gebhart/patrepeval huggingface dataset:
Eukaryotic DNA topoisomerases: two forms of type I DNA topoisomerases from HeLa cell nuclei. (1981)

Two type I DNA topoisomerases have been purified to homogeneity from the nuclei of HeLa cells. One topoisomerase has a peptide molecular weight of 100,000 and the other, a molecular weight of 67,000. Several lines of evidence indicate that these two topoisomerases are closely related, (a) Both exhibit similar enzymatic activities on DNA. (b) The chromatographic properties of the two topoisomerases during purification are similar. (c) Mild proteolysis of the purified molecular weight 100,000 topoisomerase in vitro generates a group of protein bands of molecular weight approximately 67,000, and these bands retain topoisomerase activity. (d) The peptides formed by partial proteolysis of the 67,000 topoisomerase in the presence of NaDodSO4 form a subset of those produced from the 100,000 enzyme. The 100,000 topoisomerase is the major type I enzyme in the cell. The 67,000 topoisomerase, which may be identical to the previously identified "nicking-closing" enzyme [Champoux, J. J. & Dulbecco, R. (1972) Proc. Natl. Acad. Sci. USA 69, 143-146], is probably formed by proteolysis of the 100,000 enzyme.
Ureaplasma urealyticum biovar determination in women attending a family planning clinic in Guiné‐Bissau, using polymerase chain reaction of the multiple‐banded antigen gene (2002)

Although Ureaplasma urealyticum is commonly found in the genital tract of asymptomatic women, it has been suggested that only certain subgroups of this microorganism are disease associated. Vaginal specimens were collected to determine the distribution of U. urealyticum biovars and to estimate their possible association with age, absence of lactobacilli, and tetracycline resistance. Of the 94 women studied, 40 (43%) carried U. urealyticum and were biotyped by polymerase chain reaction (PCR). Twenty-nine (73%) strains presented with parvo biovar, 10 (25%) with T960 biovar, and one (2.5%) with both biovars. Parvo biovar was predominant in all age groups and appears to be more frequent in women 20-25 years of age (41%), whereas T960 was common in women 30-35 years of age (22%). In this study, U. urealyticum was not associated with changes in vaginal flora, although the inverse apparently was true for Mycoplasma hominis. However, T960 biovar was more associated with the loss of lactobacilli than was parvo biovar. The number of T960 biovar strains that presented tetracycline (40%) or multiple (100%) resistance was higher than that of parvo biovar strains (27% and 69%, respectively).
Topical agents for idiopathic distal colitis and proctitis (2010)

Abstract Rectally administered topical agents have demonstrated efficacy in the maintenance of distal colitis (DC) and proctitis and as they are rarely associated with significant blood drug levels, side effects are infrequent. The topical 5‐aminosalicylic acid (5‐ASA) suppositories and enemas target different regions of the distal colon and are effective for proctitis and DC, respectively. They demonstrate clinical results that are better than oral 5‐ASAs and are preferred to topical steroids with better clinical, endoscopic and histological outcomes, without the risk of adrenal suppression. Disease resistant to topical agents, however, can be extremely difficult to manage. The addition of oral 5ASAs, steroids, immunosuppressants and the anti‐tumor necrosis factor‐α agents may be effective, but can result in significant side effects and not all patients will respond to the therapies. It is for these patients that new and novel therapies are required. Novel topical agents have been proposed for the management of resistant DC. These agents included butyrate, cyclosporine, and nicotine enemas, as well as tacrolimus suppositories, and tacrolimus, ecabet sodium, arsenic, lidocaine, bismuth, rebamipide and thromboxane enemas. While some of these agents appear to demonstrate impressive outcomes, the majority have only been examined in small open‐labeled studies. There is thus a desperate need for more randomized double‐blinded placebo controlled studies to investigate the clinical utility of these topical therapies. This review summarizes the efficacy of the established topical therapies, and explores the available data on the new and novel topical agents for the management of DC and proctitis.
Solid probe assisted nanoelectrospray ionization mass spectrometry for biological tissue diagnostics (2012)

To perform remote and direct sampling for mass spectrometry, solid probe assisted nanoelectrospray ionization (SPA-nanoESI) has been newly developed. After capturing the sample on the tip of the needle by sticking it to the biological tissue, the needle was inserted into the solvent-preloaded nanoESI capillary from the backside. NanoESI gave abundant ion signals for human kidney tissues and the liver of a living mouse. The method is easy to operate and versatile because any biological specimen could be sampled away from the mass spectrometer. Minimal invasiveness is another merit of this method.
Type v collagen synthesis and deposition by chicken embryo corneal fibroblasts in vitro (1989)

Chick embryo corneal fibroblasts were grown in culture to study the processes whereby fibroblasts regulate the deposition and organization of the collagenous, secondary stroma. The effects of an existing type I collagen substratum, cell density, and serum concentration on type V collagen synthesis were investigated. Type V collagen represented approximately 20% of the total fibrillar collagen synthesized, regardless of whether the cells were subcultured, grown on untreated or collagen-coated plastic, grown under confluent or subconfluent conditions, or grown in the presence of low (0.1%) or high (10.0%) serum concentrations. The synthesis of type V collagen remained constant at 20% of the total collagen when cells were grown in 1.0% serum, even though total collagen synthesis increased nearly twofold when compared to total synthesis in 0.1% or 10.0% serum. Immunocytochemistry with anti-collagen, type-specific monoclonal antibodies revealed a homogeneous population of cells synthesizing types I and V collagen. The fibrils deposited by cells grown in a three-dimensional collagen matrix contained a helical epitope on the type V molecule that was inaccessible unless the fibrillar structure was disrupted, mimicking the situation in situ. The production in vitro of heterotypic fibrils, with a constant I/V ratio and molecular packing mimicking the natural stroma, offers opportunities for studying in more detail this important process, which is essential for optical transparency.
Synthesis and tritium radiolabelling of fluorinated analogues of myo-inositol (1992)

Syntheses have been developed for a set of six myo-inositol analogues from myo-inositol in which single hydroxy groups have been replaced by fluorine (monodeoxy-fluoro-myo-inositols). Except for 2-deoxy-2-fluoro-myo-inositol 32 and lD-4-deoxy-4-fluoro-myo-inositol 23, the monodeoxy-fluoro-myo-inositols were substrates for the enzyme inositol dehydrogenase [EC 1.1.1.18], which catalyses the oxidation of the axial 2-position of myo-inositol to give scyllo-inosose. This enzyme was used to exchange tritium radiolabel from myo-[2-3H]inositol to the monodeoxy-fluoro-myo-inositol. 1D-4-Deoxy-4-fluoro-myo-inositol and 2-deoxy-2-fluoro-myo-inositol were radiolabelled chemically.
Monoclonal antibodies to herpes simplex virus type 1 proteins, including the immediate-early protein ICP 4 (1981)

Monoclonal antibodies were prepared against herpes simplex virus type 1 (strain 14012) by two immunization procedures. Procedure A utilized infectious virus propagated in mouse cells, and procedure B utilized mouse cells infected with herpes simplex virus in the presence of cycloheximide and harvested 1 h after removal of the inhibitor. A total of 52 monoclonal antibodies were obtained against 10 herpes simplex virus proteins, including four glycosylated proteins (a 110,000-molecular-weight protein, gB, gC, and gD) and six nonglycosylated proteins (a 68,000-molecular-weight protein, ICP 9, ICP 8, ICP 6, ICP 5, and the immediate-early ICP 4). The antibodies were assayed against herpes simplex virus types 1 and 2 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of radioimmunoprecipitates, immunofluorescence, and neutralization. Using the reagents prepared, we concluded that the 110,000-molecular-weight protein, gD, ICP 9, ICP 9, ICP 6, and the 68,000-molecular-weight protein express both type-specific and cross-reactive antigenic determinants. In contrast, nine antibodies against gB all cross-reacted with herpes simplex virus type 2, whereas eight antibodies to gC all reacted type specifically.
Defining the optimal animal model for translational research using gene set enrichment analysis (2016)

The mouse is the main model organism used to study the functions of human genes because most biological processes in the mouse are highly conserved in humans. Recent reports that compared identical transcriptomic datasets of human inflammatory diseases with datasets from mouse models using traditional gene-to-gene comparison techniques resulted in contradictory conclusions regarding the relevance of animal models for translational research. To reduce susceptibility to biased interpretation, all genes of interest for the biological question under investigation should be considered. Thus, standardized approaches for systematic data analysis are needed. We analyzed the same datasets using gene set enrichment analysis focusing on pathways assigned to inflammatory processes in either humans or mice. The analyses revealed a moderate overlap between all human and mouse datasets, with average positive and negative predictive values of 48 and 57% significant correlations. Subgroups of the septic mouse models (i.e., Staphylococcus aureus injection) correlated very well with most human studies. These findings support the applicability of targeted strategies to identify the optimal animal model and protocol to improve the success of translational research.
Surface Plasmon Interference Nanolithography (2005)

A new nanophotolithography technique based on the interference of surface plasmon waves is proposed and demonstrated by using computer simulations. The wavelengths of the surface plasmon waves at metal and dielectric interfaces can reach the nanometer scale while their frequencies remain in the optical range. As a result, the resolution of this surface plasmon interference nanolithography (SPIN) can go far beyond the free-space diffraction limit of the light. Simulation results show that one-dimensional and two-dimensional periodical structures of 40-100 nm features can be patterned using interfering surface plasmons launched by 1D gratings. Detailed characteristics of SPIN such as field distribution and contrast are also investigated.
Ionomycin-activated Calpain Triggers Apoptosis (2002)

Ubiquitous calpains (mu- and m-calpain) have been repeatedly implicated in apoptosis, but the underlying mechanism(s) remain(s) to be elucidated. We examined ionomycin-induced cell death in LCLC 103H cells, derived from a human large cell lung carcinoma. We detected hallmarks of apoptosis such as membrane blebbing, nuclear condensation, DNA ladder formation, caspase activation, and poly-(ADP-ribose)polymerase cleavage. Apoptosis was prevented by preincubation of the cells with the calpain inhibitor acetyl-calpastatin 27-peptide and the caspase inhibitor Z-DEVD-fmk, implicating both the calpains and caspases in the apoptotic process. The apoptotic events correlated in a calpastatin-inhibitable manner with Bid and Bcl-2 decrease and with activation of caspases-9, -3, and -7. In vitro both ubiquitous calpains cleaved recombinant Bcl-2, Bid, and Bcl-x(L) at single sites truncating their N-terminal regions. Binding studies revealed diminished interactions of calpain-truncated Bcl-2 and Bid with immobilized intact Bcl-2 family proteins. Moreover, calpain-cleaved Bcl-2 and Bid induced cytochrome c release from isolated mitochondria. We conclude that ionomycin-induced calpain activation promotes decrease of Bcl-2 proteins thereby triggering the intrinsic apoptotic pathway.
The Wax Ester Synthase/Acyl Coenzyme A:Diacylglycerol Acyltransferase from Acinetobacter sp. Strain ADP1: Characterization of a Novel Type of Acyltransferase (2005)

The wax ester synthase/acyl coenzyme A (acyl-CoA):diacylglycerol acyltransferase (WS/DGAT) catalyzes the final steps in triacylglycerol (TAG) and wax ester (WE) biosynthesis in the gram-negative bacterium Acinetobacter sp. strain ADP1. It constitutes a novel class of acyltransferases which is fundamentally different from acyltransferases involved in TAG and WE synthesis in eukaryotes. The enzyme was purified by a three-step purification protocol to apparent homogeneity from the soluble fraction of recombinant Escherichia coli Rosetta (DE3)pLysS (pET23a::atfA). Purified WS/DGAT revealed a remarkably low substrate specificity, accepting a broad range of various substances as alternative acceptor molecules. Besides having DGAT and WS activity, the enzyme possesses acyl-CoA:monoacylglycerol acyltransferase (MGAT) activity. The sn-1 and sn-3 positions of acylglycerols are accepted with higher specificity than the sn-2 position. Linear alcohols ranging from ethanol to triacontanol are efficiently acylated by the enzyme, which exhibits highest specificities towards medium-chain-length alcohols. The acylation of cyclic and aromatic alcohols, such as cyclohexanol or phenylethanol, further underlines the unspecific character of this enzyme. The broad range of possible substrates may lead to biotechnological production of interesting wax ester derivatives. Determination of the native molecular weight revealed organization as a homodimer. The large number of WS/DGAT-homologous genes identified in pathogenic mycobacteria and their possible importance for the pathogenesis and latency of these bacteria makes the purified WS/DGAT from Acinetobacter sp. strain ADP1 a valuable model for studying this group of proteins in pathogenic mycobacteria.
Two-step targeting of xenografted colon carcinoma using a bispecific antibody and 188Re-labeled bivalent hapten: biodistribution and dosimetry studies. (2001)

This study indicates that 188Re can be used for radiolabeling of hapten in two-step radioimmunotherapy protocols with the AES technique. 188Re has a greater range than 131I, which should allow the treatment of solid tumors around 1 cm in diameter. Although the method used for hapten radiolabeling did not provide optimal tumor uptake, the use of a bifunctional chelating agent associated with AG 8.1 should solve this problem.
Synovial sarcoma--a misnomer. (1984)

For an evaluation of the putative histogenetic relationship of synovia and synovial sarcomas, normal synovia, villonodular synovitis, and synovial sarcomas were compared for their patterns of expression of intermediate filaments of keratin and vimentin type and epithelial membrane antigen and for lectin binding sites. The lining cells in both normal synovia and villonodular synovitis reacted with anti-vimentin antibodies, but not with antibodies to different types of keratins or epithelial membrane antigen. The cleft-lining cells in synovial sarcoma, on the other hand, showed only keratin positivity, and epithelial membrane antigen could also be detected in these cells. Nonneoplastic synovial lining cells bound peanut agglutinin (PNA), Ricinus communis agglutinin (RCA), soybean agglutinin (SBA), concanavalin A (Con A), and wheat germ agglutinin (WGA) conjugates, but not Ulex europaeus I lectin (UEA I). In contrast, the epithelial-like cleft lining cells in synovial sarcomas showed an apical cytoplasmic binding of PNA, UEA I, RCA, and SBA, and binding of WGA to the whole cytoplasm but did not bind Con A. The distinct differences between synovial lining cells and synovial sarcoma cells speak against synovial cell features in synovial sarcoma. These results indicate that synovial sarcoma is a carcinosarcomalike tumor with true epithelial differentiation, and the term "synovial sarcoma" apparently is a misnomer that should be abandoned.
Enzyme replacement with PEGylated cystathionine β-synthase ameliorates homocystinuria in murine model (2016)

Homocystinuria, which typically results from cystathionine β-synthase (CBS) deficiency, is the most common defect of sulfur amino acid metabolism. CBS condenses homocysteine and serine to cystathionine that is then converted to cysteine. Individuals with homocystinuria have markedly elevated plasma levels of homocysteine and methionine and reduced concentrations of cystathionine and cysteine. Clinical disease manifestations include thromboembolism and neuropsychiatric, ocular, and skeletal complications. Here, we have shown that administration of PEGylated CBS into the circulation of homocystinuria model mice alters the extra- and intracellular equilibrium of sulfur amino acids, resulting in a decrease of approximately 75% in plasma total homocysteine (tHcy) and normalization of cysteine concentrations. Moreover, the decrease in homocysteine and the normalization of cysteine in PEGylated CBS-treated model mice were accompanied by improvement of histopathological liver symptoms and increased survival. Together, these data suggest that CBS enzyme replacement therapy (ERT) is a promising approach for the treatment of homocystinuria and that ERT for metabolic diseases may not necessitate introduction of the deficient enzyme into its natural intracellular compartment.
Comparative Study of Liver Gene Transfer With AAV Vectors Based on Natural and Engineered AAV Capsids (2015)

Vectors based on the clade E family member adeno-associated virus (AAV) serotype 8 have shown promise in patients with hemophilia B and have emerged as best in class for human liver gene therapies. We conducted a thorough evaluation of liver-directed gene therapy using vectors based on several natural and engineered capsids including the clade E AAVrh10 and the largely uncharacterized and phylogenically distinct AAV3B. Included in this study was a putatively superior hepatotropic capsid, AAVLK03, which is very similar to AAV3B. Vectors based on these capsids were benchmarked against AAV8 and AAV2 in a number of in vitro and in vivo model systems including C57BL/6 mice, immune-deficient mice that are partially repopulated with human hepatocytes, and nonhuman primates. Our studies in nonhuman primates and human hepatocytes demonstrated high level transduction of the clade E-derived vectors and equally high transduction with vectors based on AAV3B. In contrast to previous reports, AAVLK03 vectors are not superior to either AAV3B or AAV8. Vectors based on AAV3B should be considered for liver-directed gene therapy when administered following, or before, treatment with the serologically distinct clade E vectors.
Streamlined approach to creating yeast artificial chromosome libraries from specialized cell sources. (1990)

The study of tumor-specific chromosomal abnormalities has been severely impeded by an inability to link cytogenetic to molecular data. Restriction fragment length polymorphism mapping of any particular chromosomal rearrangement to the resolution limit of genetic methodology generates sets of probes that frequently are still too widely spaced to render the rearrangement breakpoints accessible to molecular isolation. The stable propagation of genomic fragments of up to one million base pairs in size as yeast artificial chromosomes (YACs) represents an important development in this regard. However, existing YAC libraries have been made from karyotypically normal sources making the localization and cloning of specific rearrangement breakpoints much more difficult. As a solution to this problem, we present an improved method for creating YAC libraries that can utilize specialized tumor-derived materials and that can be executed effectively in a small laboratory setting. Procedures that enabled more consistent DNA insert size selection and enhanced yeast transformation frequency were employed to generate a human YAC library from a neuroepithelioma cell line containing a characteristic t(11;22) chromosomal translocation. Approximately 40,000 colonies with an average insert size of 330 kilobase pairs were created. This library was screened with two single-copy probes that bracket the translocation breakpoint. YAC clones ranging from 370 to 550 kilobase pairs that were specific for each single-copy probe were identified. Specialized YAC libraries will make many more tumor-specific chromosomal abnormalities accessible to molecular isolation.
Antibacterial and Antimembrane Activities of Cecropin A in Escherichia coli (2000)

The ability of cecropin A to permeabilize and depolarize the membranes of Escherichia coli ML-35p bacteria has been compared to its bactericidal activity in an extension of earlier studies performed on synthetic lipid vesicle membranes (L. Silvestro, K. Gupta, J. H. Weiser, and P. H. Axelsen, Biochemistry 36:11452-11460, 1997). Our results indicate that differences in the concentration dependences of membrane permeabilization and depolarization seen in synthetic vesicles are not manifested in whole bacteria. The concentration dependences of both phenomena roughly correlate with bactericidal activity, suggesting that the bactericidal mechanism of cecropin A is related to membrane permeabilization.
Ultra-High Throughput Synthesis of Nanoparticles with Homogeneous Size Distribution Using a Coaxial Turbulent Jet Mixer (2014)

High-throughput production of nanoparticles (NPs) with controlled quality is critical for their clinical translation into effective nanomedicines for diagnostics and therapeutics. Here we report a simple and versatile coaxial turbulent jet mixer that can synthesize a variety of NPs at high throughput up to 3 kg/d, while maintaining the advantages of homogeneity, reproducibility, and tunability that are normally accessible only in specialized microscale mixing devices. The device fabrication does not require specialized machining and is easy to operate. As one example, we show reproducible, high-throughput formulation of siRNA-polyelectrolyte polyplex NPs that exhibit effective gene knockdown but exhibit significant dependence on batch size when formulated using conventional methods. The coaxial turbulent jet mixer can accelerate the development of nanomedicines by providing a robust and versatile platform for preparation of NPs at throughputs suitable for in vivo studies, clinical trials, and industrial-scale production.
Analysis of the fine specificity and cross-reactivity of monoclonal anti-lipid A antibodies. (1986)

We have investigated the fine specificity of anti-lipid A antibodies to identify conserved lipid A antigens. Because lipid A derived from many different Gram-negative bacteria has similar biologic activities, the conserved regions may be of particular importance for the immunostimulatory and toxic properties of lipid A. We found that five of nine antibodies bound to a wide variety of Gram-negative bacteria. All these widely cross-reactive antibodies bound to the same antigenic site within lipid A. Polymyxin B, an inhibitor of lipid A activity, bound to this site as well. The widely cross-reactive antibodies bound to native and base-hydrolyzed lipid A equally well, and also bound to the monosaccharide precursor lipid X. The less cross-reactive antibodies recognized base-hydrolyzed lipid A poorly, and did not recognize lipid X at all. Other investigators have shown that lipid X has some of the activities of lipid A in vitro and can inhibit the lethal toxicity of LPS in vivo. On the basis of this study, we suggest that lipid X contains a conserved lipid A epitope as well.