gebhart/patrepeval huggingface dataset:
A 2‐μm DNA‐based marker recycling system for multiple gene dispruption in the yeast Saccharomyces cerevisiae (1999)

A molecular FRT (Flp recombinase recognition target)-based cassette system for multiple gene disruption in the yeast Saccharomyces cerevisiae was developed. FRT DNA sequences were designed with different core mutations and subsequently cloned in direct orientation upstream and downstream of a marker gene to serve as template for the amplification of a set of different gene disruption cassettes. After each disruption, the marker can be easily eliminated from its integration site by in vivo site-specific recombination between the two identical, mutated FRT sequences flanking the marker, leaving behind one FRT sequence with a particular point mutation. Since recombination between two FRTs with a different core mutation is extremely rare, the possibility of chromosome rearrangements, due to site-specific recombination between residual FRTs, is very low. In strains containing 2-μm ([cir+]) the site-specific reaction is catalysed by the endogenous Flp gene product, whereas in strains without 2-μm ([cir0]), the FLP gene is carried on the cassette, together with the marker gene. This system can be applied for haploid and diploid [cir+] and [cir0] strains. Copyright © 1999 John Wiley & Sons, Ltd.
Rapid facile solid-phase immunobead assay for screening ciguatoxic fish in the market place. (1992)

The precision of the solid-phase immunobead assay (Ciguatect) to detect toxins associated with ciguatera poisoning have been evaluated through analysis of toxic and non-toxic fish obtained from fishing areas around the Hawaiian Islands. The Ciguatect test kit has been optimized for application to field/marketplace screening of ciguatoxic fish. Twelve parrot, surgeon, and amberjack fish fillet and fish extract test portions containing various concentrations of toxins were distributed to participating laboratories for analysis. The presence or absence of ciguatera-related toxins is determined by binding the toxins to a membrane attached to a plastic strip and exposing the toxin ladened membrane to a monoclonal antibody-colored latex bead complex which has a high specificity for ciguatera-related toxins. The intensity of the color on the membrane denotes the presence of the toxins in the fish or fish extract. Toxic components in the fish were confirmed by extraction, column purification, and toxicity testing using the brine shrimp (Artemia sp.) assay. Okadaic acid was used to standardize both the S-PIA and brine shrimp assays. For determination of ciguatoxin and related polyether toxins in parrot, surgeon, and amberjack fish fillets, the relative standard deviations for repeatability (RSDR) were 13.5, 9.0 and 4.3%, respectively, and the relative standard deviations for reproducibility (RSDR) were 44.4, 29.7 and 14.3%, respectively, for concentrations ranging from 1-4 ng/test strip. For determination of ciguatoxin and related polyether toxins in parrot, surgeon, and amberjack fish extracts, the RSDR were 5.8, 4.8, and 3.7%, respectively, and the RSDR were 11.9, 9.9, and 7.6%, respectively, for concentrations ranging from 3-5 ng/test strip.(ABSTRACT TRUNCATED AT 250 WORDS)
Sutterella parvirubra sp. nov. and Megamonas funiformis sp. nov., isolated from human faeces (2008)

Three strains of anaerobic, non-spore-forming, Gram-negative coccobacilli (YIT 11816T, YIT 11817 and YIT 11818) were isolated from human faeces. On the basis of 16S rRNA gene sequence similarity, these strains were shown to belong to the family Alcaligenaceae and to be related to the type strain of Sutterella stercoricanis (94.9 %) and to Sutterella wadsworthensis WAL 7877 (94.3 %); the similarity to strains of any other species with a validly published name within the family Alcaligenaceae was less than 92 %. Biochemical data supported the affiliation of these strains to the genus Sutterella. These strains therefore represent a novel species, for which the name Sutterella parvirubra sp. nov. is proposed; the type strain is YIT 11816T (=DSM 19354T =JCM 14724T). The cells of another isolate, strain YIT 11815T, were non-spore-forming, Gram-negative, very large rods, 1x5-200 microm in size, with or without a central, subterminal or terminal swelling of 2-4 microm diameter when grown in a broth medium supplemented with glucose. Based on comparative 16S rRNA gene sequencing, this bacterium is a member of the family Acidaminococcaceae, and most closely related to Megamonas hypermegale (95.3 % similarity to the type strain). Interestingly, the 16S rRNA gene sequence of strain YIT 11815T showed 99 % similarity to sequences of uncultured colonic bacteria. A 16S rRNA gene sequence divergence value of >3 % from known cultured species suggested that isolate YIT 11815T represents a novel species, for which the name Megamonas funiformis sp. nov. is proposed; the type strain is YIT 11815T (=DSM 19343T =JCM 14723T).
In Vivo Intravascular Imaging with OCT: Comparison with Ultrasound (2000)

A true clinical need exists for a high resolution imaging modality to characterize coronary microstructure. In this study, OCT imaging was performed of the in in vivo rabbit aorta examining clot, atherosclerosis, and intravascular stents. The performance of OCT was superior to that of high frequency ultrasound.
Suicide plasmid vehicles for insertion mutagenesis in Rhizobium meliloti and related bacteria (1983)

We describe the construction and use of a set of plasmid vectors of the transposons Tn1, Tn5, and Tn9 that are suicidal in Rhizobium species and therefore suitable for mutagenesis with these three transposons. The vectors are composed of the p15A replicon which functions in Escherichia coli but not in Rhizobium species and a region encoding the N type of bacterial conjugation system which is very efficient in matings between E. coli and Rhizobium species. The usefulness of the vectors has been most extensively assessed in Rhizobium meliloti. It is likely that they will be useful for mutagenesis and genome manipulation in other bacteria as well.
Identification of an immediate early gene, pghs-B, whose protein product has prostaglandin synthase/cyclooxygenase activity. (1992)

We have characterized a growth factor-inducible gene, pghs-B, isolated by differential screening of a lambda complementary DNA library from RNA of serum-stimulated NIH 3T3 cells which encodes a 604-amino acid protein presenting high similarity with prostaglandin G/H synthase (PGHS). Induction of both pghs-B mRNA and protein is rapid and remains at high levels for several hours. The increase in pghs-B mRNA is mainly due to transcriptional activation of the gene. PGHS-B has been expressed in the baculovirus system and has been demonstrated to be involved in prostaglandin synthesis and to be inhibited by indomethacin, demonstrating that PGHS-B is indeed an enzyme related to PGHS. The pghs-B gene maps to the [1G-1H2] region of the murine genome.
Increasing Cas9-mediated homology-directed repair efficiency through covalent tethering of DNA repair template (2017)

The CRISPR-Cas9 system is a powerful genome-editing tool in which a guide RNA targets Cas9 to a site in the genome where the Cas9 nuclease then induces a double stranded break (DSB) 1,2 . The potential of CRISPR-Cas9 to deliver precise genome editing is hindered by the low efficiency of homology-directed repair (HDR), which is required to incorporate a donor DNA template encoding desired genome edits near the DSB 3,4 . We present a strategy to enhance HDR efficiency by covalently tethering a single-stranded donor oligonucleotide (ssODN) to the Cas9/guide RNA ribonucleoprotein (RNP) complex via a fused HUH endonuclease 5 , thus spatially and temporally co-localizing the DSB machinery and donor DNA. We demonstrate up to an 8-fold enhancement of HDR using several editing assays, including repair of a frameshift and in-frame insertions of protein tags. The improved HDR efficiency is observed in multiple cell types and target loci, and is more pronounced at low RNP concentrations.
Five-bit parallel operation of optical quantization and coding for photonic analog-to-digital conversion (2011)

We report the attempt of optical quantization and coding in 5-bit parallel format for photonic A/D conversion. The proposed system is designed to realize generation of 32 different optical codes in proportion to the corresponding signal levels when fed a certain range of amplitude-varied input pulses to the setup. Optical coding in a bit-parallel format made it possible, that provides 5 bit optical codes from 32 optical quantized pulses. The 5-bit parallel operation of an optical quantization and coding module with 5 multi-ports was tested in our experimental setup.
Endodontic failures--changing the approach. (1996)

The underlying reason for endodontic failures is almost invariably due to bacterial infection. The bacteria may be situated within a previously missed or uninstrumented portion of a root canal, infiltrate via a leaky coronal restoration and root filling, or cause contamination from an extra-radicular infection. Management of the failing root canal filling begins with the identification of the source of persistent infection. Should the infection be present within the root canal system, such as a missed canal, orthograde retreatment is the choice of treatment. This is also true for asymptomatic cases which had been inadequately obturated and which require the placement of a dowel into the canal for restorative reasons. Periapical surgery is best reserved for cases with no sign of healing after orthograde retreatment and those with extra-radicular infection. This paper discusses the relationship between endodontics and restorative dentistry, treatment planning for endodontic failures, and the reported rates of success with orthograde and surgical retreatments.
An Inverted Metal-Organic Framework with Compartmentalized Cavities Constructed by Using an Organic Bridging Unit Derived from the Solid State We are grateful to the National Science Foundation (CAREER Award, L.R.M., DMR-0133138) and the University of Iowa for funding. Acknowledgement is also made to the Donors of The Petroleum Research Fund, administered by the American Chemical Society, for support of this research. (2002)

Gridlock: A porous metal–organic framework with an interior tailored supramolecularly with organic groups is described (see structure; two grids have been differentiated using cyan and gray, while the yellow spheres represent included methyl groups). The approach relies on inverting the role of a secondary building unit (SBU) and an organic linker such that the organic linker serves as a node and the SBU serves as a linear bridge. The organic node used to construct the framework has been obtained by way of a template-directed solid-state organic synthesis.
Unbalance of intestinal microbiota in atopic children (2012)

Depleted in key immunomodulatory symbionts, the atopy-associated microbiota can represent an inflammogenic microbial consortium which can contribute to the severity of the disease. Our data open the way to the therapeutic manipulation of the intestinal microbiota in the treatment of atopy by means of pharmaceutical probiotics.
Theory and Behavior of Multiple Unit Discriminative Auctions (1984)

ABSTRACT This paper reports the results of controlled experiments designed to test the Harris‐Raviv generalization of the Vickrey theory of bidding in multiple unit discriminative auctions. The paper also discusses further development of the theory—in a way suggested by the experimental results—to include bidders with distinct risk preferences.
Networks and pathways in pigmentation, health, and disease (2009)

Extensive studies of the biology of the pigment-producing cell (melanocyte) have resulted in a wealth of knowledge regarding the genetics and developmental mechanisms governing skin and hair pigmentation. The ease of identification of altered pigment phenotypes, particularly in mouse coat color mutants, facilitated early use of the pigmentary system in mammalian genetics and development. In addition to the large collection of developmental genetics data, melanocytes are of interest because their malignancy results in melanoma, a highly aggressive and frequently fatal cancer that is increasing in Caucasian populations worldwide. The genetic programs regulating melanocyte development, function, and malignancy are highly complex and only partially understood. Current research in melanocyte development and pigmentation is revealing new genes important in these processes and additional functions for previously known individual components. A detailed understanding of all the components involved in melanocyte development and function, including interactions with neighboring cells and response to environmental stimuli, will be necessary to fully comprehend this complex system. The inherent characteristics of pigmentation biology as well as the resources available to researchers in the pigment cell community make melanocytes an ideal cell type for analysis using systems biology approaches. In this review, the study of melanocyte development and pigmentation is considered as a candidate for systems biology-based analyses.
The dsRNA binding protein family: critical roles, diverse cellular functions (2003)

The dsRNA binding proteins (DRBPs) comprise a growing family of eukaryotic, prokaryotic, and viral-encoded products that share a common evolutionarily conserved motif specifically facilitating interaction with dsRNA. Proteins harboring dsRNA binding domains (DRBDs) have been reported to interact with as little as 11 bp of dsRNA, an event that is independent of nucleotide sequence arrangement. More than 20 DRBPs have been identified and reportedly function in a diverse range of critically important roles in the cell. Examples include the dsRNA-dependent protein kinase PKR that functions in dsRNA signaling and host defense against virus infection and DICER, which is implicated in RNA interference (RNAi) -mediated gene silencing. Other DRBPs such as Staufen, adenosine deaminase acting on RNA (ADAR), and spermatid perinuclear RNA binding protein (SPNR) are known to play essential roles in development, translation, RNA editing, and stability. In many cases, homozygous and even heterozygous disruption of DRBPs in animal models results in embryonic lethality. These results implicate the recognition of dsRNA as an evolutionarily conserved mechanism important in the regulation of gene expression and in host defense and underscore the diversity of essential biological tasks performed by dsRNA-related processes in the cell.
Classifying Hepatitis B Virus Genotypes (2003)

In 1988, hepatitis B virus (HBV) was classified into four genotypes by a sequence divergence in the entire genome exceeding 8%, and designated by capital letters of the alphabet from A to D. There are seven genotypes of HBV (A-G) at present, and an eighth is on the horizon. They have an uneven geographical distribution, and only a few of them are prevalent in a given area of the world. Thus genotype A is frequent in northwest Europe, Sub-Saharan Africa, India and the North, Central and South America, B as well as C are common in Southeast Asia and Oceania, and D is prevalent in the Mediterranean area, Central Asia and South America. Genotype E is restricted to West Africa, and F is localized in Central and South America. The distribution of genotype G added to the alphabet list very recently has yet to be determined. Coinfection with HBV of distinct genotypes is not infrequent and found in about 10% of infected individuals, and is responsible for intertypic recombination of HBV genomes. The mutation for a stop codon in the precore region (G1896A) for aborting the translation of hepatitis B e antigen (HBeAg) is prohibited in HBV genomes of genotype A, as well as some of genotypes C and F, because they possess C at position 1858 that makes a Watson-Crick pair with G at position 1896. Hence, seroconversion to antibody to HBeAg is forbidden or delayed in individuals who carry them. Evidence is accumulating as regards the influence of HBV genotypes on the progression of chronic hepatitis B and response to antiviral therapies. HBV isolates even of the same genotype can differ in virological and clinical characteristics, and therefore, the genotype needs to be classified further into subtypes, especially if they are clinically relevant.
Brain Distribution and Toxicological Evaluation of a Systemically Delivered Engineered Nanoscale Ceria (2010)

Engineered nanoscale ceria is used as a diesel fuel catalyst. Little is known about its mammalian central nervous system effects. The objective of this paper is to characterize the biodistribution of a 5-nm citrate-stabilized ceria dispersion from blood into brain and its pro- or antioxidant effects. An approximately 4% aqueous ceria dispersion was iv infused into rats (0, 100, and up to 250 mg/kg), which were terminated after 1 or 20 h. Ceria concentration, localization, and chemical speciation in the brain were assessed by inductively coupled plasma mass spectrometry, light and electron microscopy (EM), and electron energy loss spectroscopy (EELS). Pro- or antioxidative stress effects were assessed as protein carbonyls, 3-nitrotyrosine, and protein-bound 4-hydroxy-2-trans-nonenal in hippocampus, cortex, and cerebellum. Glutathione reductase, glutathione peroxidase, manganese superoxide dismutase, and catalase levels and activities were measured in hippocampus. Catalase levels and activities were also measured in cortex and cerebellum. Na fluorescein and horseradish peroxidase (HRP) were given iv as blood-brain barrier (BBB) integrity markers. Mortality was seen after administration of 175-250 mg ceria/kg. Twenty hours after infusion of 100 mg ceria/kg, brain HRP was marginally elevated. EM and EELS revealed mixed Ce(III) and Ce(IV) valence in the freshly synthesized ceria in vitro and in ceria agglomerates in the brain vascular compartment. Ceria was not seen in microvascular endothelial or brain cells. Ceria elevated catalase levels at 1 h and increased catalase activity at 20 h in hippocampus and decreased catalase activity at 1 h in cerebellum. Compared with a previously studied approximately 30-nm ceria, this ceria was more toxic, was not seen in the brain, and produced little oxidative stress effect to the hippocampus and cerebellum. The results are contrary to the hypothesis that a smaller engineered nanomaterial would more readily permeate the BBB.
Integrin Antagonists and Other Low Molecular Weight Compounds as Inhibitors of Angiogenesis: New Drugs in Cancer Therapy (1997)

Arthritis, rheumatism, and diabetic retinopathy, conditions accompanied by excessive angiogenesis, may be amenable to treatment with the same drugs proposed for cancer therapy. A promising new concept in tumor treatment is the application of integrin antagonists such as 1 and other low molecular weight compounds with antiangiogenic activity. A number of drugs are currently in preclinical and clinical trials.
Endogenous Inhibitors and Germination of<i>Beta vulgaris</i> (1984)

The nature and importance of endogenous germination inhibitors in rubbed triploid monogerm sugar beet fruits were studied. Experimental evidence suggests that germination inhibitors do not play an important role in the prevention of germination of rubbed fruits. Putative inhibitory compounds known to occur in sugar beet extracts were found to have little effect on germination. Measures to leach out water soluble compounds also had little effect on germination. Concentrated fruit extracts were found to inhibit the germination of sugar beet seeds by virtue of their osmotic potentials, and this was related to the salt content of the fruit extracts. However, a positive relationship was found between salt content and the original germination of the fruit lines. This relationship could have important consequences for assessment of fruit maturity and subsequent germination behaviour at harvest. The causes of poor germination in rubbed fruit lie not in the presence of inhibitory compounds in the fruit coat but in some other property of the fruit.
Predicting the topology of eukaryotic membrane proteins (1993)

We show that the so-called 'positive inside' rule, i.e. the observation that positively charged amino acids tend to be more prevalent in cytoplasmic than in extra-cytoplasmic segments in transmembrane proteins [von Heijne, G. (1986) EMBO J. 5, 3021-3027], seems to hold for all polar segments in multi-spanning eukaryotic membrane proteins irrespective of their position in the sequence and hence can be used in conjunction with hydrophobicity analysis to predict their transmembrane topology. Further, as suggested by others, we confirm that the net charge difference across the first transmembrane segment correlates well with its orientation [Hartmann, E., Rapoport, T. A. and Lodish H. F. (1989) Proc. Natl Acad. Sci. USA 86, 5786-5790], and that the overall amino-acid composition of long polar segments can also be used to predict their cytoplasmic or extra-cytoplasmic location [Nakashima, H. and Nishikawa, K. (1992) FEBS Lett. 303, 141-146]. We present an approach to the topology prediction problem for eukaryotic membrane proteins based on a combination of these methods.
Catalytic CC, CN, and CO Ullmann‐Type Coupling Reactions: Copper Makes a Difference (2008)

Copper makes the difference: Important challenges have been overcome in copper-catalyzed Ullmann reactions since its renaissance in the early 2000s. Significant advances in this field have recently been made in regards to carrying out enantioselective and chemoselective arylation of nucleophiles (Nu) by using a copper catalyst (see scheme).
Structure of the sialylated L3 lipopolysaccharide of Neisseria meningitidis (1993)

The L3 immunotype lipopolysaccharide (LPS) of Neisseria meningitidis was subjected to degradation procedures, which produced a number of different oligosaccharide fragments. The high resolution 1H and 13C NMR spectroscopic analyses of these oligosaccharides yielded structural information on a number of different regions of the LPS. For example, from one oligosaccharide, it was found that the endogenous sialylation of the meningococcal LPS occurs at O-3 of the terminal beta-D-galactopyranosyl residue of its lacto-N-neotetraose antenna in the alpha-D-configuration. From another, it was also established that the dominant structural feature responsible for L3 epitope specificity is the presence of a phosphorylethanolamine substituent at O-3 of the penultimate heptopyranosyl residue of its other antenna. In addition from information obtained with another oligosaccharide the structure of the 3-deoxy-D-manno-octulosonic acid disaccharide region of the L3 LPS was also elucidated. From all the above cumulative data plus some published data, it was then possible to reconstruct the complete structure of the entire native L3 LPS.
BACILLUS CALMETTE-GUERIN VERSUS CHEMOTHERAPY FOR THE INTRAVESICAL TREATMENT OF PATIENTS WITH CARCINOMA IN SITU OF THE BLADDER: A META-ANALYSIS OF THE PUBLISHED RESULTS OF RANDOMIZED CLINICAL TRIALS (2005)

Intravesical BCG significantly reduces the risk of short and long-term treatment failure compared with intravesical chemotherapy. Therefore, it is considered to be the intravesical agent of choice in the treatment of CIS.
Upstream traffic transmitter using injection-locked Fabry-Perot laser diode as modulator for WDM access networks (2002)

An upstream-traffic transmitter based on a Fabry-Perot laser diode (FP-LD) as modulator is proposed and demonstrated for wavelength division multiplexed (WDM) access networks. By injection-locking the FP-LD with the downstream wavelength at the optical network unit (ONU), the original downstream data can be largely suppressed while the upstream data can be transmitted on the same injection-locked wavelength by simultaneously directly-modulating the FP-LD.