gebhart/patrepeval huggingface dataset:
Saponin adjuvant enhancement of antigen-specific immune responses to an experimental HIV-1 vaccine (1992)

The adjuvant activity of a single highly purified saponin from the soap bark tree Quillaja saponaria was evaluated by using it as a component in an experimental vaccine containing rHIV-1 envelope protein (HIV-1 160D) adsorbed to alum. BALB/c mice immunized with experimental vaccine formulations containing the saponin adjuvant QS-21 produced significantly higher titers of antibodies than mice vaccinated with only the alum-adsorbed HIV-1 160D. Potent amnestic antibody responses to HIV-1 viral proteins were also induced. Ag-specific proliferative responses to recombinant proteins and to three variants of HIV-1 were significantly increased using QS-21 as an adjuvant. Alum-adsorbed HIV-1 160D failed to induce measurable proliferative responses to inactivated HIV-1 viruses, but group-specific proliferative responses were raised when the QS-21 adjuvant was used in the vaccine formulation. MHC class I restricted CTL specific for the immunodominant V-3 loop were induced but only when the QS-21 adjuvant was included in the vaccine formulation. The production of serine esterase by Ag-activated splenic mononuclear cells, indicating the maturation of precursor CTL, was used as a secondary measure of CTL activity, and this response was also increased. The specificity of antibody responses was not significantly broadened using QS-21; the adjuvant increased the immune recognition of epitopes throughout the HIV-1 glycoprotein 160. However, the specificity of the proliferation and serine esterase responses was broadened, suggesting that the QS-21 augmented cell-mediated immune responses specific for epitopes outside of the V-3 loop. Additionally, the QS-21 adjuvant appeared to induce recognition of weakly immunogenic epitopes that were not recognized using only alum-adsorbed HIV-1 160D. The ability of QS-21 to augment both antibody and cell-mediated immune responses suggests that this adjuvant could be a valuable component in subunit vaccines.
Atomic Resolution with Atomic Force Microscope (1987)

The atomic force microscope (AFM) is a promising new method for studying the surface structure of both conductors and insulators. In mapping a graphite surface with an insulating stylus, we have achieved a resolution better than 2.5 Å.
Association Between Serum Uric Acid, Metabolic Syndrome, and Carotid Atherosclerosis in Japanese Individuals (2005)

The prevalence of metabolic syndrome showed a graded increase according to serum uric acid values in both genders. In men who did not have metabolic syndrome, uric acid was found to be an independent risk factor for incidence of carotid plaque.
Electro-conductive enzyme membrane (1989)

An electro-conductive enzyme membrane has been synthesized at a platinum electrode surface by electrochemical polymerization of pyrrole in the presence of glucose oxidase, while retaining enzyme activity and reversible electron transfer between the enzyme molecules and the electrode.
Detection of antibodies to common antigens of pathogenic and commensal Neisseria species (1989)

Sera from 29 children and six adults were used to investigate the nature of antigenic cross-reactivity between Neisseria polysaccharea, N. lactamica and N. meningitidis B,15P1.16 by immunoblotting. Major common antigens of 68-70 Kda, 60-65 Kda and 15-20 Kda were detected. Antibody directed against them uniformly decreased after absorption of the sera with the three different Neisseria species. Antigens of 55 Kda and 35 Kda specific to N. meningitidis, and one of 43 Kda specific to N. lactamica, were also demonstrated. Antibody against all antigens was more prevalent in bactericidal than in non-bactericidal sera, although these differences were statistically not significant. Differences in antibody prevalence between carriers of Neisseria spp. and non-carriers of these organisms were even less marked. Examination of sera by whole-cell enzyme-linked immunosorbent assay against N. meningitidis B,15P1.16 and N. lactamica gave an absorbance ratio of 1:1. Only four sera from children showed no reactivity against the meningococcal strain. These common antigens are likely to be important in vaccine development.
Biodiesel production by direct methanolysis of oleaginous microbial biomass (2007)

Abstract Biodiesel is a renewable fuel conventionally prepared by transesterification of pre‐extracted vegetable oils and animal fats of all resources with methanol, catalyzed by strong acids or bases. This paper reports on a novel biodiesel production method that features acid‐promoted direct methanolysis of cellular biomass of oleaginous yeasts and filamentous fungi. The process was optimized for tuning operation parameters, such as methanol dosage, catalyst concentration, reaction temperature and time. Up to 98% yield was reached with reaction conditions of 70 °C, under ambient pressure for 20 h and a dried biomass to methanol ratio 1:20 (w/v) catalyzed by either 0.2 mol L −1 H 2 SO 4 or 0.4 mol L −1 HCl. Cetane numbers for these products were estimated to range from 56 to 59. This integrated method is thus effective and technically attractive, as dried microbial biomass as feedstocks omits otherwise tedious and time‐consuming oil extraction processes. Copyright © 2007 Society of Chemical Industry
Identification of the alpha 3 chain of type IV collagen as the common autoantigen in antibasement membrane disease and Goodpasture syndrome. (1995)

Antiglomerular basement membrane (GBM) antibodies can cause glomerulonephritis or pulmonary hemorrhage by themselves or Goodpasture syndrome when they occur together. It is unknown if variations in antibody reactivity contribute to the different patterns of organ involvement seen in this disease. This study examines the reactivity of the alpha 1-alpha 6 NC1 domains of Type IV collagen, the putative autoantigen, in sera from patients with anti-GBM antibodies after various clinical presentations of lung hemorrhage and renal injury. Serum or plasma containing anti-GBM antibodies from 35 patients with combined glomerulonephritis and pulmonary hemorrhage, 19 with glomerulonephritis alone, and 4 with pulmonary hemorrhage alone were compared with samples from 19 normal controls and 32 patients with other kidney diseases. Four different immunologic assays were performed with bovine alpha 1-alpha 6(IV) and recombinant human type alpha 1-alpha 5(IV) collagen NC1 domains. The study found that the anti-GBM antibodies from all patients reacted with the alpha 3(IV) NC1 (85% exclusively). Additional limited reactivity with the alpha 1(IV) NC1 and alpha 4(IV) NC1 was found in 15 and 3%, respectively. This non-alpha 3(IV) NC1 reactivity was most frequent in the patients with anti-GBM antibodies and glomerulonephritis alone. None of the patients had reactivity to other basement membrane components like laminin, fibronectin, heparan sulfate proteoglycan, entactin, or the 7S and triple helical fragments of Type IV collagen. The observed alpha-chain NC1 reactivity was confined to patients with anti-GBM antibodies with no additional reactivities detected among a large number of other kidney diseases controls. The correlation of alpha 1-alpha 6(IV) NC1 reactivity in a large number of patients with anti-GBM antibodies defined by classic assays definitively establishes that reactivity to alpha 3(IV) NC1 domains is both sufficient and necessary for the expression of autoimmune disease directed to the NC1 domain of Type IV collagen. On the basis of the evidence, the classification of antibasement membrane disease and Goodpasture syndrome as anti-Type IV collagen disease is proposed.
Experimental investigations on the impedance and radiation properties of a three-element concentric microstrip square-ring antenna (1996)

Experimental investigation on an electromagnetically coupled concentric microstrip square-ring antenna (CMSRA) has been presented. Our previous work on concentric microstrip annular-ring resonators revealed that the impedance and radiation bandwidth can be improved considerably. A three-element CMSRA has been designed and its measured impedance and radiation patterns have been compared with those of a single square-ring antenna having a dimension equal to the largest element of the CMSRA. The effect of change of feed location has also been studied. Results show that the total percent bandwidth (BW) for the concentric microstrip square ring antenna is larger with respect to the single-ring antenna, and this effect is very much prominent at a particular feed location. © 1996 John Wiley & Sons, Inc.
Interaction of milk proteins with inulin (2002)

By L.A. SCHALLER-POVOLNY and D.E. SMITH Department of Food Science and Nutrition University of Minnesota St. Paul, MN, USA 55108 Data collected from polyacrylamide electrophoresis indicated that inulin and milk proteins are involved in interactions with each other. The milk protein that did not interact with inulin was a-lactalbumin. The findings of this study touched the surface concerning the understanding of the type of interactions that may be involved to form the protein-inulin complex. Further research would help to obtain a better understanding of not only the type or types of interactions occurring among milk proteins and inulin, but increase the understanding of the interaction between proteins and carbohydrates in general. lnteraktion von Milchproteinen und lnulin Dalen der Polyacrylamid-Elektrophorese zeigten, dass lnulin und Milchproteine lnteraktionen aufweisen. a-Lakt­albumin interagierte jedoch nicht mit lnulin. Die Befunde dieser Studie beri.lhren die Oberflache tor das Verstandnis der Art von lnteraktionen, die dazu beitragen, den Protein-lnulin-Komplex zu bilden. Weitere Untersuchungen konnten zu einem besseren Verstandnis nicht nur der Art oder der Arlen von lnteraktionen zwischen Milchproteinen und lnulin, son­dern auch der lnteraktionen zwischen Proteinen und Kohlenhydraten im allgemeinen beitragen. 21 Protein carbohydrate interaction 21 Protein-Kohlenhydratinteraktionen (inulin/milk proteins) (lnulin/Milchproteine)
Entering the Postgenome Era (1995)

Genet]icists can now identify about half the estimated 100,000 genes in the human genome, but they don't have a clue about what most of them actually do. Now, two new techniques described in this issue of Science could transform research on gene function. They offer two different ways of detecting the expression of hundreds or thousands of genes at a time, thereby allowing researchers to determine which genes are turned on in particular tissues, and at what levels. And that provides a quick way of assessing how gene expression patterns change during development, disease, and other physiological conditions.
A Diastereodivergent Synthetic Strategy for the Syntheses of Communesin F and Perophoramidine (2014)

An efficient, unified, and stereodivergent approach toward communesin F and perophoramidine was examined. The C(3) all-carbon quaternary center of an oxindole was smoothly constructed by base-promoted indolone-malonate alkylation chemistry. The complementary relative stereochemistry of the crucial vicinal quaternary centers found in communesin F and perophoramidine was selectively installed by substrate-controlled decarboxylative allylic alkylations.
System to independently modify excitation and/Or spectrum of speech waveform without explicit pitch extraction (1982)

A new speech analysis/synthesis system is described which is capable of independent manipulation of the fundamental frequency and spectral envelope of a speech waveform. The system deconvolves the original speech with the spectral envelope estimate to obtain a model for the excitation. Hence, explicit pitch extraction is not required. As a consequence, the transformed speech is more natural sounding than would be the case if the excitation were modeled as a sequence of pulses during voiced segments or pseudorandom noise during unvoiced segments. The system has applications in the areas of voice modification, baseband-excited vocoders, time-scale modification, and frequency compression as an aid to the partially deaf.
Mnk2 and Mnk1 Are Essential for Constitutive and Inducible Phosphorylation of Eukaryotic Initiation Factor 4E but Not for Cell Growth or Development (2004)

Mnk1 and Mnk2 are protein kinases that are directly phosphorylated and activated by extracellular signal-regulated kinase (ERK) or p38 mitogen-activated protein (MAP) kinases and implicated in the regulation of protein synthesis through their phosphorylation of eukaryotic translation initiation factor 4E (eIF4E) at Ser209. To investigate their physiological functions, we generated mice lacking the Mnk1 or Mnk2 gene or both; the resulting KO mice were viable, fertile, and developed normally. In embryonic fibroblasts prepared from Mnk1-Mnk2 DKO mice, eIF4E was not detectably phosphorylated at Ser209, even when the ERK and/or p38 MAP kinases were activated. Analysis of embryonic fibroblasts from single KO mice revealed that Mnk1 is responsible for the inducible phosphorylation of eIF4E in response to MAP kinase activation, whereas Mnk2 mainly contributes to eIF4E's basal, constitutive phosphorylation. Lipopolysaccharide (LPS)- or insulin-induced upregulation of eIF4E phosphorylation in the spleen, liver, or skeletal muscle was abolished in Mnk1(-/-) mice, whereas the basal eIF4E phosphorylation levels were decreased in Mnk2(-/-) mice. In Mnk1-Mnk2 DKO mice, no phosphorylated eIF4E was detected in any tissue studied, even after LPS or insulin injection. However, neither general protein synthesis nor cap-dependent translation, as assayed by a bicistronic reporter assay system, was affected in Mnk-deficient embryonic fibroblasts, despite the absence of phosphorylated eIF4E. Thus, Mnk1 and Mnk2 are exclusive eIF4E kinases both in cultured fibroblasts and adult tissues, and they regulate inducible and constitutive eIF4E phosphorylation, respectively. These results strongly suggest that eIF4E phosphorylation at Ser209 is not essential for cell growth during development.
Structure of the hamster low density lipoprotein receptor gene. (1992)

The metabolism of low density lipoprotein (LDL) in the hamster is substantially similar to that of the human. To extend the usefulness of the hamster as an experimental model, the hamster LDL receptor gene was isolated and characterized. The gene is composed of 18 exons and 17 introns which span 26 kilobases. The introns occur at precisely the same positions as those previously determined for the human LDL receptor gene. The 18 exons of the hamster gene predict an LDL receptor protein of 854 amino acids that is similar in organization and sequence to those predicted from the cDNAs of rat, rabbit, cow, and human. Within the 5'-flanking region of the hamster LDL receptor gene are three highly conserved imperfect direct repeat sequences of 16 nucleotides each that in the human gene have been demonstrated to regulate transcription. In addition, a similar arrangement of direct repeat sequences was also isolated from the 5'-flanking region of the rat LDL receptor gene using the polymerase chain reaction. These results indicate a strong sequence and structural conservation of the LDL receptor among several species and further support the hamster as an experimental model for the study of human LDL-cholesterol metabolism.
Population pharmacokinetic analysis from phase I and phase II studies of the humanized monovalent antibody, MetMAb, in patients with advanced solid tumors. (2011)

2571 Background: MetMAb is a recombinant, humanized, monovalent monoclonal antibody directed against the tyrosine kinase Met, based on the human IgG (k) framework sequences, and is the first monovalent antibody in clinical development. The unique monovalent design of MetMAb reduces the potential for Met activation, found with bivalent anti-Met antibodies. The main objective of the analyses was to characterize the pharmacokinetics (PK) of MetMAb. Methods: MetMAb was administered intravenously once every 3 weeks (q3wk). The noncompartment and population PK analyses were performed using patient data from a Phase I dose escalation study (1, 4, 10, 20, 30 mg/kg as a single agent, 10 and 15 mg/kg with bevacizumab (bev) 15 mg/kg q3wk) and a Phase II study in 2nd/3rd line NSCLC patients (15 mg/kg q3wk with erlotinib 150 mg daily). Potential PK drug-drug interaction (DDI) was assessed for coadministration of MetMAb with bev or erlotinib. Results: MetMAb showed linear PK in the dose range of 4-30 mg/kg. The clearance (CL) was faster (~2-fold) at 1 mg/kg compared with the other dose groups, suggesting that the target-mediated CL pathway played a major role at the low dose. In the linear-dose range, the mean CL values were in the range of 6.8-9.9 mL/day/kg, about 1.5- to 2-fold faster than the range reported for typical bivalent IgG antibodies. The mean elimination half-life is in the range of 8-12 days. In the Phase II study, over 90% patients achieved the target steady state trough concentrations (i.e., 15 ug/mL based on preclinical studies) with the mean value of about 73 ug/mL. Cross-study comparison did not show significant PK DDI for MetMAb in combination with bev or erlotinib. Although minimal and transient anti-therapeutic antibody (ATA) responses were detected in 7 out of 98 MetMAb-treated patients, the MetMAb PK profiles did not appear to be impacted in the ATA-positive patients. Conclusions: This is the first report of monovalent antibody PK from Phase I and II studies. Although slightly faster CL and shorter half-life were observed compared with typical bivalent antibodies, the PK profile supports q2wk or q3wk dosing regimens to achieve an effective and safe exposure in patients.
“Control” laboratory rodents are metabolically morbid: Why it matters (2010)

Failure to recognize that many standard control rats and mice used in biomedical research are sedentary, obese, glucose intolerant, and on a trajectory to premature death may confound data interpretation and outcomes of human studies. Fundamental aspects of cellular physiology, vulnerability to oxidative stress, inflammation, and associated diseases are among the many biological processes affected by dietary energy intake and exercise. Although overfed sedentary rodents may be reasonable models for the study of obesity in humans, treatments shown to be efficacious in these animal models may prove ineffective or exhibit novel side effects in active, normal-weight subjects.
Sequence Homology Among Sperm Antigens Involved in Mammalian Fertilization: Search for a Common Epitope for Immunocontraception (1994)

Sequence homology was searched among the nine cDNAs/deduced amino acid sequences encoding for the eight fertilization-related sperm antigens: namely, lactate dehydrogenase (LDH-C4), galactosyltransferase (GT), SP-10, rabbit sperm autoantigen (RSA), guinea pig (g)PH-20, cleavage signal protein (CS-1), HSA-63, human (h)PH-20, and AgX-1, respectively. Most significant identity (> 50%) was found between HSA-63 and SP-10 (59.8%), and between gPH-20 and hPH-20 (61.1%); followed by identity between SP-10 and GT (34.7%); and then between AgX-1 and hPH-20 (39.4%). All others had identity < 25%. The significance of these sequence homologies among the sperm antigens in the development of an antisperm contraceptive vaccine is discussed.
The insulin-like effect of hydrogen peroxide on pathways of lipid synthesis in rat adipocytes. (1979)

In addition to the well known insulin-like effects of certain concentrations of H2O2 on glucose transport and oxidation in isolated rat adipocytes, the present work demonstrates that lipid synthesis from glucose is also enhanced over a narrow range of H2O2 concentrations (0.15 to 0.5 mM) added to the incubation medium. As in the case of insulin, H2O2 was found to stimulate greater glucose incorporation into glyceride-fatty acid than incorporation into glyceride-glycerol. As part of a multifaceted regulation of lipogenesis, H2O2, like insulin, increased the amount of pyruvate dehydrogenase in the active form without increasing the total amount of pyruvate dehydrogenase. Pyruvate dehydrogenase activity increased within 5 min of H2O2 incubation, reached a maximum at 15 min and declined thereafter as the H2O2 disappeared from the incubation medium. While medium glucose per se was found to activate the enzyme, it is unlikely that the effect of H2O2 was mediated by the known enhancement of glucose transport since the effects on the enzyme were maximal in the absence of glucose in the incubation medium. These findings add to the growing list of insulin effects that are reproduced by H2O2, and strengthen the hypothesis that assigns H2O2 the role of "second messenger" of insulin.
Diode-pumped singly resonant continuous-wave optical parametric oscillator with wide continuous tuning of the near-infrared idler wave (2000)

We demonstrate wide, continuous tuning of the single-frequency idler wave of a cw singly resonant optical parametric oscillator (SRO). The SRO consists of a periodically poled LiNbO(3) crystal for quasi-phase matching in a four-mirror signal-resonant ring cavity. The SRO, excited by 2.25 W of 924-nm radiation from an InGaAs diode laser, generates as much as 200 mW of single-frequency 2.1-mum idler radiation. We tune the idler frequency continuously within a range as large as 56 GHz by changing the wavelength of the diode pump laser. The versatility of this continuously tunable single-frequency infrared source is demonstrated by recording of N(2)O rovibrational absorption lines near 2.1 mum.
Family-wide Structural Characterization and Genomic Comparisons Decode the Diversity-oriented Biosynthesis of Thalassospiramides by Marine Proteobacteria (2016)

The thalassospiramide lipopeptides have great potential for therapeutic applications; however, their structural and functional diversity and biosynthesis are poorly understood. Here, by cultivating 130 Rhodospirillaceae strains sampled from oceans worldwide, we discovered 21 new thalassospiramide analogues and demonstrated their neuroprotective effects. To investigate the diversity of biosynthetic gene cluster (BGC) architectures, we sequenced the draft genomes of 28 Rhodospirillaceae strains. Our family-wide genomic analysis revealed three types of dysfunctional BGCs and four functional BGCs whose architectures correspond to four production patterns. This correlation allowed us to reassess the "diversity-oriented biosynthesis" proposed for the microbial production of thalassospiramides, which involves iteration of several key modules. Preliminary evolutionary investigation suggested that the functional BGCs could have arisen through module/domain loss, whereas the dysfunctional BGCs arose through horizontal gene transfer. Further comparative genomics indicated that thalassospiramide production is likely to be attendant on particular genes/pathways for amino acid metabolism, signaling transduction, and compound efflux. Our findings provide a systematic understanding of thalassospiramide production and new insights into the underlying mechanism.
Brighthouse (2008)

Brighthouse is a column-oriented data warehouse with an automatically tuned, ultra small overhead metadata layer called Knowledge Grid, that is used as an alternative to classical indexes. The advantages of column-oriented data storage, as well as data compression have already been well-documented, especially in the context of analytic, decision support querying. This paper demonstrates additional benefits resulting from Knowledge Grid for compressed, column-oriented databases. In particular, we explain how it assists in query optimization and execution, by minimizing the need of data reads and data decompression.