gebhart/patrepeval huggingface dataset:
Catalytic, Mild, and Selective Oxyfunctionalization of Linear Alkanes: Current Challenges (2012)

Selective catalysts for sustainable oxidation of alkanes are highly demanded because of the abundance of these molecules in the environment, the possibility to transform them into higher-value compounds, such as chemicals or synthetic fuels, and the fact that, kinetically speaking, this is a difficult reaction. Numerous chemical and biological catalysts have been developed in the lasts decades for this purpose, rendering the overview over this field of chemistry difficult. After giving a definition of the ideal catalyst for alkane oxyfunctionalization, this review aims to present the catalysts available today that are closest to ideal.
Microbic Superinfection in Relapse of Inflammatory Bowel Disease (1992)

To assess the association between symptomatic relapse of inflammatory bowel disease (IBD) and superinfection with enteropathogenic microorganisms, we determined prospectively the incidence of infections with enteropathogenic bacteria, protozoa, and helminths in patients with confirmed longstanding IBD. Sixty-four patients with IBD (49 with Crohn's disease [CD] and 15 with ulcerative colitis [UC]) were consecutively enrolled in the study when relapse occurred. Multiple biopsies for histological and microbiological investigations were taken from all patients who were evaluated by colonoscopy. Parallel stool specimens were investigated for the presence of enteropathogenic bacteria, protozoa, and helminths. In six patients, we detected Clostridium difficile or toxin B (five CD, one UC), in one patient Campylobacter jejuni (CD), and in another patient Salmonella typhimurium (UC). Enteropathogenic Escherichia coli were isolated from three patients. Investigation of biopsies for Mycobacteria, microscopic examination of stool samples for helminths, and immunofluorescence for chlamydia were negative in all patients. In summary, as we found enteropathogenic microorganisms so infrequently in patients with relapse of IBD, despite intensive microbiological screening by tissue sampling for detection of gut adherent bacteria, we believe that microorganisms play only a minor role in the exacerbation of IBD.
Nonfucosylated Therapeutic IgG1 Antibody Can Evade the Inhibitory Effect of Serum Immunoglobulin G on Antibody-Dependent Cellular Cytotoxicity through its High Binding to FcγRIIIa (2006)

Our data showed that nonfucosylated IgG1, not including fucosylated counterparts, can evade the inhibitory effect of plasma IgG on ADCC through its high FcgammaRIIIa binding. Hence, nonfucosylated IgG1 exhibits strong therapeutic potential through dramatically enhanced ADCC at low doses in humans in vivo.
DNA-damaging agents stimulate gene expression at specific loci in Escherichia coli. (1980)

Operon fusions in Escherichia coli were obtained that showed increased beta-galactosidase expression in response to treatment with the DNA-damaging agent mitomycin C. These fusions were generated by using the Mud(ApR, lac) vector [Casadaban, M.J. & Cohen, S.N. (1979) Proc. Natl. Acad. Sci. USA 76, 4530-4533] to insert the lactose structural genes randomly into the bacterial chromosome. Induction of beta-galactosidase in these strains, which carried fusions of lac to these din (damage-inducible) loci, was (i) triggered by UV light as well as by mitomycin C and (ii) abolished by either a recA- or a lexA- mutation. Similar characteristics of induction were observed when the lactose genes were fused to a prophage lambda promoter by using Mud(ApR, lac). These results indicate that E. coli contains a set of genes that, like prophage lambda genes, are expressed in response to DNA-damaging agents and regulated by the recA and lexA gene products. These din genes map at five bacterial loci. One din::Mud(ApR, lac) insertion results in a UV-sensitive phenotype and may be within the uvrA transcriptional unit.
Micropositioners for microscopy applications and microbiology based on piezoelectric actuators (2002)

Founded in 1683 in Leiden, the Netherlands, Brill is a leading international academic publisher in the Humanities, Social Sciences, International Law, and Biology. With offices in the Netherlands, Germany, Austria, the USA and Asia, Brill today publishes more than 360 journals and 2,000 new books and reference works each year as well as a large number of databases and primary source research collections.
Effect of helium ion implantation and annealing on the relaxation behavior of pseudomorphic Si1−xGex buffer layers on Si (100) substrates (2002)

The influence of He implantation and annealing on the relaxation of Si0.7Ge0.3 layers on Si (100) substrates is investigated. Proper choice of the implantation energy results in a narrow defect band ≈100 nm underneath the substrate/epilayer interface. During annealing at 700–1000 °C, He-filled bubbles are created, which act as sources for misfit dislocations. Efficient annihilation of the threading dislocations is theoretically predicted, if a certain He bubble density with respect to the buffer layer thickness is maintained. The variation of the implantation dose and the annealing conditions changes density and size of spherical He bubbles, resulting in characteristic differences of the dislocation structure. Si1−xGex layers with Ge fractions up to 30 at. % relax the initial strain by 70% at an implantation dose of 2×1016 cm−2 and an annealing temperature as low as 850 °C. Simultaneously, a low threading dislocation density of 107 cm−2 is achieved. The strain relaxation mechanism in the presence of He filled bubbles is discussed.
Efficient Incremental Induction of Decision Lists - Can Incremental Learning Outperform Non-Incremental Learning? (1996)

Although incremental learning has many advantages in theory, it is not in practice as widely used as non-incremental learning for real-world applications. One major reason for this situation is the lack of incremental algorithms that can perform as fast as non-incremental algorithms in general. In this paper, we present an effective yet very efficient incremental algorithm CDL4 for learning decision lists whose complexity is O(dn 2 ), where d is the number of attributes and n the number of training instances. On the experiments we have conducted, CDL4&amp;apos;s performance is as fast and accurate as the best non-incremental learning algorithms for batch tasks, and is much faster than the best-known incremental and non-incremental learning algorithms for serial tasks. We also show that efficient incremental algorithms can provide new research opportunities for learners to actively select training instances for better accuracy and higher speed, and that incremental learning may eventually out...
Modification of adenine and cytosine derivatives with bromoacetaldehyde. (1980)

Bromoacetaldehyde reacted with adenosine 5'-phosphate and cytidine more rapidly than chloroacetaldehyde to give 1, N6-ethenoadenosine 5'-phosphate and 3, N4-ethenocytidine, respectively. The pH-dependence of the rates of these reactions was similar to that of the chloroacetaldehyde modifications reported in the literature ; i.e. the reactions proceed smoothly in the pH range of 5 to 7. When applied to polynucleotides, bromoacetaldehyde reacted with adenine and cytosine residues located in single-stranded regions but not with those in double-stranded regions. Guanosine 5'-phosphate reacted with bromoacetaldehyde at pH 7 but only very slowly at pH 5. Bromoacetaldehyde may be useful as a more reactive subtitute for chloroacetaldehyde. Bromoacetaldehyde showed little mutagenic activity when assayed on Salmonella typhymurium TA 100.
Characterization of a Replication-Defective Human Immunodeficiency Virus Type 1 att Site Mutant That Is Blocked after the 3′ Processing Step of Retroviral Integration (2000)

Two activities of retroviral integrase, 3' processing and DNA strand transfer, are required to integrate viral cDNA into a host cell chromosome. Integrase activity has been analyzed in vitro using purified protein and recombinant DNA substrates that model the U3 and U5 ends of viral cDNA or by using viral preintegration complexes (PICs) that form during virus infection. Numerous studies have investigated changes in integrase or viral DNA for effects on both 3' processing and DNA strand transfer activities using purified protein, but similar analyses have not been carried out using PICs. Here, we analyzed PICs from human immunodeficiency virus type 1 (HIV-1) strain 604del, an integration-defective mutant lacking 26 bp of U5, and revE1, a revertant of 604del containing an additional 19-bp deletion, for levels of 3' processing activity that occurred in infected cells and for levels of in vitro DNA strand transfer activity. Whereas revE1 supported one-third to one-half of the level of wild-type DNA strand transfer activity, the level of 604del DNA strand transfer activity was undetectable. Surprisingly, integrase similarly processed the 3' ends of 604del and revE1 in vivo. We therefore conclude that 604del is blocked in its ability to replicate in cells after the 3' processing step of retroviral integration. Whereas Western blotting showed that wild-type, revE1, and 604del PICs contained similar levels of integrase protein, Mu-mediated PCR footprinting revealed only minimal protein-DNA complex formation at the ends of 604del cDNA. We propose that 604del is replication defective because proteins important for DNA strand transfer activity do not stably associate with this cDNA after in vivo 3' processing by integrase.
Uncoupling protein 3 and fatty acid metabolism (2001)

A role for uncoupling protein (UCP) 3 in fatty acid metabolism is reviewed within the context of our proposal, first put forward in 1998, that this homologue of UCP1 may be involved in the regulation of lipids as fuel substrate rather than in the mediation of thermogenesis. Since then, the demonstrations of muscle-type differences in UCP3 gene regulation in response to dietary manipulations (starvation, high-fat feeding) or to pharmacological interferences with the flux of lipid substrates between adipose-tissue stores and skeletal-muscle mitochondrial oxidation are all in accord with this proposed role for UCP3 in regulating lipids as fuel substrate. However, given the current limitations of gene-knockout technology for evaluating/interpreting the functional importance of genes encoding mitochondrial membrane proteins, the transition from 'associative' to 'cause-and-effect' evidence for a physiological role of UCP3 in regulating fatty acid metabolism will have to await the development of assays that are sensitive to changes in UCP3 activity. Furthermore, in evaluating the physiological regulators of UCP3, the available evidence points to the existence of adipose-derived factor(s) which, independently of circulating levels of free fatty acids, initiates events leading to the transcription of genes encoding UCP3 and key enzymes of lipid oxidation in the fast glycolytic or fast oxidative-glycolytic muscles, i.e. in the bulk of the skeletal-muscle mass. It is proposed that in tissues where UCP3 co-exists with UCP2 (skeletal muscle, brown adipose tissue, heart) they may act in concert in the overall regulation of lipid oxidation, concomitant to the prevention of lipid-induced oxidative damage.
IR Spectroscopic Studies of Adsorption of Dithiol-Containing Ligands on CdS Nanocrystal Films in Aqueous Solutions (2007)

The adsorption of the ligands alpha-lipoic acid, dihydrolipoic acid, and dithiothreitol to films of deposited CdS nanoparticles was studied in situ by ATR-IR spectroscopy. For alpha-lipoic acid and dihydrolipoic acid, the spectra of the adsorbed species closely resemble those of the respective solution species. However, for dithiothreitol, the spectrum of the adsorbed species is significantly different from that of the solution species and is attributed to an interruption of intermolecular hydrogen bonding upon adsorption to the CdS. The S-H stretching absorption of the dihydrolipoic acid solution species at pH=8.6 is observed at 2542 cm(-1). The corresponding absorptions for dithiothreitol occur at 2578 and 2528 cm(-1) and are attributed to monomers and dimers. Adsorption of dihydrolipoic acid and dithiothreitol is found to occur via both thiol functional groups and an additional interaction between the carboxylate and the CdS surface. The adsorption of alpha-lipoic acid to CdS in the presence of light proceeds with photo-oxidation of the CdS surface and reductive cleavage of the disulfide bond of alpha-lipoic acid to produce some adsorbed dihydrolipoic acid and thiosulfate. The adsorption of alpha-lipoic acid to CdS in the absence of visible light shows no photo-oxidation and suggests that adsorption occurs via retention of the disulfide bond. The adsorption isotherm data for dihydrolipoic acid and dithiothreitol gave good fits to the Langmuir isotherm, with adsorption constants higher than those for monothiol-containing ligands on CdS. The Langmuir adsorption constant for n-octanoic acid on CdS indicates that the additional interaction between the carboxylate group of dihydrolipoic acid and the CdS is weak in comparison with the dithiol interaction with CdS.
Cloning and Functional Expression of a Human Y4 Subtype Receptor for Pancreatic Polypeptide, Neuropeptide Y, and Peptide YY (1995)

The pancreatic polypeptide family includes pancreatic polypeptide (PP), neuropeptide Y (NPY), and peptide YY (PYY). Members of the PP family regulate numerous physiological processes, including appetite, gastrointestinal transit, anxiety, and blood pressure. Of the multiple Y-type receptors proposed for PP family members, only the Y1 subtype has been cloned previously. We now report the cloning of an additional Y-type receptor, designated Y4, by homology screening of a human placental genomic library with transmembrane (TM) probes derived from the rat Y1 gene. The Y4 genomic clone encodes a predicted protein of 375 amino acids that is most homologous to Y1 receptors from human, rat, and mouse (42% overall; 55% in TM). 125I-PYY binding to transiently expressed Y4 receptors was saturable (pKd = 9.89) and displaceable by human PP family derivatives: PP (pKi = 10.25) approximately PP2-36 (pKi = 10.06) > PYY (pKi = 9.06) approximately [Leu31,Pro34]NPY (pKi = 8.95) > NPY (pKi = 8.68) > PP13-36 (pKi = 7.13) > PP31-36 (pKi = 6.46) > PP31-36 free acid (pKi < 5). Human PP decreased [cAMP] and increased intracellular [Ca2+] in Y4-transfected LMTK- cells. Y4 mRNA was detected by reverse transcriptase-polymerase chain reaction in human brain, coronary artery, and ileum, suggesting potential roles for Y4 receptors in central nervous system, cardiovascular, and gastrointestinal function.
Small-molecule Antagonists of the Orexin Receptors (2014)

The orexin-1 and orexin-2 receptors are two G protein-coupled receptors that bind the neuropeptides orexin-A and orexin-B. Dual antagonism of the receptors by small molecules is clinically efficacious in the treatment of insomnia, where the most advanced molecule suvorexant has recently been approved. The scope of this article is to review the small molecule orexin receptor antagonist patent literature between January 2012 and January 2014.
An Experimental Study of SBH with Gapped Probes (1999)

Sequencing by Hybridization (SBH) has been proposed as a means of automating the task of DNA sequencing. The original SBH proposal was able to sequence DNA of length about 2^k nucleotides with a cost O(4^k) (in linear time). Preparata and Upfal have recently proposed a new method, which was predicted to be able to sequence DNA of length O(4^k), still for a cost O(4^k). This work describes a simulation of the method developed to test the theoretical results.
Macromolecular basis for homocystein-induced changes in proteoglycan structure in growth and arteriosclerosis. (1972)

Cell culture monolayers deficient in cystathionine synthetase bound more inorganic sulfate than normal cell monolayers during growth to confluence; this was correlated with the production of granular proteoglycan by the abnormal cells and fibrillar proteoglycan by normal cells. Homocysteine was demonstrated to be an active precursor of esterified sulfate, confirming our previous finding of this sulfation pathway in liver. The cell cultures deficient in cystathionine synthetase were found to assume an abnormal cellular distribution on the surface of the culture dish, resembling the distribution assumed by neoplastic cells with loss of contact inhibition; the degree of abnormality of the cellular distribution was correlated with the amount of granular proteoglycan produced by the cells and the amount of inorganic sulfate binding by the cell monolayers. Pyridoxine was found to increase the growth rate of cell cultures from a patient with pyridoxineresponsive homocystinuria and to increase the production of fibrillar proteoglycan by the cells; no effect of pyridoxine was observed in the cell cultures from a patient who failed to respond to pyridoxine therapy. The findings suggest that the change in macromolecular conformation of cellular proteoglycans from fibrillar to granular is due to increased sulfation of the carbohydrate envelope of the molecule. The significance of the findings is related to the pathogenesis of homocystinuria, the phenomenon of contact inhibition, the action of growth hormone and initiation of arteriosclerotic plaques.
Permanent and panerythroid correction of murine β thalassemia by multiple lentiviral integration in hematopoietic stem cells (2002)

Achieving long-term pancellular expression of a transferred gene at therapeutic level in a given hematopoietic lineage remains an important goal of gene therapy. Advances have recently been made in the genetic correction of the hemoglobinopathies by means of lentiviral vectors and large locus control region (LCR) derivatives. However, panerythroid beta globin gene expression has not yet been achieved in beta thalassemic mice because of incomplete transduction of the hematopoietic stem cell compartment and position effect variegation of proviruses integrated at a single copy per genome. Here, we report the permanent, panerythroid correction of severe beta thalassemia in mice, resulting from a homozygous deletion of the beta major globin gene, by transplantation of syngeneic bone marrow transduced with an HIV-1-derived [beta globin gene/LCR] lentiviral vector also containing the Rev responsive element and the central polypurine tract/DNA flap. The viral titers produced were high enough to achieve transduction of virtually all of the hematopoietic stem cells in the graft with an average of three integrated proviral copies per genome in all transplanted mice; the transduction was sustained for >7 months in both primary and secondary transplants, at which time approximately 95% of the red blood cells in all mice contained human beta globin contributing to 32 +/- 4% of all beta-like globin chains. Hematological parameters approached complete phenotypic correction, as assessed by hemoglobin levels and reticulocyte and red blood cell counts. All circulating red blood cells became and remained normocytic and normochromic, and their density was normalized. Free alpha globin chains were completely cleared from red blood cell membranes, splenomegaly abated, and iron deposit was almost eliminated in liver sections. These findings indicate that virtually complete transduction of the hematopoietic stem cell compartment can be achieved by high-titer lentiviral vectors and that position effect variegation can be mitigated by multiple events of proviral integration to yield balanced, panerythroid expression. These results provide a solid foundation for the initiation of human clinical trials in beta thalassemia patients.
A New Type of a Multifunctional β-Oxidation Enzyme in Euglena (2003)

The biochemical and molecular properties of the beta-oxidation enzymes from algae have not been investigated yet. The present study provides such data for the phylogenetically old alga Euglena (Euglena gracilis). A novel multifunctional beta-oxidation complex was purified to homogeneity by ammonium sulfate precipitation, density gradient centrifugation, and ion-exchange chromatography. Monospecific antibodies used in immunocytochemical experiments revealed that the enzyme is located in mitochondria. The enzyme complex is composed of 3-hydroxyacyl-coenzyme A (-CoA) dehydrogenase, 2-enoyl-CoA hydratase, thiolase, and epimerase activities. The purified enzyme exhibits a native molecular mass of about 460 kD, consisting of 45.5-, 44.5-, 34-, and 32-kD subunits. Subunits dissociated from the complete complex revealed that the hydratase and the thiolase functions are located on the large subunits, whereas two dehydrogenase functions are located on the two smaller subunits. Epimerase activity was only measurable in the complete enzyme complex. From the use of stereoisomers and sequence data, it was concluded that the 2-enoyl-CoA hydratase catalyzes the formation of L-hydroxyacyl CoA isomers and that both of the different 3-hydroxyacyl-CoA dehydrogenase functions on the 32- and 34-kD subunits are specific to L-isomers as substrates, respectively. All of these data suggest that the Euglena enzyme belongs to the family of beta-oxidation enzymes that degrade acyl-CoAs via L-isomers and that it is composed of subunits comparable with subunits of monofunctional beta-oxidation enzymes. It is concluded that the Euglena enzyme phylogenetically developed from monospecific enzymes in archeons by non-covalent combination of subunits and presents an additional line for the evolutionary development of multifunctional beta-oxidation enzymes.
Pyruvate decarboxylase: An indispensable enzyme for growth of Saccharomyces cerevisiae on glucose (1996)

In Saccharomyces cerevisiae, the structural genes PDC1, PDC5 and PDC6 each encode an active pyruvate decarboxylase. Replacement mutations in these genes were introduced in a homothallic wild-type strain, using the dominant marker genes APT1 and Tn5ble. A pyruvate-decarboxylase-negative (Pdc-) mutant lacking all three PDC genes exhibited a three-fold lower growth rate in complex medium with glucose than the isogenic wild-type strain. Growth in batch cultures on complex and defined media with ethanol was not impaired in Pdc- strains. Furthermore, in ethanol-limited chemostat cultures, the biomass yield of Pdc- and wild-type S. cerevisiae were identical. However, Pdc- S. cerevisiae was unable to grow in batch cultures on a defined mineral medium with glucose as the sole carbon source. When aerobic, ethanol-limited chemostat cultures (D = 0 center dot 10 h-1) were switched to a feed containing glucose as the sole carbon source, growth ceased after approximately 4 h and, consequently, the cultures washed out. The mutant was, however, able to grow in chemostat cultures on mixtures of glucose and small amounts of ethanol or acetate (5% on a carbon basis). No growth was observed when such cultures were used to inoculate batch cultures on glucose. Furthermore, when the mixed-substrate cultures were switched to a feed containing glucose as the sole carbon source, wash-out occurred. It is concluded that the mitochondrial pyruvate dehydrogenase complex cannot function as the sole source of acetyl-CoA during growth of S. cerevisiae on glucose, neither in batch cultures nor in glucose-limited chemostat cultures.
Management of Venous Thromboembolism (1996)

Venous thromboembolism, which includes deep-vein thrombosis (usually involving leg veins) and pulmonary embolism, is a common cause of death. Treatment of affected patients reduces the incidence of fatal pulmonary embolism, but therapy should be based on the severity of disease and the potential for side effects. Decisions about the duration of therapy should be made by balancing the risks of continuing therapy against the risk of recurrence. In this review, the care of patients with venous thromboembolism will be discussed, with emphasis on recent advances.DiagnosisApproximately 75 percent of patients who present with suspected venous thrombosis or pulmonary embolism . . .