gebhart/patrepeval huggingface dataset:
Purification and Characterization of Cinnamoyl-Coenzyme A:NADP Oxidoreductase in Eucalyptus gunnii (1994)

Cinnamoyl-coenzyme A:NADP oxidoreductase (CCR, EC 1.2.1.44), the entry-point enzyme into the monolignol biosynthetic pathway, was purified to apparent electrophoretic homogeneity from differentiating xylem of Eucalyptus gunnii Hook. The purified protein is a monomer of 38 kD and has an isoelectric point of 7. Although Eucalyptus gunnii CCR has approximately equal affinities for all possible substrates (p-coumaroyl-coenzyme A, feruloyl-coenzyme A, and sinapoyl-coenzyme A), it is approximately three times more effective at converting feruloyl-coenzyme A than the other substrates. To gain a better understanding of the catalytic regulation of Eucalyptus CCR, a variety of compounds were tested to determine their effect on CCR activity. CCR activity is inhibited by NADP and coenzyme A. Effectors that bind lysine and cysteine residues also inhibit CCR activity. As a prerequisite to the study of the regulation of CCR at the molecular level, polyclonal antibodies were obtained.
Electrochemical Biosensor Array for the Identification of Microorganisms Based on Lectin−Lipopolysaccharide Recognition (2001)

Rapid identification of bacterial strains remains a well-known problem in applied medicine and, for viable pathogens, is an important diagnostic goal. We have investigated an electrochemical biosensor array, in which transduction is based on respiratory cycle activity measurements, where the microorganism's native respiratory chain is interrupted with non-native external oxidants. The selective biochemical recognition agents employed in this study are lectins that, once immobilized, recognize and bind to cell surface lipopolysaccharides. Porous membranes with different surface properties were examined as potential immobilization supports for these lectins. Optimizations performed using concanavalin A and E. coli JM105 show that immobilization methods involving pre-activated membranes significantly reduce the time required to create a functional lectin layer on the membrane surface. Overall, we found general agreement between agglutination test results and the electrochemical assessment of lectin-cell binding. Chronocoulometric measurements were made for cells captured on lectin-modified Immunodyne ABC membranes physically affixed to Pt working electrodes. This lectin-based sensor array was exposed to viable cells of gram-negative and gram-positive bacteria as well as yeast, and chronocoulometric measurements were used to generate a pattern of responses for each organism toward each lectin. Principal component analysis was used to classify the chronocoulometric results for the different microbial strains. With this new method, six microbial species (Baccilus cereus, Staphylococcus aureus, Proteus vulgaris, Escherichia coli, Enterobacter aerogenes, Saccharomyces cerevisiae) were readily distinguished.
Cyclic Steaming in Heavy Oil Diatomite (1995)

ABSTRACT Chevron currently uses cyclic steaming as a recovery method to produce economically its heavy oil diatomite resource in the Cymric field, San Joaquin Valley, California. A highly instrumented, cyclically steaming well from this field was simulated in this study to delineate important production mechanisms, to optimize operations, and to improve reser­ voir management. The model was constrained, as much as possible, by the available measured data. Results show that fluid flow from the well to the reservoir is primarily through the hydraulic fracture induced by the in­ jected steam. Parameters with unique importance to model­ modeling cyclic steaming in diatomites are: ( 1) induced fracture dimension (length and height), (2) matrix permeability, (3) oil/water capillary pressure, (4) grid size perpendicular to fracture face, and (5)producing bottomhole pressures. Additionally, parameters important for conventional steam injection processes, such as relative permeabilities and injected steam volume, quality, and rate, are important for diatomites also. Oil production rates and steam/oil ratios calculated by this model compare reasonably with field data.
Illegal use of beta-adrenergic agonists: European Community. (1998)

The use of veterinary medicinal products within the European Community is governed by a series of directives and regulations that describe the requirements for safety, quality, and efficacy of these products. Veterinary therapeutic use of beta-agonists has only been approved in the case of clenbuterol for bronchodilatation in horses and calves and for tocolysis in cows. No beta-agonists have been permitted in the European Community for growth-promoting purposes in farm animals. Surveillance for the presence of residues of veterinary agents in food-producing animals and meat is regulated by the Directive 86/469/EEC containing specific guidelines for sampling procedures on farms and in slaughterhouses. The level and frequency of sampling is dependent on the category of compounds and animal species. When positive samples have been identified (above certain action levels), sampling intensity is increased. Results of monitoring programs in EU member states during 1992 and 1993 for the occurrence of residues of beta-agonists in food-producing animals vary substantially with respect to the percentages of positive samples, ranging from 0 to 7%. The variability is partly explained by differences in sampling strategies, detection methods, and action levels applied. Identification of the proper matrices for sampling and detection of beta-agonists is important. In the case of clenbuterol, hair and choroid retinal tissue are appropriate tissues because clenbuterol accumulates in these matrices. A clear decrease in the use of clenbuterol in cattle has been observed in The Netherlands, Germany, Northern Ireland, and Spanish Basque Country over the last 3 yr. This is partly due to intensified surveillance activities at farms and slaughterhouses by governmental agencies and production sector organizations. There are data on human intoxication following consumption of liver or meat from cattle treated with beta-agonists. At the concentrations of clenbuterol measured in contaminated liver and meat samples, pharmacological effects may be expected in humans after consuming 100 to 200 g of product. The use of highly active beta-agonists as growth promoters is not appropriate because of the potential hazard for human and animal health, as was recently concluded at the scientific Conference on Growth Promotion in Meat Production (Nov. 1995, Brussels).
Cross-Feeding betweenBifidobacterium longumBB536 and Acetate-Converting, Butyrate-Producing Colon Bacteria during Growth on Oligofructose (2006)

In vitro coculture fermentations of Bifidobacterium longum BB536 and two acetate-converting, butyrate-producing colon bacteria, Anaerostipes caccae DSM 14662 and Roseburia intestinalis DSM 14610, with oligofructose as the sole energy source, were performed to study interspecies interactions. Two clearly distinct types of cross-feeding were identified. A. caccae DSM 14662 was not able to degrade oligofructose but could grow on the fructose released by B. longum BB536 during oligofructose breakdown. R. intestinalis DSM 14610 could degrade oligofructose, but only after acetate was added to the medium. Detailed kinetic analyses of oligofructose breakdown by the last strain revealed simultaneous degradation of the different chain length fractions, in contrast with the preferential degradation of shorter fractions by B. longum BB536. In a coculture of both strains, initial oligofructose degradation and acetate production by B. longum BB536 took place, which in turn also allowed oligofructose breakdown by R. intestinalis DSM 14610. These and similar cross-feeding mechanisms could play a role in the colon ecosystem and contribute to the combined bifidogenic/butyrogenic effect observed after addition of inulin-type fructans to the diet.
The Role of an Epithelial Neutrophil-Activating Peptide-78-Like Protein in Rat Adjuvant-Induced Arthritis (1999)

The chemokine, epithelial neutrophil-activating peptide-78 (ENA-78), is a potent neutrophil chemotaxin whose expression is increased in inflamed synovial tissue and fluid in human rheumatoid arthritis compared with osteoarthritis. Since ENA-78 has been implicated in the pathogenesis of RA, we examined the expression of an ENA-78-like protein during the development of rat adjuvant-induced arthritis (AIA). Using an ELISA assay, we found increased levels of antigenic ENA-78-like protein in the sera of AIA animals compared with control normal animals by day 7 postadjuvant injection. ENA-78-like protein levels continued to increase as AIA developed. ENA-78-like protein levels in joint homogenates were increased in AIA animals later in the development of the disease, by day 18 during maximal arthritis, compared with control animals. Expression of ENA-78-like protein in both the AIA serum and joint correlated with the progression of inflammation of the joints. Anti-human ENA-78 administered before disease onset modified the severity of AIA, while administration of anti-ENA-78 after clinical onset of AIA did not modify the disease. These data support a role for an ENA-78-like protein as an important chemokine in the progression and maintenance of AIA.
An implantable neural stimulator for Intraspinal MicroStimulation (2012)

This paper reports on a wireless stimulator device for use in animal experiments as part of an ongoing investigation into intraspinal stimulation (ISMS) for restoration of walking in humans with spinal cord injury. The principle behind using ISMS is the activation of residual motor-control neural networks within the spinal cord ventral horn below the level of lesion following a spinal cord injury. The attractiveness to this technique is that a small number of electrodes can be used to induce bilateral walking patterns in the lower limbs. In combination with advanced feedback algorithms, ISMS has the potential to restore walking for distances that exceed that produced by other types of functional electrical stimulation. Recent acute animal experiments have demonstrated the feasibility of using ISMS to produce the coordinated walking patterns. Here we described a wireless implantable stimulation system to be used in chronic animal experiments and for providing the basis for a system suitable for use in humans. Electrical operation of the wireless system is described, including a demonstration of reverse telemetry for monitoring the stimulating electrode voltages.
Nontemplated Nucleotide Additions Distinguish the Small RNA Composition in Cells from Exosomes (2014)

Functional biomolecules, including small noncoding RNAs (ncRNAs), are released and transmitted between mammalian cells via extracellular vesicles (EVs), including endosome-derived exosomes. The small RNA composition in cells differs from exosomes, but underlying mechanisms have not been established. We generated small RNA profiles by RNA sequencing (RNA-seq) from a panel of human B cells and their secreted exosomes. A comprehensive bioinformatics and statistical analysis revealed nonrandomly distributed subsets of microRNA (miRNA) species between B cells and exosomes. Unexpectedly, 3' end adenylated miRNAs are relatively enriched in cells, whereas 3' end uridylated isoforms appear overrepresented in exosomes, as validated in naturally occurring EVs isolated from human urine samples. Collectively, our findings suggest that posttranscriptional modifications, notably 3' end adenylation and uridylation, exert opposing effects that may contribute, at least in part, to direct ncRNA sorting into EVs.
The Development of Recombinant Human Serum Albumin (1998)

We have developed a fermentation process for recombinant human serum albumin (rHSA) production using an expression strain of the methylotrophic yeast Pichia pastoris. The high productivity of the process enables it to compete with the production of plasma derived HSA. After purification of the rHSA, the content of yeast derived contaminants was less than 1 ng/250 mg of rHSA. The results from structural analyses suggested that purified rHSA possessed an identical conformation to plasma derived HSA. Furthermore, no neoantigenicity different from that of plasma derived HSA was observed. The efficacy and safety of rHSA were tested in clinical studies, and it was shown that there was no difference between rHSA and plasma derived HSA in a comparison study. The high efficacy of rHSA with little or no adverse reaction was confirmed in these studies.
The clinical practice of risk reduction for Alzheimer's disease: A precision medicine approach (2018)

Like virtually all age-related chronic diseases, late-onset Alzheimer's disease (AD) develops over an extended preclinical period and is associated with modifiable lifestyle and environmental factors. We hypothesize that multimodal interventions that address many risk factors simultaneously and are individually tailored to patients may help reduce AD risk. We describe a novel clinical methodology used to evaluate and treat patients at two Alzheimer's Prevention Clinics. The framework applies evidence-based principles of clinical precision medicine to tailor individualized recommendations, follow patients longitudinally to continually refine the interventions, and evaluate N-of-1 effectiveness (trial registered at ClinicalTrials.gov NCT03687710). Prior preliminary results suggest that the clinical practice of AD risk reduction is feasible, with measurable improvements in cognition and biomarkers of AD risk. We propose using these early findings as a foundation to evaluate the comparative effectiveness of personalized risk management within an international network of clinician researchers in a cohort study possibly leading to a randomized controlled trial.
Heterologous Expression of Arabidopsis UDP-Glucosyltransferases in Saccharomyces cerevisiae for Production of Zearalenone-4- O -Glucoside (2006)

Zearalenone, a secondary metabolite produced by several plant-pathogenic fungi of the genus Fusarium, has high estrogenic activity in vertebrates. We developed a Saccharomyces cerevisiae bioassay strain that we used to identify plant genes encoding UDP-glucosyltransferases that can convert zearalenone into zearalenone-4-O-glucoside (ZON-4-O-Glc). Attachment of the glucose moiety to zearalenone prevented the interaction of the mycotoxin with the human estrogen receptor. We found that two of six clustered, similar UGT73C genes of Arabidopsis thaliana encode glucosyltransferases that can inactivate zearalenone in the yeast bioassay. The formation of glucose conjugates seems to be an important plant mechanism for coping with zearalenone but may result in significant amounts of "masked" zearalenone in Fusarium-infected plant products. Due to the unavailability of an analytical standard, the ZON-4-O-Glc is not measured in routine analytical procedures, even though it can be converted back to active zearalenone in the digestive tracts of animals. Zearalenone added to yeast transformed with UGT73C6 was converted rapidly and efficiently to ZON-4-O-Glc, suggesting that the cloned UDP-glucosyltransferase could be used to produce reference glucosides of zearalenone and its derivatives.
X-ray excited optical luminescence (XEOL) detection of x-ray absorption fine structure (XAFS) (1998)

The x-ray excited optical luminescence (XEOL) from a variety of rare-earth ions was used as a detection mode for the collection of L-edge x-ray absorption fine-structure (XAFS) data. In order to understand the source of the observed optical signal, advantage is taken of the known luminescent response of f ions in a variety of transparent host materials. Whereas some samples exhibit an optical response that is indistinguishable from the transmission XAFS data, other samples show marked differences between the data obtained with the two different detection schemes. The unexpected optical luminescence of a Gd2O3 sample is traced to a Eu impurity. An optical spectrum of 0.4% Tb in Gd2O2S, excited by x-ray photons at the Gd edge, is used to demonstrate that the optical signal may arise from an ion different from the absorbing ion. The implications of this energy transfer are discussed in terms of the suitability of XEOL as a detection scheme for XAFS spectroscopy.
Phase II clinical trial of a murine monoclonal antibody cytotoxic for gastrointestinal adenocarcinoma. (1985)

A murine monoclonal antibody (MAb) which binds to human metastatic gastrointestinal adenocarcinomas can be administered safely and has tumor effects in some patients. Its therapeutic effect was assessed in 20 patients with measurable advanced colorectal carcinoma that was refractory to prior surgical resection, chemotherapy, and/or radiotherapy. All patients had agreed to receive no other therapy at the time of MAb administration and follow-up evaluation. In one patient, tumor at all known sites responded after a single i.v. injection of antibody. One other patient had a marked reduction in a hepatic metastasis where binding of 131I-labeled F(ab')2 MAb fragments was demonstrated but not in his abdominal wall metastases where no MAb binding could be demonstrated. In a third patient, stabilization persisting for 12 mo of an aggressively growing tumor was observed. The antibody was well tolerated in all patients, although 10 patients mounted an anti-murine immunoglobulin antibody response.
Free-Volume Model of the Amorphous Phase: Glass Transition (1961)

Free volume vf is defined as that part of the thermal expansion, or excess volume Δv̄ which can be redistributed without energy change. Assuming a Lennard-Jones potential function for a molecule within its cage in the condensed phase, it can be shown that at small Δv̄ considerable energy is required to redistribute the excess volume; however, at Δv̄ considerably greater than some value δv̄g (corresponding to potentials within the linear region), most of the volume added can be redistributed freely. The transition from glass to liquid may be associated with the introduction of appreciable free volume into the system. Free volume will be distributed at random within the amorphous phase and there is a contribution to the entropy from this randomness which is not present in the entropy of the crystalline phase. According to our model all liquids would become glasses at sufficiently low temperature if crystallization did not intervene. Therefore whether or not a glass forms is determined by the crystallization kinetic constants and the cooling rate of the liquid. The experience on the glass formation is consistent with the generalization: at a given level of cohesive energy the glass-forming tendency of a substance in a particular class is greater the less is the ratio of the energy to the entropy of crystallization.
Functional metagenomics reveals novel salt tolerance loci from the human gut microbiome (2012)

Metagenomics is a powerful tool that allows for the culture-independent analysis of complex microbial communities. One of the most complex and dense microbial ecosystems known is that of the human distal colon, with cell densities reaching up to 10(12) per gram of faeces. With the majority of species as yet uncultured, there are an enormous number of novel genes awaiting discovery. In the current study, we conducted a functional screen of a metagenomic library of the human gut microbiota for potential salt-tolerant clones. Using transposon mutagenesis, three genes were identified from a single clone exhibiting high levels of identity to a species from the genus Collinsella (closest relative being Collinsella aerofaciens) (COLAER_01955, COLAER_01957 and COLAER_01981), a high G+C, Gram-positive member of the Actinobacteria commonly found in the human gut. The encoded proteins exhibit a strong similarity to GalE, MurB and MazG. Furthermore, pyrosequencing and bioinformatic analysis of two additional fosmid clones revealed the presence of an additional galE and mazG gene, with the highest level of genetic identity to Akkermansia muciniphila and Eggerthella sp. YY7918, respectively. Cloning and heterologous expression of the genes in the osmosensitive strain, Escherichia coli MKH13, resulted in increased salt tolerance of the transformed cells. It is hoped that the identification of atypical salt tolerance genes will help to further elucidate novel salt tolerance mechanisms, and will assist our increased understanding how resident bacteria cope with the osmolarity of the gastrointestinal tract.
The 5′ RNA Terminus of Spleen Necrosis Virus Stimulates Translation of Nonviral mRNA (2000)

The RU5 region at the 5' RNA terminus of spleen necrosis virus (SNV) has been shown to facilitate expression of human immunodeficiency virus type 1 (HIV) unspliced RNA independently of the Rev-responsive element (RRE) and Rev. The SNV sequences act as a distinct posttranscriptional control element to stimulate gag RNA nuclear export and association with polyribosomes. Here we sought to determine whether RU5 functions to neutralize the cis-acting inhibitory sequences (INSs) in HIV RNA that confer RRE/Rev dependence or functions as an independent stimulatory sequence. Experiments with HIV gag reporter plasmids that contain inactivated INS-1 indicated that neutralization of INSs does not account for RU5 function. Results with luciferase reporter gene (luc) plasmids further indicated that RU5 stimulates expression of a nonretroviral RNA that lacks INSs. Northern blot and RT-PCR analyses indicated that RU5 does not increase the steady-state levels or nuclear export of the luc transcript but rather that the U5 region facilitates efficient polyribosomal association of the mRNA. RU5 does not function as an internal ribosome entry site in bicistronic reporter plasmids, and it requires the 5'-proximal position for efficient function. Our results indicate that RU5 contains stimulatory sequences that function in a 5'-proximal position to enhance initiation of translation of a nonretroviral reporter gene RNA. We speculate that RU5 evolved to overcome the translation-inhibitory effect of the highly structured encapsidation signal and other replication motifs in the 5' untranslated region of the retroviral RNA.
Functional magnetic resonance imaging: A review of methodological aspects and clinical applications (2003)

This paper gives an overview of the recent literature on methodological developments of functional magnetic resonance imaging (fMRI) and recent trends in clinical applications. With the recent introduction of high-field systems and methodological developments leading to more robust signal behavior, fMRI is in a transition state from a research modality for use by experts to a standard procedure with useful applications in patient management. Compared to the use in neuroscientific research, which is often based on BOLD techniques alone, the application in patients is distinguished by a multiparametric characterization of the brain using a combination of several techniques. Neuronal fiber tracking based on diffusion anisotropy measurements, in particular, has already turned out to provide relevant supplementary information to the BOLD-based cortical activation maps.
A hyperbranched conjugated Schiff base polymer network: a potential negative electrode for flexible thin film batteries (2016)

A hyperbranched conjugated Schiff base polymer network was synthesized by condensation between 4,4',4''-nitrilotribenzaldehyde and p-phenylenediamine. The material exhibits excellent rate capability and long cycle life for lithium storage. Coupled with lower electrode potential (0.7 V vs. Li(+)/Li), it may be well suited for fully flexible thin film polymeric batteries as the negative electrode.