gebhart/patrepeval huggingface dataset:
Synthetic and natural Escherichia coli free lipid A express identical endotoxic activities (1985)

The recently chemically synthesized Escherichia coli lipid A and the natural free lipid A of E. coli were compared with respect to their endotoxic activities in the following test systems: lethal toxicity, pyrogenicity, local Shwartzman reactivity, Limulus amoebocyte lysate gelation capacity, tumour necrotizing activity, B cell mitogenicity, induction of prostaglandin synthesis in macrophages, and antigenic specificity. It was found that synthetic and natural free lipid A exhibit identical activities and are indistinguishable in all tests.
Quantitation of Viral DNA by Real-Time PCR Applying Duplex Amplification, Internal Standardization, and Two-Color Fluorescence Detection (2001)

A real-time PCR method was developed to quantitate viral DNA that includes duplex amplification, internal standardization, and two-color fluorescence detection without the need to generate an external standardization curve. Applied to human parvovirus B19 DNA, the linear range was from 10(2) to at least 5 x 10(6) copies per ml of sample. The coefficient of variation was 0.29 using a run control of 2,876 copies per ml. The method reduces the risk of false-negative results, yields high precision, and is applicable for other DNA targets.
The psoralen-DNA photoreaction. Characterization of the monoaddition products from 8-methoxypsoralen and 4,5',8-trimethylpsoralen (1982)

The isolation and structural characterization are described of the major monoaddition products formed in the photoreaction of two naturally occurring psoralens, 8-methoxypsoralen and 4,5',8-trimethylpsoralen, with high molecular weight, double-stranded DNA. Hydrolysis of the psoralen-modified DNA and subsequent chromatography resulted in the isolation of four modified nucleosides from each psoralen. Structural characterization was accomplished by mass spectrometry and 1H NMR analysis. The major products, accounting for 44-52% of the covalently bound psoralen, are two diastereomeric thymidine adducts formed by cycloaddition between the 5,6 double bond of the pyrimidine and the 4',5' (furan) double bond of the psoralen. A minor product, less than 2% of the covalently bound psoralen, is a furan-side adduct to deoxyuridine, derived from an initially formed deoxycytidine adduct by hydrolytic deamination. A fourth product is a thymidine adduct where cycloaddition has taken place between the 5,6 double bond of the pyrimidine and the 3,4 (pyrone) double bond of the psoralen. This pyrone-side adduct accounts for 19% of the covalently bound 8-methoxypsoralen but for less than 3% of the covalently bound 4,5'8-trimethylpsoralen. All of the isolated adducts have cis-syn stereochemistry. The stereochemistry and product distribution of the adducts are determined in part by the constraints imposed by the DNA helix on the geometry of the noncovalent intercalation complex formed by psoralen and DNA prior to irradiation.
Schizophrenia (2007)

Schizophrenia is one of the most serious and frightening of all mental illnesses. No other disorder arouses as much anxiety in the general public, the media, and doctors. Effective treatments are available, yet patients and their families often find it hard to access good care. In the United Kingdom, as in many parts of the world, this is often due to poor service provision, but sometimes it is simply down to misinformation. In this review, we clarify the causes and presentation of schizophrenia, summarise the treatments that are available, and try to clear up a few myths. We searched the online electronic databases Web of Knowledge, the Cochrane Library, and the current National Institute for Health and Clinical Excellence (NICE) guidelines for suitable evidence based material. The name schizophrenia derives from the early observation that the illness is typified by “the disconnection or splitting of the psychic functions.”w1 Unfortunately, this has led to the misconception that the illness is characterised by a “split personality,” which it is not. Box 1 lists the common symptoms of schizophrenia. #### Box 1 Definitions of symptoms of schizophrenia ##### Positive symptoms ###### Lack of insight ###### Hallucination ###### Delusions ###### Thought disorder
Production from first-calf beef heifers fed a maintenance or low level of prepartum nutrition and ruminally undegradable or degradable protein postpartum (1991)

Two experiments were conducted in consecutive years to determine the effects of prepartum nutrient level and postpartum ruminally undegraded protein intake on nutrient status, milk production, subsequent calf production, and reproductive performance of 126 crossbred, primiparous beef heifers. Prepartum treatments were low nutrient intake (LN) (approximately 2.5 kg of TDN, .5 kg of CP animal-1.d-1 and maintenance nutrient intake (MN) (5 kg of TDN, 1 kg of CP animal-1.d-1), which were fed for 75 d before parturition. Two postpartum protein supplements were formulated to provide 250 g/d of ruminally degradable protein (RD) and one to supply ruminally undegraded protein (UD) at 250 g/d of additional UD CP compared to the RD supplement. Cholesterol was lower (P less than .01) in heifers given UD than in heifers given RD. Blood urea nitrogen was higher (P less than .01) for UD-fed heifers than for RD-fed heifers and was higher in LN heifers (P less than .06) than in MN heifers. Milk production did not differ (P greater than .11) as a result of LN, MN, UD, or RD. Postpartum cow weight gain was greatest (P less than .01) for UD and LN heifers. The percentage of heifers bred during the first estrous cycle of the breeding season was greater (P less than .02) for UD than for RD. Overall, prepartum nutrition did not interact with postpartum protein supplement, nor did it have any effect on postpartum interval, whereas UD increased cow weight gain postpartum and reduced postpartum interval.
Utilization of No‐Kor Needles for Slit‐Micrografting (1994)

The No-Kor vented needle is an excellent tool for the development of micrograft recipient sites. It demonstrates advantages over both hypodermic needles and Bard Parker blades.
Occasional memory cytotoxic T-cell responses of patients with human papillomavirus type 16-positive cervical lesions against a human leukocyte antigen-A *0201-restricted E7-encoded epitope. (1996)

Most cervical carcinoma (Cxca) cells constitutively express human papillomavirus type 16 (HPV16) E6 and E7 oncoproteins. These proteins are, therefore, attractive targets for T cell-based immunotherapy. Previously, we identified HVP16 E7-encoded CTL epitopes. In patients with cervical intraepithelial neoplasia or Cxca, little is known concerning T-cell activity against viruses in general and against HPV16 in particular. Here, we have screened the blood of 10 healthy donor controls and of 22 patients with HPV16+ cervical lesions for the presence of CTLs directed against HPV16 E7- and control influenza virus matrix-derived epitopes presented by HLA-A *0201. We detected influenza virus-specific CTLs in all donors and in the majority of patients, indicating that most patients have functioning T-cell responses despite their lesions or therapeutic interventions. Moreover, we show that patients with HPV16+ lesions occasionally have memory CTLs against a HPV16 E7-encoded epitope (sequence YMLD-LQPETT), providing evidence for natural CTL immunity against HPV16 in patients with cervical lesions. Combined, these findings raise possibilities for vaccination with HPV16 E7-encoded peptides to induce or augment CTL responses for treatment or prevention of Cxca.
The development of genetically modified K562 cells as artificial antigen presenting cells for NKT cells (P4310) (2013)

Abstract CD1d-restricted type-I Natural Killer T cells (NKTs) have been shown to mediate anti-tumor immune responses in mouse models and are associated with improved outcome in several types of cancer. However, the therapeutic application of NKTs has been limited by low numbers and functional defects of these cells in patients with cancer. To provide a means for effective ex-vivo NKT-cell expansion for cell and gene therapy applications we explored native and engineered properties of K562 cells to function as artificial antigen presenting cells (aAPC). K562 cells express an activating allele of HLA-C and propagate NK cells which compete with NKTs in the same culture. Therefore, we used zinc finger nucleases to delete the endogenous HLA-C gene in K562 cells and transduced parental and HLA-Cnull K562 cells with CD1d cDNA followed by single cell sorting and clonal expansion. The clones exhibited a range of CD1d expression. They were pulsed with a NKT ligand, αGalactosylceramide and tested as aAPC for NKTs using CFSE proliferation assay. We found that aAPC clones with an intermediate level of CD1d expression induced the highest rate of NKT-cell proliferation. No difference was observed between K562/CD1d and HLA-CnullK562/CD1d clones when purified NKTs were used as responders. In contrast to K562/CD1d, HLA-CnullK562/CD1d clones did not expand NK cells when added to primary PBMC. Therefore, these HLAnullCD1d+ aAPC can be used to selectively expand primary NKTs for adoptive cell therapy.
Organization of Intracellular Reactions with Rationally Designed RNA Assemblies (2011)

The rules of nucleic acid base-pairing have been used to construct nanoscale architectures and organize biomolecules, but little has been done to apply this technology in vivo. We designed and assembled multidimensional RNA structures and used them as scaffolds for the spatial organization of bacterial metabolism. Engineered RNA modules were assembled into discrete, one-dimensional, and two-dimensional scaffolds with distinct protein-docking sites and used to control the spatial organization of a hydrogen-producing pathway. We increased hydrogen output as a function of scaffold architecture. Rationally designed RNA assemblies can thus be used to construct functional architectures in vivo.
N-(4-Acetylphenyl)acetohydroxamic acid (1987)

C10HuNO s, Mr= 193.20, monoclinic, P2~/n, a=23.539(5), b=8.473(2), c=9.540A, fl=99.44(2) ° , V=1876.9 (7) A 3, z=8, D x- 1.367 gcm -3, Ni-filtered Cu K~ 2 -- 1.5418 A, /t -- 7-55 cm -~, F(000) = 816, T= 138 (2) K, R = 0.057 for 3018 data. The hydroxamate groups of the two crystallographically unique molecules have a trans conformation. Both molecules are roughly planar and have similar molecular conformations and identical dimensions, which are compared with those of other N-substituted acetohydroxamic acids. The molecules are linked by two intermolecular hydrogen bonds with lengths 2.631 (2)and 2.636 (2)A. Introduction. Under iron-limiting conditions, micro- organisms produce a variety of small chelating agents which solubilize ferric iron in the environment and transport the iron to the cell. Many of these metabolites chelate the iron through hydroxamic acid groups. Both naturally occurring and synthetic hydroxamic acids have been used as therapeutic agents for treatment of iron overload (Anderson & Hiller, 1977). Crystal structures of synthetic hydroxamic acids with a trans conformation include N,N'-dihydroxy-N,N'-diiso- propylhexanediamide (hipa) (Smith & Raymond, 1980), N-(4-cyanophenyl)acetohydroxamic acid (p- cnpa) (Mocherla, Powell, Barnes & van der Helm, 1983) and N-(3-cyanophenyl)acetohydroxamic acid (m-cnpa) (Mocharla, Powell & van der Helm, 1984). This article describes the crystal and molecular struc- ture of N-(4-acetylphenyl)acetohydroxamic acid (apa).
The FLP protein of the 2-micron plasmid of yeast. Purification of the protein from Escherichia coli cells expressing the cloned FLP gene. (1985)

Most laboratory strains of the yeast Saccharomyces cerevisiae contain many copies of an autonomously replicating plasmid called 2-micron circle DNA. This plasmid codes for a site-specific recombinase, the FLP protein which promotes recombination across two 599-base pair inverted repeats of the plasmid DNA. We have cloned the FLP gene under the control of a strong Escherichia coli promoter and have hyperproduced the protein in that organism. Cell-free extracts from this source promote highly efficient site-specific recombination in vitro and we have used this activity to purify the FLP protein substantially. The enzyme acts efficiently on circular and linear substrates and requires only monovalent or divalent cations for activity.
TGF-β, Smad3 and the process of progressive fibrosis (2007)

Transient adenovirus-mediated gene transfer of active TGF-beta1 (transforming growth factor-beta1) induces severe and progressive fibrosis in rodent lung without apparent inflammation. Alternatively, transfer of IL-1beta (interleukin 1beta) induces marked tissue injury and inflammation, which develops into progressive fibrosis, associated with an increase in TGF-beta1 concentrations in lung fluid and tissue. Both vector treatments induce a fibrotic response involving myofibroblasts and progressive matrix deposition starting at the peri-bronchial site of expression and extending over days to involve the entire lung and pleural surface. Administration of the TGF-beta1 vector to the pleural space induces progressive pleural fibrosis, which minimally extends into the lung parenchyma. The mechanisms involved in progressive fibrosis need to account for the limitation of fibrosis to specific organs (lung fibrosis and not liver fibrosis or vice versa) and the lack of effect of anti-inflammatory treatments in regulating progressive fibrosis. TGF-beta1 is a key cytokine in the process of fibrogenesis, using intracellular signalling pathways involving the ALK5 receptor and signalling molecules Smad2 and Smad3. Transient gene transfer of either TGF-beta1 or IL-1beta to Smad3-null mouse lung provides little evidence of progressive fibrosis and no fibrogenesis-associated genes are induced. These results suggest that mechanisms of progressive fibrosis involve factors presented within the context of the matrix that define the microenvironment for progressive matrix deposition.
Candida albicans and its metabolite gliotoxin inhibit platelet function via interaction with thiols (2010)

Platelets bind to Candida albicans, the major cause of candidiasis. But in contrast to other microorganisms the fungus does not aggregate platelets. Gliotoxin (GT), which possesses immunosuppressive properties, is produced by various fungi, including the opportunistic pathogens Aspergillus fumigatus and C. albicans . Its mode of action involves the formation of mixed disulfides with host proteins. Disulfide exchanges play an important role in platelet activation. Therefore, the effect of C. albicans and GT on platelet function was tested. C. albicans yeast cells (5,000-10,000 cells/microl) and GT, in pathophysiologically relevant concentrations (0.05-0.5 microM), inhibited platelet fibrinogen binding, anti gp IIb/IIIa antibody PAC-1 binding, aggregation and procoagulant activity in a dose-dependent manner. Alpha granule release, measured via CD62P surface expression, was not affected. Addition of reduced glutathione partially counteracted the effect of C. albicans and GT on platelet fibrinogen binding and platelet aggregation. The C. albicans metabolite GT features antithrombotic properties in addition to its immunosuppressive functions. Since treatment with reduced glutathione partially counteracted the inhibitory effect of C. albicans yeast cells and GT on platelet fibrinogen binding, the antithrombotic activity is likely to depend on the disulfide bridge of this mycotoxin. GT production by C. albicans could contribute to its survival in the blood stream during vascular infections. The knowledge of the underlying mechanisms of the antithrombotic properties might help to treat fungal infections as well as thrombosis.
Cell surface ADP-ribosyltransferase regulates lymphocyte function-associated molecule-1 (LFA-1) function in T cells (1996)

Post-translational modifications are important in regulating the functions of signal proteins. This is well established for intracellular proteins, but little is known in the case of extracellular domains of cell surface molecules. We recently described a cell surface protein, mono-ADP-ribosyltransferase (ADPRT), on cytotoxic T cells and showed that it mediates attachment of ADP-ribose to cell surface proteins. Concomitantly, cytolytic activity and cell proliferation are inhibited. Here we report that one of the principal proteins modified by this enzyme is lymphocyte function-associated molecule-1 (LFA-1). While both chains are ADP-ribosylated on the extracellular domain of the molecule, persistence of the modification differs between the chains. Label is released from the beta-chain by 1 h, yet remains for at least 6 h on the alpha-chain. Loss of label is suppressed by phosphodiesterase inhibitors such as ADP-ribose and p-nitrophenylthymidine 5'-monophosphate, pointing to the involvement of this class of enzyme. Modification of LFA-1 requires expression of the cell surface ADPRT and causes the loss of epitopes recognized by alpha- and beta-chain-specific Abs. Concomitantly, the generation of inositol phosphates induced by Ab cross-linking of LFA-1 is significantly inhibited. Consistent with this effect, anti-LFA-1-induced homotypic cell adhesion is also inhibited. These effects are not seen in cells from which the ADPRT was removed by phospholipase C. Moreover, cells lacking the cell surface ADPRT are not inhibited by NAD in the cell adhesion assay, but gain this property upon transfection with the ADPRT gene. It is concluded that the cell surface protein mono-ADPRT regulates LFA-1 functions.
Regulation of B Lymphocyte Responses to Foreign and Self-Antigens by the CD19/CD21 Complex (2000)

The membrane protein complex CD19/CD21 couples the innate immune recognition of microbial antigens by the complement system to the activation of B cells. CD21 binds the C3d fragment of activated C3 that becomes covalently attached to targets of complement activation, and CD19 co-stimulates signaling through the antigen receptor, membrane immunoglobulin. CD21 is also expressed by follicular dendritic cells and mediates the long-term retention of antigen that is required for the maintenance of memory B cells. Understanding of the biology of this receptor complex has been enriched by analyses of genetically modified mice; these analyses have uncovered roles not only in positive responses to foreign antigens, but also in the development of tolerance to self-antigens. Studies of signal transduction have begun to determine the basis for the coreceptor activities of CD19. The integration of innate and adaptive immune recognition at this molecular site on the B cell guides the appropriate selection of antigen by adaptive immunity and emphasizes the importance of this coreceptor complex.
Effect of short-term ethanol on the proliferative response of Swiss 3T3 cells to mitogenic growth factors (2000)

Both adaptive and deleterious responses of cells to ethanol are likely triggered by short-term interactions of the cells with ethanol. Many studies have demonstrated the direct effect of ethanol on growth factor-stimulated cell proliferation. Using Swiss 3T3 cells whose growth was inhibited by ethanol in a concentration-dependent manner, we further investigated the molecular mechanisms of acute ethanol treatment by examining its effect on EGF- and PDGF-mediated cellular signaling systems for the mitogenic function. Tyrosine autophosphorylation of the growth factor receptors was partially prevented by ethanol in intact cells. When ethanol was included before or after EGF stimulation, no effect on the receptor signaling was observed. Here we also report that ethanol inhibits activation of ERK induced by both EGF and PDGF. EGF-induced JNK activation was reduced but PDGF-induced rapid JNK activation was delayed by the addition of ethanol. The balance between its inhibitory and stimulatory effect on the signaling molecules might determine the rate of cell growth.
Talbot array illuminators with liquid crystal displays (1997)

First we show that a binary amplitude grating, altered by a suitable discrete phase modulation is transformed, by Fresnel diffraction, into another binary grating with reduced opening ratio. We employ this process as the basis for discussing segmented versions of Talbot array illuminators that can be displayed with liquid crystal displays.
Novel Glycerolipids and Glycolipids from the Surface Lipids ofNicotiana benthamiana (1992)

Journal Article Novel Glycerolipids and Glycolipids from the Surface Lipids of Nicotiana benthamiana Get access Toshiake Matsuzaki, Toshiake Matsuzaki Tobacco Science research Laboratory, Japan Tobacco Inc., Umegaoka 6–2, Midori-ku, Yokohama 227, Japan Search for other works by this author on: Oxford Academic Google Scholar Yasuhiro Shinozaki, Yasuhiro Shinozaki Tobacco Science research Laboratory, Japan Tobacco Inc., Umegaoka 6–2, Midori-ku, Yokohama 227, Japan Search for other works by this author on: Oxford Academic Google Scholar Manabu Hagimori, Manabu Hagimori Tobacco Science research Laboratory, Japan Tobacco Inc., Umegaoka 6–2, Midori-ku, Yokohama 227, JapanApplied Plant Research Laboratory, Japan Tobacco Inc., Oaza Idei 1900, Oyama, Tochigi 323, Japan Search for other works by this author on: Oxford Academic Google Scholar Tetsuya Tobita, Tetsuya Tobita Tobacco Science research Laboratory, Japan Tobacco Inc., Umegaoka 6–2, Midori-ku, Yokohama 227, Japan Search for other works by this author on: Oxford Academic Google Scholar Hitoshi Shigematsu, Hitoshi Shigematsu Tobacco Science research Laboratory, Japan Tobacco Inc., Umegaoka 6–2, Midori-ku, Yokohama 227, Japan Search for other works by this author on: Oxford Academic Google Scholar Akira Koiwai Akira Koiwai Tobacco Science research Laboratory, Japan Tobacco Inc., Umegaoka 6–2, Midori-ku, Yokohama 227, JapanLife Science Research Laboratory, Japan Tobacco Inc., Umegaoka 6–2, Midori-ku, Yokohama 227, Japan Search for other works by this author on: Oxford Academic Google Scholar Bioscience, Biotechnology, and Biochemistry, Volume 56, Issue 10, 1 January 1992, Pages 1565–1569, https://doi.org/10.1271/bbb.56.1565 Published: 01 January 1992 Article history Published: 01 January 1992 Received: 05 March 1992
Discontinuous Mechanism of Transcription Elongation (1994)

During transcription elongation, three flexibly connected parts of RNA polymerase of Escherichia coli advance along the template so that the front-end domain is followed by the catalytic site which in turn is followed by the RNA product binding site. The advancing enzyme was found to maintain the same conformation throughout extended segments of the transcribed region. However, when the polymerase traveled across certain DNA sites that seemed to briefly anchor the front-end domain, cyclic shifting of the three parts, accompanied by buildup and relief of internal strain, was observed. Thus, elongation proceeded in alternating laps of monotonous and inchworm-like movement with the flexible RNA polymerase configuration being subject to direct sequence control.