gebhart/patrepeval huggingface dataset:
Phytase fromAspergillus terreus (1968)

1) Aspergillus terreus No. 9A-1 was cultivated by a shaking method and the optimal cultural conditions for the phytase production were concluded as follows: Composition of medium; rice bran 30 g, ammonium sulfate 3 g, distilled water 1.0 liter; initial pH 5.5; shaking condition; 50 ml of medium/500 ml vol. flask; 120 oscil./min, 90 hr. 2) Phytase from Asp. terreus was purified by ammonium sulfate precipitation, acetone precipitation and chromatography on SE-Sephadex C-50 and Sephadex G-200 columns. The enzyme was purified about 520-folds with the yield of 20% from the broth. The purified enzyme was homogeneous by column chromatography, ultracentrifugation and electrophoresis. 3) This purified preparation of phytase showed following properties, a) Optimal pH for the reaction was 4.5; b) optimal temperature for the reaction was about 70°C; c) the enzyme was stable in the range of pH from 1.2 to 9.0
The post-antibiotic sub-MIC effect in vitro and in vivo (1993)

The post-antibiotic effect (PAE) has been recognized as a pharmacodynamic parameter which may influence optimal dosage intervals. During the post-antibiotic phase, various bacteria have been shown to be very sensitive to a repeated exposure to the same antibiotic. A long period of growth suppression may be obtained when a low concentration (< or = 0.3 x MIC) is added to bacteria previously exposed to a supra-inhibitory concentration. This phenomenon has been named the post-antibiotic sub-MIC effect (PA SME). Since a period with sub-inhibitory concentrations will often exist between the doses when intermittent dosing of antibiotics is used, the PA SME probably reflects the in-vivo situation more closely than the PAE. The published literature on the PA SME is reviewed and its possible role in antibiotic dosing discussed.
Phosphorylation Site Dynamics of Early T-cell Receptor Signaling (2014)

In adaptive immune responses, T-cell receptor (TCR) signaling impacts multiple cellular processes and results in T-cell differentiation, proliferation, and cytokine production. Although individual protein-protein interactions and phosphorylation events have been studied extensively, we lack a systems-level understanding of how these components cooperate to control signaling dynamics, especially during the crucial first seconds of stimulation. Here, we used quantitative proteomics to characterize reshaping of the T-cell phosphoproteome in response to TCR/CD28 co-stimulation, and found that diverse dynamic patterns emerge within seconds. We detected phosphorylation dynamics as early as 5 s and observed widespread regulation of key TCR signaling proteins by 30 s. Development of a computational model pointed to the presence of novel regulatory mechanisms controlling phosphorylation of sites with central roles in TCR signaling. The model was used to generate predictions suggesting unexpected roles for the phosphatase PTPN6 (SHP-1) and shortcut recruitment of the actin regulator WAS. Predictions were validated experimentally. This integration of proteomics and modeling illustrates a novel, generalizable framework for solidifying quantitative understanding of a signaling network and for elucidating missing links.
Role of endothelial-leukocyte adhesion molecule 1 (ELAM-1) in neutrophil-mediated lung injury in rats. (1991)

Two murine monoclonal antibodies (CL-3 and CL-37, both F(ab')2) to human endothelial-leukocyte adhesion molecule-1 (ELAM-1) were found to react immunohistochemically with rat pulmonary artery endothelial cells that had been pretreated with tumor necrosis factor (TNF alpha). CL-3, but not CL-37, blocked in vitro adherence of neutrophils to TNF alpha-treated endothelial cells and the killing of TNF alpha-treated rat endothelial cells by phorbol ester activated neutrophils. In rats treated systemically with CL-3, there was a 70% reduction in accumulation of neutrophils in glycogen-induced peritoneal exudates. Treatment of animals with CL-37 anti-ELAM-1 did not reduce neutrophil accumulation under the same conditions. When IgG immune complex deposition was induced in dermis and in lungs of rats, treatment with CL-3 anti-ELAM-1 markedly reduced vascular injury as measured by changes in vascular permeability (leakage of 125I-albumin) and hemorrhage (extravasation of 51Cr-red blood cells). The protective effects of CL-3 anti-ELAM-1 were related to greatly diminished recruitment of neutrophils (as assessed morphologically, by tissue extraction of myeloperoxidase, and by retrieval, via bronchoalveolar lavage, of neutrophils from lung). CL-37 had no protective effects in vivo after deposition of immune complexes in lung. Using either CL-3 or CL-37 anti-ELAM-1, immunohistochemical analysis of lungs undergoing IgG immune complex-induced injury revealed a striking upregulation of ELAM-1 in the lung vasculature (venules and interstitial capillaries), with a peak intensity developing between 3 and 4 h after deposition of immune complexes in lung. Vascular beds of spleen, liver, and kidney failed to show upregulation of ELAM-1 under these same conditions. The immunohistochemical reactivity of rat lung was abolished if the anti-ELAM-1 preparation was first absorbed with monolayers of human umbilical vein endothelial cells that had been pretreated with TNF alpha. Untreated human endothelial cells failed to cause loss of lung reactivity of the anti-ELAM-1 preparation. These data indicate that ELAM-1 is upregulated in the pulmonary vasculature of rats during deposition of immune complexes and that ELAM-1 appears to play an obligate role in the recruitment of neutrophils.
Dna methylation status of the MUC1 gene coding for a breast‐cancer‐associated protein (1995)

The MUC1 gene codes for protein products that are highly expressed in human breast-cancer tissue and that serve as tumor markers for disease progression. The factors contributing to the disease-specific over-expression of the MUC1 gene are under intensive investigation and are yet to be determined. A large transcribed region of the human MUC1 gene is a CpG island that consists of 60-bp tandemly repeating units, each of which contains one SmaI restriction site. The methylation status of regulatory regions, upstream to the transcriptional start site, is essential for the regulation of gene expression. We therefore evaluated whether the methylation status of the various regions of the MUC1 gene may affect its expression. Using SmaI, and its isoschizomer XmaI endonucleases, we demonstrated that in peripheral-blood leukocytes (PBL-DNA) that do not express the MUC1 gene, the repeat array is completely methylated, whereas the same sequences are entirely non-methylated in breast-tumor-tissue DNA (BT-DNA). In contrast, sequences upstream and downstream to the repeat array showed no difference in the methylation pattern in PBL-DNA and BT-DNA. Hypomethylation within the repeat array was also observed in other epithelial tissues that express the MUC1 gene at much lower levels to those seen in breast-cancer tissue. These studies demonstrate that hypomethylation of the tandem repeat array is an absolute requirement for MUC1 gene expression in epithelial tissues, although in breast-cancer tissue additional regulatory mechanisms must pertain for its over-expression.
Bacterial Survival in Suspension in Polyethylene Glycol Solutions (1966)

SUMMARY: The % survivals of Escherichia coli (B, Jepp, commune), Serratia marcescens (uk8) and Aerobacter aerogenes (Hinshelwood), in the presence of polyethylene glycol were studied as a function of molecular weight and % polyethylene glycol. Polyethylene glycol is shown to cause a loss of viability; experiments are described which suggest loci for its action.
Quantitative Imaging Test Approval and Biomarker Qualification: Interrelated but Distinct Activities (2011)

http://radiology.rsna.org/lookup/suppl/doi:10.1148/radiol.10100800/-/DC1.
A randomized three-way cross-over study in healthy pituitary-suppressed women to compare the bioavailability of human chorionic gonadotrophin (Pregnyl) after intramuscular and subcutaneous administration (1998)

The objective of this study was to compare the bioavailability of s.c. and i.m. administration of human chorionic gonadotrophin (HCG; Pregnyl). In a randomized, single-centre, three-way cross-over study, 18 healthy pituitary-suppressed volunteers were assigned to single HCG injections of 5000 and 10,000 IU i.m. and 10,000 IU s.c. Rate (Cmax, t(max)) and extent [area under curve from zero to infinity (AUC(0-infinity))] of absorption of HCG were determined. Serum immunoactive HCG increased from 0.4-0.5 IU/l at baseline to mean peak concentrations, which were reached 20 h after injection of 156 IU/l with 5000 IU i.m., of 307 IU/l with 10,000 IU i.m. and of 339 IU/l with 10,000 IU s.c. Eight days after administration, < 10% of the maximum HCG activity was found for each regimen. The elimination half-life (t(1/2)) was on average 32-33 h, irrespective of the treatment regimen. Intramuscular and s.c. injections of 10,000 IU HCG were bioequivalent with respect to AUC(0-infinity). The Cmax and t(max) were also similar between the two administration routes but bioequivalence could not be proven due to intersubject variability. Intramuscular doses of 5000 IU and 10,000 IU HCG were dose-proportional. Since s.c. HCG is bioequivalent to i.m. HCG with respect to extent of absorption (its major pharmacokinetic variable) and is well tolerated, the s.c. administration route may be effectively and safely used in assisted reproduction. Moreover, since s.c. injection can be performed by the patients themselves, acceptability may be enhanced.
Enhanced antigen‐specific primary CD4+ and CD8+ responses by codelivery of ovalbumin and toll‐like receptor ligand monophosphoryl lipid A in poly(D,L‐lactic‐co‐glycolic acid) nanoparticles (2006)

The purpose of this research was to investigate the use of biodegradable poly(D,L-lactic-co-glycolic acid) nanoparticles (PLGA-NP) as a vaccine delivery system to codeliver antigen, ovalbumin (OVA) along with monophosphoryl lipid A (MPLA) as adjuvant for induction of potent CD4(+) and CD8(+) T cell responses. The primary CD4(+) T responses to OVA/MPLA NP were investigated using OVA-specific T cells from DO11.10 transgenic mice. Following adoptive transfer of these cells, mice were immunized s.c. by NP formulations. For assessing the CD8(+) responses, bone marrow derived dendritic cells (DCs) were pulsed with different OVA formulations, then, cocultured with CD8(+) T cells from OT-1 mice. T cell proliferation/activation and IFN-gamma secretion profile have been examined. Particulate delivery of OVA and MPLA to the DCs lead to markedly increase in in vitro CD8(+) T cell T cell proliferative responses (stimulation index >3000) and >13-folds increase in in vivo clonal expanded CD4(+) T cells. The expanded T cells were capable of cytokine secretion and expressed an activation and memory surface phenotype (CD62L(lo), CD11a(hi), and CD44(hi)). Codelivery of antigen and MPLA in PLGA-NP offers an effective method for induction of potent antigen specific CD4(+) and CD8(+) T cell responses.
Neoglycoproteins as carriers for antiviral drugs: synthesis and analysis of protein-drug conjugates (1991)

In order to investigate whether neoglycoproteins can potentially act as carriers for targeting of antiviral drugs to certain cell types in the body, various neoglycoproteins were synthesized using thiophosgene-activated p-aminophenyl sugar derivatives. These neoglycoproteins were conjugated with the 5'-monophosphate form of the antiviral drug AZT. For a proper characterization of these preparations, both protein and drug content have to be determined. Comparison of the Lowry and the Bio-Rad protein assays revealed that for both the neoglycoprotein carriers themselves and the AZTMP conjugates, the Lowry assay yielded the most reliable and reproducible results. It was demonstrated that both the reagent used for drug conjugation (ECDI) as well as the introduction of phenyl-sugar groups in the protein interfered with the analysis of bound nucleotide as based on spectral differences between protein and protein-drug conjugate. Therefore, we developed a rapid HPLC system for determination of the drug-protein coupling ratio through acid hydrolysis of the covalently bound nucleotide. With the ECDI-mediated conjugation of 5'-monophosphate drug derivatives to neoglycoproteins, products with molar ratios of drug to protein ranging from 1.2 to 5.6 were obtained. The drug-neoglycoprotein conjugates appeared to be fairly stable during storage, in lyophilized form, at -20 degrees C. The anti-HIV-1 activity of the neoglycoprotein-drug conjugates, as determined in vitro in MT-4 cells, was shown to be dependent on glycosylation of the albumin and also on the kind of sugar present in the neoglycoprotein. The anti-HIV-1 activity of the AZTMP-mannose-albumin conjugate exceeded that of the parent drug by more than 4 times.
A brief survey of papers on scheduling for pipelined processors (1990)

Most microprocessors introduced into the market in the past few years employ pipelining to enhance execution speed. Moreover, many of these processors use multiple pipelined functional units. This paper surveys several heuristics reported in the literature on the topic of code optimization and reordering for exploiting instruction level parallelism in pipelined processors. Five methods are described in detail and several others are briefly reviewed
Mineral metabolism and growth (2001)

Although research into mineral metabolism has exploded in the last 2 decades, resulting in dramatic improvement in the treatment of bone diseases, mineral metabolism in relation to growth has been surprisingly neglected until the last few years. We review here recent advances in our understanding of calcium, magnesium, chromium, iron, and zinc, and their relation to growth using molecular biology and improved stable isotope techniques.
Relationship between sex and antibodies to high mobility group proteins 1 and 2 in juvenile idiopathic arthritis. (2000)

The results suggest that females with JIA are more likely to be ANA positive than males and more likely than males to have antibodies to HMG-1.
Construction and cloning of rat albumin structural gene sequences. (1979)

A recombinant plasmid containing a DNA segment complementary to rat liver albumin mRNA has been constructed, cloned, and used to examine the organization of albumin gene. The 18S fraction of total liver poly(A)-containing RNA was copied into a double-stranded cDNA by avian myeloblastosis virus reverse transcriptase and Escherichia coli DNA polymerase I. The cDNA was inserted into the HindIII site of the plasmid pBR322 via the addition of specific oligonucleotide linkers. Recombinant plasmids were screened by hybrid arrest of mRNA translation and hybridization with specific cDNAs. Thereby, a plasmid was identified that contained a 1200-nucleotide insert corresponding to a segment adjacent to the 5'-terminal region of albumin mRNA. The inserted sequence was used as a hybridization probe to detect five EcoRI fragments of genomic DNA which encode albumin mRNA. These were compared to eight EcoRI fragments identified within the rat genome by albumin cDNA. We conclude that the albumin gene (or genes) is interrupted at more than one site in the coding DNA by intervening sequences. Furthermore, we were able to distinguish those fragments that encode the 5' and 3' ends of the mRNA.
Identification of a common ecotropic viral integration site, Evi-1, in the DNA of AKXD murine myeloid tumors. (1988)

AKXD-23 recombinant inbred mice develop myeloid tumors at a high frequency, unlike other AKXD recombinant inbred strains which develop B-cell lymphomas, T-cell lymphomas, or both. AKXD-23 myeloid tumors are monoclonal, and their DNA contains somatically acquired proviruses, suggesting that they are retrovirally induced. We identified a common site of ecotropic proviral integration that is present in the DNA of all AKXD-23 myeloid tumors that were analyzed and in the DNA of all myeloid tumors that occur in AKXD strains other than AKXD-23. We designated this locus Evi-1 (ecotropic viral integration site 1). Rearrangements in the Evi-1 locus were also detected in the DNA of a number of myeloid tumors and myeloid cell lines isolated from strains other than AKXD. In contrast, few Evi-1 rearrangements were detected in the DNA of T- or B-cell tumors. Evi-1 may thus identify a new proto-oncogene locus that is involved in myeloid disease.
Preparation and Structure ofβ-Peptides Consisting of Geminally Disubstitutedβ2,2- andβ3,3-Amino Acids: A Turn Motif forβ-Peptides (1998)

We report on the synthesis of new and previously described β-peptides (1 – 6), consisting of up to twelve β2,2- or β3,3-geminally disubstituted β-amino acids which do not fit into any of the secondary structural patterns of β-peptides, hitherto disclosed. The required 2,2- and 3,3-dimethyl derivatives of 3-aminopropanoic acid are readily obtained from 3-methylbut-2-enoic acid and ammonia (Scheme 1) and from Boc-protected methyl 3-aminopropanoate by enolate methylation (Scheme 2). Protected (Boc for solution-, Fmoc for solid-phase syntheses) 1-(aminomethyl)cycloalkanecarboxylic-acid derivatives (with cyclopropane, cyclobutane, cyclopentane, and cyclohexane rings) are obtained from 1-cyanocycloalkanecarboxylates and the corresponding dihaloalkanes (Scheme 3). Fully 13C- and 15N-labeled 3-amino-2,2-dimethylpropanoic-acid derivatives were prepared from the corresponding labeled precursors (see asterixed formula numbers and Scheme 4). Coupling of these amino acids was achieved by methods which we had previously employed for other β-peptide syntheses (intermediates 18 – 23). Crystal structures of Boc-protected geminally disubstituted amino acids (16a – d) and of the corresponding tripeptide (23a), as well as NMR and IR spectra of an isotopically labeled β-hexapeptide (2a*) are presented (Figs. 1 – 4) and discussed. The tripeptide structure contains a ten-membered H-bonded ring which is proposed to be a turn-forming motif for β-peptides (Fig. 2).
The Smallest Known Genomes of Multicellular and Toxic Cyanobacteria: Comparison, Minimal Gene Sets for Linked Traits and the Evolutionary Implications (2010)

Cyanobacterial morphology is diverse, ranging from unicellular spheres or rods to multicellular structures such as colonies and filaments. Multicellular species represent an evolutionary strategy to differentiate and compartmentalize certain metabolic functions for reproduction and nitrogen (N(2)) fixation into specialized cell types (e.g. akinetes, heterocysts and diazocytes). Only a few filamentous, differentiated cyanobacterial species, with genome sizes over 5 Mb, have been sequenced. We sequenced the genomes of two strains of closely related filamentous cyanobacterial species to yield further insights into the molecular basis of the traits of N(2) fixation, filament formation and cell differentiation. Cylindrospermopsis raciborskii CS-505 is a cylindrospermopsin-producing strain from Australia, whereas Raphidiopsis brookii D9 from Brazil synthesizes neurotoxins associated with paralytic shellfish poisoning (PSP). Despite their different morphology, toxin composition and disjunct geographical distribution, these strains form a monophyletic group. With genome sizes of approximately 3.9 (CS-505) and 3.2 (D9) Mb, these are the smallest genomes described for free-living filamentous cyanobacteria. We observed remarkable gene order conservation (synteny) between these genomes despite the difference in repetitive element content, which accounts for most of the genome size difference between them. We show here that the strains share a specific set of 2539 genes with >90% average nucleotide identity. The fact that the CS-505 and D9 genomes are small and streamlined compared to those of other filamentous cyanobacterial species and the lack of the ability for heterocyst formation in strain D9 allowed us to define a core set of genes responsible for each trait in filamentous species. We presume that in strain D9 the ability to form proper heterocysts was secondarily lost together with N(2) fixation capacity. Further comparisons to all available cyanobacterial genomes covering almost the entire evolutionary branch revealed a common minimal gene set for each of these cyanobacterial traits.
Anthrax lethal factor cleaves MKK3 in macrophages and inhibits the LPS/IFNγ‐induced release of NO and TNFα (1999)

The lethal toxin of Bacillus anthracis consists of two proteins, PA and LF, which together induce lethal effects in animals and cause macrophage lysis. LF is a zinc-endopeptidase which cleaves two mitogen-activated protein kinase kinases (MAPKKs), Mek1 and Mek2, within the cytosol. Here, we show that also MKK3, another dual-specificity kinase that phosphorylates and activates p38 MAP kinase, is cleaved by LF in macrophages. No direct correlation between LF-induced cell death and cleavage of these MAPKKs was found in macrophage cell lines and primary peritoneal cells exhibiting different sensitivity to LF. However, we present the first evidence that sublytic doses of LF cleave Meks and cause a substantial reduction in the production of NO and tumour necrosis factor-alpha induced by lipopolysaccharide/interferon gamma. We suggest that this effect of LF is relevant during the first stages of B. anthracis infection, when a reduction of the inflammatory response would permit growth and diffusion of the bacterium.
Frequency Dependence of Ultrasonic Cavitation (1954)

On the basis of a simplified model an explanation for the high-frequency limit of ultrasonic cavitation is suggested and compared with published experimental data.
Monoclonal Antibodies against Dengue 2 Virus E-Glycoprotein Protect Mice against Lethal Dengue Infection (1987)

A panel of 11 murine monoclonal antibodies directed against dengue type 2 was evaluated for antigen specificity by dot immunobinding assay and Western blot analysis and for in vitro and in vivo biological activities. Nine of the 11 monoclonal antibodies reacted with viral E-glycoprotein based on the Western blot analysis; one reacted with a 36 Kd protein present in dengue-infected C6/36 mosquito cells. The nine E-glycoprotein-reactive monoclonal antibodies also neutralized dengue 2 virus in a plaque reduction assay. Of the neutralizing monoclonal antibodies, five passively protected mice in vivo against lethal intracerebral dengue 2 challenge. The protective monoclonal antibodies were directed against viral determinants that fell into at least three spatially separate families of epitopes on E-glycoprotein, the antigenicities of which were preserved after heat/detergent denaturation.
The dynamics of wire array Z-pinch implosions (1999)

Wire array Z-pinch dynamics are studied in experiments with 16-mm diameter arrays of between 8 and 64, 15-μm diameter aluminum wires, imploded in 200–260 ns by a 1.4-MA current pulse. Side-on laser probing shows early development of noncorrelated m=0-like instabilities with an axial wavelength ∼0.5 mm in individual wires. End-on interferometry (r-θ plane) shows azimuthal merging of the plasma with a density of 1017 cm−3 in 90–65 ns for 8–64 wires, respectively. At the same time low-density plasma reaches the array axis and forms a precursor pinch by 120–140 ns. At 0.7–0.85 of the implosion time a global m=0 instability with a wavelength of 1.7–2.3 mm was detected in soft x-ray gated images, laser probing, and optical streaks. The time when the instability reaches the observable level corresponds to the number of e-foldings for the growth of the classical Rayleigh–Taylor instability of ∫γ dt∼5.6–7. The scaling of this number with the number of wires is consistent with the instability growth from the seed level determined by the averaging of uncorrelated density perturbations in individual wires. Preliminary results from a 4×4 array permit the simultaneous observation by laser probing of the characteristic bubble and spike structure of the magneto Rayleigh–Taylor instability.