gebhart/patrepeval huggingface dataset:
NRED: a database of long noncoding RNA expression (2008)

In mammals, thousands of long non-protein-coding RNAs (ncRNAs) (>200 nt) have recently been described. However, the biological significance and function of the vast majority of these transcripts remain unclear. We have constructed a public repository, the Noncoding RNA Expression Database (NRED), which provides gene expression information for thousands of long ncRNAs in human and mouse. The database contains both microarray and in situ hybridization data, much of which is described here for the first time. NRED also supplies a rich tapestry of ancillary information for featured ncRNAs, including evolutionary conservation, secondary structure evidence, genomic context links and antisense relationships. The database is available at http://jsm-research.imb.uq.edu.au/NRED, and the web interface enables both advanced searches and data downloads. Taken together, NRED should significantly advance the study and understanding of long ncRNAs, and provides a timely and valuable resource to the scientific community.
A Simple and Effective Chemical Phosphorylation Procedure for Biomolecules (1987)

Abstract A general chemical phosphorylation method based on P(III) chemistry has been developed. The system is demonstrated for the phosphorylation of oligonucleotides, directly after their synthesis on a solid support, and for the O ‐phosphorylation of serine, threonine, and tyrosine as well as for a serine‐containing peptide.
The leukocidin pore: Evidence for an octamer with four LukF subunits and four LukS subunits alternating around a central axis (2005)

The staphylococcal alpha-hemolysin (alphaHL) and leukocidin (Luk) polypeptides are members of a family of related beta-barrel pore-forming toxins. Upon binding to susceptible cells, alphaHL forms water-filled homoheptameric transmembrane pores. By contrast, Luk pores are formed by two classes of subunit, F and S, rendering a heptameric structure displeasing on symmetry grounds at least. Both the subunit stoichiometry and arrangement within the Luk pore have been contentious issues. Here we use chemical and genetic approaches to show that (1) the predominant, or perhaps the only, form of the Luk pore is an octamer; (2) the subunit stoichiometry is 1:1; and (3) the subunits are arranged in an alternating fashion about a central axis of symmetry, at least when a fused LukS-LukF construct is used. The experimental approaches we have used also open up new avenues for engineering the arrangement of the subunits of beta-barrel pore-forming toxins.
Generalized wavelet product integral for rendering dynamic glossy objects (2006)

We consider real-time rendering of dynamic glossy objects with realistic shadows under distant all-frequency environment lighting. Previous PRT approaches pre-compute light transport for a fixed scene and cannot account for cast shadows on high-glossy objects occluded by dynamic neighbors. In this paper, we extend double/triple product integral to generalized multi-function product integral . We represent shading integral at each vertex as the product integral of multiple functions, involving the lighting, BRDF, local visibility and dynamic occlusions. Our main contribution is a new mathematical representation and analysis of multi-function product integral in the wavelet domain. We show that multi-function product integral in the primal corresponds to the summation of the product of basis coefficients and integral coefficients. We propose a novel generalized Haar integral coefficient theorem to evaluate arbitrary Haar integral coefficients. We present an efficient sub-linear algorithm to render dynamic glossy objects under time-variant all-frequency lighting and arbitrary view conditions in a few seconds on a commodity CPU, orders of magnitude faster than previous techniques. To further accelerate shadow computation, we propose a Just-in-time Radiance Transfer (JRT) technique. JRT is a new generalization to PRT for dynamic scenes. It is compact and flexible, and supports glossy materials. By pre-computing radiance transfer vectors at runtime, we demonstrate rendering dynamic view-dependent all-frequency shadows in real-time.
Evaluation of novel sorbent systems for joint hemodialysis and hemoperfusion. (1977)

Hemodialysis is not very effective at removing middle molecular weight species and certain drugs such as salicylates and barbiturates. Carbon hemoperfusion is ineffective in removing urea and water, even when coated microparticles can be generated. To use the advantages of hemodialysis and carbon hemoperfusion without their disadvantages, cuprophan tubular membranes and fibers containing activated carbon have been manufactured. A device called the Hemocarbodialyser, consisting of a sorbent and dialyzing carbon membrane wound onto a coli dialyzer, has been evaluated by the authors. From preliminary results, the Hemocarbodialyser has been shown to be efficient at removing vitamin B12, has high ultrafiltration, and has high dialysance of creatinine and uric acid. The use of activated carbon and aluminum oxide fibers was also evaluated, indicating that fibers containing sorbents, as well as the Hemocarbodialyser, may have clinical importance in the near future, when joint hemodialysis and hemoperfusion is required in hepatic failure, uremia, and acute poisoning.
Insulated gold scanning tunneling microscopy probes for recognition tunneling in an aqueous environment (2012)

Chemically functionalized probes are required for tunneling measurements made via chemical contacts ("Recognition Tunneling"). Here, we describe the etching of gold STM probes suitable for chemical functionalization with moieties bearing thiol groups. Insulated with high density polyethylene, these probes may be used in aqueous electrolytes with sub pA leakage currents. The area of the exposed probe surface was characterized via the saturation current in an electroactive solution (0.1 M K(3)Fe(CN)(6)). Twenty five percent of the probes had an exposed region of 10 nm radius or less.
Construction and immunogenicity in a prime–boost regimen of a Semliki Forest virus-vectored experimental HIV clade A vaccine (2003)

A novel, experimental subunit human immunodeficiency virus (HIV) vaccine, SFV.HIVA, was constructed. This consists of Semliki Forest virus (SFV), which is a suitable vaccine vector for use in humans, and a passenger gene encoding HIVA, which is an immunogen derived from HIV-1 clade A that is being currently tested in clinical trials of combined DNA- and modified vaccinia virus Ankara (MVA)-vectored vaccines in Oxford (UK) and Nairobi (Kenya). In the mouse, the SFV.HIVA vaccine was highly immunogenic for T cell-mediated immune responses and induced T cell memory that lasted for at least 6 months. SFV.HIVA was also compared to the vaccines currently used in the clinical trials and was shown to be as effective in T cell induction as pTHr.HIVA DNA but less immunogenic than MVA.HIVA. When tested in a prime-boost regimen, SFV.HIVA-induced responses could be boosted by MVA.HIVA. This work is a part of a long-term effort to build a panel of subunit vaccines expressing a common immunogen, which will allow both a direct comparison of various vaccine vectors and combined vaccination regimens in humans and provide more flexibility and/or a potential optimization of vaccinations for individuals based on their pre-existing anti-vector immunity.
The msp1 beta multigene family of Anaplasma marginale: nucleotide sequence analysis of an expressed copy (1991)

A gene for the beta subunit of the immunoprotective surface antigen MSP-1 of Anaplasma marginale was previously cloned and expressed in Escherichia coli. A nucleic acid probe based on this gene detects A. marginale infection in carrier cattle and in the tick vector. We report here the sequence and structural features of the cloned msp1 beta gene and expressed polypeptide. The gene codes for a polypeptide of 756 amino acids that contains domains of tandemly repeated sequence and glutamine-rich regions at the N and C termini. The cloned copy is a member of a multigene family with multiple restriction fragment length polymorphisms in isolates of this rickettsia from different geographical regions. The availability of the sequence will allow use of the polymerase chain reaction in diagnostic assays and the preparation and testing of different vaccine constructs in cattle.
Cloning, Expression in Yeast, and Functional Characterization of CYP81B1, a Plant Cytochrome P450 That Catalyzes In-chain Hydroxylation of Fatty Acids (1998)

Several omega and in-chain fatty acid hydroxylases have been characterized in higher plants. In microsomes from Helianthus tuberosus tuber the omega-2, omega-3, and omega-4 hydroxylation of lauric acid is catalyzed by one or a few closely related aminopyrine- and MnCl2-inducible cytochrome P450(s). To isolate the cDNA and determine the sequences of the(se) enzyme(s), we used antibodies directed against a P450-enriched fraction purified from Mn2+-induced tissues. Screening of a cDNA expression library from aminopyrine-treated tubers led to the identification of a cDNA (CYP81B1) corresponding to a transcript induced by aminopyrine. CYP81B1 was expressed in yeast. A systematic exploration of its function revealed that it specifically catalyzes the hydroxylation of medium chain saturated fatty acids, capric (C10:0), lauric (C12:0), and myristic (C14:0) acids. The same metabolites were obtained with transgenic yeast and plant microsomes, a mixture of omega-1 to omega-5 monohydroxylated products. The three fatty acids were metabolized with high and similar efficiencies, the major position of attack depending on chain length. When lauric acid was the substrate, turnover was 30.7 +/- 1.4 min-1 and Km(app) 788 +/- 400 nM. No metabolism of long chain fatty acids, aromatic molecules, or herbicides was detected. This new fatty acid hydroxylase is typical from higher plants and differs from those already isolated from other living organisms.
Measurement of free form of insulin-like growth factor I in human plasma. (1991)

A method to measure free form of insulin-like growth factor I (IGF-I) in human plasma using octadecylsilyl silica (Sep-Pak C18) cartridge has been developed. IGF-I was adsorbed by Sep-Pak C18 cartridge and eluted with 75% ethanol--0.01 M HCl. Labeled and non-labeled IGF-I were recovered in yields 92.5 +/- 2.1% (Mean +/- SEM) and 94.4 +/- 6.3% after adsorption to and elution from the Sep-Pak, respectively. When EDTA plasma was applied to the Sep-Pak, less than 5% of total IGF-I was recovered in the eluate. However, when acid-ethanol extracted plasma was applied to the Sep-Pak, IGF-I was recovered in yields greater than 75% of total IGF-I. When the Sep-Pak eluate was gel filtered, 88.4 +/- 4.0% of immunoreactive IGF-I eluted in the same fraction as synthetic IGF-I did, but the fraction passed through the Sep-Pak was observed as a high molecular weight form (bound form) of IGF-I. These data indicate that this Sep-Pak method does not extract all of the IGF-I in plasma, but extracts mainly the free form IGF-I. Using this method, IGF-I values of free form (fIGF-I) in EDTA plasma were measured. The fIGF-I values in normal adults, patients with acromegaly, and patients with growth hormone (GH)-deficiency were 2.4 +/- 0.1, 13.8 +/- 1.6, and 1.1 +/- 0.1 ng/ml, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)
Finding the visibility graph of a simple polygon in time proportional to its size (1987)

Let P be a given simple polygon with n sides. The visibility graph of P has an edge between every pair of polygon vertices that can be connected by an open segment in the interior of P. We describe an algorithm that finds the visibility graph of P in O(m + n log log n) time, where m is the number of edges in the visibility graph. Because m can be as small as O(n), the algorithm improves on the more general visibility algorithms of Asano et al. [AAGHI] and Welzl [W], which take T(n2) time.
PHOTOSENSITIZATION BY SYNTHETIC DIPORPHYRINS AND DICHLORINS in vivo AND in vitro (1991)

A group of polycarboxylic diporphyrins, two dichlorins and a porphyrin-chlorine dimer, with rings linked by methylene groups, were examined to help identify structures which can mediate photodynamic tumor eradication in vivo. Among the features sought were short persistence of normal tissue photosensitization and substantial absorbance at wavelengths longer than 630 nm. Both objectives were achieved, with pertinent structure-activity relationships partly characterized. The relative hydrophobicity of the different sensitizers was an important determinant of their accumulation in cell culture, but not of in vivo effectiveness. These compounds showed affinity for protein and high-density lipoprotein components of serum. Their distribution may be mediated by a different mechanism than that which occurs with more hydrophobic sensitizers like hematoporphyrin derivative which have greater affinity for low-density lipoproteins and less for protein components of serum, as compared with the products examined in this study.
Strategies for Covalent Multilayer Growth. 1. Polymer Design and Characterization (2002)

We describe the synthesis and characterization of several maleimide−vinyl ether and maleimide−primary alkene alternating copolymers capable of being incorporated into covalently bound multilayer assemblies. Synthetic control over the monomer substituents allows substantial versatility in the choice of layer formation chemistry and in polymer properties. We report on the copolymerization of substituted allyl-, allyloxy-, vinyl-, and vinyloxy- monomers with a variety of N-substituted maleimides. The substituted maleimides were prepared by reaction of maleic anhydride with selected aromatic amines. Polymerization yields are typically in the range of 75−95% consumption of the monomers. 1H NMR, FTIR, and UV−visible spectroscopies were used to characterize the polymers.
Reversing insect adaptation to transgenic insecticidal plants (2001)

The refuge-high-dose strategy for delaying insect adaptation to transgenic plants produces non-transgenic plants that enable survival of susceptible individuals. Previous theoretical work has suggested three requirements for success of the refuge-high-dose strategy: a low initial frequency of the resistance allele, extensive mating between resistant and susceptible adults and recessive inheritance of resistance. In order to understand an observed decrease in resistance frequency and improve the potential for managing resistance better, we used analytical and simulation models for exploring the conditions that prevent or reverse the evolution of resistance, even when resistance is not rare initially. Assuming random mating and recessive or nearly recessive inheritance of resistance, the factors favouring reversal of resistance are non-recessive costs of resistance, low initial resistance allele frequency, large refuges, incomplete resistance and density-independent population growth in refuges.
A System for the Enhancement of Adenovirus Mediated Gene Transfer to Uro-Epithelium (2002)

Primary urothelial cells and bladder carcinoma cells can be efficiently transfected using an adenoviral vector with similar infectivity. In vitro viral infection shows that the efficiency of adenoviral transfection is significantly reduced in the presence of pentosan polysulfate, a GAG analog. Adenoviral mediated gene transfer to bladder urothelium is enhanced by HCl pretreatment.
Transplantation of Chondrocytes Utilizing a Polymer-Cell Construct to Produce Tissue-Engineered Cartilage in the Shape of a Human Ear (1997)

This study evaluates the feasibility of growing tissue-engineered cartilage in the shape of a human ear using chondrocytes seeded onto a synthetic biodegradable polymer fashioned in the shape of a 3-year-old child's auricle. A polymer template was formed in the shape of a human auricle using a nonwoven mesh of polyglycolic acid molded after being immersed in a 1% solution of polylactic acid. Each polyglycolic acid-polylactic acid template was seeded with chondrocytes isolated from bovine articular cartilage and then implanted into subcutaneous pockets on the dorsa of 10 athymic mice. The three-dimensional structure was well maintained after removal of an external stent that had been applied for 4 weeks. Specimens harvested 12 weeks after implantation and subjected to gross morphologic and histologic analysis demonstrated new cartilage formation. The overall geometry of the experimental specimens closely resembled the complex structure of the child's auricle. These findings demonstrate that polyglycolic acid-polylactic acid constructs can be fabricated in a very intricate configuration and seeded with chondrocytes to generate new cartilage that would be useful in plastic and reconstructive surgery.
The immunodeficiency of chronic lymphocytic leukaemia (2008)

There has been little done to develop better vaccination strategies in patients with CLL, and although effective antimicrobials have been developed to protect against opportunistic infections, many are both expensive and inconvenient. More work is necessary to define precisely which patients should be offered them and when.
CD5-mediated specific delivery of DNA to T lymphocytes: compartmentalization augmented by adenovirus (1995)

Specific DNA delivery has been achieved via interactions between an asialoorosomucoid-polylysine conjugate and the asialoglycoprotein receptor. We have now extended this technology to another cell type. In order to achieve DNA delivery uniquely to T cells, we have employed an antibody-polylysine conjugate which binds and is internalized via CD5. Binding analyses of the T101 monoclonal antibody to Jurkat cells and freshly isolated human peripheral T lymphocytes were performed and Scatchard plots revealed Kd values of 1.4 and 1.2 pM, respectively. To introduce DNA into the T cell, a complex of T101-polylysine and the luciferase plasmid was formed (T101-PL-DNA). 125I-labeled antibody alone or T101-PL-DNA complexes were both shown to internalize. Subcellular fractionation indicated that the complex remained in the endosomal compartment of the cell for up to 90 min. However, with the addition of adenovirus particles, there was a decrease of labeled complex in the endosomal fraction over time suggesting it was no longer 'tethered' to the endosome vesicle. In vitro transfections confirmed this result showing the addition of adenovirus particles during incubation resulted in increased expression of the luciferase protein. Without adenovirus, there was limited expression of the transduced gene. These data revealed that T101 can deliver DNA via an antibody-PL conjugate. The addition of adenovirus allowed the DNA to escape the endosome enabling expression of the reporter gene.
Isolation of a Protein Complex Containing Translation Initiation Factor Prt1 from Saccharomyces cerevisiae (1995)

Translation initiation factor Prt1 was purified from a ribosomal salt wash fraction of Saccharomyces cerevisiae cells by ammonium sulfate precipitation, DEAE chromatography, phosphocellulose chromatography, sucrose density gradient centrifugation, and non-denaturing polyacrylamide gel electrophoresis. Prt1 protein cofractionates with four other polypeptides during all steps of purification suggesting that it is part of a protein complex containing polypeptide subunits with apparent molecular masses of 130, 80, 75 (Prt1), 40, and 32 kDa. Deletion of the first AUG codon in the published sequence of the PRT1 gene results in the synthesis of functional Prt1 protein indicating that the actual molecular mass of the Prt1 subunit is 82.7 kDa. This is in agreement with results from primer extension experiments reported earlier by Keierleber et al. (Keierleber, C., Wittekind, M., Qin, S., and McLaughlin, C. S. (1986) Mol. Cell. Biol. 6, 4419-4424). The Prt1-containing protein complex is an active translation factor as shown by its ability to restore translation in a cell-free system derived from a temperature-sensitive prt1 mutant strain in which endogenous Prt1 activity is inactivated by heating the extract to 37 degrees C. The question of whether the Prt1-containing protein complex represents the yeast homologue of mammalian translation initiation factor eIF-3 is discussed.
Thin-film piezoelectric-on-substrate resonators and narrowband filters (2008)

A new class of micromachined devices called thin-film piezoelectric-on-substrate (TPoS) resonators is introduced, and the performance of these devices in RF and sensor applications is studied. TPoS resonators benefit from high electromechanical coupling of piezoelectric transduction mechanism and superior acoustic properties of a substrate such as single crystal silicon. Therefore, the motional impedance of these resonators are significantly smaller compared to typical capacitively-transduced counterparts while they exhibit relatively high quality factor and power handling and can be operated in air. The combination of all these features suggests TPoS resonators as a viable alternative for current acoustic devices.&#13;\nIn this thesis, design and fabrication methods to realize dispersed-frequency lateral-extensional TPoS resonators are discussed. TPoS devices are fabricated on both silicon-on-insulator and thin-film nanocrystalline diamond substrates. The performance of these resonators in simple and low-power oscillators is measured and compared. Furthermore, a unique coupling technique for implementation of high frequency filters is introduced in which dual resonance modes of a single resonant structure are coupled. The measured results of this work show that these filters are suitable candidates for single-chip implementation of multiple-frequency narrow-band filters with high out-of-band rejection in a small footprint.
A new approach to imidazole derivatives (1991)

Cycloadditions reactions of mesoionic 1,3-oxazolium-5-olates with N-(phenylmethylene) benzenesulphonamides give substituted imidazoles via elimination of carbon dioxide and benzenesulphinic acid; structural assignments were confirmed by 2D NOESY experiments
The Regulated Expression of Epstein--Barr Virus. III. Proteins Specified by EBV During the Lytic Cycle (1981)

The experiments show that 30 virus-induced or virus-specified proteins were synthesized in Raji cells after superinfection with Epstein-Barr virus (EBV) derived from P3HR1 cells. Using a combination of pulse labelling, application of cycloheximide blocks at different times post-infection, treatment with amino acid analogues and inhibition of DNA synthesis it was shown that three groups of proteins appear in Raji cells after superinfection; the synthesis of the proteins in any one group appears to be coordinately regulated. Amongst the six virus-induced proteins which were synthesized immediately after release from an early cycloheximide block one would expect to find those proteins essential for the transition from EBNA to EA synthesis. Using human sera with differing specificities for the various antigen groups 11 proteins were identified as being specifically precipitated by sera having high titres against the EBV-induced early antigen complex.