gebhart/patrepeval huggingface dataset:
Antitumor Agents. Part 184. Syntheses and antitubulin activity of compounds derived from reaction of thiocolchicone with amines: Lactams, alcohols, and ester analogs of allothiocolchicinoids (1998)

Abstract 7‐ O ‐Substituted analogs of deaminodeoxycolchinol thiomethyl ether were synthesized and evaluated for their inhibitory effects on tubulin polymerization in vitro . Ketone 9 , a key compound in this study, was derived from thiocolchicone 6 by reaction with aniline. Reaction of compound 6 with MeNH 2 or BuNH 2 gave tetracyclic lactams 7 and 8 , respectively. Optically active alcohols 11a and 11b were obtained from racemic 11 by chemical resolution including a separation of the comphanate diastereoisomers 12a and 12b , followed by basic hydrolysis. The (a R ,7 R )‐configuration of 12b was verified by X‐ray crystallographic analysis. Almost all racemic and optically active 7‐ O ‐acyl or 7‐ O ‐aroyl compounds had strong inhibitory effects on the tubulin polymerization reaction, with IC 50 values from 1.7 to 5.1 μM. A few agents, such as the lactams 7 and 8 , the camphanates 12a and 12b , the cyclohexanecarboxylates 19a and 19b , and, most notably, the (7 S )‐benzoate 15a , had negligible effects on polymerization, yielding IC 50 values greater than 40μ M . Ketone 9 showed strong inhibition of tubulin polymerization comparable to that of thiocolchicone ( 6 ). Optically active alcohol 11a and acyl esters 13a and 14a with a (7 S )‐configuration were more active than the (7 R )‐esters 13b and 14b . However, the esters 15a – 17a with a (7 S )‐configuration were less active than the (7 R )‐isomers 15b – 17b , in which the (7 R )‐benzoate 15b was at least 15‐fold more inhibitory than the (7 S )‐isomer 15a . For the most part, the agents causing strongest inhibition of polymerization also caused the greatest inhibition of [ 3 H]colchicine binding. NMR and optical rotatory data indicate that, in polar solvents, the equilibrium in esters with a 7‐ O ‐aroyl substituent, i.e. , 15a , b , 16a , b , and 17a , b , is reversed from (a S ) to (a R ) or from (a R ) to (a S ), as compared to nonpolar solvents.
Structure and Localization of Genes Encoding Aberrant and Normal Epidermal Growth Factor Receptor RNAs from A431 Human Carcinoma Cells (1985)

A431 cells have an amplification of the epidermal growth factor (EGF) receptor gene, the cellular homolog of the v-erb B oncogene, and overproduce an aberrant 2.9-kilobase RNA that encodes a portion of the EGF receptor. A cDNA (pE15) for the aberrant RNA was cloned, sequenced, and used to analyze genomic DNA blots from A431 and normal cells. These data indicate that the aberrant RNA is created by a gene rearrangement within chromosome 7, resulting in a fusion of the 5' portion of the EGF receptor gene to an unidentified region of genomic DNA. The unidentified sequences are amplified to about the same degree (20- to 30-fold) as the EGF receptor sequences. In situ hybridization to chromosomes from normal cells and A431 cells show that both the EGF receptor gene and the unidentified DNA are localized to the p14-p12 region of chromosome 7. By using cDNA fragments to probe DNA blots from mouse-A431 somatic cell hybrids, the rearranged receptor gene was shown to be associated with translocation chromosome M4.
Mitochondrial uncoupling proteins. (1999)

The mechanisms explaining the imperfect coupling of respiration to ADP phosphorylation in mitochondria are not well understood. In the case of a thermogenic organ such as brown adipose tissue, heat production results from a regulated uncoupling of respiration due to a specific uncoupler present in the inner mitochondrial uncoupling protein, referred to as uncoupling protein (UCP)-1. UCP1 functions as a proton translocator regulated by fatty acids. Two UCP homologues were identified very recently; UCP2 is expressed in most organs, whereas UCP3 expression is restricted to skeletal muscle and brown adipose tissue. Experimental data support the respiration uncoupling activity of UCP2 and UCP3. Physiological and genetic data are in agreement with thermogenic activity of the two proteins, although other physiological data favor a role for UCP2 and UCP3 in lipid handling rather than in energy expenditure. UCP2 and UCP3 may also be involved in inflammation, immune response and fever. Many hormones and certain pharmacological regulators affect expression level of UCP2 and/or UCP3 gene.
Current concepts of PLP and its role in the nervous system (1998)

Proteolipid protein (PLP) and its smaller isoform DM20 constitute the major myelin proteins of the CNS. Mutations of the X-linked Plp gene cause the heterogeneous syndromes of Pelizaeus-Merzbacher disease (PMD) and spastic paraplegia (SPG) in man and similar dysmyelinating disorders in a range of animal species. A variety of mutations including missense mutations, deletions, and duplications are responsible. Missense mutations cause a predicted alteration in primary structure of the encoded protein(s) and are generally associated with early onset of signs and generalised dysmyelination. The severity of the phenotype varies according to the particular codon involved and the influence of uncharacterised modifying genes. There is some evidence that the dysmyelination results from the altered protein acquiring a novel function deleterious to the oligodendrocyte's function. Transgenic mice carrying extra copies of the Plp gene provide a valid model of PMD/SPG due to gene duplication. Depending on the gene dosage, the phenotype can vary from early onset of severe and lethal dysmyelination through to a very late onset of a tract-specific demyelination and axonal degeneration. Mice with a null mutation of the Plp gene assemble and maintain normal amounts of myelin but develop a progressive axonopathy, again demonstrating tract specificity. The results indicate that the functions of PLP are far from clear. There is good evidence that it is involved in the formation of the intraperiod line of myelin, and the results from the knockout and transgenic mice suggest a role in the interaction of oligodendrocyte and axon.
Perturbation of rRNA Synthesis in the bap28 Mutation Leads to Apoptosis Mediated by p53 in the Zebrafish Central Nervous System (2006)

Zebrafish is a powerful vertebrate model system for using forward genetics to elucidate mechanisms of early development. We have used chemical mutagenesis to screen for mutants that show defects in the CNS. Here we describe the isolation of the bap28 mutation that leads to abnormalities in the brain starting at midsomitogenesis stages. Mutant embryos display excess apoptosis primarily in the central nervous system (CNS) and die by days 6-7 after fertilization. The mutation was positionally cloned and shown to affect a gene that encodes a large protein with high similarity to the uncharacterized human protein BAP28 and lower similarity to yeast Utp10. Utp10 is a component of a nucleolar U3 small nucleolar RNA-containing RNP complex that is required for transcription of ribosomal DNA and for processing of 18 S rRNA. We show that zebrafish Bap28 likewise is required for rRNA transcription and processing, with a major effect on 18 S rRNA maturation. We suggest that bap28 is required for cell survival in the CNS through its role in rRNA synthesis and processing. Inhibition of p53 protein expression in bap28 mutants led to embryos with morphologically normal appearance, suggesting that p53 is involved in triggering apoptosis in the bap28 mutant CNS. The bap28 mutation provides a genetic approach to study the role of ribosome biogenesis in the development of a vertebrate embryo.
De-regulation of common housekeeping genes in hepatocellular carcinoma (2007)

As shown here in the case of HCV-induced HCC, the most constantly expressed gene is the arginine/serine-rich splicing factor 4 (SFRS4). The utilization of at least two genes for normalization is robust and advantageous, because they can compensate for slight differences of their expression when not co-regulated. The combination of ribosomal protein large 41 (RPL41) and SFRS4 used for normalization led to very similar results as SFRS4 alone and is a very good choice for reference in this disease as shown on four differentially expressed genes.
Percutaneous balloon aortic valvotomy. (1993)

We report our first case of percutaneous balloon aortic valvotomy in a 72-year-old Chinese female with critical aortic stenosis and carcinoma of the stomach. The presence of critical aortic stenosis (mean aortic pressure gradient of 65 mmHg and an aortic valve area of 0.5 cm2) placed her at a high risk for gastrectomy. After balloon valvotomy of the aortic valve, the mean pressure gradient fell to 21 mmHg and the aortic valvular area increased to 1.0 cm2. She improved clinically and subsequently underwent surgery with no haemodynamic complication. Overseas experience has shown that percutaneous balloon valvotomy can be done with little technical difficulty and excellent patient tolerance, resulting in good haemodynamic and clinical improvement and a low acute complication rate. Present follow-up data however suggest significant mortality and restenosis rates at the end of one year. Percutaneous balloon aortic valvotomy (PBAV) has a significant though narrowly defined role in the management of patients with severe calcific aortic stenosis.
A vaccinia replication system for producing recombinant hepatitis C virus (2004)

This cell culture system is capable of producing high titer recombinant HCV.
Molecular Recognition by Self-Assembled Monolayers of Cavitand Receptors (1994)

It is shown by angle-resolved x-ray photoelectron spectroscopy that cavitands derived from resorcin[4]arenes provided with four dialkylsulfide chains form stable monolayers on gold surfaces that are well organized by self-assembly. The cavitand headgroups at the surface of the resorcin[4]arene monolayer act as molecular recognition sites for small organic molecules with remarkable selectivity for perchloroethylene (C(2)Cl(4)). Comparative thermal desorption experiments indicate binding sites with high interaction energies of C(2)Cl(4) at the surface of the resorcin[4]arene monolayers. Fast and reversible "host-guest" interactions were found by the monitoring of extremely small mass changes (in the nanogram range) with a quartz microbalance oscillator provided with gold electrodes coated by resorcin[4]arene monolayers.
A chromosomal Agrobacterium tumefaciens gene required for effective plant signal transduction (1990)

The vir gene products of Agrobacterium tumefaciens carry out the transfer of T-DNA to the plant genome. Effective transcriptional induction of the vir genes by plant signal molecules is controlled by two vir gene products, VirA and VirG. In this study we have identified and cloned a chromosomal region which is also required for vir gene induction. Transposon insertions within this region reduce induction significantly and strongly attenuate virulence, resulting in a restricted host range for infection. The reduction in vir gene transcription can be partially overcome by high concentrations of the inducer molecule acetosyringone. Expression of virG at low pH and low phosphate concentrations, which is independent of plant signals, is not affected by these mutations. Sequence analysis of the region revealed two divergent open reading frames, which we have designated chvE and ORF1. Several transposon insertions mapped in chvE; this resulted in attenuated virulence. chvE codes for a putative protein which is homologous to two periplasmic receptor proteins involved in chemotaxis and uptake of sugars. Whether ORF1 is required for virulence is uncertain. One transposon insertion resulting in avirulence maps in or near the 5' end of ORF1, and several which do not affect virulence map in its 3' end. ORF1 codes for a putative protein which is homologous to a family of transcriptional activator proteins.
Interleukin‐1‐inducible MCPIP protein has structural and functional properties of RNase and participates in degradation of IL‐1β mRNA (2009)

In human monocyte-derived macrophages, the MCPIP gene (monocyte chemoattractant protein-induced protein) is strongly activated by interleukin-1beta (IL-1beta). Using bioinformatics, a PIN domain was identified, spanning amino acids 130-280; such domains are known to possess structural features of RNases. Recently, RNase properties of MCPIP were confirmed on transcripts coding for interleukins IL-6 and IL-12p40. Here we present evidence that siRNA-mediated inhibition of the MCPIP gene expression increases the level of the IL-1beta transcript in cells stimulated with LPS, whereas overexpression of MCPIP exerts opposite effects. Cells with an increased level of wild-type MCPIP showed lower levels of IL-1beta mRNA. However, this was not observed when mutant forms of MCPIP, either entirely lacking the PIN domain or with point mutations in this domain, were used. The results of experiments with actinomycin D indicate that lower levels of IL-1beta mRNA are due to shortening of the IL-1beta transcript half-life, and are not related to the presence of AU-rich elements in the 3' UTR. The interaction of the MCPIP with transcripts of both IL-1beta and MCPIP observed in an RNA immunoprecipitation assay suggests that this novel RNase may be involved in the regulation of expression of several genes.
Double-stranded-RNA-dependent protein kinase and TAR RNA-binding protein form homo- and heterodimers in vivo. (1995)

The yeast two-hybrid system and far-Western protein blot analysis were used to demonstrate dimerization of human double-stranded RNA (dsRNA)-dependent protein kinase (PKR) in vivo and in vitro. A catalytically inactive mutant of PKR with a single amino acid substitution (K296R) was found to dimerize in vivo, and a mutant with a deletion of the catalytic domain of PKR retained the ability to dimerize. In contrast, deletion of the two dsRNA-binding motifs in the N-terminal regulatory domain of PKR abolished dimerization. In vitro dimerization of the dsRNA-binding domain required the presence of dsRNA. These results suggest that the binding of dsRNA by PKR is necessary for dimerization. The mammalian dsRNA-binding protein TRBP, originally identified on the basis of its ability to bind the transactivation region (TAR) of human immunodeficiency virus RNA, also dimerized with itself and with PKR in the yeast assay. Taken together, these results suggest that complexes consisting of different combinations of dsRNA-binding proteins may exist in vivo. Such complexes could mediate differential effects on gene expression and control of cell growth.
Molecular cloning of RhD cDNA derived from a gene present in RhD- positive, but not RhD-negative individuals (1993)

The Rh blood group system plays a major role in immune and nonimmune hemolytic states. Although an Rh cDNA has been previously cloned, there is no information on which Rh antigenic protein it encodes. Using polymerase chain reaction (PCR) amplification, we have identified this original Rh clone, here designated Rh21, and an additional Rh cDNA clone, Rh13, that is 96% nucleotide- and 92% amino acid-identical to Rh21, with the substitutions scattered throughout the sequence. A molecular genetic approach was used to match this Rh clone with an Rh specificity. The mRNA transcript for Rh13 was present in reticulocytes from RhD-positive individuals, but was absent from the reticulocytes of RhD-negative individuals. Using conventional screening of genomic libraries, as well as PCR cloning, partial genomic clones for these two Rh cDNAs were obtained. Based on PCR analysis and Southern blots, the Rh21 gene was present in all individuals, but an intact Rh13 gene was only present in RhD-positive and not RhD-negative individuals. Thus, by correlating the presence of Rh mRNA and gene sequences with individual Rh phenotypes, we were able to establish that the new Rh13 cDNA clone represents the RhD protein.
Functional characterization of two stromal cell lines that support B lymphopoiesis. (1990)

Bone marrow stromal cells have well documented effects on the production of B lymphocytes, but whether or not stromal cell signals are involved in the pre-B to B cell transition is unclear. The potential of two stromal cell lines, S10 and S17, in this process was examined. Initial experiments, using a short term liquid culture, indicated that S10 and S17 stroma efficiently supported the generation of clonable B cells (B lymphocyte CFU) from their immediate precursors in fresh bone marrow. The contribution of macrophages and other accessory cells in those experiments was minimized through use of a colony assay system that permits the direct effects of stromal cell signals on single B cell progenitors to be evaluated. The results indicated that soluble mediators from the S10 and S17 lines could support colony formation from fresh or cultured surface Ig- bone marrow cells. Colonies supported by S17 stroma appeared on day 15 and contained cells that expressed the B220 Ag; surface IgM expression was never observed. S10 supported colonies appeared on day 7 and routinely included surface IgM+ cells. Individual colonies were capable of undergoing additional growth when picked and replated directly onto the different stroma. Those colonies replated onto S10 stroma generated surface IgM expressing cells in up to 60% of experiments, but colonies transferred onto the S17 cell line included B cells only 10% of the time. These data demonstrate that stromal cells alone can provide the signals necessary for generating a surface IgM+ B cell from precursors but that not all stromal cell lines are equally efficient at doing so.
Haemophilia A and haemophilia B: molecular insights (2002)

This review focuses on selected areas that should interest both the scientist and the clinician alike: polymorphisms within the factor VIII and factor IX genes, their linkage, and their ethnic variation; a general assessment of mutations within both genes and a detailed inspection of the molecular pathology of certain mutations to illustrate the diverse cause-effect relations that exist; a summary of current knowledge on molecular aspects of inhibitor production; and an introduction to the new areas of factor VIII and factor IX catabolism. An appendix defining various terms encountered in the molecular genetics of the haemophilias is included, together with an appendix providing accession numbers and locus identification links for accessing gene and sequence information in the international nucleic acid databases.
Half tetrad analysis in alfalfa using multiple restriction fragment length polymorphism markers. (1996)

A maximum likelihood approach of half tetrad analysis (HTA) based on multiple restriction fragment length polymorphism (RFLP) markers was developed. This procedure estimates the relative frequencies of 2n gametes produced by mechanisms genetically equivalent to first division restitution (FDR) or second division restitution and simultaneously locates the centromere within a linkage group of RFLP marker loci. The method was applied to the diploid alfalfa clone PG-F9 (2n = 2x = 16) previously selected because of its high frequency of 2n egg production. HTA was based on four RFLP loci for which PG-F9 was heterozygous with codominant alleles that were absent in the tetraploid tester. Models including three linked and one unlinked RFLP loci were developed and tested. Results of the HTA showed that PG-F9 produced 6% FDR and 94% second division restitution 2n eggs. Information from a marker locus belonging to one linkage group was used to more precisely locate the centromere on a different linkage group. HTA, together with previous cytological analysis, indicated that in PG-F9, FDR 2n eggs are likely produced by diplospory, a mechanism common among apomictic species. The occurrence of FDR 2n eggs in plant species and their importance for crop evolution and breeding is discussed together with the potential applicability of multilocus HTA in the study of reproductive mutants.
Mining developer communication streams (2014)

This paper explores the concepts of modelling a software development project as a process that results in the creation of a continuous stream of data. In terms of the Jazz repository used in this research, one aspect of that stream of data would be developer communication. Such data can be used to create an evolving social network characterized by a range of metrics. This paper presents the application of data stream mining techniques to identify the most useful metrics for predicting build outcomes. Results are presented from applying the Hoeffding Tree classification method used in conjunction with the Adaptive Sliding Window (ADWIN) method for detecting concept drift. The results indicate that only a small number of the available metrics considered have any significance for predicting the outcome of a build.
Deficient interleukin 2 production in rheumatoid arthritis: association with active disease and systemic complications. (1988)

Interleukin 2 (IL-2) production and proliferative responses of peripheral blood mononuclear cells (PBMC) stimulated with three concentrations of PHA were measured in 75 patients with rheumatoid arthritis (RA) and 25 normal controls. All patients were on a standard therapeutic regime, and were assessed for disease activity by clinical and laboratory criteria. Rheumatoid cells showed significantly lower IL-2 production and proliferation than normal PBMC at all PHA doses. These differences were not attributable to different kinetics. Within the rheumatoid population, both IL-2 levels and proliferation were lower in patients with active disease than those with inactive RA. Patients with extra-articular disease showed the most pronounced defects. Proliferative responses showed an inverse correlation with clinical indices of disease activity but not with measures of the acute phase response. Rheumatoid patients had higher proportions of CD4+, TFR+ and Tac+ lymphocytes than controls. Both proliferative responses and IL2- levels showed a positive relationship with the proportion of CD4+ cells, and an inverse relationship with Tac+ lymphocytes. Monocyte depletion and partial reconstitution resulted in an increase of both proliferation and IL-2 production, which was more marked in RA patients, suggesting that depressed IL-2 production may relate in part to monocyte effects. However, this cannot completely explain the magnitude of the defects observed, because normal monocytes did not increase the responses of rheumatoid lymphocytes, neither did rheumatoid monocytes suppress the responses of normal lymphocytes.
Imaging of chemiluminescent reactions in mesoscale silicon‐glass microstructures (1994)

Chemiluminescent reactions in mesoscale analytical structures (chips) containing micrometre-sized interconnecting channels and chambers (pL-nL total volume) were imaged. The chips were fabricated by bonding Pyrex glass to etched pieces of silicon using a high-temperature diffusive bonding technique. In initial experiments light emission from an enhanced chemiluminescent horseradish peroxidase reaction and from a peroxyoxalate reaction contained in straight channels (300 microns wide x 20 mu deep; volume 70.2 nL) and open chambers (812 microns wide, 400 microns deep, 5.2 mm long) linked by channels (100 microns wide, 20 microns deep) to an exit and entry port were studied using a specially modified microplate holder and an Amerlite microplate luminometer. Light emission from more complex structures (two chambers interconnected by a branching channel 100 microns wide, 20 microns deep) filled with a solution containing alkaline phosphatase, Emerald, and CSPD was imaged using a Photometrics Star 1 CCD camera. Detailed investigation of the detection and spatial resolution of the signal was performed on a Berthold Luminograph LB 980 using both the enhanced chemiluminescent horseradish peroxidase reaction and a peroxyoxalate reaction. We successfully resolved light emission from silicon structures with dimensions 100 microns wide and 20 microns deep. These simple silicon structures served as models for more complex designs that will be used for simultaneous multi-analyte assays in which an imaging system resolves and quantitates light emission from different locations on a silicon-glass analytical device.