gebhart/patrepeval huggingface dataset:
Toxicity and Bioavailability of Metals in the Missouri River Adjacent to a Lead Refinery (2001)

This study is an evaluation of the potential environmental impacts of contaminated groundwater from the ASARCO metals refining facility adjacent to the Missouri River in Omaha, Nebraska. Surface waters, sediments, and sediment pore waters were collected from the Burt-Izard drain, which transects the facility, and from the Missouri River adjacent to the facility. Groundwater was also collected from the facility. Waters and sediments were analyzed for inorganic contaminants, and the toxicity of the waters was evaluated with the Ceriodaphnia dubia 7- day test. Concentrations of several elemental contaminants were highly elevated in the groundwater, but not in river sediment pore waters. Lead concentrations were moderately elevated in whole sediment at one site, but lead concentrations in pore waters were low due to apparent sequestration by acid-volatile sulfides. The groundwater sample was highly toxic to C. dubia, causing 100% mortality. Even at the lowest groundwater concentration tested (6.25%) C. dubia survival was reduced; however, at that concentration, reproduction was not significantly different from upstream porewater reference samples. Sediment pore waters were not toxic, except reproduction in pore water collected from one downstream site was somewhat reduced. The decrease in reproduction could not be attributed to measured elemental contaminants.
Enhancing biocompatibility and corrosion resistance of Mg implants via surface treatments (2011)

Oxide coating layers were formed on a pure magnesium (Mg) substrate through anodization and micro-arc oxidation (MAO) in order to enhance the biocompatibility and reduce the degradation rate. A thin, smooth MgO coating layer was formed after the anodization. On the other hand, when the Mg was treated using the MAO process, a relatively thick, rough MgO layer was formed. The corrosion properties were investigated using electrochemical and ion release tests in a simulated body fluid. Both the anodization and the MAO treatment enhanced the corrosion resistance of the Mg specimens. However, the MgO layers that formed on the surface were not stable enough to render favorable environments for cell growth. The anodized and MAO-treated specimens were post-treated in a cell-culturing medium in order to improve the stability of the coating layer. The biocompatibility was evaluated using in vitro cell tests, including cell attachment, DNA measurement, and alkaline phosphatase (ALP) activity tests. The DNA levels of the surface-treated Mg were about 6-10 times higher than the bare Mg. The ALP activity levels were also more than double after either the anodization or the MAO followed by the post-treatments. These results demonstrated that the biocompatibility and the corrosion resistance of Mg were significantly improved by the series of surface treatments.
Tm^3+ cladding-doped fiber for selective wavelength filtering in high-power pump lasers (2004)

Scattering and reflection of transmission band power in a fiber amplifier cause increased bit-error rates through multiple path interference (MPI). We report a passive method for reducing MPI contributions from the front facet of a 980-nm fiber-Bragg-grating-stabilized pump laser by use of a Tm3+-doped fiber pigtail between the diode facet and the fiber Bragg grating. Optical return loss in the C band is reduced to below -30 dB.
High-performance long wave infrared bolometer fabricated by wafer bonding (2010)

A novel microbolometer with peak responsivity in the longwave infrared region of the electromagnetic radiation is under development at Sensonor Technologies. It is a focal plane array of pixels with a 25&mu;m pitch, based on monocrystalline Si/SiGe quantum wells as IR sensitive material. The novelty of the proposed 3D process integration comes from the choice of several of the materials and key processes involved, which allow a high fill factor and provide improved transmission/absorption properties. Together with the high TCR and low 1/f noise provided by the thermistor material, they will lead to bolometer performances beyond those of existing devices. The thermistor material is transferred from the handle wafer to the read-out integrated circuit (ROIC) by wafer bonding. The low thermal conductance legs that connect the thermistor to the ROIC are fabricated prior to the transfer bonding and are situated under the pixel. Depending on the type of the transfer bonding used, the plugs connecting the legs to the thermistor are made before or after this bonding, resulting in two different configurations of the final structure. Using a low temperature oxide bonding and subsequent plugs formation result in through-pixel plugs. Pre-bonding plugs formation followed by thermo-compression bonding result in under-pixel plugs. The pixels are subsequently released by anhydrous vapor HF of the sacrificial oxide layer. The ROIC wafer containing the released FPAs is bonded in vacuum with a silicon cap wafer, providing hermetic encapsulation at low cost. Antireflection coatings and a thin layer getter are deposited on the cap wafer prior to bonding, ensuring high performance of the bolometer.
Reduced thermal dependence of the sensitivity of a planar Hall sensor (2019)

The ability to stabilize the sensitivity of a magnetoresistance sensor in unstable thermal environments is a key parameter in many high precision measurements. Here, we propose a method to stabilize the sensitivity of a highly sensitive and low noise magnetic sensor based on a planar Hall Effect crossed junction. The stability is achieved by controlling the interplay between Zeeman energy, exchange bias energy, and anisotropy energy as a function of the temperature of the sensor stack comprising a trilayer structure NiFe/Cu/IrMn (10/0.12/10 nm). The high thermal stability of the sensor sensitivity of 4.5 ± 0.15 × 10−3 V/A/T/K is achieved when the external magnetic field is set around ±2 ± 0.04 mT and the applied current is fixed at 20 mA in the temperature range of 110 K–360 K. This method improves the magnetic sensor detection by about an order of magnitude, enabling its deployment in various research fields, particularly to study magnetic properties of small quantities of magnetic materials toward the detection of single magnetic objects, which was impossible before.
Genetic architecture of human plasma lipidome and its link to cardiovascular disease (2019)

Understanding genetic architecture of plasma lipidome could provide better insights into lipid metabolism and its link to cardiovascular diseases (CVDs). Here, we perform genome-wide association analyses of 141 lipid species (n = 2,181 individuals), followed by phenome-wide scans with 25 CVD related phenotypes (n = 511,700 individuals). We identify 35 lipid-species-associated loci (P <5 ×10<sup>-8</sup>), 10 of which associate with CVD risk including five new loci-COL5A1, GLTPD2, SPTLC3, MBOAT7 and GALNT16 (false discovery rate<0.05). We identify loci for lipid species that are shown to predict CVD e.g., SPTLC3 for CER(d18:1/24:1). We show that lipoprotein lipase (LPL) may more efficiently hydrolyze medium length triacylglycerides (TAGs) than others. Polyunsaturated lipids have highest heritability and genetic correlations, suggesting considerable genetic regulation at fatty acids levels. We find low genetic correlations between traditional lipids and lipid species. Our results show that lipidomic profiles capture information beyond traditional lipids and identify genetic variants modifying lipid levels and risk of CVD.
Faster and More Accurate Sequence Alignment with SNAP (2011)

We present the Scalable Nucleotide Alignment Program (SNAP), a new short and long read aligner that is both more accurate (i.e., aligns more reads with fewer errors) and 10-100x faster than state-of-the-art tools such as BWA. Unlike recent aligners based on the Burrows-Wheeler transform, SNAP uses a simple hash index of short seed sequences from the genome, similar to BLAST's. However, SNAP greatly reduces the number and cost of local alignment checks performed through several measures: it uses longer seeds to reduce the false positive locations considered, leverages larger memory capacities to speed index lookup, and excludes most candidate locations without fully computing their edit distance to the read. The result is an algorithm that scales well for reads from one hundred to thousands of bases long and provides a rich error model that can match classes of mutations (e.g., longer indels) that today's fast aligners ignore. We calculate that SNAP can align a dataset with 30x coverage of a human genome in less than an hour for a cost of $2 on Amazon EC2, with higher accuracy than BWA. Finally, we describe ongoing work to further improve SNAP.
SeMoPS (2011)

Many experts consider that efficient and effective mobile payment solutions will empower existing e- and m-commerce efforts and unleash the true potential of mobile business. Recently, different mobile payment approaches appear to the market addressing particular needs, but up to now no global mobile payment solution exists. SEMOPS is a secure mobile payment service with an innovative technology and business concept that aims to fully address the challenges the mobile payment domain poses and become a global mobile payment service. We present here a detailed description of the approach, its implementation, and features that diversify it from other systems. We discuss on its business model and try to predict its future impact. The aim is to provide an insight of a new mobile payment service and discuss implementation decisions and scenarios.Request access from your librarian to read this chapter's full text.
Antigen Is Required for Maturation and Activation of Pathogenic Anti-DNA Antibodies and Systemic Inflammation (2011)

Systemic lupus erythematosus is an autoimmune disease characterized by autoantibodies and systemic inflammation that results in part from dendritic cell activation by nucleic acid containing immune complexes. There are many mouse models of lupus, some spontaneous and some induced. We have been interested in an induced model in which estrogen is the trigger for development of a lupus-like serology. The R4A transgenic mouse expresses a transgene-encoded H chain of an anti-DNA Ab. This mouse maintains normal B cell tolerance with deletion of high-affinity DNA-reactive B cells and maturation to immunocompetence of B cells making nonglomerulotropic, low-affinity DNA-reactive Abs. When this mouse is given estradiol, normal tolerance mechanisms are altered; high-affinity DNA-reactive B cells mature to a marginal zone phenotype, and the mice are induced to make high titers of anti-DNA Abs. We now show that estradiol administration also leads to systemic inflammation with increased B cell-activating factor and IFN levels and induction of an IFN signature. DNA must be accessible to B cells for both the production of high-affinity anti-DNA Abs and the generation of the proinflammatory milieu. When DNase is delivered to the mice at the same time as estradiol, there is no evidence for an abrogation of tolerance, no increased B cell-activating factor and IFN, and no IFN signature. Thus, the presence of autoantigen is required for positive selection of autoreactive B cells and for the subsequent positive feedback loop that occurs secondary to dendritic cell activation by DNA-containing immune complexes.
Human Colon Adenocarcinoma Cells. II. Tumorigenic and Organoid Expression In Vivo and In Vitro2 (1977)

A human colon epithelial tumor cell line (LS174T) recultured in vitro following passage through hamsters displayed differences in its cell doubling time and synthesis of carcinoembryonic antigen when compared with the cells grown solely in vitro. These animal-passaged cells more closely resembled the parent tumor cell line (LS180) derived from the primary tumor than LS174T, the trypsinized variant of LS180. Analysis of lactate dehydrogenase isoenzymes indicated that the tumor cells recovered from the hamsters were free of xenogeneic host tissue. Furthermore, LS174T grafted to athymic (nude) mice grew as a mucinous adenocarcinoma microscopically resembling the original tumor. The altered growth potential of LS174T was also demonstrated on confluent feeder monolayers of normal cells and by uninhibited multiplication in vitro. These results suggest that, at least in this one case, short-term passage of long-term cultured cells into xenogeneic hosts may effect a phenotypic reversion such that the cells regain properties observed in the primary tumor and the initial in vitro explant.
D‐Isomeric replacements within the 6–9 core sequence of ac‐[Nle4]‐α‐MSH4–11‐NH2: A topological model for the solution conformation of α‐melanotropin (1986)

Abstract Analogs of Ac‐[Nle 4 ]‐α‐MSH 4–11 ‐NH 2 and Ac‐[Nle 4 , D ‐Phe 7 ]‐α‐MSH 4–11 ‐NH 2 were prepared with D ‐isomeric replacements at the His 6 , Arg 8 , and Trp 9 residues. The requirement for an indole moiety at position 9 also was evaluated by replacement with L ‐leucine in both parent fragment analogs. D ‐isomeric replacements at positions 6 and 8 in either series were detrimental to biological potency in frog ( Rana pipiens ) and lizard skin ( Anolis carolinensis ) in vitro melanotropic assays. However, Ac‐[Nle 4 , D ‐Trp 9 ]‐α‐MSH 4–11 ‐NH 2 and Ac‐[Nle 4 , D ‐Phe 7 , D ‐Trp 9 ]‐α‐MSH 4–11 ‐NH 2 were equipotent and 10 × more potent than Ac‐[Nle 4 ]‐α‐MSH 4–11 ‐NH 2 , respectively, in the lizard skin bioassay, and 30 and 1900 times more potent in the frog skin bioassay. Ac‐[Nle 4 , D ‐Phe 7 , D ‐Trp 9 ]‐α‐MSH 4–11 ‐NH 2 was 3 × more potent than α‐MSH in the frog skin bioassay. Proton nmr studies in aqueous solution revealed a marked preservation of the backbone conformation of these linear analogs. Chemical‐shift variations due to the through‐space anisotropic influence of the core aromatic amino acid residues permitted evaluation of side‐chain topology. The observed topology was consistent with nonhydrogen‐bonded β‐like structure (ϕ = −139°, ψ = +135° for L ‐amino acids; ϕ = +139°, ψ = −135° for D ‐amino acids) as the predominant solution conformation. The biological and conformational data suggest that high melanotropic potency requires a close spatial arrangement of the His 6 , Phe 7 , and Arg 8 side chains.
Enantioselective Synthesis of (S)-γ-Fluoroleucine Ethyl Ester (2006)

A concise synthesis of (S)-γ-fluoroleucine ethyl ester is reported. An enantioselective Ti-catalyzed ene reaction of ethyl glyoxylate with isobutene afforded the desired α-hydroxy ester in excellent enantioselectivity. Addition of HF to the terminal double bond gave the fluorinated intermediate, which was subsequently converted into the final product by triflation, SN2 substitution by BnNH2 and benzyl group deprotection using Pearlman’s catalyst. The final product was obtained in 95% ee and 25% overall yield in five steps.
Design and fabrication of the vacuum ultraviolet nonlinear metasurfaces (2020)

Nonlinear metasurface devices for generation and manipulation of coherent vacuum ultraviolet (VUV) light will be reported in this talk. The approaches for design, fabrication, and measurement of the metasurface devices with different working principles will be discussed. Our ultracompact metasurfaces are capable of efficiently generating VUV light via various nonlinear processes with effective nonlinear coefficients much better than general nonlinear medias in the targeted regime. They pave the way toward highly efficient and versatile miniaturized VUV nanodevices.
Stepwise Design of γ-Secretase Modulators with an Advanced Profile by Judicious Coordinated Structural Replacements and an Unconventional Phenyl Ring Bioisostere (2020)

Starting from RO6800020 (<b>1</b>), our former γ-secretase modulator (GSM) lead compound, we utilized sequential structural replacements to improve the potency (IC<sub>50</sub>), pharmacokinetic properties including the free fraction (fraction unbound (fu)) in plasma, and <i>in vivo</i> efficacy. Importantly, we used novel CF<sub>3</sub>-alkoxy groups as bioisosteric replacements of a fluorinated phenyl ring and properties such as lipophilicity, solubility, metabolic stability, and free fraction could be balanced, maintaining low Pgp efflux needed for CNS penetration. In addition, by reducing aromaticity, we prevented phototoxicity. Additional substitution in the triazolopyridine core disturbed the binding to phosphatidylinositol 4-kinase, catalytic β (PIK4CB). We also introduced less lipophilic head heterocycles devoid of covalent binding (CVB) liability. After these changes, further modifications to the trifluoroethoxy bioisosteric replacement allowed rebalancing of properties, such as lipophilicity, and also potency. Our optimization strategy culminated with <i>in vivo</i> active RO7101556 (<b>18B</b>) having excellent properties and being selected as an advanced candidate.
Immunogenicity and Protective Efficacy of a Live Attenuated H5N1 Vaccine in Nonhuman Primates (2009)

The continued spread of highly pathogenic H5N1 influenza viruses among poultry and wild birds, together with the emergence of drug-resistant variants and the possibility of human-to-human transmission, has spurred attempts to develop an effective vaccine. Inactivated subvirion or whole-virion H5N1 vaccines have shown promising immunogenicity in clinical trials, but their ability to elicit protective immunity in unprimed human populations remains unknown. A cold-adapted, live attenuated vaccine with the hemagglutinin (HA) and neuraminidase (NA) genes of an H5N1 virus A/VN/1203/2004 (clade 1) was protective against the pulmonary replication of homologous and heterologous wild-type H5N1 viruses in mice and ferrets. In this study, we used reverse genetics to produce a cold-adapted, live attenuated H5N1 vaccine (AH/AAca) that contains HA and NA genes from a recent H5N1 isolate, A/Anhui/2/05 virus (AH/05) (clade 2.3), and the backbone of the cold-adapted influenza H2N2 A/AnnArbor/6/60 virus (AAca). AH/AAca was attenuated in chickens, mice, and monkeys, and it induced robust neutralizing antibody responses as well as HA-specific CD4+ T cell immune responses in rhesus macaques immunized twice intranasally. Importantly, the vaccinated macaques were fully protected from challenge with either the homologous AH/05 virus or a heterologous H5N1 virus, A/bar-headed goose/Qinghai/3/05 (BHG/05; clade 2.2). These results demonstrate for the first time that a cold-adapted H5N1 vaccine can elicit protective immunity against highly pathogenic H5N1 virus infection in a nonhuman primate model and provide a compelling argument for further testing of double immunization with live attenuated H5N1 vaccines in human trials.
Utilizing Radar Measured Velocity Fields to Forecast Turbine Wind Speeds (2015)

U.S. Department of Energy
Laser spectroscopy methods in the development of laser sensor elements for underwater robotics (2017)

Laser technologies that are used for the development of sensor elements for Remotely Operated Vehicles (ROVs) are presented, as well as the latest developments in underwater robotics where laser spectroscopy methods are applied to environmental monitoring. A submersible laser spectrometer unit intended for studying Raman scattering and laser-induced fluorescence (LIF) spectra is presented. The spectrometer was developed as an element of an ROV sensor system for remote detection and measurements of organic matter concentrations in sea water and underwater objects. The results of environmental tests of the submersible LIF spectrometer in various marine areas, including the Arctic, are described.
A split, conditionally active mimetic of IL-2 reduces the toxicity of systemic cytokine therapy (2022)

The therapeutic potential of recombinant cytokines has been limited by the severe side effects of systemic administration. We describe a strategy to reduce the dose-limiting toxicities of monomeric cytokines by designing two components that require colocalization for activity and that can be independently targeted to restrict activity to cells expressing two surface markers. We demonstrate the approach with a previously designed mimetic of cytokines interleukin-2 and interleukin-15-Neoleukin-2/15 (Neo-2/15)-both for trans-activating immune cells surrounding targeted tumor cells and for cis-activating directly targeted immune cells. In trans-activation mode, tumor antigen targeting of the two components enhanced antitumor activity and attenuated toxicity compared with systemic treatment in syngeneic mouse melanoma models. In cis-activation mode, immune cell targeting of the two components selectively expanded CD8<sup>+</sup> T cells in a syngeneic mouse melanoma model and promoted chimeric antigen receptor T cell activation in a lymphoma xenograft model, enhancing antitumor efficacy in both cases.
Rolic<sup>®</sup> LCMO Photo Alignment Technology: Mechanism and Application to Large LCD Panels (2011)

Rolic® Light Controlled Molecular Orientation (LCMO) technology is the basis for todays advanced mass production technologies for large LCD-TV panel, high-resolution 3D patterned-retarders and high-resolution optical security devices. This fundamental technology allows an easy achievement of high resolution azimuthal LC-director patterns with defined bias angles, from homogeneous planar to homeotropic orientation, depending on the target application [1-7]. In addition to the control of bias angles, LCD panel manufacturers require alignment layers with a wide range of optimized properties. Thin alignment films must be easily coatable and should have high photosensitivity in order to achieve fast processing. The photoalignment film should also have high stability and good electrical properties such as Voltage Holding Ratio (VHR), Residual DC (RDC) and image sticking. Because of in-situ photo crosslinking during processing [1, 2], our proprietary LCMO photoalignment technology is shown to be thermally and optically stable. Last years, enormous progress has been made in the development of advanced materials that meet all requirements for mass production of large-area flat panel displays. LCMO-VA technology, for vertical alignment LCDs, is the basis for the state of the art UV 2 A production technology recently used in the manufacturing of advanced new generation LCD-TV panel displays with reduced production costs and low energy consumption [8, 9]. LCMO-VA mechanism and performances of state of the art materials will be discussed.