gebhart/patrepeval huggingface dataset:
Parallel Stranded DNA (1988)

A series of four hairpin deoxyoligonucleotides was synthesized with a four-nucleotide central loop (either C or G) flanked by the complementary sequences d(T)10 and d(A)10. Two of the molecules contain either a 3'-p-3' or 5'-p-5' linkage in the loop, so that the strands in the stem have the same, that is, parallel (ps) polarity. The pair of reference oligonucleotides have normal phosphodiester linkages throughout and antiparallel (aps) stem regions. All the molecules adopt a duplex helical structure in that (i) the electrophoretic mobilities in polyacrylamide gels of the ps and aps oligomers are similar. (ii) The ps hairpins are substrates for T4 polynucleotide kinase, T4 DNA ligase, and Escherichia coli exonuclease III. (iii) Salt-dependent thermal transitions are observed for all hairpins, but the ps molecules denature 10 degrees C lower than the corresponding aps oligomers. (iv) The ultraviolet absorption and circular dichroism spectra are indicative of a base-paired duplex in the stems of the ps hairpins but differ systematically from those of the aps counterparts. (v) The bis-benzimidazole drug Hoechst-33258, which binds in the minor groove of B-DNA, exhibits very little fluorescence in the presence of the ps hairpins but a normal, enhanced emission with the aps oligonucleotides. In contrast, the intercalator ethidium bromide forms a strongly fluorescent complex with all hairpins, the intensity of which is even higher for the ps species. (vi) The pattern of chemical methylation is the same for both the ps and aps hairpins. The combined results are consistent with the prediction from force field analysis of a parallel stranded right-handed helical form of d(A)n.d(T)n with a secondary structure involving reverse Watson-Crick base pairs and a stability not significantly different from that of the B-DNA double helix. Models of the various hairpins optimized with force field calculations are described.
Deposition of molybdenum thin films by an alternate supply of MoCl5 and Zn (1998)

Molybdenum thin films were deposited onto both soda lime glass and Al2O3 film by an alternate supply of MoCl5 and Zn. Zinc was used as a reducing agent. The film growth was performed over a temperature range of 400–500 °C in order to study the temperature effect on the growth. In addition to the growth temperature, the purge length after zinc was also seen to have a considerable effect on the growth. The films were analyzed by energy dispersive x-ray spectroscopy, scanning electron microscopy, elastic recoil detection analysis, x-ray diffraction and four point resistance measurements in order to determine their chemical and physical characteristics.
Rapid Identification of Staphylococcus aureus by Using Fluorescent Staphylocoagulase Assays (1999)

Two rapid (1-h) assays for the detection of Staphylococcus aureus staphylocoagulase were developed by using the fluorogenic thrombin substrates N-t-boc-Val-Pro-Arg-7-amido-4-methylcoumarin (VPA) and N-t-boc-beta-benzyl-Asp-Pro-Arg-7-amido-4-methylocoumarin (BB). The assays were compared to the tube coagulase test and latex agglutination (LA) (Sanofi Diagnostics Pasteur, Guildford, Surrey, United Kingdom) by using 406 clinical isolates of staphylococci, and they produced positive and negative predictive values of 99.2 and 99. 1% for LA, 98.9 and 92.7% for VPA, and 98.9 and 99.1% for BB. Fluorescent assays used colonies from solid media, thereby eliminating the need for broth cultures, and were performed in microtiter trays, thus making them suitable for large-scale screening.
A specific inhibitor for tyrosine protein kinase from Pseudomonas. (1986)

An effective antitumor substance is one of the most exciting targets for researchers in the chemotherapeutic field.
Ecient and Flexible Search Using Text and Metadata CSIRO Mathematical and Information Sciences Technical Report 2000/83 (2000)

Digital libraries and intranets often include a wide mix of document types, ranging from catalog entries consisting entirely of metadata, to documents with both substantial text content and thorough metadata tagging, to documents with hardly any metadata at all. This paper describes a retrieval model for use in such environments which can accommodate searches in a variety of metadata schemata. It uses both content search and three-valued satisfaction of metadata constraints (yes, no and maybe). In this model queries may include explicit metadata constraints as well as free text terms. The latter may impose additional implicit constraints as well as contributing to content relevance scores. Result lists are presented in tiers, in which the top tier corresponds to full satisfaction of all constraints and subsequent tiers are derived by progressive relaxation of constraints. An ecient and scalable implementation of the model has been developed and has been in production use on the Australian National University intranet since July 1999. Details of the implementation are given and performance results are presented.
Double-stranded RNA-dependent protein kinase and 2-5A system are both activated in interferon-treated, encephalomyocarditis virus-infected HeLa cells (1985)

Activation of the interferon-inducible, double-stranded RNA-dependent protein kinase was monitored in monolayer cultures of control and interferon-treated HeLa cells infected with encephalomyocarditis virus. The extent of phosphorylation in the intact cell of the alpha-subunit of eucaryotic protein synthesis initiation factor eIF2 by the kinase was determined for the first time in this type of system, using a two-dimensional immunoblot technique. Virus protein synthesis and the kinetics of activation of the ppp(A2'p)nA (n greater than or equal to 2) system were analyzed in parallel. Enhanced phosphorylation of eIF2-alpha was obvious at 9 h and increased by 12 h postinfection. ppp(A2'p)nA and ppp(A2'p)nA-mediated rRNA cleavage were observed from 6 h. No viral protein synthesis was detected in cells in which a general inhibition of protein synthesis developed with time. It can be concluded that both the kinase and ppp(A2'p)nA system are active in interferon-treated, encephalomyocarditis virus-infected HeLa cells.
Clinical comparison of Omafilcon A with four control materials. (1997)

We hypothesize that the reduced spoliation seen with the Omafilcon A lens relates to the biomimetic nature of the material which incorporates phosphorylcholine.
Repair of 20‐mm long rabbit radial bone defects using BMP‐derived peptide combined with an α‐tricalcium phosphate scaffold (2006)

In previous studies, we have reported that the BMP-2-derived peptide KIPKASSVPTELSAISTLYL, corresponding to BMP-2 residues 73-92, binds to a BMP-2-specific receptor, and elevates both alkaline phosphatase activity and osteocalcin mRNA in the murine mesenchymal cell line, C3H10T1/2. This 73-92 peptide conjugated to a covalently crosslinked alginate gel induced ectopic bone formation in rat calf muscle, and activated osteoblasts to promote the repair of rat tibial bone defects. Here, we report repair of 20-mm long rabbit radial bone defects using the 73-92 peptide combined with a porous alpha-tricalcium phosphate (TCP) scaffold. In vitro, the 73-92 peptide was released from the porous alpha-TCP scaffold over more than one week. In vivo, radiomorphometric analysis showed that the 73-92 peptide combined with the porous alpha-TCP scaffold promoted calcification in the implanted area in a dose-dependent manner, and that 5 mg of the 73-92 peptide induced connection of 20-mm long defects, defects of critical size, 12 weeks after implantation. Histological examination revealed newly formed bone and a marrow cavity in the implanted area. The area of bone denser than 690 mg/cm(3) induced by the 73-92 peptide was nearly equal to that of the contralateral radius.
Activation of the HIV-1 LTR by T Cell Mitogens and the Trans-Activator Protein of HTLV-I (1987)

To investigate the mechanism by which immune activation augments replication of the human immunodeficiency virus type 1 (HIV-1) in infected T cells, four different classes of T cell mitogens were evaluated for their effects on the HIV-1 long terminal repeat (LTR). Phytohemagglutinin (PHA), a mitogenic lectin; phorbol 12-myristic 13-acetate, a tumor promoter; ionomycin, a calcium ionophore; and tat-1, the trans-activator protein from the human T cell leukemia/lymphoma virus type I (HTLV-I) each stimulated the HIV-1 LTR. Studies of deleted forms of the LTR supported a central role in these responses for the HIV-1 enhancer, which alone was sufficient for mitogen inducibility, but also suggested that other 5' positive and negative regulatory elements contribute to the overall magnitude of the response. Synergistic activation of the HIV-1 LTR (up to several thousandfold) was observed with combinations of these mitogens and the HIV-1--derived tat-III protein. Cyclosporin A, an immunosuppressive agent, inhibited PHA-mediated activation of the HIV-1 LTR but was without effect in the presence of other mitogens. Thus, HIV-1 gene expression and replication appear to be regulated, via the HIV-1 LTR, by the same mitogenic signals that induce T cell activation.
Bacterial-Reactive T Regulatory Cells Inhibit Pathogenic Immune Responses to the Enteric Flora (2002)

We showed previously that cecal bacterial Ag (CBA)-specific CD4(+) T cells induce colitis when transferred into SCID mice. The purpose of this study was to generate and characterize CBA-specific regulatory T cells in C3H/HeJBir (Bir) mice. CD4(+) T cells were stimulated with CBA-pulsed APC in the presence of IL-10 every 10-14 days. After four or more cycles, these T cells produced high levels of IL-10, low levels of IL-4 and IFN-gamma, and no IL-2, consistent with the phenotype of T regulatory-1 (Tr1) cells. Bir Tr1 cells proliferated poorly, but their proliferation was dependent on CD28-B7 interactions and was MHC class II-restricted. Transfer of Bir Tr1 cells into SCID mice did not result in colitis, and cotransfer of Bir Tr1 T cells with pathogenic Bir CD4(+) Th1 cells prevented colitis. Bir Tr1 cells inhibited proliferation and IFN-gamma production of a CBA-specific Th1 cell line in vitro. Such inhibition was partly due to IL-10 and TGFbeta1, but cognate interactions with either APCs or Th1 cells were also involved. Normal intestinal lamina propria CD4(+) T cells had Tr1-like activity when stimulated with CBA-pulsed APCs. We conclude that CD4(+) T cells with the properties of Tr1 cells are present in the intestinal lamina propria and hypothesize that these cells maintain intestinal immune homeostasis to the enteric flora.
Four-Dimensional Modulation and Stokes Direct Detection of Polarization Division Multiplexed Intensities, Inter Polarization Phase and Inter Polarization Differential Phase (2016)

We propose and experimentally demonstrate modulation and Stokes space direct-detection (DD) of four orthogonal dimensions or degrees of freedom (DOF) of a single laser being the intensity on two orthogonal polarizations, the inter-polarization phase and the inter-polarization differential phase. At the transmitter, a dual-polarization in-phase quadrature-phase (DP-IQ) modulator driven by a 4-channel digital-to-analog converter is employed to imprint the transmitted data onto the aforementioned four DOF. Transmitted symbols for each polarization are drawn from multi-ring/multi-phase constellations, e.g., 2-ring/4-ary phase shift keying (PSK) or 2-ring/8PSK, resulting in a polarization division multiplexed (PDM) format with intensity, inter-polarization phase, and inter-polarization differential phase modulation (PDM-IM-IPM-IDPM). At the receiver, a novel DD front-end 1 1 A direct-detection front-end refers to a family of receivers that employ a self-beating mechanism in which the received signal beats with itself or its polarization tributaries beat with themselves. Unlike a coherent front-end, a direct-detection front-end does not incorporate a local oscillator (LO) laser.
Three-dimensional photoresist image simulation on flat surfaces (1985)

A simulation procedure for three-dimensional (3-D) photoresist images on flat substrates is developed. The procedure consists of three parts, i.e., two-dimensional (2-D) distribution of projected light intensity, 3-D photosensitizer concentration distribution, and 3-D photoresist development. For the former two simulations, conventional procedures have been employed. The last development simulation is carried out by extending the ray tracing model to three dimensions. A successful result is obtained for the resist system with a weak standing-wave effect.
Measurement of clay surface areas by polyvinylpyrrolidone (PVP) sorption and its use for quantifying illite and smectite abundance (2004)

Abstract A new method has been developed for quantifying smectite abundance by sorbing polyvinylpyrrolidone (PVP) on smectite particles dispersed in aqueous solution. The sorption density of PVP-55K on a wide range of smectites, illites and kaolinites is ∼0.99 mg/m 2 , which corresponds to ∼0.72 g of PVP-55K per gram of montmorillonite. Polyvinylpyrrolidone sorption on smectites is independent of layer charge and solution pH. PVP sorption on SiO 2 , Fe 2 O 3 and ZnO normalized to the BET surface area is similar to the sorption densities on smectites. γ-Al 2 O 3 , amorphous Al(OH) 3 and gibbsite have no PVP sorption over a wide range of pH, and sorption of PVP by organics is minimal. The insensitivity of PVP sorption densities to mineral layer charge, solution pH and mineral surface charge indicates that PVP sorption is not localized at charged sites, but is controlled by more broadly distributed sorption mechanisms such as Van der Waals’ interactions and/or hydrogen bonding. Smectites have very large surface areas when dispersed as single unit-cell-thick particles (∼725 m 2 /g) and usually dominate the total surface areas of natural samples in which smectites are present. In this case, smectite abundance is directly proportional to PVP sorption. In some cases, however, the accurate quantification of smectite abundance by PVP sorption may require minor corrections for PVP uptake by other phases, principally illite and kaolinite. Quantitative XRD can be combined with PVP uptake measurements to uniquely determine the smectite concentration in such samples.
Learning a Deep Compact Image Representation for Visual Tracking (2013)

In this paper, we study the challenging problem of tracking the trajectory of a moving object in a video with possibly very complex background. In contrast to most existing trackers which only learn the appearance of the tracked object on-line, we take a different approach, inspired by recent advances in deep learning architectures, by putting more emphasis on the (unsupervised) feature learning problem. Specifically, by using auxiliary natural images, we train a stacked de-noising autoencoder offline to learn generic image features that are more robust against variations. This is then followed by knowledge transfer from offline train-ing to the online tracking process. Online tracking involves a classification neural network which is constructed from the encoder part of the trained autoencoder as a feature extractor and an additional classification layer. Both the feature extrac-tor and the classifier can be further tuned to adapt to appearance changes of the moving object. Comparison with the state-of-the-art trackers on some challenging benchmark video sequences shows that our deep learning tracker is more accurate while maintaining low computational cost with real-time performance when our MATLAB implementation of the tracker is used with a modest graphics process-ing unit (GPU). 1
In Situ identification of mineral resources with an X-ray-optical "Hand-Lens" instrument (1997)

The recognition of material resources on a planetary surface requires exploration strategies not dissimilar to those employed by early field geologists who searched for ore deposits primarily from surface clues. In order to determine the location of mineral ores or other materials, it will be necessary to characterize host terranes at regional or subregional scales. This requires geographically broad surveys in which statistically significant numbers of samples are rapidly scanned from a roving platform. To enable broad-scale, yet power-conservative planetary-surface exploration, we are developing an instrument that combines x-ray diffractometry (XRD), x-ray fluorescence spectrometry (XRF), and optical capabilities; the instrument can be deployed at the end of a rover's robotic arm, without the need for sample capture or preparation. The instrument provides XRD data for identification of mineral species and lithological types; diffractometry of minerals is conducted by ascertaining the characteristic lattice parameters or d-spacings of mineral compounds. D-spacings of 1.4 to 25 angstroms can be determined to include the large molecular structures of hydrated minerals such as clays. The XRF data will identify elements ranging from carbon (Atomic Number = 6) to elements as heavy as barium (Atomic Number = 56).
Mosaicplasty: long-term follow-up. (2005)

The successful treatment of chondral and osteochondral defects of the weightbearing surfaces is a challenge for orthopaedic surgeons. Autologous osteochondral transplantation is one method that can be used to create a hyaline or hyaline-like repair in the defect area. Ten years of clinical experience with autologous osteochondral mosaicplasty are described. Clinical scores, imaging techniques, arthroscopy, histological examination of biopsy samples, and cartilage stiffness measurements were used to evaluate the clinical outcomes and quality of the transplanted cartilage in a total of 831 patients who underwent mosaicplasty. According to our investigations, good-to-excellent results were achieved in 92% of the patients treated with femoral condylar implantations, in 87% of those treated with tibial resurfacing, in 79% of those treated with patellar and/or trochlear mosaicplasties, and in 94% of those treated with talarprocedures. Long-term donor-site disturbances, which were assessed using the Bandi score, showed that patients had 3% morbidity after mosaicplasty. Sixty-nine of 83 patients who were followed arthroscopically showed congruent gliding surfaces, histological evidence of the survival of the transplanted hyaline cartilage, and fibrocartilage filling of the donor sites. Four deep infections and 36 painful postoperative hemarthroses were experienced as complications arising from the surgical procedures. On the basis of both these promising results and also those of other similar studies, autologous osteochondral mosaicplasty would appears to be an alternative for the treatment of small and medium-sized focal chondral and osteochondral defects of the weightbearing surfaces of the knee and other weightbearing synovial joints.
Heterointerfaces in III-V semiconductor nanowhiskers (2003)

We have investigated heterostructures formed within Vapor-Liquid-Solid grown III-V nanowhiskers. The growth conditions that are typical for chemical beam epitaxy facilitate the creation of atomically abrupt interfaces. In this paper we investigate the properties of heterostructure interfaces including switching of either the column-V material (As, P) or the column-III material (In, Ga).
PANCREATIC GENE EXPRESSION IN DIFFERENTIATING EMBRYONIC STEM CELLS. (2000)

Odorico, Jon S.1; Jacobson, Lynn M.1; Lumelsky, Nadya1; Hullett, Debra A.1; Thomson, James A.2; Kahan, Brenda W.1 Author Information
Challenges in Modern Drug Discovery: A Case Study of Boceprevir, an HCV Protease Inhibitor for the Treatment of Hepatitis C Virus Infection (2008)

More than 170 million people worldwide are affected by the hepatitis C virus (HCV). The disease has been described as a "silent epidemic" and "a serious global health crisis". HCV infection is a leading cause of chronic liver disease such as cirrhosis, carcinoma, or liver failure. The current pegylated interferon and ribavirin combination therapy is effective in only 50% of patients. Its moderate efficacy and apparent side effects underscore the need for safer and more effective treatments. The nonstructural NS3 protease of the virus plays a vital role in the replication of the HCV virus. The development of small molecule inhibitors of NS3 protease as antiviral agents has been intensively pursued as a viable strategy to eradicate HCV infection. However, it is a daunting task. The protease has a shallow and solvent-exposed substrate binding region, and the inhibitor binding energy is mainly derived from weak lipophilic and electrostatic interactions. Moreover, lack of a robust in vitro cell culture system and the absence of a convenient small animal model have hampered the assessment of both in vitro and in vivo efficacy of any antiviral compounds. Despite the tremendous challenges, with access to a recently developed cell-based replicon system, major progress has been made toward a more effective small molecule HCV drug. In our HCV program, facing no leads from our screening effort, a structure-based drug design approach was carried out. An alpha-ketoamide-type electrofile was designed to trap the serine hydroxyl of the protease. Early ketoamide inhibitors mimicked the structures of the peptide substrates. With the aid of X-ray structures, we successfully truncated the undecapeptide lead that had a molecular weight of 1265 Da stepwise to a tripeptide with a molecular weight of 500 Da. In an attempt to depeptidize the inhibitors, various strategies such as hydrazine urea replacement of amide bonds and P2 to P4 and P1 to P3 macrocyclizations were examined. Further optimization of the tripeptide inhibitors led to the identification of the best moieties for each site: primary ketoamide at P', cyclobutylalanine at P1, gem-dimethylcyclopropylproline at P2, tert-leucine at P3, and tert-butyl urea as capping agent. The combination of these led to the discovery of compound 8 (SCH 503034, boceprevir), our clinical candidate. It is a potent inhibitor in both enzyme assay (Ki* = 14 nM) and cell-based replicon assay (EC 90 = 0.35 microM). It is highly selective (2200x) against human neutrophil elastase (HNE). Boceprevir is well tolerated in humans and demonstrated antiviral activity in phase I clinical trials. It is currently in phase II trials. This Account details the complexity and challenges encountered in the drug discovery process.