gebhart/patrepeval huggingface dataset:
Lunasin Concentration in Different Soybean Genotypes, Commercial Soy Protein, and Isoflavone Products (2004)

Lunasin is a unique and novel cancer preventive peptide originally isolated from soy. Information on lunasin concentration of soybean cultivars and commercial soy proteins would be useful in developing lunasin-enriched cultivars and soy products. We report the development of an enzyme-linked immunosorbent assay (ELISA) method to identify lunasin and quantify the variations in concentration in 144 selected, diverse soybean accessions from the U.S. Department of Agriculture Soybean Germplasm Collection, several commercially available soy protein fractions and isoflavone-enriched products. With synthetic lunasin and monoclonal antibody, ELISA shows a linear concentration range of 24-72 ng/mL, good reproducibility, a detection limit of 8 ng/mL, and a recovery of 90% on spiked soy samples. Lunasin concentrations in the tested materials range from 0.10 to 1.33 g/100 g flour. Differences that exceeded 100% have been observed among accessions of similar maturity that were grown in the same environment, indicating that genetic differences in soybeans exist for lunasin. The mean of 23 major ancestral lines of U.S. cultivars is similar to the mean of 16 modern cultivars selected to represent the current diversity of the crop, but the highest values were found within the ancestral and exotic accessions. Soy protein concentrate, isolate, and hydrolyzate contain 2.81 +/- 0.30, 3.75 +/- 0.43, and 4.43 +/- 0.59 g lunasin/100 g flour, respectively, while soy flour and soy flakes contain 1.24 +/- 0.22 g lunasin/100 g flour. Isoflavone-enriched products contain very little or no lunasin. The relative mass (M(r)) of lunasin in the samples is 5.45 +/- 0.25 kDa. The wide range of lunasin concentrations within the Glycine max species indicates that the levels of this important bioactive peptide can be genetically manipulated. Furthermore, soy isolates and hydrolyzed soy proteins contain the highest concentrations of lunasin.
DNA-Templated Assembly of Helical Cyanine Dye Aggregates:  A Supramolecular Chain Polymerization (2004)

Symmetrical cationic cyanine dyes assemble in cooperative fashion into helical supramolecular polymers using DNA as a template. The dyes assemble into cofacial dimers within the minor groove of the DNA and assembly of one dimer facilitates assembly of additional dimers directly adjacent to the first. Growth of the polymer ceases when the end of the DNA is reached or when the DNA sequence blocks dimerization of the dye. Thus, this process can be thought of as a supramolecular analogue of a chain polymerization. This Account describes how polymerization depends on the dye structure and DNA sequence and also summarizes the interesting optical properties exhibited by these chiral, helical materials.
Pharmacologic therapy for stop mutations: how much CFTR activity is enough? (2004)

It is as yet unknown how much corrected mutant CFTR must reach the apical membrane to induce a clinically relevant beneficial effect. The future goal is to maximize the effect of stop-codon supressors on CFTR while minimizing side effects, but further studies must be performed to find a safer compound that may be administered in small children from the time of diagnosis.
Phylotype-level 16S rRNA analysis reveals new bacterial indicators of health state in acute murine colitis (2012)

Human inflammatory bowel disease and experimental colitis models in mice are associated with shifts in intestinal microbiota composition, but it is unclear at what taxonomic/phylogenetic level such microbiota dynamics can be indicative for health or disease. Here, we report that dextran sodium sulfate (DSS)-induced colitis is accompanied by major shifts in the composition and function of the intestinal microbiota of STAT1(-/-) and wild-type mice, as determined by 454 pyrosequencing of bacterial 16S rRNA (gene) amplicons, metatranscriptomics and quantitative fluorescence in situ hybridization of selected phylotypes. The bacterial families Ruminococcaceae, Bacteroidaceae, Enterobacteriaceae, Deferribacteraceae and Verrucomicrobiaceae increased in relative abundance in DSS-treated mice. Comparative 16S rRNA sequence analysis at maximum possible phylogenetic resolution identified several indicator phylotypes for DSS treatment, including the putative mucin degraders Akkermansia and Mucispirillum. The analysis additionally revealed strongly contrasting abundance changes among phylotypes of the same family, particularly within the Lachnospiraceae. These extensive phylotype-level dynamics were hidden when reads were grouped at higher taxonomic levels. Metatranscriptomic analysis provided insights into functional shifts in the murine intestinal microbiota, with increased transcription of genes associated with regulation and cell signaling, carbohydrate metabolism and respiration and decreased transcription of flagellin genes during inflammation. These findings (i) establish the first in-depth inventory of the mouse gut microbiota and its metatranscriptome in the DSS colitis model, (ii) reveal that family-level microbial community analyses are insufficient to reveal important colitis-associated microbiota shifts and (iii) support a scenario of shifting intra-family structure and function in the phylotype-rich and phylogenetically diverse Lachnospiraceae in DSS-treated mice.
Remotely pollable Geiger-Müller detector for continuous monitoring of iodine-131 therapy patients. (1998)

Monitoring patients with the described remotely pollable GM detector is an accurate and easy-to-implement technique that could conceivably lead to shortened hospital stays for (131)I therapy inpatients. Continuous quantitative data obtained are useful for kinetic and dosimetric analyses, which may be applied to study other gamma-emitting radiopharmaceuticals as well. The flexibility of the technique may permit its use in the monitoring of therapy on an outpatient basis, where allowed.
Rapid determination of renal filtration function using an optical ratiometric imaging approach (2007)

Glomerular filtration rate (GFR), which measures the amount of plasma filtered through the kidney within a given time, is an essential and clinically important indicator of kidney function. Here, we report a new ratiometric measurement technique based on intravital fluorescence microscopy that allows rapid evaluations of renal function in rodent models. By using this technique, plasma clearance rates of a fluorescent GFR marker can be measured in less than 5 min following a bolus infusion of a fluorescent dye mixture into the bloodstream. The plasma clearance kinetics of the GFR marker showed consistent values when measured in healthy animals at locations both in the kidney and from the skin. In addition, by using this technique, we were able to rapidly determine renal function with acute renal failure animal models and with other animal models where kidney filtration functions were altered. The measured plasma clearance kinetics using this technique correlated with expected changes in kidney function. We found this ratiometric approach offers improved accuracy and speed for quantifying renal function compared with the approach using single fluorescent probes, and the measurement can be done noninvasively from the skin. This approach also offers a high sensitivity for determining plasma clearance rate of a fluorescent compound. This feature is important for rapidly quantifying small differences in plasma clearance when kidney function is changing.
The structure of PA48009: The revised structure of duramycin. (1990)

PA48009, a lanthionine-containing peptide antibiotic was isolated from the culture broth of Streptoverticillium griseoverticillatum PA-48009, and identified as duramycin. Determination of the structure using both Edman degradations and 2D NMR spectroscopy showed the need to revise the structure of duramycin given in literature. Duramycin (PA48009) was different from lanthiopeptin (Ro 09-0198, cinnamycin) only by a Lys/Arg exchange at position 2.
Pharmacokinetic/Pharmacodynamic Modeling in Drug Development (2000)

We propose a framework for considering the role of pharmacokinetic/pharmacodynamic modeling in drug development and an appraisal of its current and potential impact on that activity. After some introduction, definitions, and background information on drug development, we discuss subject-matter models that underlie pharmacokinetic/pharmacodynamic modeling and show how they determine appropriate statistical models. We discuss the broad role modeling can play in drug development, enhancing primarily the "learning" steps, i.e. acquiring the information needed for the label and for planning efficient confirmatory clinical trials. Examples of past applications of modeling to drug development are presented in tabular form, followed by a discussion of some practical issues in application. Modeling will not reach its potential utility until it is manifest as a visible and separate work unit within a drug development program. We suggest that that work unit is the "in numero" study: a protocol-driven exercise designed to extract additional information, and/or answer a specific drug-development question, through an integrated model-based (meta-) analysis of existent raw data, often pooled across separate (clinical) studies.
Identification of Three Essential Regulatory Gene Loci Governing Expression of Staphylococcus epidermidis Polysaccharide Intercellular Adhesin and Biofilm Formation (2000)

The formation of adherent multilayered biofilms embedded into a glycocalyx represents an essential factor in the pathogenesis of Staphylococcus epidermidis biomaterial-related infections. Using biofilm-producing S. epidermidis 1457 and transposon Tn917 carried on plasmid pTV1ts, we isolated nine isogenic biofilm-negative transposon mutants. Transduction by S. epidermidis phage 71 was used to prove the genetic linkage of transposon insertions and altered phenotypes. Mapping of the different transposon insertions by Southern hybridization and pulsed-field gel electrophoresis indicated that these were inserted in four unlinked genetic loci. According to their phenotypes, including quantitative differences in biofilm production in different growth media, in the amount of the polysaccharide intercellular adhesin (PIA) produced, in the hemagglutination titers, and in the altered colony morphology, the mutants could be separated into four phenotypic classes corresponding with the genetic classes. Synthesis of PIA was not detectable with class I and II mutants, whereas the amount of PIA produced reflected the residual degree of biofilm production of class III and IV mutants in different growth media. Chromosomal DNA flanking the transposon insertions of five class I mutants was cloned and sequenced, and the insertions were mapped to different locations of icaADBC, representing the synthetic genes for PIA. Expression of icaADBC from a xylose-dependent promoter in the different isogenic mutant classes reconstituted biofilm production in all mutants. In a Northern blot analysis no icaADBC-specific transcripts were observed in RNA isolated from mutants of classes II, III, and IV. Apparently, in addition to icaADBC, three other gene loci have a direct or indirect regulatory influence on expression of the synthetic genes for PIA on the level of transcription.
Targeting key angiogenic pathways with a bispecific Cross MA b optimized for neovascular eye diseases (2016)

Anti-angiogenic therapies using biological molecules that neutralize vascular endothelial growth factor-A (VEGF-A) have revolutionized treatment of retinal vascular diseases including age-related macular degeneration (AMD). This study reports preclinical assessment of a strategy to enhance anti-VEGF-A monotherapy efficacy by targeting both VEGF-A and angiopoietin-2 (ANG-2), a factor strongly upregulated in vitreous fluids of patients with retinal vascular disease and exerting some of its activities in concert with VEGF-A. Simultaneous VEGF-A and ANG-2 inhibition was found to reduce vessel lesion number, permeability, retinal edema, and neuron loss more effectively than either agent alone in a spontaneous choroidal neovascularization (CNV) model. We describe the generation of a bispecific domain-exchanged (crossed) monoclonal antibody (CrossMAb; RG7716) capable of binding, neutralizing, and depleting VEGF-A and ANG-2. RG7716 showed greater efficacy than anti-VEGF-A alone in a non-human primate laser-induced CNV model after intravitreal delivery. Modification of RG7716's FcRn and FcγR binding sites disabled the antibodies' Fc-mediated effector functions. This resulted in increased systemic, but not ocular, clearance. These properties make RG7716 a potential next-generation therapy for neovascular indications of the eye.
The Metabolism of Glucose by the Alga Ochromonas malhamensis. (1956)

The single-drop technique that was used for apply-
Recent Development in Oxy-Combustion Technology and Its Applications to Gas Turbine Combustors and ITM Reactors (2012)

For decreasing greenhouse gas (mainly CO2) emissions, several approaches have been evaluated and reviewed for capturing CO2 in the utility industry, namely, carbon capture and storage technology (CCS), including precombustion capture, oxy-fuel combustion, and postcombustion capture. As a promising CCS technology, oxy-fuel combustion can be used to existing and new power plants. In oxy-combustion, a fuel is oxidized in a nearly nitrogen-free, diluted mixture such that the products consist mainly of CO2 and water vapor, enabling a relatively simple and inexpensive condensation separation process, and then, CO2 could be captured easily. There are two main approaches available to utilize the oxy-combustion technology, one of them is through the use of air separation units to separate O2, which will be used in the combustion process, and the other application is the ion transport membrane (ITM) reactor technology. This membrane separates oxygen from oxygen containing upstream (typically air). The oxygen transports through the membrane to a downstream permeate side containing fuel, with CO2 as inert carrier gas and the combustion starts in the permeate side of the membrane. In the present review paper, the oxy-fuel combustion technology status for clean power generation and carbon capture is introduced, starting with the available carbon capture technologies and comparison between them. This is followed by a detailed review of research work that considers the oxy-fuel combustion process itself, with a particular focus on the applications to this technology in ITM reactors and gas turbine combustors. This work also presents a detailed analysis for the most recent advancement in the ITM reactors technology with more analysis related to the membrane separation mechanism, the available permeation equations in the literature and the membrane performance regarding separation only and ITM reactor applications. The new coefficients oxygen permeation equation model is introduced in this work by fitting the experimental data available in the literature for a LSCF-1991 ion transport membrane. Because of new challenges presented by oxy-fuel combustion, as opposed to air-fuel combustion, research pertaining to the analysis of oxy-fuel combustion in real systems such as gas turbines is also discussed in the present work.
Relative bioavailability of controlled-release oral morphine sulfate during naltrexone blockade. (1995)

The effect of naltrexone hydrochloride on the bioavailability of 60 mg controlled-release oral morphine sulfate in normal volunteers was determined using a randomized, 2-way crossover, analytically blinded study design. Although naltrexone did not qualitatively alter the concentration-time curve for controlled-release morphine, the area under the plasma morphine concentration-time curve from 0-24 h (AUC0-24) was significantly greater (p < 0.01) for morphine given with naltrexone (265 ng x h/ml) than for morphine given alone (215 ng x h/ml). Compared to morphine given alone, the apparent absorption half-life of morphine was decreased from 0.94-0.58 h (p = 0.01) and Cmax was increased from 28.17 ng/ml to 32.26 ng/ml (p = 0.04) during naltrexone blockade, whereas the Tmax and apparent elimination half-life of morphine were not significantly affected. The minimal differences in morphine bioavailability indicate naltrexone may be useful in comparative bioavailability studies of high-dose opioids in opioid-naive normal volunteers.
A Generalization of RTM Inverse Scattering Imaging Conditions (2013)

Reverse time migration (RTM) imaging can have significant artifacts which are generated by backscattered and turning waves, where the source and receiver wavefields are in phase. This paper gives a tutorial on an inverse scattering based imaging condition, in which a significant reduction of these artifacts can be achieved. The basic principle has been discussed by others, but we give a simple explanation of the components of the method and then extend it to be more generally applicable to shot, stacks and angle domains. The method is based on an imaging kernel that is the weighted combination of two separate imaging kernels – the time derivative product and the gradient dot product of the source and receiver wavefields respectively. Applications of this method are given for the cases of imaging of single shots, the sum of shots and RTM angle data.
Role of human epidermal growth factor receptor 2 in gastric cancer: Biological and pharmacological aspects (2014)

Amplification of the human epidermal growth factor receptor 2 (HER2) gene and overexpression of the HER2 protein is found in 15%-20% of patients with gastric and gastroesophageal junction cancer. The degree of HER2 overexpression and amplification varies with the location of the carcinoma, with higher expression in the gastroesophageal and proximal parts compared to the distal parts of the stomach. Further, HER2 overexpression and amplification also seems to be related to the Lauren histological classification, with higher levels found in the intestinal phenotype compared to the diffuse and mixed types. The prognostic properties of HER2 overexpression and amplification are still under debate, but a large number of studies seem to indicate that HER2 is a negative prognostic factor. The usefulness of HER2 targeted therapy in gastric cancer was demonstrated in the ToGA trial, where HER2-positive patients with advanced gastric and gastroesophageal junction adenocarcinoma were randomized to receive 5-FU/capecitabine and cisplatin, either alone or in combination with trastuzumab. A statically significant gain in overall survival was seen in patients who received the combined treatment of trastuzumab and chemotherapy. Patients with a strong overexpression of the HER2 protein (IHC3+) specifically benefited from the treatment, with a median overall survival of 17.9 mo. As a consequence of the positive results of the ToGA trial, patients with advanced gastric or gastroesophageal junction adenocarcinoma are now routinely tested for HER2. The ToGA trial must be characterized as a landmark in the treatment of gastric cancer and it has paved the way for a number of new HER2 targeted compounds such as pertuzumab, ado-trastuzumab emtansine, lapatinib, afatinib, and dacomitinib, which are currently undergoing phase II and III clinical testing. Overall, this review will discuss the current status of HER2 in gastric and gastroesophageal junction cancer and the future direction in relation to HER2 target therapy.
Transfer RNA-dependent amino acid biosynthesis: An essential route to asparagine formation (2002)

Biochemical experiments and genomic sequence analysis showed that Deinococcus radiodurans and Thermus thermophilus do not possess asparagine synthetase (encoded by asnA or asnB), the enzyme forming asparagine from aspartate. Instead these organisms derive asparagine from asparaginyl-tRNA, which is made from aspartate in the tRNA-dependent transamidation pathway [Becker, H. D. & Kern, D. (1998) Proc. Natl. Acad. Sci. USA 95, 12832-12837; and Curnow, A. W., Tumbula, D. L., Pelaschier, J. T., Min, B. & Söll, D. (1998) Proc. Natl. Acad. Sci. USA 95, 12838-12843]. A genetic knockout disrupting this pathway deprives D. radiodurans of the ability to synthesize asparagine and confers asparagine auxotrophy. The organism's capacity to make asparagine could be restored by transformation with Escherichia coli asnB. This result demonstrates that in Deinococcus, the only route to asparagine is via asparaginyl-tRNA. Analysis of the completed genomes of many bacteria reveal that, barring the existence of an unknown pathway of asparagine biosynthesis, a wide spectrum of bacteria rely on the tRNA-dependent transamidation pathway as the sole route to asparagine.
CpG DNA rescue from anti-IgM-induced WEHI-231 B lymphoma apoptosis via modulation of I kappa B alpha and I kappa B beta and sustained activation of nuclear factor-kappa B/c-Rel. (1998)

Unmethylated CpG dinucleotides in particular base contexts in oligonucleotides (CpG DNA) rescue WEHI-231 cells from anti-IgM-induced cell cycle arrest and apoptosis. Anti-IgM rapidly elevated the levels of NFkappaB p50/c-Rel heterodimers followed by a decline of p50/c-Rel heterodimers by 3 h and a concomitant increase of p50/p50 homodimers. In contrast, CpG DNA induced and maintained the levels of p50/c-Rel heterodimers in the presence or absence of anti-IgM, while control non-CpG DNA failed to induce NFkappaB activation. Anti-IgM induced IkappaB alpha degradation followed by increased IkappaB alpha protein levels. The levels of IkappaB beta were increased after anti-IgM treatment. In contrast, CpG DNA, but not non-CpG DNA, induced sustained IkappaB alpha and IkappaB beta degradation in the presence or absence of anti-IgM. Inhibition of IkappaB degradation blocked CpG DNA-induced NFkappaB activation and expression of c-myc. Prevention of NFkappaB activation by inhibiting IkappaB degradation also suppressed the ability of CpG DNA to rescue WEHI-231 cells from anti-IgM-induced apoptosis. These results indicate that CpG DNA-mediated sustained activation of NFkappaB depends on the degradation of IkappaB alpha and IkappaB beta and is required for the CpG DNA-mediated anti-apoptosis gene expression and the protection against anti-IgM-induced apoptosis of WEHI-231 cells.
Arenoviruses in Vero Cells: Ultrastructural Studies (1970)

Thin-section electron microscopy was carried out on Vero green monkey kidney cell cultures infected with some viruses of the newly constituted arenovirus group. Junin, Machupo, Amapari, Pichinde, Parana, Tamiami, and Latino viruses were morphologically identical and indistinguishable from lymphocytic choriomeningitis virus, the prototype virus of the group. Virus particles were round, oval, or pleomorphic, 60 to 280 nm in diameter, and matured via budding from plasma membranes. Most characteristically, particles contained various amounts of homogeneous, 20- to 25-nm, dense granules; these granules in large masses also formed distinctive intracytoplasmic inclusions. In negative-contrast preparations from infected Vero cell culture supernatant fluids, several of the viruses appeared as pleomorphic membrane-bound forms with rather pronounced surface projections. Most particles were between 90 and 220 nm in diameter, although some reached 350 nm in their longest dimension. Internal structure was not resolved by negative-contrast electron microscopy. All observations supported the current delineation of a distinct arenovirus group.
Review of Fission Engine Concepts (1972)

Covers advancements in spacecraft and tactical and strategic missile systems, including subsystem design and application, mission design and analysis, materials and structures, developments in space sciences, space processing and manufacturing, space operations, and applications of space technologies to other fields.
Application of ultrasonic scalpel in gynecologic operative laparoscopy. (2001)

The ultrasonic scalpel can be safely applied for gynecologic operative laparoscopy and should be used widely.