gebhart/patrepeval huggingface dataset:
METHODOLOGY OF THE ONE‐STAGE ASSAY OF FACTOR VIII(VIII:C) (1984)

ABSTRACT: In this chapter several aspects of the one‐stage assay for Factor VIII coagulant activity (VIII:C) are discussed, based both on a survey of the literature and on experimental data. Special attention is paid to the variables present in the assay system and their influence on coagulation times and Factor VIII estimates. Recommendations are given on how to carry out the assay properly and finally two examples of an assay system are presented.
Spliceosome-mediated RNA trans-splicing in gene therapy and genomics (2000)

In human cells, the majority of the primary transcripts synthesized by RNA polymerase II contain interruptions in the coding sequences, which are known as introns. The spliceosome, a macromolecular enzyme, precisely and efficiently removes these introns in a process known as pre-messenger RNA splicing. This enzyme is also capable of recombining two RNAs in trans in a process known as spliceosome-mediated RNA trans -splicing. In this review, we highlight technologies that take advantage of this RNA trans -splicing, from gene therapy to genomics.
Mouse tumor rejection antigens P815A and P815B : Two epitopes carried by a single peptide (1992)

Abstract Mouse mastocytoma P815 expresses several distinct tumor rejection antigens recognized by syngeneic cytolytic T lymphocytes (CTL). Two of these tumor rejection antigens, P815A and P815B, are encoded by gene P1A, the sequence of which was reported previously. Tumor cell variants having lost one or both of these antigens were isolated by in vitro selection with CTL and also by collecting tumor cells that progressed in vivo after escaping a nearly complete immune rejection process. The structure of gene P1A in these antigen‐loss variants was examined. Several A − B − variants presented a complete or partial deletion of the gene. One variant that had lost only antigen A displayed a point mutation in the first exon. Peptides were synthesized that corresponded to the normal sequence located in the region of this point mutation. They sensitized target cells to both anti‐A and anti‐B CTL. The homologous peptide encoded by the mutated gene of the P815 A − B + variant sensitized cells only to anti‐B CTL. We conclude that anti‐A and anti‐B CTL recognize on the same peptide two distinct epitopes that are affected differently by the mutation.
Alcell® lignin solubility in ethanol–water mixtures (1995)

Abstract The lignin solubility in aqueous solutions of different ethanol concentrations was studied. The concept of the solubility parameter was applied to account for the effect of ethanol concentration on the lignin solubility. Experimental results showed that the lignin solubility increased strongly as the ethanol concentration increased from 9.5 to 47.5% then, it increased much more slowly until a maximum was reached at an ethanol concentration of about 70%. Further increase in the ethanol concentration resulted in a slight decrease in the lignin solubility. Based on the lignin molecular formula, the solubility parameter (δ‐value) of the ALCELL® lignin was 13.7 (cal/cm 3 ) 1/2 . The δ‐value of aqueous ethanol solutions of increased ethanol concentration was calculated and was found to decrease continuously from 22.31 (cal/cm 3 ) 1/2 for pure water to 12.08 (cal/cm 3 ) 1/2 for pure ethanol. The effect of ethanol concentration on the solubility of the ALCELL lignin was then explained based on the theory that lignin exhibited the maximum solubility when the δ‐value of the solvent was close to that of the ALCELL lignin and the H‐bonding capacity of the solutions with different ethanol concentrations was similar. © 1995 John Wiley &amp; Sons, Inc.
Active Serine Involved in the Stabilization of the Active Site Loop in the Humicola lanuginosa Lipase (1998)

We have investigated the binding properties of and dynamics in Humicola lanuginosa lipase (Hll) and the inactive mutant S146A (active Ser146 substituted with Ala) using fluorescence spectroscopy and molecular dynamics simulations, respectively. Hll and S146A show significantly different binding behavior for phosphatidylcholine (PC) and phosphatidylglycerol (PG) liposomes. Generally, higher binding affinity is observed for Hll than the S146A mutant. Furthermore, depending on the matrix, the addition of the transition state analogue benzene boronic acid increases the binding affinity of S146A, whereas only small changes are observed for Hll suggesting that the active site lid in the latter opens more easily and hence more lipase molecules are bound to the liposomes. These observations are in agreement with molecular dynamics simulations and subsequent essential dynamics analyses. The results reveal that the hinges of the active site lid are more flexible in the wild-type Hll than in S146A. In contrast, larger fluctuations are observed in the middle region of the active site loop in S146A than in Hll. These findings reveal that the single mutation (S146A) of the active site serine leads to substantial conformational alterations in the H. lanuginosa lipase and different binding affinities.
Controlling Chemical Reactivity with Antibodies (1993)

The remarkable specificity of an antibody molecule has been used to accomplish highly selective functional group transformations not attainable by current chemical methods. An antibody raised against an amine-oxide hapten catalyzes the reduction of a diketone to a hydroxyketone with greater than 75:1 regioselectivity for one of two nearly equivalent ketone moieties. The antibody-catalyzed reaction is highly stereoselective, affording the hydroxyketone in high enantiomeric excess. Similarly, the reduction of ketones containing branched and aryl substituents, including the highly symmetrical 1-nitrophenyl-3-phenyl-2-propanone, was enantioselective. The simple strategy presented herein may find general applicability to the regio- and stereoselective reduction of a broad range of compounds.
Luminescence of ruthenium(II) polypyridyls: evidence for intercalative binding to Z-DNA (1991)

Photophysical studies have been undertaken to characterize the binding interactions of enantiomers of Ru(phen)3(2+), Ru(DIP)3(2+), and racemic Ru(bpy)2dppz2+ (where phen = 1,10-phenanthroline, DIP = 4,7-diphenylphenanthroline, and dppz = dipyridophenazine) with Z-form poly d(GC). Parallel enhancements in steady state luminescent intensity and a lengthening of luminescent lifetimes are seen for ruthenium enantiomers with Z-DNA as for B-DNA but with enantioselectivities reversed. Greater enhancements are seen for delta-isomers with the right-handed helix but for lambda-isomers with the left-handed helix. Ru(bpy)2dppz2+, an avid intercalator in B-DNA, displays no luminescence free in aqueous solution, but luminesces brightly bound to either B- or Z-poly d(GC). Stern-Volmer quenching studies also support the enantioselective preference in binding to B-DNA by delta-isomers and a reversal with binding to Z-DNA preferentially by the lambda-isomers. Steady state polarization studies indicate a rigid association of the complexes with both B- and Z-DNA on the time-scale of their emission and again with symmetrical enantioselectivities for the left and right-handed helices. Given the well characterized intercalative association of the complexes with B-DNA, the parallel results seen here with Z-DNA point strongly to a comparable intercalative association with the Z-form helix. That molecules may interact with Z-DNA through intercalation has not been demonstrated previously and now requires consideration in describing the range of interactions of small molecules and proteins with Z-DNA.
Synergizing Pesticides To Reduce Use Rates (1993)

There is great need to reduce pesticide inputs to save costs, reduce environmental loads, and lower the selection pressures resulting in rapid evolution of resistance. This can often be done by judiciously chosen mixtures; with synergism given the economic definition of a mixture that gives more cost-effective pest control than the sum of the separate components. Pesticides are often used alone at high rates to control the most recalcitrant pests in the infestation spectrum, where a low rate of a second pesticide can be complimentary and even synergistic. Herbicide mixtures based on field weed spectra matched to the best available compounds are more prevalent in Europe than in the U.S.A. High use rates are often required to overcome endogenous degradation pathways in certain pests, and inhibitors of the offending pathways can be biorationally chosen to synergistically lower rates. This requires a better knowledge of the reasons for the lack-of-action of pesticides in target pests, an area insufficiently researched There are already compounds known that enhance pesticide penetration, that block pesticide degradation by monooxygenases, glutathione transferases, as well as compounds that block detoxification of the active oxygen species generated by many herbicides.
High-Temperature Polybenzimidazole Fuel Cell Membranes via a Sol−Gel Process (2005)

A sol−gel process is described to produce phosphoric acid (PA)-doped polybenzimidazole (PBI) films that operate as fuel cell membranes above 150 °C for extended periods of time without the need for feed gas humidification. When solutions of high molecular weight heterocylic polymers such as polybenzimidazoles in polyphosphoric acid (PPA) were cast into films, a transition from solution state to gel state was observed during the hydrolysis of the solvent from PPA (a good solvent for PBI) to PA (a poor solvent for PBI). The resulting membranes retained high levels of phosphoric acid in the gel structure and exhibited high ionic conductivities and stable mechanical properties at elevated temperatures. Preliminary fuel cell tests have demonstrated the feasibility of such PBI membranes from the sol−gel process for operating a fuel cell at temperatures above 150 °C without any feed gas humidification or pressure requirements for more than 1000 h.
Large-scale mRNA expression profiling in the common ice plant, Mesembryanthemum crystallinum, performing C3 photosynthesis and Crassulacean acid metabolism (CAM) (2008)

The common ice plant (Mesembryanthemum crystallinum L.) has emerged as a useful model for molecular genetic studies of Crassulacean acid metabolism (CAM) because CAM can be induced in this species by water deficit or salinity stress. Non-redundant sequence information from expressed sequence tag data was used to fabricate a custom oligonucleotide microarray to compare large-scale mRNA expression patterns in M. crystallinum plants conducting C(3) photosynthesis versus CAM. Samples were collected every 4 h over a 24 h time period at the start of the subjective second day from plants grown under constant light and temperature conditions in order to capture variation in mRNA expression due to salinity stress and circadian clock control. Of 8455 genes, a total of 2343 genes (approximately 28%) showed a significant change as judged by analysis of variance (ANOVA) in steady-state mRNA abundance at one or more time points over the 24 h period. Of these, 858 (10%) and 599 (7%) exhibited a greater than two-fold ratio (TFR) increase or decrease in mRNA abundance, respectively. Functional categorization of these TFR genes revealed that many genes encoding products that function in CAM-related C(4) acid carboxylation/decarboxylation, glycolysis/gluconeogenesis, polysaccharide, polyol, and starch biosynthesis/degradation, protein degradation, transcriptional activation, signalling, stress response, and transport facilitation, and novel, unclassified proteins exhibited stress-induced increases in mRNA abundance. In contrast, salt stress resulted in a significant decrease in transcript abundance for genes encoding photosynthetic functions, protein synthesis, and cellular biogenesis functions. Many genes with CAM-related functions exhibited phase shifts in their putative circadian expression patterns following CAM induction. This report establishes an extensive catalogue of gene expression patterns for future investigations aimed at understanding the complex, transcriptional hierarchies that govern CAM-specific expression patterns. A novel graph-theoretic approach called 'Max Clique Builder' is introduced that identifies and organizes sets of coordinately regulated genes, such as those encoding subunits of the vacuolar H(+)-ATPase complex, into tighter functionally related clusters with more similar expression patterns compared with standard hierarchical clustering methods.
Transcription Mapping of the Kaposi’s Sarcoma-Associated Herpesvirus (Human Herpesvirus 8) Genome in a Body Cavity-Based Lymphoma Cell Line (BC-1) (1998)

Kaposi's sarcoma-associated herpesvirus (KSHV) gene transcription in the BC-1 cell line (KSHV and Epstein-Barr virus coinfected) was examined by using Northern analysis with DNA probes extending across the viral genome except for a 3-kb unclonable rightmost region. Three broad classes of viral gene transcription have been identified. Class I genes, such as those encoding the v-cyclin, latency-associated nuclear antigen, and v-FLIP, are constitutively transcribed under standard growth conditions, are unaffected by tetradecanoylphorbol acetate (TPA) induction, and presumably represent latent viral transcripts. Class II genes are primarily clustered in nonconserved regions of the genome and include small polyadenylated RNAs (T0.7 and T1.1) as well as most of the virus-encoded cytokines and signal transduction genes. Class II genes are transcribed without TPA treatment but are induced to higher transcription levels by TPA treatment. Class III genes are primarily structural and replication genes that are transcribed only following TPA treatment and are presumably responsible for lytic virion production. These results indicate that BC-1 cells have detectable transcription of a number of KSHV genes, particularly nonconserved genes involved in cellular signal transduction and regulation, during noninduced (latent) virus culture.
Maize DELLA Proteins dwarf plant8 and dwarf plant9 as Modulators of Plant Development (2010)

DELLA proteins are nuclear-localized negative regulators of gibberellin signaling found ubiquitously throughout higher plants. Dominant dwarfing mutations of DELLA proteins have been primarily responsible for the dramatic increases in harvest index of the 'green revolution'. Maize contains two genetic loci encoding DELLA proteins, dwarf plant8 (d8) and dwarf plant 9 (d9). The d8 gene and three of its dominant dwarfing alleles have been previously characterized at the molecular level. Almost 20 years after the initial description of the mutant, this investigation represents the first molecular characterization of d9 and its gibberellin-insensitive mutant, D9-1. We have molecularly, subcellularly and phenotypically characterized the gene products of five maize DELLA alleles in transgenic Arabidopsis. In dissecting the molecular differences in D9-1, a critical residue for normal DELLA function has been uncovered, corresponding to E600 of the D9 protein. The gibberellin-insensitive D9-1 was found to produce dwarfing and, notably, earlier flowering in Arabidopsis. Conversely, overexpression of the D9-1 allele delayed flowering in transgenic maize, while overexpression of the d9 allele led to earlier flowering. These results corroborate findings that DELLA proteins are at the crux of many plant developmental pathways and suggest differing mechanisms of flowering time control by DELLAs in maize and Arabidopsis.
Structural and Functional Analysis of the Human HDAC4 Catalytic Domain Reveals a Regulatory Structural Zinc-binding Domain (2008)

Histone deacetylases (HDACs) regulate chromatin status and gene expression, and their inhibition is of significant therapeutic interest. To date, no biological substrate for class IIa HDACs has been identified, and only low activity on acetylated lysines has been demonstrated. Here, we describe inhibitor-bound and inhibitor-free structures of the histone deacetylase-4 catalytic domain (HDAC4cd) and of an HDAC4cd active site mutant with enhanced enzymatic activity toward acetylated lysines. The structures presented, coupled with activity data, provide the molecular basis for the intrinsically low enzymatic activity of class IIa HDACs toward acetylated lysines and reveal active site features that may guide the design of class-specific inhibitors. In addition, these structures reveal a conformationally flexible structural zinc-binding domain conserved in all class IIa enzymes. Importantly, either the mutation of residues coordinating the structural zinc ion or the binding of a class IIa selective inhibitor prevented the association of HDAC4 with the N-CoR.HDAC3 repressor complex. Together, these data suggest a key role of the structural zinc-binding domain in the regulation of class IIa HDAC functions.
The Myxoma Virus-soluble Interferon- γ Receptor Homolog, M-T7, Inhibits Interferon- γ in a Species-specific Manner (1995)

The myxoma virus M-T7 protein contains significant sequence similarity to the ligand binding domain of the mammalian interferon-gamma receptors, and functions as a soluble homolog which can bind and inhibit the biological activities of rabbit interferon-gamma (Upton, C., Mossman, K., and McFadden, G. (1992) Science 258:1369-1372). M-T7, the most abundantly secreted protein from myxoma virus-infected cells, was shown to be expressed in significant biological amounts as a typical poxvirus early gene product, efficiently secreted at early times of infection to levels that exceed 5 x 10(7) molecules/cell, and function as a stable inhibitory protein in infected cell supernatants until late times of infection. M-T7 was specific in binding and inhibiting rabbit interferon-gamma, and did not bind either human or murine interferon-gamma. Scatchard analysis of rabbit interferon-gamma binding curves yielded a single high affinity binding site on M-T7, with a Kd of 1.2 x 10(-9) M, which is comparable to the affinity between soluble forms of cellular interferon-gamma receptors and their cognate ligands. In comparison, rabbit interferon-gamma was shown to bind its cellular receptor with a Kd of 5.9 x 10(-10) M, again comparable to the affinity of membrane bound forms of other mammalian interferon-gamma receptors for interferon-gamma. Thus, the myxoma virus M-T7 protein is a functional soluble interferon-gamma receptor homolog which binds and inhibits interferon-gamma with high affinity in a species-specific manner.
Cell Transplantation for the Treatment of Acute Myocardial Infarction Using Vascular Endothelial Growth Factor–Expressing Skeletal Myoblasts (2001)

This combined strategy of cell transplantation with gene therapy could be of importance for the treatment of acute myocardial infarction.
Cystatin C as a biomarker for estimating glomerular filtration rate (2015)

Cystatin C has some advantages over serum creatinine in estimating GFR. The use of cystatin C as a confirmatory biomarker in deciding medication dosages or as a confirmatory test in patients with an uncertain diagnosis of chronic kidney disease may be beneficial.
Fusobacterium nucleatumand T Cells in Colorectal Carcinoma (2015)

The amount of tissue F nucleatum is inversely associated with CD3+ T-cell density in colorectal carcinoma tissue. On validation, our human population data may provide an impetus for further investigations on potential interactive roles of Fusobacterium and host immunity in colon carcinogenesis.
DNA watermarks: A proof of concept (2008)

From our experiments we conclude that the DNA watermarks produced by DNA-Crypt do not influence the translation from mRNA into protein. By analyzing the vacuolar morphology, growth rate and ability to sporulate we confirmed that the resulting Vam7 protein was functionally active.
Evaluation of the gamma dose distribution comparison method (2003)

The gamma tool was developed to quantitatively compare dose distributions, either measured or calculated. Before computing gamma, the dose and distance scales of the two distributions, referred to as evaluated and reference, are renormalized by dose and distance criteria, respectively. The renormalization allows the dose distribution comparison to be conducted simultaneously along dose and distance axes. The gamma quantity, calculated independently for each reference point, is the minimum distance in the renormalized multidimensional space between the evaluated distribution and the reference point. The gamma quantity degenerates to the dose-difference and distance-to-agreement tests in shallow and very steep dose gradient regions, respectively. Since being introduced, the gamma quantity has been used by investigators to evaluate dose calculation algorithms, and compare dosimetry measurements. This manuscript examines the gamma distribution behavior in two dimensions and evaluates the gamma distribution in the presence of data noise. Noise in the evaluated distribution causes the gamma distribution to be underestimated relative to the no-noise, condition. Noise in the reference distribution adds noise in the gamma distribution in proportion to the normalized dose noise. In typical clinical use, the fraction of points that exceed 3% and 3 mm can be extensive, so we typically use 5% and 2-3 mm in clinical evaluations. For clinical cases, the calculation time is typically 5 minutes for a 1 x 1 mm2 interpolated resolution on an 800 MHz Pentium 4 for a 14.1 x 15.2 cm2 radiographic film.
Mitochondrial DNA Alterations in Cancer (2002)

A number of studies have demonstrated the presence of mitochondrial DNA (mtDNA) mutations in cancer cells. In this article, we review mitochondrial genomic aberrations reported in solid tumors of the breast, colon, stomach, liver, kidney, bladder, head/neck, and lung. The tantalizing association of tumors with mtDNA mutations implicates these mutations in the process of carcinogenesis. Alterations in expression of mtDNA transcripts in a variety of cancer types are also reviewed. In solid tumors, elevated expression of mtDNA-genes coding for subunits of the mitochondrial electron respiratory chain may reflect mitochondrial adaptation to perturbations in cellular energy requirements. The role of mtDNA mutations and altered expression of mitochondrial genes in carcinogenesis is discussed. Mitochondrial DNA mutations can initiate a cascade of events leading to a continuous increase in the production of reactive oxygen species (persistent oxidative stress), a condition that probably favors tumor development.
Endogenous Nitric Oxide Protects Bacteria Against a Wide Spectrum of Antibiotics (2009)

Bacterial nitric oxide synthases (bNOS) are present in many Gram-positive species and have been demonstrated to synthesize NO from arginine in vitro and in vivo. However, the physiological role of bNOS remains largely unknown. We show that NO generated by bNOS increases the resistance of bacteria to a broad spectrum of antibiotics, enabling the bacteria to survive and share habitats with antibiotic-producing microorganisms. NO-mediated resistance is achieved through both the chemical modification of toxic compounds and the alleviation of the oxidative stress imposed by many antibiotics. Our results suggest that the inhibition of NOS activity may increase the effectiveness of antimicrobial therapy.
Ultrasonic Levitation by Stepped Circular Vibrating Plate (1990)

A high intensity ultrasound field was produced by a new type sound source called a stepped circular vibrating plate, and the experimental results on levitation in air by ultrasound energy are described. The density of samples, frequencies and sample dimensions were varied. The minimum threshold of sound pressure required for levitating the samples was found proportional to sample density, and was also inversely proportional to the ultrasonic frequency used.