gebhart/patrepeval huggingface dataset:
Hyperactive transposase mutants of the <i>Himar</i> <i>1</i> mariner transposon (1999)

Mariner-family transposable elements are active in a wide variety of organisms and are becoming increasingly important genetic tools in species lacking sophisticated genetics. The Himar1 element, isolated from the horn fly, Haematobia irritans, is active in Escherichia coli when expressed appropriately. We used this fact to devise a genetic screen for hyperactive mutants of Himar1 transposase that enhance overall transposition from approximately 4- to 50-fold as measured in an E. coli assay. Purified mutant transposases retain their hyperactivity, although to a lesser degree, in an in vitro transposition assay. Mutants like those described herein should enable sophisticated analysis of the biochemistry of mariner transposition and should improve the use of these elements as genetic tools, both in vivo and in vitro.
SAT-748 Advantages and Limitations of an Integrative Measurement for All Serum Androgens and Anti-Androgens (2020)

Abstract Background: Analytic measurements of a hormone in bodily fluids are a cornerstone of clinical evaluation. However, clinical presentation may be affected also by currently unmeasured modulators of hormonal function. An alternative could be to measure the cumulative effect of all factors present in a bodily fluid on the function of a hormone receptor. Prior studies showed an androgen receptor (AR) BioAssay to accurately measure urine androgens in males undergoing testosterone (T) supplementation (1). The factors integrated by the AR BioAssay include androgens, anti-androgens and, in serum, androgen binding proteins affecting ligand availability. Methods: The AR BioAssay was exposed to male and female serum samples obtained from the CDC’s Hormone Standardization (HoSt) Program, and to female serum samples from the UCSF PCOS Tissue Bank registry. AR activity was quantified against a testosterone standard curve and recorded as ‘T-equivalent’ (‘T-eq’) androgen activity units. Results: In 40 CDC HoSt sera added directly (no extraction) to AR BioAssay cells, androgen activities ranged from 2.57 to 298 ng ‘T-eq’/dl. In the 20 ‘male’ CDC HoSt sera (T&gt;150 ng/dl), the androgen activity measurements were uniformly less (0.35 ± 0.10) that of the T-measurement. By contrast, in the 20 ‘female’ CDC HoSt sera, in which T concentrations are typically lower than the affinity of T for sex hormone binding globulins such that more of the T is available to the AR BioAssay, the measured androgen levels were on average 1.45-fold higher than the T concentration. This androgen to T comparison showed high variability in females with 5 of 20 CDC HoSt samples having androgen concentrations more than double that of T (maximum, 6.1-fold). In female serum samples from the PCOS registry, androgens were higher in patients with a PCOS diagnosis (57.7 +/-17.6 ng ‘T-eq’/dl; n = 23) compared to women not meeting formal PCOS criteria (38.1 +/-10.8 ng ‘T-eq’/dl; n = 4); androgen values again averaged 1.40-fold (maximum, 4.9-fold) that of the T measurements, regardless of PCOS diagnosis. Conclusions: Androgen-binding globulins appear to most influence androgen activity levels in male serum. In females, the lower T concentrations may minimize the impact of androgen-binding proteins and permit the impact of non-T androgens to be more pronounced with possible clinical consequence. Further investigations are needed to determine whether functional androgen measurements may improve clinical diagnosis of certain conditions. Reference: (1) Bailey et al (2016) PLoS One11(3):e0151860
Oncolytic targeting of androgen-sensitive prostate tumor by the respiratory syncytial virus (RSV): consequences of deficient interferon-dependent antiviral defense (2011)

We demonstrated that RSV is potentially a useful therapeutic tool in the treatment of androgen-sensitive and androgen-independent prostate cancer. Moreover, impaired IFN-mediated antiviral response is the likely cause of higher viral burden and resulting oncolysis of androgen-sensitive prostate cancer cells.
Adenovirus based HPV L2 vaccine induces broad cross-reactive humoral immune responses (2018)

Oncogenic high-risk human papillomavirus (HPV) infections cause a substantial number of genital and non-genital cancers worldwide. Approximately 70% of all cervical cancers are caused by the high-risk HPV16 and 18 types. The remaining 30% can be attributed to twelve other high-risk HPV-types. Highly efficacious 2-valent, 4-valent and 9-valent L1 protein based prophylactic HPV vaccines are available however with limited cross-protection. To further increase the coverage, development of a multivalent cross-protective HPV vaccine is currently focused on the conserved N-terminus of HPV's L2 protein. We have developed a vaccine candidate based on the rare human adenovirus type 35 (HAdV35) vector that displays a concatemer of L2 protein epitopes from four different HPV-types via protein IX (pIX). A mix of two heterologous HAdV35 pIX-L2 display vectors present highly conserved linear epitopes of nine HPV-types. Each HAdV35 pIX-L2 display vector exhibits a good manufacturability profile. HAdV35 pIX-L2 display vaccine vectors were immunogenic and induced neutralizing antibodies against HPV-types included in the vaccine and cross-neutralizing antibodies against distant a HPV-type not included in the vaccine in mice. The HAdV35 pIX-L2 display vectors offer an opportunity for a multivalent HAdV-based prophylactic HPV vaccine.
Star-type polarizer with equal-power splitting function for each polarization based on polarization-dependent defects in two-dimensional photonic-crystal waveguides (2016)

We propose a star-type polarizer with equal-power splitting function for each polarization based on polarization-dependent defects (PDDs) in two-dimensional photonic-crystal waveguides (PCWs). The structure is designed by combining two Y-type PCWs, and two types of PDDs are introduced into the PCWs respectively to provide polarization functions. By using finite-element method and optimizing the parameters of the PDDs, it is demonstrated that different polarizations can only transmit through their own PCWs and output with identical power distributions, i.e., the structure can function as polarizer and equal-power splitter for each polarization at the same time. In addition, by scanning the wavelength of the structure, it is proved that the proposed splitter can work in a wide range of wavelength while keeping high output transmission for both the TE and TM polarizations. Such a structure is useful for polarization-relative multi-channel signal processing for optical communications in the mid- and far-infrared wavelength regions.
Multimodal local search in Speak4it (2011)

Speak4it is a consumer-oriented mobile search application that leverages multimodal input and output to allow users to search for and act on local business information. It supports true multimodal integration where user inputs can be distributed over multiple input modes. In addition to specifying queries by voice e.g. bike repair shops near the golden gate bridge users can combine speech and gesture, for example, gas stations + <route drawn on display> will return the gas stations along the specified route traced on the display. We describe the underlying multimodal architecture and some challenges of supporting multimodal interaction as a deployed mobile service.
Comparison of nodule characteristics on CT and radiographic images (2004)

The purpose of this study is to identify the difference in nodule characteristics manifested on computed topography (CT) and X-ray images and to evaluate the ability of radiographic features to differentiate between benign and malignant nodules, when compared to the features extracted from CT. We collected 79 consecutive computed radiographic (CR) chest images with one or more CT-documented lung nodules. Upon viewing the CT slices, corresponding nodules were localized on CR images by an experienced chest radiologist. Of the 79 CT nodules (19 benign, 60 malignant), 61 (14 benign, 47 malignant) were considered to be definitely visible on the CR, and the rest were considered to be invisible or did not qualify for distinct feature assessment. Eleven nodule features each were visually extracted from CT and CR images. These features were used to characterize the nodule in terms of size, shape, lobulation, spiculation, density, etc. Correlation between the CT and CR features was calculated for the 61 definitely CR-visible nodules. Receiver operating characteristics (ROC) analysis was performed to evaluate the ability of these features in the task of differentiating between benign and malignant nodules. Results showed that CR and CT images agreed well in characterizing nodules in terms of shape, lobulation, spiculation and density features. We found that 40-50% of the cases had same CR and CT ratings and 41-51% of cases were rated by a difference of one between their ratings on CT and CR for shape (3-point scale), lobulation (4-point scale) and speculation (4-point scale) features. Ninety-two percent of the cases had same CT and CR ratings on the density feature. Size yielded a correlation coefficient of 0.84. In the task of differentiating between benign and malignant lung nodules, ROC analysis of individual features yielded an A<sub>z</sub> value ranging from 0.52 to 0.77 for the 14 CT features and from 0.52 to 0.75 for the CR features. In addition, we examined the characteristics of the 18 nodules that were excluded from feature analysis. On average, these 18 nodules were smaller in size (15.2 mm measured from CT) than the 61 CR-visible nodules (23.5 mm). We found that CR features agreed reasonably well with CT features and their ability to differentiate between benign and malignant nodules were similar to that of the CT features.
High-Energy Fragmentation in Nanophotonic Ion Production by Laser-Induced Silicon Microcolumn Arrays (2009)

Laser-induced silicon microcolumn arrays (LISMA) exhibit nanophotonic ion production in laser desorption ionization experiments (Walker et al., Angew. Chem., Int. Ed. 2009, 48, 1669) for small-to-medium-size molecules. Although these surfaces are known to promote fragmentation of adsorbates at high laser fluences, the nature, extent, and origin of peptide ion decomposition remains unknown. Here we demonstrate that peptide ions, e.g., bradykinin, leucine enkephalin, angiotensin I, substance P, and various tripeptides, desorbed from these substrates show an increasing degree of fragmentation as the fluence is raised. Compared to other ion fragmentation methods, LISMA shows similarity to high-energy collision activated dissociation (CAD), ion decomposition produced by metastable atom beams, and surface induced dissociation (SID). While some of the produced fragments are associated with high-energy decomposition channels, for example, the abundant a5 fragment produced from singly protonated bradykinin ion, other ions in the same spectra (e.g., the ammonia loss from the protonated bradykinin ion) are predominantly produced by low energy processes. To explore the role of internal energy in the fragmentation of ions produced from LISMA, the survival yields of eight benzyl-substituted benzylpyridinium thermometer ions were also studied as a function of laser fluence and surface derivatization. The corresponding internal energies were determined using the Rice−Ramsperger−Kassel−Marcus formalism. On both native and silane-derivatized surfaces, the thermometer ions showed stable internal energy values over a wide range of laser fluences. This presented a strong contrast to the behavior of the peptides that yielded high-energy fragments at increased fluence. As the thermometer ions did not record an increase in internal energy, the enhanced fragmentation of the peptides was indicative of alternative high-energy mechanisms.
Nonlithographic approach to nanostructure fabrication using a scanned electrospinning source (2003)

We have used deposited polymeric nanofibers as nonlithographic templates for the fabrication of semiconductor nanostructures. We deposited oriented poly(methyl methacrylate) (PMMA) fibers, with diameters ranging from 85 to 350 nm, on the surface of various substrates using a microfabricated electrospinning source. By utilizing the small apex of a microfabricated source, a stable Taylor cone was formed as an electrostatically driven source of polymer solution directed toward the substrate. By attaching the target substrate to a rotating counter electrode, isolated and oriented PMMA fibers were deposited. We used these fibers as etch masks to pattern nanostructures in the surface of a silicon wafer. This method provides a simple, nonlithographic approach to forming nanostructures on a wide variety of substrates, such as silicon, aluminum, silicon dioxide, silicon nitride, and glass. The fiber deposition can be oriented with respect to surface features, allowing for realization of nanodevice architectures.
Visna virus encodes a post-transcriptional regulator of viral structural gene expression. (1990)

Visna virus is an ungulate lentivirus that is distantly related to the primate lentiviruses, including human immunodeficiency virus type 1 (HIV-1). Replication of HIV-1 and of other complex primate retroviruses, including human T-cell leukemia virus type I (HTLV-I), requires the expression in trans of a virally encoded post-transcriptional activator of viral structural gene expression termed Rev (HIV-1) or Rex (HTLV-I). We demonstrate that the previously defined L open reading frame of visna virus encodes a protein, here termed Rev-V, that is required for the cytoplasmic expression of the incompletely spliced RNA that encodes the viral envelope protein. Transactivation by Rev-V was shown to require a cis-acting target sequence that coincides with a predicted RNA secondary structure located within the visna virus env gene. However, Rev-V was unable to function by using the structurally similar RNA target sequences previously defined for Rev or Rex and, therefore, displays a distinct sequence specificity. Remarkably, substitution of this visna virus target sequence in place of the HIV-1 Rev response element permitted the Rev-V protein to efficiently rescue the expression of HIV-1 structural proteins, including Gag, from a Rev- proviral clone. These results suggest that the post-transcriptional regulation of viral structural gene expression may be a characteristic feature of complex retroviruses.
Superconductivity in Boron-Doped Diamond (2006)

The discovery of superconductivity in diamond opened up a new field of superconductivity in doped semiconductor. Using the chemical vapor deposition (CVD) method, polycrystalline and homoepitaxial superconducting diamond films have been successfully synthesized. These films show relatively high superconducting transition temperatures, particularly in homoepitaxial (111) film that showed the highest superconducting transition temperature of Tc = 11.4 K. Since high quality and large films can be obtained by the CVD method, many fundamental physical measurements were carried out to understand the mechanism of superconductivity in diamond. In this report, the recent data about superconducting properties of heavily boron-doped diamond are discussed.
Effect of High Shear Mixing Parameters and Degassing Temperature on the Morphology of Epoxy-Clay Nanocomposites (2013)

Epoxy-clay nanocomposites were prepared by high shear mixing method using Nanomer I.30E nanoclay as nano-reinforcement in diglycidyl ether of bisphenol A (DGEBA). The effect of mixing speed and time on the nature and degree of clay dispersion were investigated by varying the mixing speed in the range of 500-8000 RPM and mixing time in the range of 15-90 minutes. The effect of degassing temperature on the morphology of the resultant nanocomposites was also studied. Scanning and transmission microscopy (SEM & TEM) along with x-ray diffraction (XRD) have been used to characterize the effect of shear mixing speed, mixing time and degassing temperature on the structure of the resultant nanocomposites. The SEM, TEM and XRD examinations demonstrated that the degree of clay dispersion was improved with increasing the high shear mixing speed and mixing time. The results showed that the optimum high shear mixing speed and mixing time were 6000 rpm and 60 min, respectively. It was observed that the structure of the nanocomposites that have been degassed at 65oC was dominated by ordered intercalated morphology while disordered intercalated with some exfoliated morphology was found for the sample degassed at 100oC for the first 2 hours of the degassing process.
A Water‐Borne Adhesive Modeled after the Sandcastle Glue of <i>P. californica</i> (2008)

Polyacrylate glue protein analogs of the glue secreted by Phragmatopoma californica, a marine polycheate, were synthesized with phosphate, primary amine, and catechol sidechains with molar ratios similar to the natural glue proteins. Aqueous mixtures of the mimetic polyelectrolytes condensed into liquid complex coacervates around neutral pH. Wet cortical bone specimens bonded with the coacervates, oxidatively crosslinked through catechol sidechains, had bond strengths nearly 40% of the strength of a commercial cyanoacrylate. The unique material properties of complex coacervates may be ideal for development of clinically useful adhesives and other biomaterials.
Abstract 14163: Oxidized Phospholipids and Lipoprotein-Associated Phospholipase A2 in Plasma, ApoB-containing and ApoAI -containing Lipoprotein Subfractions in Patients with Familial Hypercholesterolemia: Effect of LDL Apheresis (2010)

Objectives: Lp(a) is a causal, genetic risk factor for cardiovascular disease (CVD) and is enriched in pro-inflammatory oxidized phospholipids (OxPL) and lipoprotein-associated phospholipase A2 (Lp-PLA2). Epidemiologic outcomes studies have shown that the OxPL, Lp(a) and Lp-PLA2 collectively mediate additive risk for CVD. To derive new insights into these findings, we evaluated the impact of apheresis on lipoprotein-associated OxPL and Lp-PLA2 mass in pts with familial hypercholesterolemia (FH). Methods: Patients with FH (n=18) on chronic LDL apheresis were divided into three groups according to low ( Results: In plasma and subfractions, OxPL were present primarily on Lp(a), but minimally on non-Lp(a)-apoB or apoAI. OxPL were almost exclusively detected in density 1.059-1.094 g/ml where Lp(a) is prevalent and in proportion to the amount of Lp(a) present. In plasma and subfractions, Lp-PLA2 was present primarily on apoB particles; however the proportion of Lp-PLA2 decreased in apoB-containing subfractions but progressively increased in Lp(a) as Lp(a) plasma levels increased. LDL apheresis resulted in significant reductions of OxPL and Lp-PLA2 in plasma, in apoB-containing subfractions and on isolated apoB and Lp(a). Conclusions: By physical separation and immunological techniques, OxPL are primarily present on the Lp(a) particle. Lp-PLA2 is present primarily on apoB-containing particles but the proportion on Lp(a) increases as plasma Lp(a) levels increase. These data suggest that Lp(a), OxPL and Lp-PLA2 are pathophysiologically linked, particularly as Lp(a) levels increase, and provide a rationale for understanding their interactive role in mediating atherothrombosis and CVD in humans.
Sugar Beet Pectins: Chemical Structure and Gelation through Oxidative Coupling (1986)

Pectins were isolated from sugar beet pulp by sequential extraction with water, oxalate, acid, and alkali. They were found to be fairly low molecular mass products with a high degree of acetylation and a relatively high neutral sugar content. Neutral sugars were determined and their location in "hairy fragments" of the pectin molecules was studied by enzymic and chemical degradation experiments. Acetyl ester groups are bound to the anhydrogalacturonide backbone mainly. Feruloyl ester groups appear to be linked to the neutral sugar side chains. These can be used in the formation of cross-links with hydrogen peroxide and peroxidase or with ammonium persulfate. The products obtained are either pectin solutions with increased intrinsic viscosity or pectin gels. Cross-linked pectins isolated from these gels have an extremely high water-absorbing capacity.
Environment‐Adaptable Rotational Energy Harvesters Based on Nylon‐core Coiled Carbon Nanotube Yarns (2023)

Owing to increasing amount of research on energy harvesting, studies on harvesters for practical application and their performance are attracting attention. Therefore, studies on the use of continuous energy as an energy source for energy-harvesting devices are being conducted, and fluid flows, e.g., wind, river flow, and sea wave, are widely used as input energy sources for continuous energy harvesting. A new energy-harvesting technology has emerged based on the mechanical stretch and release of coiled carbon nanotube (CNT) yarns, which generate energy based on the change in the electrochemical double-layer capacitance. First, this CNT yarn-based mechanical energy harvester is demonstrated, which is applicable to various environments where fluid flow exists. This environment-adaptable harvester uses rotational energy as the mechanical energy source and is tested in river and ocean environments. Moreover, an attachable-type harvester for the application of the existing rotational system is devised. In the case of a slow rotational environment, a square-wave strain-applying harvester has been implemented, which can convert sinusoidal strain motion into square-wave strain motion for high output voltages. To achieve high performance of practical harvesting applications, a scale-up method for powering signal-transmitting devices has been implemented.
VirtualScan: Test Compression Technology Using Combinational Logic and One-Pass ATPG (2008)

IC testing based on a full-scan design methodology and ATPG is the most widely used test strategy today. However, rapidly growing test costs are severely challenging the applicability of scan-based testing. Both test data size and number of test cycles increase drastically as circuit size grows and feature size shrinks. For a full-scan circuit, test data volume and test cycle count are both proportional to the number of test patterns N and the longest scan chain length L. To reduce test data volume and test cycle count, we can reduce N, L, or both. Earlier proposals focused on reducing the number of test patterns N through pattern compaction. All these proposals assume a 1-to-1 scan configuration, in which the number of internal scan chains equals the number of external scan I/O ports or test channels (two ports per channel) from ATE. Some have shown that ATPG for a circuit with multiple clocks using the multicapture clocking scheme, as opposed to one-hot clocking, generates a reduced number of test patterns.