gebhart/patrepeval huggingface dataset:
Enzyme-Linked Small-Molecule Detection Using Split Aptamer Ligation (2012)

Here we report an aptamer-based analogue of the widely used sandwich enzyme-linked immunosorbent assay (ELISA). This assay utilizes the cocaine split aptamer, which is comprised of two DNA strands that only assemble in the presence of the target small molecule. One split aptamer fragment is immobilized on a microplate, then a test sample is added containing the second split aptamer fragment. If cocaine is present in the test sample, it directs assembly of the split aptamer and promotes a chemical ligation between azide and cyclooctyne functional groups appended to the termini of the split aptamer fragments. Ligation results in covalent attachment of biotin to the microplate and provides a colorimetric output upon conjugation to streptavidin-horseradish peroxidase. Using this assay, we demonstrate detection of cocaine at concentrations of 100 nM-100 μM in buffer and 1-100 μM human blood serum. The detection limit of 1 μM in serum represents an improvement of two orders of magnitude over previously reported split aptamer-based sensors and highlights the utility of covalently trapping split aptamer assembly events.
Efficient access to optical bandwidth wavelength routing on directed fiber trees, rings, and trees of rings (2002)

We address efficient access to bandwidth in WDM (wavelength division multiplexing) optical networks. We consider tree topologies, ring topologies, as well as trees of rings. These are topologies of concrete practical relevance for which undirected underlying graph models have been studied before by P. Raghavan and E. Upfal (1993). As opposed to previous studies (A. Aggarwal et al., 1993; R. Pankaj, 1992; P. Raghavan and E. Upfal, 1993), we consider directed graph models. Directedness of fiber links is dictated by physical directedness of optical amplifiers. For trees, we give a polynomial time routing algorithm that satisfies requests of maximum load L/sub max/ per fiber link using no more than 15L/sub max//8/spl les/15OPT/8 optical wavelengths. This improves a 2L/sub max/ scheme that is implicit by P. Raghavan and E. Upfal by extending their undirected methods to our directed model. Alternatively stated, for fixed W wavelength technology, we can load the network up to L,, 8W/15 rather than W/2. In engineering terms, this is a so called "6.66% increase of bandwidth" and it is considered substantial. For rings, the approximation factor is 2OPT. For trees of rings, the approximation factor is 15OPT/4. Technically, optical routing requirements give rise to novel coloring paradigms. Our algorithms involve matchings and multicolored alternating cycles, combined with detailed potential and averaging analysis.
The development of a new measure of L2 vocabulary knowledge (1993)

With the increasing interest on the part of both researchers and language teaching specialists in the study of vocabulary acquisition by L2 learners, there is a need to have suitable instruments to measure learners' knowledge of words. The purpose of this article is to report on an investigation of a new test format, which was designed to go beyond conventional vocabulary test items - that simply allow for a yes/no judgement on whether a word is known - by providing a practical way of assessing the quality of word knowledge, that is, how well particular words are known.
Microstructure and optical properties of free-standing porous silicon films: Size dependence of absorption spectra in Si nanometer-sized crystallites (1993)

We have studied the microstructure and optical properties of free-standing porous Si thin films fabricated by electrochemical anodization. Raman-spectroscopy and transmission-electron-microscopy examinations show that Si crystallite spheres with diameters of several nanometers are dispersed in the amorphous phase. The blueshift of the optical-absorption spectrum is observed for decreasing average diameter of the Si crystallites. However, there is no clear size dependence of the peak energy of the broad photoluminescence (PL) spectrum. Spectroscopic analysis strongly suggests that the photogeneration of carriers occurs in the c-Si core, whose band gap is modified by the quantum-confinement effect, while the strong PL comes from the near-surface region of small crystallites.
Construction of a mobilizable Yersinia enterocolitica virulence plasmid (1983)

Virulence of Yersinia enterocolitica O:8 is associated with pO:8, a 42-megadalton plasmid. We constructed a mobilizable pO:8 derivative by successive in vitro and in vivo genetic manipulations. The in vitro constructed hybrid molecule pRK290B8-5 consisting of the mobilizable vector pRK290B and a 2.9-megadalton BamHI fragment of pO:8 was conjugally transferred to a Y. enterocolitica strain of serotype O:8 which harbored the virulence plasmid pO:8. From Yersinia transconjugants, a cointegrate was isolated which apparently formed by homologous recombination between the two component plasmids. The cointegrate was mobilized into plasmidless Y. enterocolitica strains of different serotypes. The transconjugants of serotype O:8 were found to express all four plasmid-associated phenotypes: (i) mouse lethality (Ml), (ii) conjunctivitis provocation in the guinea pig eye (Con), (iii) calcium requirement for growth at 37 degrees C (Mox), and (iv) agglutinogens (Ag8). The transconjugants of serotype O:3 expressed the phenotypes Con, Mox, and Ag8 but were nonlethal for mice (Ml-). The transconjugants of serotype O:5 remained avirulent for mice (Ml-) and for the guinea pig eye (Con-) but expressed the phenotypes Mox and Ag8. These data show that the virulence plasmid is probably not functionally interchangeable within different serotypes of Y. enterocolitica.
Stearoyl-CoA desaturase-1: a novel key player in the mechanisms of cell proliferation, programmed cell death and transformation to cancer (2010)

As part of a shift toward macromolecule production to support continuous cell proliferation, cancer cells coordinate the activation of lipid biosynthesis and the signaling networks that stimulate this process. A ubiquitous metabolic event in cancer is the constitutive activation of the fatty acid biosynthetic pathway, which produces saturated fatty acids (SFAs) and monounsaturated fatty acids (MUFAs) to sustain the increasing demand of new membrane phospholipids with appropriate acyl composition. In cancer cells, the tandem activation of the fatty acid biosynthetic enzymes adenosine triphosphate citrate lyase, acetyl-CoA carboxylase (ACC) and fatty acid synthase (FAS) leads to increased synthesis of SFA and their further conversion into MUFA by stearoyl-CoA desaturase (SCD) 1. The roles of adenosine triphosphate citrate lyase, ACC and FAS in the pathogenesis of cancer have been a subject of extensive investigation. However, despite early experimental and epidemiological observations reporting elevated levels of MUFA in cancer cells and tissues, the involvement of SCD1 in the mechanisms of carcinogenesis remains surprisingly understudied. Over the past few years, a more detailed picture of the functional relevance of SCD1 in cell proliferation, survival and transformation to cancer has begun to emerge. The present review addresses the mounting evidence that argues for a key role of SCD1 in the coordination of the intertwined pathways of lipid biosynthesis, energy sensing and the transduction signals that influence mitogenesis and tumorigenesis, as well as the potential value of this enzyme as a target for novel pharmacological approaches in cancer interventions.
Identification of YidC Residues That Define Interactions with the Sec Apparatus (2013)

In bacteria, a subset of membrane proteins insert into the membrane via the Sec apparatus with the assistance of the widely conserved essential membrane protein insertase YidC. After threading into the SecYEG translocon, transmembrane segments of nascent proteins are thought to exit the translocon via a lateral gate in SecY, where YidC facilitates their transfer into the lipid bilayer. Interactions between YidC and components of the Sec apparatus are critical to its function. The first periplasmic loop of YidC interacts directly with SecF. We sought to identify the regions or residues of YidC that interact with SecY or with additional components of the Sec apparatus other than SecDF. Using a synthetic lethal screen, we identified residues of YidC that, when mutated, led to dependence on SecDF for viability. Each residue identified is highly conserved among YidC homologs; most lie within transmembrane domains. Overexpression of SecY in the presence of two YidC mutants partially rescued viability in the absence of SecDF, suggesting that the corresponding wild-type YidC residues (G355 and M471) participate in interactions, direct or indirect, with SecY. Staphylococcus aureus YidC complemented depletion of YidC, but not of SecDF, in Escherichia coli. G355 of E. coli YidC is invariant in S. aureus YidC, suggesting that this highly conserved glycine serves a conserved function in interactions with SecY. This study demonstrates that transmembrane residues are critical in YidC interactions with the Sec apparatus and provides guidance on YidC residues of interest for future structure-function analyses.
Effect of Oral CNSA-001 (sepiapterin, PTC923) on gastric accommodation in women with diabetic gastroparesis: A randomized, placebo-controlled, Phase 2 trial (2021)

CNSA-001 improved gastric accommodation in women with diabetic gastroparesis. Further evaluation of CNSA-001 in gastroparesis is warranted; ClinicalTrials.gov number, NCT03712124.
Structure of Patulodin, a New Azaphilone Epoxide, Produced by Penidllium urticae (1995)

Penicillium urticae is knownas a producer of a variety of secondary metabolites, such as patulin, griseofulvm or patulolides1}. During biosynthetic studies of patulin by Sekiguchi et al.9 P. urticae P3 was isolated as one of the patulin minus mutants2). Recently, we found that a spontaneous mutant from strain P3, named P3Y, started producing at the same time a yellow compound and
The organization of 3' splice-site sequences in mammalian introns. (1989)

A model pre-mRNA substrate was used to carry out a detailed investigation of the functional organization of sequences at the 3' end of mammalian introns. This analysis revealed a difference in the sequence requirements for the first and second steps of the splicing reaction (lariat formation and exon ligation, respectively). Maximal efficiencies of lariat formation require a pyrimidine stretch directly adjacent to the branch site. In addition, efficient lariat formation can be specified in at least two distinct ways, one that requires the AG dinucleotide at the 3' splice junction, and the other that does not: If the pyrimidine stretch is short (14 nucleotides), an adjacent AG is essential; in contrast, the AG is not required in the presence of a long pyrimidine stretch (26 nucleotides). In a pre-mRNA containing a long pyrimidine stretch, efficient lariat formation is observed when the branch site is located greater than 100 nucleotides upstream from the AG or when the AG is preceded by a purine stretch. Although splicing usually takes place at the first AG downstream from the branch site, both distance and sequence play roles in the efficiency of this reaction.
A 80ns 5V-only dynamic RAM (1979)

The design and technology of a +5V-only 16K dynamic RAM with a typical access time of 80ns will be described. Power dissipation is 16.5mW standby and 140mW active.
The Isolation, Characterization, and Lipid-aggregating Properties of a Citrulline Containing Myelin Basic Protein (1989)

Human myelin basic protein was fractionated into its various charge isomers by CM52 cation exchange chromatography. Approximately 25-30% of the total charge applied to the column appeared in the void volume. This material termed "C-8," was further purified by reversed phase high performance liquid chromatography. Amino acid analyses of C-8 revealed low Arg (7 residue % in C-8 compared to 11-12 residue % in C-1) and increased Glx residues. The low Arg was accounted for by a corresponding amount of citrulline. Sequence analysis after chemical fragmentation (cyanogen bromide and BNPS-skatole) and enzymatic (cathepsin D and carboxypeptidase S-1) digestion localized the citrulline at residues 25, 31, 122, 130, 159, and 170 of the amino acid sequence. The effect of this loss of positive charge on the ability of the protein to aggregate lipid vesicles was demonstrated with vesicles composed of phosphatidylcholine (92.2 mol %) and phosphatidylserine (7.8 mol %). C-1 was the most effective charge isomer, and C-8 was the least effective. The ability of these charge isomers to aggregate vesicles correlated with the net positive charge on each. Vesicles composed of phosphatidylcholine alone were not aggregated by lipophilin or any of the charge isomers. However, when lipophilin was incorporated into phosphatidylcholine vesicles (50% w/w), small, optically clear suspensions of vesicles were formed. None of C-1, C-2, or C-3 aggregated these vesicles, but C-8 produced rapid vesicle aggregation. Since the substitution of citrulline for Arg would generate several relatively long apolar sequences, these would enhance the ability of C-8 to interact with the hydrophobic lipophilin molecule, promoting vesicle aggregation by hydrophobic interactions. The mechanism by which citrulline is generated in myelin is not known, although enzymatic conversion has been described in other systems. Studies are underway to elucidate the mechanism by which this post-translational modification is generated.
An optical tweezer actuated, nanoaperture-grid based Optofluidic Microscope implementation method (2007)

We report a novel grid based Optofluidic Microscope (OFM) method where a closely spaced 2D grid of nanoapertures (diameter = 100 nm, separation = 2.5 mum) provided patterned illumination. We achieved a one-to-one mapping of the light transmissions through the nanoapertures onto a high-speed CCD camera. By optically tweezing a targeted sample across the grid in a controlled fashion and recording the time varying light reception from the nanoapertures, we were able to generate high-resolution images of the sample. The achievable resolution limit of the prototype was ~ 110 nm (Sparrow's criterion) under optimal conditions. We demonstrated the technique by imaging polystyrene beads and pollen spores.
RISK FACTORS IN DENGUE SHOCK SYNDROME: A PROSPECTIVE EPIDEMIOLOGIC STUDY IN RAYONG, THAILAND (1984)

In January 1980, the municipal area of Rayong, Thailand, and contiguous suburban villages were chosen for a long-term study on dengue epidemiology. From 3,185 children randomly sampled in schools and households, the population prevalence of neutralizing antibody to the four dengue serotypes was estimated. To estimate the incidence of infection with each dengue virus serotype (dengue seroconversions), first grade children were re-bled in January 1981 (cohort study). Children admitted to hospital were studied for dengue virus isolation and antibody responses in paired sera. An epidemic of dengue occurred in 1980. Plaque reduction neutralization tests of 1,009 pre-epidemic sera from children aged less than 1-10 years of age determined that 3.3% were immune to dengue 1, 13.2% to dengue 2, 6.4% to dengue 3, and 5.8% to dengue 4. Examination of pre- and post-epidemic cohort blood samples revealed that the incidence of dengue infection in 251 seronegative children was 39.4% (15.1% dengue 1, 11.1% dengue 2, 2.0% dengue 3, 4.8% dengue 4, and 6.4% two or more dengue viruses). Among the 52,935 residents of the study area, there were 22 cases of virologically and clinically confirmed dengue shock syndrome, in children 15 years or younger. All 22 shock syndrome cases had secondary type antibody responses. Eight of 22 had been included in the random serologic sample prior to onset of shock; five had been immune to dengue 1, two to dengue 3, one to dengue 4, and none to dengue 2. Despite the high rate of dengue 1 infections in 1980, only dengue 2 viruses were recovered from dengue shock syndrome cases, including two dengue 1 immune children with pre-illness serum specimens. Although the pre-epidemic prevalence of antibodies to dengue 1 was the lowest to any type, children with this immunologic background contributed disproportionately to shock cases. In descending order of magnitude, risk factors for dengue shock syndrome in Rayong were secondary infections with dengue 2 which followed primary infections with dengue 1, dengue 3, or dengue 4.
Phylogenetic Perspectives in Innate Immunity (1999)

The concept of innate immunity refers to the first-line host defense that serves to limit infection in the early hours after exposure to microorganisms. Recent data have highlighted similarities between pathogen recognition, signaling pathways, and effector mechanisms of innate immunity in Drosophila and mammals, pointing to a common ancestry of these defenses. In addition to its role in the early phase of defense, innate immunity in mammals appears to play a key role in stimulating the subsequent, clonal response of adaptive immunity.
Photonic crystal fiber with a hybrid honeycomb cladding (2004)

We consider an air-silica honeycomb lattice and demonstrate a new approach to the formation of a core defect. Typically, a high or low-index core is formed by adding a high-index region or an additional air-hole (or other low-index material) to the lattice, but here we discuss how a core defect can be formed by manipulating the cladding region ratherthan the core region itself. Germanium-doping of the honeycomb lattice has recently been suggested for the formation of a photonic band-gap guiding silica-core and here we experimentally demonstrate how an index-guiding silica-core can be formed by fluorine-doping of the honeycomb lattice.
Analysis of the Role of Glutamine 190 in the Catalytic Mechanism of Murine Leukemia Virus Reverse Transcriptase (1999)

To determine the catalytic role of Gln(190), a member of the highly conserved LPQG motif in Moloney murine leukemia virus reverse transcriptase, we carried out site-directed mutagenesis of this residue to generate Q190N and Q190A. Both mutant proteins exhibited a significant loss in their polymerase and pyrophosphorolysis activities with a more pronounced effect noted with the Gln --> Asn substitution. The catalytic efficiencies of the mutants exhibited a 40-70-fold reduction with poly(rC) and poly(dC) templates in the presence of Mg(2+) and a 10-20-fold reduction with poly(rA) template in the presence of Mn(2+). Interestingly, the K(m) for NTP exhibited only a moderate 3-10-fold increase irrespective of the template-primer and the metal ion. Photoaffinity labeling of both the mutant and the WT enzymes exhibited an identical affinity for RNA.DNA and DNA.DNA template-primers. However, unlike the WT enzyme, the mutant enzymes exhibited a significantly reduced ability to catalyze the nucleotidyltransferase reaction on the covalently immobilized template-primer. An examination of the rate constants for the first and the second nucleotide for the mutant enzymes indicated dissimilar rates, indicating that Gln(190) may be involved in a rate-limiting, conformational change step both before and after the phosphodiester bond formation. Furthermore, the processivity of DNA synthesis by the mutant enzymes was decreased severely, which may result from the lower catalytic efficiency as well as translocation defect.
Percutaneous transhepatic liver biopsy with tract embolization. (1996)

PBTE produces excellent diagnostic specimens. The high complication rate empirically appears to be related to the degree of coagulopathy and operator experience.
Advances in the Enzymatic Reduction of Ketones (2007)

Historically, biocatalytic ketone reductions involved the use of Baker's yeast. Within the last five years, a significant and growing number of isolated ketoreductases have become available that have rendered yeast-based reductions obsolete. The broad substrate range and exquisite selectivities of these enzymes repeatedly outperform other ketone reduction chemistries, making biocatalysis the general method of choice for ketone reductions. Presented here is a summary of our understanding of the capabilities and limitations of these enzymes.
Complete polarisation control of GaAs gain-guidedtop-surface emittingvertical cavity lasers (1997)

Complete polarisation control is demonstrated in circular gain-guided top-surface emitting vertical cavity lasers by etching a line near the cavity aperture. The etch orientation determines the dominant polarisation state of emission by modifying the spontaneous emission coupling into each polarisation state. This is sufficient to pin the polarisation in monomode and multimode devices.
Potent cytodifferentiating agents related to hexamethylenebisacetamide. (1991)

Bishydroxamic acids are effective inducers of differentiation in murine erythroleukemia cells. Flexible analogs of suberic acid bisdimethylamide are approximately 100 times as active as the parent compound or hexamethylenebisacetamide. They also induce differentiation of human promyelocytic leukemia cells (HL-60) and a subclone of human colon carcinoma cells (HT-29-U4). Some rigid bishydroxamic acids with benzene rings in the spacers are even more active toward murine erythroleukemia cells but show curious biological differences. In contrast to the flexible molecules, those with benzene spacers show poor activity toward HL-60 cells; they also have different geometric requirements, and they are not additive with hexamethylenebisacetamide in their effect. It is likely that rigid bishydroxamic acids, with a benzene ring spacer, induce differentiation by a different mechanism in spite of their chemical resemblance to the flexible bisamide and bishydroxamic acid inducers.
Preparation and Acylation of Highly Functionalized Copper Derivatives of 3‐Iodoindazoles Leading to Polyfunctional 3‐Acylindazoles. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Indications for Antifibrinolytic Therapy (1975)

* Presented at the Postgraduate Course and Workshop “Progress in Fibrinolysis”, Milan, March 6–8, 1975.
Gene expression prediction using low-rank matrix completion (2016)

This method has potentially far-reaching applications including how bio-medical data is sourced and generated, and transcriptomic prediction by optimisation. We show that gene expression data can be computationally constructed, thereby potentially reducing the costs of gene expression profiling. In conclusion, this method shows great promise of opening new avenues in research on low-rank matrix completion in biological sciences.
Intramolecular Interaction between Hydroxyl Group and Carbonyl Moiety in Keto-alcohols (1968)

Abstract The O–H stretching absorption (νO–H) spectra of some keto-alcohols have been examined. The νO–H shift to the lower frequency due to the intramolecular O–H··· bonding can roughly be correlated to the geometry of the hydroxyl group relative to the n-electrons on the carbonyl oxygen. When the bonding is forbidden because of the conformational restriction, a weaker interaction between the hydroxyl group and the π-electrons on the carbonyl group is observable as the lower shift of the νO–H by 10–30 cm−1 as far as the conformation is favorable for the interaction.
Dielectric characteristics of fluorinated ultradry SiO2 (1989)

Improvement of dielectric breakdown characteristics and hot-electron-induced interface degradation of metal-oxide-semiconductor capacitors having fluorinated ultradry oxides has been demonstrated. The fluorine is introduced through HF surface treatment of Si prior to oxidation. Secondary-ion mass spectrometry data indicate that SiF distribution is peaked both at the surface of the oxide and at the SiO2/Si interface in the fluorinated ultradry oxide. The possible role of fluorine on the improvement of the dielectric characteristics will be discussed.