. The waveguide based assay is fully self-contained in a small, exchangeable cartridge that is optically coupled to the sensor detection system making ROB simple to use and offering the possibility of inexpensive, disposable sensor elements. Using assays for cholera toxin we compare results using flourimetry of vesicle solutions against results for our waveguide based test-bed and prototype sensor systems.
Bursts of Bipolar Microsecond Pulses Inhibit Tumor Growth (2015)

Irreversible electroporation (IRE) is an emerging focal therapy which is demonstrating utility in the treatment of unresectable tumors where thermal ablation techniques are contraindicated. IRE uses ultra-short duration, high-intensity monopolar pulsed electric fields to permanently disrupt cell membranes within a well-defined volume. Though preliminary clinical results for IRE are promising, implementing IRE can be challenging due to the heterogeneous nature of tumor tissue and the unintended induction of muscle contractions. High-frequency IRE (H-FIRE), a new treatment modality which replaces the monopolar IRE pulses with a burst of bipolar pulses, has the potential to resolve these clinical challenges. We explored the pulse-duration space between 250 ns and 100 μs and determined the lethal electric field intensity for specific H-FIRE protocols using a 3D tumor mimic. Murine tumors were exposed to 120 bursts, each energized for 100 μs, containing individual pulses 1, 2, or 5 μs in duration. Tumor growth was significantly inhibited and all protocols were able to achieve complete regressions. The H-FIRE protocol substantially reduces muscle contractions and the therapy can be delivered without the need for a neuromuscular blockade. This work shows the potential for H-FIRE to be used as a focal therapy and merits its investigation in larger pre-clinical models.
Biological upgrading of 3,6-anhydro-<scp>l</scp>-galactose from agarose to a new platform chemical (2020)

Recently, the utilization of renewable biomass instead of fossil fuels for producing fuels and chemicals is receiving much attention due to the global climate change. Among renewable biomass, marine algae are gaining importance as third generation biomass feedstocks owing to their advantages over lignocellulose. Particularly, red macroalgae have higher carbohydrate contents and simpler carbohydrate compositions than other marine algae. In red macroalgal carbphydrates, 3,6-anhydro-L-galactose (AHG) is the main sugar composing agarose along with D-galactose. However, AHG is not a common sugar and is chemically unstable. Thus, not only AHG but also red macroalgal biomass itself cannot be efficiently converted or utilized. Here, we biologically upgraded AHG to a new platform chemical, its sugar alcohol form, 3,6-anhydro-l-galactitol (AHGol), an anhydrohexitol. To accomplish this, we devised an integrated process encompassing a chemical hydrolysis process for producing agarobiose (AB) from agarose and a biological process for converting AB to AHGol using metabolically engineered <i>Saccharomyces cerevisiae</i> to efficiently produce AHGol from agarose with high titers and yields. AHGol was also converted to an intermediate chemical for plastics, isosorbide. To our knowledge, this is the first demonstration of upgrading a red macroalgal biomass component to a platform chemical via a new biological route, by using an engineered microorganism.
The effects of high temperature annealing on metal-induced laterally crystallized polycrystalline silicon (2000)

Metal-induced laterally crystallized (MILC) polycrystalline silicon (poly-Si) with and without a post-crystallization high temperature anneal have been studied and compared. It was revealed using transmission electron microscopy (TEM) that the anneal resulted in significant improvement in the material quality. Consequently, the electrical properties of the annealed MILC poly-Si resistors were greatly enhanced, showing conduction behavior approaching that of single-crystal Si. Thin-film transistors realized on high-temperature annealed MILC poly-Si exhibited excellent device characteristics, thus making them potentially applicable to three-dimensional (3-D) device integration. Based on the TEM observations and a detailed consideration of the mechanism of grain growth during MILC, the effects of the anneal can be explained in terms of the evolution of the unique MILC grain structure during the high temperature treatment.
Fundamental understanding of the interplay between target and sensor brings diffraction based overlay to the next level of accuracy (2021)

Driven by the increasing demand for a better on-product overlay control, the metrology specifications continue to tighten when nodes advance. Metrology accuracy budgets are reaching levels close to 1 angstrom. To obey these stringent requirements on metrology accuracy, the understanding of the interplay between the metrology target and metrology tool is of paramount importance to advance diffraction based overlay (DBO) to the next level of accuracy. In this contribution we will first present a model for the signal formation of DBO. We will show how overlay is translated into a measurable intensity asymmetry using biased gratings. When the metrology target is symmetric, the accuracy of the measurement is limited by photon shot noise only. We will show how an asymmetric target deformation leads to an overlay ambiguity that deteriorates the accuracy of the overlay metrology well beyond the fundamental photon shot noise limit. To recover from the effects of asymmetric target deformation, we will show that additional information is needed on top of the traditional single wavelength overlay reading on one target. When the target deformation is small, that additional information can, for example, come from multiple wavelengths. For large asymmetric target deformations causing a significant center-of-gravity shift, a plurality of targets or a description of the stack is needed. These specific solution directions will be discussed in detail. In conclusion, in this paper we will dive into the fundamentals of diffraction based overlay, where we explore the physics of the signal formation in diffraction based overlay in the presence of asymmetric target deformation. We will show that a better understanding of the signal formation helps to develop methods that advance diffraction based overlay metrology to the next level of accuracy, which is needed to fulfill the increasing demand for a better on product overlay control.
Piracy of adhesins: attachment of superinfecting pathogens to respiratory cilia by secreted adhesins of Bordetella pertussis (1986)

Two proteins secreted by Bordetella pertussis are known to mediate adherence of these bacteria to mammalian respiratory cilia. When either ciliated cells or other pathogenic bacteria were pretreated with these adhesins, Streptococcus pneumoniae, Haemophilus influenzae, and Staphylococcus aureus acquired the ability to adhere to cilia in vitro and in vivo. Such piracy of adhesins may contribute to superinfection in mucosal diseases such as whooping cough.
Time compression/expansion with synchronized individual pitch correction of separate components (1988)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Michael A. Klasco, Irwin H. Kornfeld; Time compression/expansion with synchronized individual pitch correction of separate components. J. Acoust. Soc. Am. 1 January 1988; 83 (1): 405. https://doi.org/10.1121/1.396212 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAcoustical Society of AmericaThe Journal of the Acoustical Society of America Search Advanced Search |Citation Search
A new frequency synthesis method based on "flying-adder" architecture (2003)

The "flying-adder" frequency and phase synthesis architecture was presented in papers published by Mair and Xiu in 2000 and Xiu and You in 2002. This architecture contains many excellent features and it can be implemented/integrated easily in a very large scale integration system. However, it has a drawback of inherent jitter on the output frequency, due to the frequency modulation of the output frequency. This brief presents a new frequency synthesis method that eliminates such jitter. The frequency accuracy of this new architecture is studied; subsequently, the frequency error upper bound is found. Furthermore, it leads to the development of a scheme that can be used to derive the frequency error distribution. The comparison to "integer-N" and "fractional-N" phase-locked loop (PLL) based frequency synthesis techniques is also presented.