gebhart/patrepeval huggingface dataset:
Genetic Immunization (1996)

Genetic immunization, the latest addition to the field of vaccinology, has shown, in a number of animal models, to be an efficacious approach to induce protective immunity to infectious diseases. The advantages of DNA vaccines are their ease of construction, the low expanse of mass production, their high temperature stability, and their ability to induce a full spectrum of exceptionally long-lasting immune responses including cytolytic T cells. Their potential disadvantages are putative safety issues such as integration into the host cell genome. The slow development of the immune response to genetic immunization will make these vaccines unsuitable for treatment of some infectious diseases such as postexposure vaccination to rabies virus, where a rapid immune response is warranted. Although only time will tell if genetic immunization provides a viable alternative for human immunization, in the meantime this approach provides immunologists with a powerful tool to gain further insight in the mechanisms that drive primary immune responses.
A test chip for ISFET/CMNOS technology development (2002)

A dedicated test chip has been designed and fabricated for assessing the compatibility of the ISFET (Ion Sensitive Field Effect Transistors) and CMNOS (Complementary Metal gate Nitride Oxide Semiconductor) technologies, in order to develop an ISFET/CMOS fabrication process. The test chip contains three sets of test structures dedicated respectively to the evaluation of the sensor performances in terms of electro-chemical characteristics, to the extraction of the CMNOS process/design (e.g. SPICE) parameters, and to the characterisation of basic analogue integrated circuit blocks for the on chip interface electronics. By using this technology single chemical sensors, arrays sensors and multi-sensors with on-chip signal conditioning for environmental and biomedical applications are currently under development in our laboratory.
Sequence dependence of protein isoprenylation (1991)

Several proteins have been shown to be post-translationally modified on a specific C-terminal cysteine residue by either of two isoprenoid biosynthetic pathway metabolites, farnesyl diphosphate or geranylgeranyl diphosphate. Three enzymes responsible for protein isoprenylation were resolved chromatographically from the cytosolic fraction of bovine brain: a farnesyl-protein transferase (FTase), which modified the cell-transforming Ras protein, and two geranyl-geranyl-protein transferases, one (GGTase-I) which modified a chimeric Ras having the C-terminal amino acid sequence of the gamma-6 subunit of heterotrimeric GTP-binding proteins, and the other (GGTase-II) which modified the Saccharomyces cerevisiae secretory GTPase protein YPT1. In a S. cerevisiae strain lacking FTase activity (ram1), both GGTases were detected at wild-type levels. In a ram2 S. cerevisiae strain devoid of FTase activity, GGTase-I activity was reduced by 67%, suggesting that GGTase-I and FTase activities derive from different enzymes but may share a common genetic feature. For the FTase and the GGTase-I activities, the C-terminal amino acid sequence of the protein substrate, the CAAX box, appeared to contain all the critical determinants for interaction with the transferase. In fact, tetrapeptides with amino acid sequences identical to the C-terminal sequences of the protein substrates for FTase or GGTase-I competed for protein isoprenylation by acting as alternative substrates. Changes in the CAAX amino acid sequence of protein substrates markedly altered their ability to serve as substrates for both FTase and GGTase-I. In addition, it appeared that FTase and GGTase-I had complementary affinities for CAAX protein substrates; that is, CAAX proteins that were good substrates for FTase were, in general, poor substrates for GGTase-I, and vice versa. In particular, a leucine residue at the C terminus influenced whether a CAAX protein was either farnesylated or geranylgeranylated preferentially. The YPT1 C terminus peptide, TGGGCC, did not compete or serve as a substrate for GGTase-II, indicating that the interaction between GGTase-II and YPT1 appeared to depend on more than the 6 C-terminal residues of the protein substrate sequence. These results identify three different isoprenyl-protein transferases that are each selective for their isoprenoid and protein substrates.
A family with tau-negative frontotemporal dementia and neuronal intranuclear inclusions linked to chromosome 17 (2006)

Over 30 different mutations have now been identified in MAPt that cause frontotemporal dementia (FTD). However, there are several families with FTD that show definite linkage to the region on chromosome 17 that contains MAPt, in which no mutation(s) has been identified. Although these families could have a complex mutation of the MAPt locus that has evaded detection it is also possible that another gene in this region is associated with FTD. This possibility is supported by neuropathological findings in these families, which consist of neuronal inclusions that are immunoreactive for ubiquitin (ub-ir) but not for tau. In addition to neuronal cytoplasmic inclusions, several chromosome 17-linked families are reported to have ub-ir neuronal intranuclear inclusions (NII); a finding which is uncommon in sporadic FTD. Here, we describe detailed clinical and neuropathological findings in a new large, multigenerational family with autosomal dominant FTD and autopsy proven tau-negative, ub-ir neuronal cytoplasmic and intranuclear inclusions. We have demonstrated that this family is linked to a 19.06 cM region of chromosome 17q21 with a maximum multipoint LOD score of 3.911 containing MAPt. By combining the results of our genetic analysis with those previously published for other families with similar pathology, we have further refined the minimal region to a 3.53 cM region of chromosome 17q21. We did not identify point mutations in MAPt by direct sequencing or any gross MAPt gene alterations using fluorescent in situ hybridization. In addition, tau protein extracted from members of this family was unremarkable in size and quantity as assessed by western blotting. Neuropathological characterization of the ub-ir NII in this family shows that they are positive for promyelocytic leukaemia protein (PML) and SUMO-1 that suggests that these inclusions form in the nuclear body and suggests a possible mechanism of neurodegeneration in tau-negative FTD linked to chromosome 17q21.
Induction of the Fatty Acid Transport Protein 1 and Acyl-CoA Synthase Genes by Dimer-selective Rexinoids Suggests That the Peroxisome Proliferator-activated Receptor-Retinoid X Receptor Heterodimer Is Their Molecular Target (2000)

The intracellular fatty acid content of insulin-sensitive target tissues determines in part their insulin sensitivity. Uptake of fatty acids into cells is a controlled process determined in part by a regulated import/export system that is controlled at least by two key groups of proteins, i.e. the fatty acid transport protein (FATP) and acyl-CoA synthetase (ACS), which facilitate, respectively, the transport of fatty acids across the cell membrane and catalyze their esterification to prevent their efflux. Previously it was shown that the expression of the FATP-1 and ACS genes was controlled by insulin and by peroxisome proliferator-activated receptor (PPAR) agonists in liver or in adipose tissue. The aim of this investigation was to determine the effects of retinoic acid derivatives on the expression of FATP-1 and ACS. In several cultured cell lines, it was shown that the expression of both the FATP-1 and ACS mRNAs was specifically induced at the transcriptional level by selective retinoid X receptor (RXR) but not by retinoic acid receptor (RAR) ligands. This effect was most pronounced in hepatoma cell lines. A similar induction of FATP-1 and ACS mRNA levels was also observed in vivo in Zucker diabetic fatty rats treated with the RXR agonist, LGD1069 (4-[1-(3,5,5,8,8-pentamethyl-5,6,7, 8-tetrahydro-2-naphthyl)ethenyl]benzoic acid). Through the use of heterodimer-selective compounds, it was demonstrated that the modulatory effect of these rexinoids on FATP-1 and ACS gene expression was mediated through activation of RXR in the context of the PPAR-RXR heterodimer. The observation that both RXR and PPAR agonists can stimulate the transcription of genes implicated in lipid metabolism, suggest that rexinoids may also act as lipid-modifying agents and support a role of the permissive PPAR-RXR heterodimer in the control of insulin sensitivity.
The NS3/4A proteinase of the hepatitis C virus: unravelling structure and function of an unusual enzyme and a prime target for antiviral therapy (1999)

The hepatitis C virus (HCV) is a major causative agent of transfusion-acquired and sporadic non-A, non-B hepatitis worldwide. Infections most often persist and lead, in approximately 50% of all patients, to chronic liver disease. As is characteristic for a member of the family Flaviviridae, HCV has a plus-strand RNA genome encoding a polyprotein, which is cleaved co- and post-translationally into at least 10 different products. These cleavages are mediated, among others, by a virally encoded chymotrypsin-like serine proteinase located in the N-terminal domain of non-structural protein 3 (NS3). Activity of this enzyme requires NS4A, a 54-residue polyprotein cleavage product, to form a stable complex with the NS3 domain. This review will describe the biochemical properties of the NS3/4A proteinase, its X-ray crystal structure and current attempts towards development of efficient inhibitors.
Comparison of methods for immobilization to carboxymethyl dextran sensor surfaces by analysis of the specific activity of monoclonal antibodies (1995)

Abstract The authors have recently described the development of a carboxymethyl dextran‐based sensor surface for biospecific interaction analysis by surface plasmon resonance. Ligands are immobilized via primary amine groups after activation of the carboxymethyl groups on the sensor surface with a mixture of N ‐hydroxysuccinimide and N ‐ethyl‐ N ′‐(dimethylaminopropyl) carbodiimide. Methods have now been developed for efficient immobilization via thiol/disulfide exchange, aldehyde coupling and biotin–avidin coupling. The specific activity of monoclonal antibodies immobilized by the four different methods was investigated by altering the immobilization conditions, e. g., activation time, protein concentration, ionic strength and the degree of modification, etc. Investigations have also been made concerning possible differences in the specific activity for antibodies immobilized using optimized conditions with respect to the four different chemistries. These studies show that, with the flexible carboxymethyl dextran matrix used here, the immobilization methods give rise to only minor differences in specific activity. Thus, with this solid support, a ‘site directed’ immobilization strategy for monoclonal antibodies has no advantage. In general the specific activity for optimized systems was approximately 75% for the binding of β2μ‐globulin to an immobilized monoclonal antibody directed against β2μ‐globulin. Reduced specific activities of immobilized antibodies induced by variation of the coupling conditions could be attributed to the deterioraton of the active site of the antibody.
CNTO 859, a humanized anti‐tissue factor monoclonal antibody, is a potent inhibitor of breast cancer metastasis and tumor growth in xenograft models (2006)

Thromboembolic complications are frequently associated with advanced cancer. Interestingly, one of the major initiators of blood coagulation, tissue factor (TF), is reported to be overexpressed in several tumor types and can be found on both tumor cells and tumor vasculature. Although the exact mechanisms have yet to be elucidated, TF expressed on tumor cells can trigger intracellular signaling events through various pathways that can lead to tumor angiogenesis, proliferation, and metastasis. There exists preclinical evidence that disruption of TF dependent signaling can effectively inhibit tumor cell migration, metastasis, and angiogenesis. Here, we report for the first time that an antibody to tissue factor can also prevent tumor growth in vivo. Prophylactic administration of CNTO 859, a humanized anti-human TF antibody, was shown to inhibit experimental lung metastasis of MDA-MB-231 human breast carcinoma cells by over 99% compared to a control antibody. Furthermore, therapeutic doses of CNTO 859 were shown to reduce tumor incidence and growth of orthotopically implanted MDA-MB-231 cells.
Crystal Structure and Function of the Isoniazid Target of Mycobacterium tuberculosis (1995)

Resistance to isoniazid in Mycobacterium tuberculosis can be mediated by substitution of alanine for serine 94 in the InhA protein, the drug's primary target. InhA was shown to catalyze the beta-nicotinamide adenine dinucleotide (NADH)-specific reduction of 2-trans-enoyl-acyl carrier protein, an essential step in fatty acid elongation. Kinetic analyses suggested that isoniazid resistance is due to a decreased affinity of the mutant protein for NADH. The three-dimensional structures of wild-type and mutant InhA, refined to 2.2 and 2.7 angstroms, respectively, revealed that drug resistance is directly related to a perturbation in the hydrogen-bonding network that stabilizes NADH binding.
Directed Mutagenesis Using the Polymerase Chain Reaction (1998)

Abstract The polymerase chain reaction (PCR) is most often used for the enzymatic amplification and direct sequencing of small quantities of nucleic acids. This technology can also be used as a quick and efficient method for introducing any desired sequence change into the DNA of interest. This unit contains two basic protocols for introducing base changes into specific DNA sequences. The first describes the incorporation of a restriction site and the second details the generation of specific point mutations. An alternate protocol describes generating point mutations by sequential PCR steps. Although the general procedure is the same in all three protocols, there are differences in the design of the synthetic oligonucleotide primers and in the subsequent cloning and analyses of the amplified fragments.
Ineffective erythropoiesis in Stat5a−/−5b−/− mice due to decreased survival of early erythroblasts (2001)

Erythropoietin (Epo) controls red cell production in the basal state and during stress. Epo binding to its receptor, EpoR, on erythroid progenitors leads to rapid activation of the transcription factor Stat5. Previously, fetal anemia and increased apoptosis of fetal liver erythroid progenitors were found in Stat5a(-/-)5b(-/-) mice. However, the role of Stat5 in adult erythropoiesis was not clear. The present study shows that some adult Stat5a(-/-)5b(-/-) mice have a near-normal hematocrit but are deficient in generating high erythropoietic rates in response to stress. Further, many adult Stat5a(-/-)5b(-/-) mice have persistent anemia despite a marked compensatory expansion in their erythropoietic tissue. Analysis of erythroblast maturation in Stat5a(-/-)5b(-/-) hematopoietic tissue shows a dramatic increase in early erythroblast numbers, but these fail to progress in differentiation. Decreased expression of bcl-x(L) and increased apoptosis in Stat5a(-/-)5b(-/-) early erythroblasts correlate with the degree of anemia. Hence, Stat5 controls a rate-determining step regulating early erythroblast survival.
Experience with rule induction and k-nearest neighbor methods for interface agents that learn (1997)

Interface agents are being developed to assist users with a variety of tasks. To perform effectively, such agents need knowledge of user preferences. An agent architecture has been developed which observes a user performing tasks, and identifies features which can be used as training data by a learning algorithm. Using the learned profile, an agent can give advice to the user on dealing with new situations. The architecture has been applied to two different information filtering domains: classifying incoming mail messages (Magi) and identifying interesting USENet news articles (UNA). This paper describes the architecture and examines the results of experimentation with different learning algorithms and different feature extraction strategies within these domains.
Organometallic Compounds of Titanium and Zirconium as Selective Nucleophilic Reagents in Organic Synthesis (1983)

Abstract The addition of carbanionic organometallic compounds (usually RLi or RMgX) to a carbonyl group—a key step in numerous syntheses—is not always straightforward. Depending on the substrate, various complications and problems may arise, but in many cases these can be remedied by addition of (RO) 3 TiCl, (RO) 3 ZrCl or (R 2 N) 3 TiX to the classic lithium and Grignard reagents. This usually leads to formation of stable organo‐titanium and ‐zirconium compounds which react highly selectively with carbonyl groups. For example, CH 3 Ti(O i Pr) 3 reacts five orders of magnitude faster with benzaldehyde than with acetophenone at room temperature; reagents of the type RTi(O i Pr) 3 add smoothly to nitro‐, ido‐, or cyano‐subsituted benzaldehyde, and the reactions may be performed in chlorinated solvents or acetonitrile; the zirconium analogues have particularly low basicity and add in high yield to α‐ and β‐tetralones or to substrates containing a nitroaldol group; the inclusion of chiral OR * groups gives enantioselective reagents (up to 90% ee ); allylic (RO 3 )Ti‐ derivatives react only at the more highly substituted carbon atom and, in addition, react diastereoselectively (up to 98% ds ) with unsymmetrical ketones. Finally, titanium reagents have also been found to effect novel transformations such as direct geminal dialkylation (CO→CMe 2 ) and alkylative amination [CO→CR(NR )]. The modification and finetuning (“taming”) of carbonyl reactivity obtainable by use of the new reagents is not dearly bought; starting materials are the cheap and harmless “titanates”, “zirconates” and the corresponding tetrachlorides.
Palladium-Catalyzed Coupling of Optically Active Amines with Aryl Bromides (1997)

The coupling of enantiomerically enriched amines with aryl bromides produces the corresponding N-aryl derivatives. The choice of ligand in the palladium-catalyzed coupling is critical to the formation of the anilines without loss of enantiomeric purity. While LnPd (L = P(o-tolyl)3) successfully catalyzes the intramolecular aryl amination of α-subsituted optically pure amines, intermolecular coupling reactions with this catalyst system gives racemized products. In contrast, intermolecular N-arylations employing LnPd (L = (±)-BINAP) gives products in good yields with no erosion of enantiopurity. A mechanism for the observed racemization is proposed. The utility of the intramolecular process is demonstrated by the synthesis of 5, an intermediate in the formal synthesis of 6, a potent ACE inhibitor.
Engineering of factors determining α‐amylase and cyclodextrin glycosyltransferase specificity in the cyclodextrin glycosyltransferase from Thermoanaerobacterium thermosulfurigenes EM1 (1998)

The starch-degrading enzymes alpha-amylase and cyclodextrin glycosyltransferase (CGTase) are functionally and structurally closely related, with CGTases containing two additional domains (called D and E) compared to the three domains of alpha-amylases (A, B and C). Amino acid residue 196 (Thermoanaerobacterium thermosulfurigenes EM1 CGTase numbering) occupies a dominant position in the active-site cleft. All alpha-amylases studied have a small residue at this position (Gly, Leu, Ser, Thr or Val), in contrast to CGTases which have a more bulky aromatic residue (Tyr or Phe) at this position, which is highly conserved. Characterization of the F196G mutant CGTase of T. thermosulfurigenes EM1 revealed that, for unknown reasons, apart from the F196G mutation, domain E as well as a part of domain D had become deleted [mutant F196G(delta'DE)]. This, nevertheless, did not prevent the purification of a stable and active mutant CGTase protein (62 kDa). The mutant protein was more similar to an alpha-amylase protein in terms of the identity of residue 196, and in the domain structure containing, however, some additional C-terminal structure. The mutant showed a strongly reduced temperature optimum. Due to a frameshift mutation in mutant F196G, a separate protein of 19 kDa with the DE domains was also produced. Mutant F196G(delta'DE) displayed a strongly reduced raw-starch-binding capacity, similar to the situation in most alpha-amylases that lack a raw-starch-binding E domain. Compared to wild-type CGTase, cyclization, coupling and disproportionation activities had become drastically reduced in the mutant F196G(delta'DE), but its saccharifying activity had doubled, reaching the highest level ever reported for a CGTase. Under industrial production process conditions, wild-type CGTase converted starch into 35% cyclodextrins and 11% linear oligosaccharides (glucose, maltose and maltotriose), whereas mutant F196G(delta'DE) converted starch into 21% cyclodextrins and 18% into linear oligosaccharides. These biochemical characteristics indicate a clear shift from CGTase to alpha-amylase specificity.
Cell surface antigens of human malignant melanoma: mixed hemadsorption assays for humoral immunity to cultured autologous melanoma cells. (1976)

We studied how frequently patients with malignant melanoma have specific antibody to cell surface antigens of cultured autologous melanoma cells as demonstrated by mixed hemadsorption assays. Of 35 patients studied over periods ranging from 1 to 36 months with Stage II, III, and IV disease, two showed consistent and high titered reactivity against autologous melanoma cells, two showed less consistent and intermediate reactivity, seven showed sporatic, low titered reactivity, and the remainder were consistently negative. A detailed analysis was carried out with the sera of one patient with sufficiently high titer against autologous melanoma cells. By direct tests and by absorption analysis with a variety of melanoma and nonmelanoma cell lines which included autologous fibroblasts, the antigen could not be demonstrated on any cell type other than the autologous melanoma.
The monoamine oxidase inhibitor phenelzine enhances the discriminative stimulus effect of nicotine in rats (2007)

In addition to delivering nicotine, tobacco smoke also inhibits monoamine oxidase (MAO). Although MAO inhibitors (MAOIs) can increase nicotine self-administration in rodents, the effects of MAOIs on the discriminative stimulus effect of nicotine are not known. This study examined the effects of three MAOIs (phenelzine, clorgyline and pargyline) with varying selectivity for MAOA and MAOB in the nicotine drug discrimination procedure in rats. Adult male Sprague-Dawley rats were trained to discriminate nicotine (0.3 mg/kg, subcutaneously) from saline in a standard, two-lever food-reinforced operant task. Once the discrimination was acquired, the ability of each MAOI to substitute for or alter the discriminative stimulus effect of nicotine was determined. In substitution tests, nicotine (0.03-0.3 mg/kg) produced full, dose-dependent substitution. Although the selective MAOA inhibitor clorgyline (3-56 mg/kg) and the selective MAOB inhibitor pargyline (3-56 mg/kg) did not elicit any nicotine-appropriate responding, partial substitution was obtained with the nonselective MAO inhibitor phenelzine (1-17 mg/kg). Phenelzine (10 mg/kg) also enhanced the discriminative stimulus effect of a low dose of nicotine (0.056 mg/kg) and prolonged the time course effect of the nicotine-training dose. These findings indicate that concomitant inhibition of MAOA and MAOB can enhance the discriminative stimulus effect of nicotine in rats.