gebhart/patrepeval huggingface dataset:
Improved p-hydroxybenzoate production by engineered Pseudomonas putida S12 by using a mixed-substrate feeding strategy (2011)

The key precursors for p-hydroxybenzoate production by engineered Pseudomonas putida S12 are phosphoenolpyruvate (PEP) and erythrose-4-phosphate (E4P), for which the pentose phosphate (PP) pathway is an important source. Since PP pathway fluxes are typically low in pseudomonads, E4P and PEP availability is a likely bottleneck for aromatics production which may be alleviated by stimulating PP pathway fluxes via co-feeding of pentoses in addition to glucose or glycerol. As P. putida S12 lacks the natural ability to utilize xylose, the xylose isomerase pathway from E. coli was introduced into the p-hydroxybenzoate producing strain P. putida S12palB2. The initially inefficient xylose utilization was improved by evolutionary selection after which the p-hydroxybenzoate production was evaluated. Even without xylose-co-feeding, p-hydroxybenzoate production was improved in the evolved xylose-utilizing strain, which may indicate an intrinsically elevated PP pathway activity. Xylose co-feeding further improved the p-hydroxybenzoate yield when co-fed with either glucose or glycerol, up to 16.3 Cmol% (0.1 g p-hydroxybenzoate/g substrate). The yield improvements were most pronounced with glycerol, which probably related to the availability of the PEP precursor glyceraldehyde-3-phosphate (GAP). Thus, it was demonstrated that the production of aromatics such as p-hydroxybenzoate can be improved by co-feeding different carbon sources via different and partially artificial pathways. Moreover, this approach opens new perspectives for the efficient production of (fine) chemicals from renewable feedstocks such as lignocellulose that typically has a high content of both glucose and xylose and (crude) glycerol.
Insole Pedometer With Piezoelectric Energy Harvester and 2 V Organic Circuits (2012)

A shoe insole pedometer, which consists of a piezoelectric energy harvester and a 2 V organic pedometer circuit, has been developed as a first step toward the application of flexible large-area energy harvesting. A pseudo-CMOS 14 bit step counter records the number of steps up to 16383 steps using the harvested power. To increase the noise margin of the pseudo-CMOS logic circuits, a negative voltage is generated by an organic charge pump circuit and is applied to the pseudo-CMOS inverters and transmission gates in the flip-flops in the step counter. A pseudo-CMOS Schmitt trigger inverter used to feed clean square pulses to the step counter is presented. This paper describes the details of the insole pedometer and provides measurement results and some discussion.
Radial Basis Functions, Multi-Variable Functional Interpolation and Adaptive Networks (1988)

Abstract : The relationship between 'learning' in adaptive layered networks and the fitting of data with high dimensional surfaces is discussed. This leads naturally to a picture of 'generalization in terms of interpolation between known data points and suggests a rational approach to the theory of such networks. A class of adaptive networks is identified which makes the interpolation scheme explicit. This class has the property that learning is equivalent to the solution of a set of linear equations. These networks thus represent nonlinear relationships while having a guaranteed learning rule. Great Britain.
Purification of a Meningeal Cell‐derived Chondroitin Sulphate Proteoglycan with Neurotrophic Activity for Brain Neurons and its Identification as Biglycan (1995)

Serum-free cultures of meningeal fibroblasts synthesize and release a chondroitin sulphate proteoglycan (CSPG) that markedly enhances survival but not adhesion of embryonic rat (embryonic day 15) neocortical neurons in vitro. The active molecule was purified from conditioned medium (meningeal cell-conditioned medium, MCM) in three steps by means of fast-performance liquid chromatography fractionation combined with a quantitative microphotometric bioassay: (i) preparative Q-Sepharose anion exchange chromatography under native conditions; (ii) rechromatography of biologically active Q-Sepharose fractions on a MonoQ column in the presence of 8 M urea; and (iii) final gel filtration of active MonoQ fractions on Superose 6 in the presence of 4 M guanidinium hydrochloride. Analytical sodium dodecyl sulphate-polyacrylamide gradient gel electrophoresis of active Superose 6 fractions revealed a single broad glycoprotein band with a molecular mass in the range of 220-340 kDa. Further characterization of the purified molecule with glycosaminoglycan:lyases revealed a core protein of 50 kDa and the nearly complete loss of neurotrophic activity after chondroitinase digestion, whereas heparitinase treatment changed neither electrophoretic mobility nor biological activity. Amino-terminal sequencing of the purified CSPG core protein revealed identity with the amino acid sequence of rat biglycan. Biglycan purified from bovine cartilage supported neuron survival with virtually the same activity as the CSPG purified from MCM (half-maximal activity approximate to 10(-8) M). In conclusion, we isolated a neurotrophic CSPG from meningeal cells with strong survival-enhancing activity for brain neurons that was identified as biglycan, a molecule not previously related to neural functions.
Ammonium sulfate precipitation combined with liquid chromatography is sufficient for purification of bovine serum albumin that is suitable for most routine laboratory applications (2013)

Introduction Bovine serum albumin (BSA) is widely used in various biochemical and immunological applications due to its high abundance in bovine plasma, structural stability, and its noninvasive stabilizing interaction with most proteins [1-5]. Albumin is used as a carrier for several molecules in drug delivery systems, a stabilizing protein to dilute
Fucosyltransferases: structure/function studies (2001)

Alpha3-fucosyltransferases (alpha3-FucTs) catalyze the final step in the synthesis of a range of important glycoconjugates that function in cell adhesion and lymphocyte recirculation. Six members of this family of enzymes have been cloned from the human genome, and their expression pattern has been shown to be highly regulated. Each enzyme has a unique acceptor substrate binding pattern, and each generates a unique range of fucosylated products. Results from a range of studies have provided information on amino acids in the FucT sequence that contribute to the differential acceptor specificity for the FucTs, and to the binding of the nucleotide sugar donor GDP-fucose. These results, in conjunction with results obtained from the analysis of the disulfide bond pattern, have provided useful clues about the spatial distribution of amino acids that influence or directly contribute to substrate binding. This information is reviewed here, and a molecular fold prediction is presented which has been constructed based on the available information and current modeling methodology.
Extraction of periodic multivariate signals: mapping of voltage-dependent dye fluorescence in the mouse heart (2003)

In many experimental circumstances, heart dynamics are, to a good approximation, periodic. For this reason, it makes sense to use high-resolution methods in the frequency domain to visualize the spectrum of imaging data of the heart and to estimate the deterministic signal content and extract the periodic signal from background noise in experimental data. In this paper, we describe the first application of a new method that we call cardiac rhythm analysis which uses a combination of principal component analysis and multitaper harmonic analysis to extract periodic, deterministic signals from high-resolution imaging data of cardiac electrical activity, We show that this method significantly increases the signal-to-noise ratio of our recordings, allowing for better visualization of signal dynamics and more accurate quantification of the properties of electrical conduction. We visualize the spectra of three cardiac data sets of mouse hearts exhibiting sinus rhythm, paced rhythm and monomorphic tachycardia. Then, for pedagogical purposes, we investigate the tachycardia more closely, demonstrating the presence of two distinct periodicities in the re-entrant tachycardia. Analysis of the tachycardia shows that cardiac rhythm analysis not only allows for better visualization of electrical activity, but also provides new opportunities to study multiple periodicities in signal dynamics.
Interleukin-1 Stimulates the Secretion of Hypothalamic Corticotropin-Releasing Factor (1987)

There is now evidence that the immune system, during times of infectious challenge, can stimulate the secretion of glucocorticoids, the adrenal steroids that mediate important aspects of the response to stress. Specifically, secretion of interleukin-1 (IL-1), a monocyte lymphokine secreted after infection, appears at least in part responsible for this effect. Glucocorticoids are secreted in response to a neuroendocrine cascade involving, first, the brain, then the pituitary, and finally the adrenal gland. In this report, human IL-1 is shown to activate the adrenocortical axis at the level of the brain, stimulating the release of the controlling hormone corticotropin-releasing factor (CRF) from the hypothalamus. Infusion of IL-1 induced a significant secretion of CRF into the circulation exiting the hypothalamus, whereas immunoneutralization of CRF blocked the stimulatory effect of IL-1 on glucocorticoid secretion. IL-1 appeared to have no acute direct stimulatory effects on the pituitary or adrenal components of this system. Furthermore, IL-1 did not cause a nonspecific release of other hypothalamic hormones. Thus, the lymphokine acts in a specific manner to activate the adrenocortical axis at the level of the brain; this effect appears to be unrelated to the known pyrogenic effects of IL-1 within the hypothalamus.
Lipocortin 1 fragment modifies pyrogenic actions of cytokines in rats (1990)

Lipocortins form a group of proteins that have been proposed as mediators of the anti-inflammatory actions of glucocorticoids. Intracerebroventricular injection of a recombinant fragment of lipocortin 1 (NH2-terminal 1-188) caused dose-dependent (0.4-1.2 micrograms) reductions in the acute increases in colonic temperature and oxygen consumption, which occurred in response to central injections of recombinant interleukin 1 beta and gamma-interferon in conscious rats. In contrast the lipocortin fragment did not affect the response to prostaglandin E2, and its activity was prevented by heat treatment or by pretreatment of animals with polyclonal antiserum raised to the fragment. Central injection of antiserum significantly enhanced the thermogenic responses to interleukin 1 beta in rats treated with dexamethasone without affecting the responses in normal animals. These results support a physiological role for lipocortin in the central effects of glucocorticoids.
Dietary approach to attenuate oxidative stress, hypertension, and inflammation in the cardiovascular system (2004)

Imbalance between production and scavenging of superoxide anion results in hypertension by the inactivation of nitric oxide, and the increased oxidative stress from the resultant peroxynitrite that is produced promotes inflammatory processes such as atherosclerosis. Induction of phase 2 proteins promotes oxidant scavenging. We hypothesized that intake of dietary phase 2 protein inducers would ameliorate both hypertension and atherosclerotic changes in the spontaneously hypertensive stroke-prone rat. For 5 days/week for 14 weeks, we fed rats 200 mg/day of dried broccoli sprouts that contained glucoraphanin, which is metabolized into the phase 2 protein-inducer sulforaphane (Group A), sprouts in which most of the glucoraphanin was destroyed (Group B), or no sprouts (Group C). After 14 weeks of treatment, no significant differences were seen between rats in Groups B and C. Rats in Group A had significantly decreased oxidative stress in cardiovascular and kidney tissues, as shown by increased glutathione (GSH) content and decreased oxidized GSH, decreased protein nitrosylation, as well as increased GSH reductase and GSH peroxidase activities. Decreased oxidative stress correlated with better endothelial-dependent relaxation of the aorta and significantly lower (20 mm Hg) blood pressure. Tissues from Groups B and C had considerable numbers of infiltrating activated macrophages, indicative of inflammation, whereas animals in Group A had few detectable infiltrating macrophages. There is interest in dietary phase 2 protein inducers as means of reducing cancer incidence. We conclude that a diet containing phase 2 protein inducers also reduces the risk of developing cardiovascular problems of hypertension and atherosclerosis.
Sequence-Specific DNA Binding by a Short Peptide Dimer (1990)

A recently described class of DNA binding proteins is characterized by the "bZIP" motif, which consists of a basic region that contacts DNA and an adjacent "leucine zipper" that mediates protein dimerization. A peptide model for the basic region of the yeast transcriptional activator GCN4 has been developed in which the leucine zipper has been replaced by a disulfide bond. The 34-residue peptide dimer, but not the reduced monomer, binds DNA with nanomolar affinity at 4 degrees C. DNA binding is sequence-specific as judged by deoxyribonuclease I footprinting. Circular dichroism spectroscopy suggests that the peptide adopts a helical structure when bound to DNA. These results demonstrate directly that the GCN4 basic region is sufficient for sequence-specific DNA binding and suggest that a major function of the GCN4 leucine zipper is simply to mediate protein dimerization. Our approach provides a strategy for the design of short sequence-specific DNA binding peptides.
Summaries of Affymetrix GeneChip probe level data (2003)

High density oligonucleotide array technology is widely used in many areas of biomedical research for quantitative and highly parallel measurements of gene expression. Affymetrix GeneChip arrays are the most popular. In this technology each gene is typically represented by a set of 11-20 pairs of probes. In order to obtain expression measures it is necessary to summarize the probe level data. Using two extensive spike-in studies and a dilution study, we developed a set of tools for assessing the effectiveness of expression measures. We found that the performance of the current version of the default expression measure provided by Affymetrix Microarray Suite can be significantly improved by the use of probe level summaries derived from empirically motivated statistical models. In particular, improvements in the ability to detect differentially expressed genes are demonstrated.
Molybdenum effector of fumarate reductase repression and nitrate reductase induction in Escherichia coli (1987)

In Escherichia coli the presence of nitrate prevents the utilization of fumarate as an anaerobic electron acceptor. The induction of the narC operon encoding the nitrate reductase is coupled to the repression of the frd operon encoding the fumarate reductase. This coupling is mediated by nitrate as an effector and the narL product as the regulatory protein (S. Iuchi and E. C. C. Lin, Proc. Natl. Acad. Sci. USA 84:3901-3905, 1987). The protein-ligand complex appears to control narC positively but frd negatively. In the present study we found that a molybdenum coeffector acted synergistically with nitrate in the regulation of frd and narC. In chlD mutants believed to be impaired in molybdate transport (or processing), full repression of phi(frd-lac) and full induction of phi(narC-lac) by nitrate did not occur unless the growth medium was directly supplemented with molybdate (1 microM). This requirement was not clearly manifested in wild-type cells, apparently because it was met by the trace quantities of molybdate present as a contaminant in the mineral medium. In chlB mutants, which are known to accumulate the Mo cofactor because of its failure to be inserted as a prosthetic group into proteins such as nitrate reductase, nitrate repression of frd and induction of narC were also intensified by molybdate supplementation. In this case a deficiency of the molybdenum coeffector might have resulted from enhanced feedback inhibition of molybdate transport (or processing) by the elevated level of the unutilized Mo cofactor. In addition, mutations in chlE, which are known to block the synthesis of the organic moiety of the Mo cofactor, lowered the threshold concentration of nitrate (< 1 micromole) necessary for frd repression and narC induction. These changes could be explained simply by the higher intracellular nitrate attainable in cells lacking the ability to destroy the effector.
Reinventing the inbox (2002)

Email was originally designed as a tool for asynchronous communication. However, its current usage goes far beyond that. One of the most commonly performed activities in email is the management of pending tasks. This research focuses on how to support this activity in email and explores alternative solutions that use different external representations of messages and associated tasks.
Direct Immunologic activities of CpG DNA and implications for gene therapy (1999)

Vertebrate immune systems have evolved the ability to detect and be activated by most microbial and viral DNAs by virtue of their content of unmethylated ‘CpG motifs’, which are selectively suppressed in vertebrate DNA. Because their CpGs are also unmethylated, the DNA in gene therapy vectors routinely induces direct immune stimulation through activating this host defense mechanism. Administration of such ‘CpG DNA’ by injection or inhalation triggers rapid activation of B cells, monocytes, macrophages, dendritic cells, and natural killer cells, along with the release of pro-inflammatory cytokines. These immune stimulatory effects can be prevented by chloroquine and other drugs that interfere with endosomal maturation or by the presence of certain neutralizing DNA sequences, which block the immune stimulatory CpG motifs. Aside from serving as the genetic code, DNA can have direct immune activities. Vertebrate immune systems have evolved a defense mechanism that is able to broadly detect most microbial and viral DNAs because of differences in the frequency and methylation of CpG dinucleotides in particular base contexts. B cells, monocytes, macrophages, and dendritic cells spontaneously take up DNA of any type. If the DNA contains these immune stimulatory ‘CpG-S motifs’, the cells become activated within minutes and begin producing pro-inflammatory cytokines such as IL-6 and IL-12 and upregulate expression of co-stimulatory molecules. This results in the activation of both innate and acquired immune responses. The pro-inflammatory effects of CpG-S motifs are opposed by CpG dinucleotides in certain distinct base contexts, termed neutralizing or CpG-N motifs. Increasing the ratio of CpG-S to CpG-N motifs enhances the immune stimulatory effects of DNA, even if the total level of CpGs in the DNA is not altered. While this is useful in generating enhanced genetic vaccines, the opposite strategy is likely to become useful for the generation of gene therapy vectors with reduced inflammatory effects. Copyright © 1999 John Wiley & Sons, Ltd.
Cloning and nucleotide sequence of a chromosomally encoded tetracycline resistance determinant, tetA(M), from a pathogenic, methicillin-resistant strain of Staphylococcus aureus (1990)

This report describes the cloning and sequencing of a chromosomally encoded tetracycline resistance determinant from a clinical isolate of methicillin-resistant Staphylococcus aureus. On the basis of the sequence, the gene is in the tet(M) class, and it was shown that the S. aureus tetA(M) gene is induced at the level of transcription.
Human Thyroid Carcinoma Cell Lines and Normal Thyrocytes: Expression and Regulation of Matrix Metalloproteinase-1 and Tissue Matrix Metalloproteinase Inhibitor-1 Messenger-RNA and Protein (1997)

Matrix metalloproteinase-1 (MMP-1) and tissue matrix metalloproteinase inhibitor 1 (TIMP-1) play an important role in remodeling the extracellular matrix in normal and pathological processes. The effect of phorbol-myristate acetate (PMA), interleukin-1 (IL-1), and tumor necrosis factor-alpha (TNF-alpha) on MMP-1 and TIMP-1 expression was studied on highly purified thyrocytes and undifferentiated 8505 C, C 643, HTh 74, SW 1736 thyroid carcinoma cells compared with thyroid-derived fibroblasts. Messenger RNA (mRNA) levels were monitored by competitive semiquantitative reverse transcriptase polymerase chain reaction (RT-PCR) after 24 hours. Culture supernatants were assayed for free and/or complexed MMP-1 and TIMP-1 after 48 hours using enzyme-linked immunosorbent assay (ELISA) systems (detection limit: <2 ng/mL). MMP-1 and TIMP-1 mRNA were present in all cell types, although thyrocytes showed MMP-1 mRNA levels near the detection limit. 8505 C expressed MMP-1 mRNA levels of up to 10(6) times those of the other cells analyzed. PMA and IL-1 increased MMP-1 mRNA in most cell types. TIMP-1 mRNA increased after treatment with PMA in all cells except 8505 C, whereas only slight effects were shown after IL-1 stimulation. MMP-1 protein was undetectable in normal thyrocyte cultures, but was secreted spontaneously by all cell lines ([ng/mL]; C 643: 15+/-7; HTh 74: 81+/-1; SW 1736: 13+/-2; 8505 C: 2097+/-320). There was a strong correlation between levels of MMP-1 mRNA and protein (r = 0.99, p < .0001). PMA and IL-1 increased MMP-1 secretion in all cell types after 48 hours. Fibroblasts ([ng/mL] 517+/-55) and the cell lines (C 643: 142+/-48; HTh 74: 115+/-13; SW 1736: 202+/-14; 8505C: 120+/-19) secreted TIMP-1 in unstimulated cultures, whereas only a trace amount was detected in thyrocyte cultures, even after PMA treatment. IL-1 upregulated TIMP-1 secretion after 48 hours in SW 1736, HTh 74, and C 643 cells. Our data suggest that in contrast to normal thyrocytes, dedifferentiated thyroid carcinoma cell lines are potential producers of MMP-1 as well as TIMP-1. High MMP-1 or MMP-1/TIMP-1 expression may play a role in tissue invasion of undifferentiated thyroid cancer cells.
Asymmetric Electrophilic α‐Amidoalkylation, VII1): Generation, Crystal Structure, and Trapping Reactions of a Chiral 6,7‐Dimethoxy‐1,2,3,4‐tetrahydroisoquinoline Derived N‐Acyliminium Ion (1990)

Abstract The camphanic acid amide 4 has efficiently been oxidized with triphenylcarbenium tetrafluoroborate ( 3 ) to yield the chiral N‐acyliminium ion 1 . Trapping reactions of 1 with the silyl nucleophiles 7a‐c and 10a‐f proceeded with stereoselective bond formation, affording the diastereomers (R)‐ 8 /(S)‐ 9a‐c and (R)‐ 11 /(S)‐ 12a‐f , respectively, with diastereoselectivities of up to 93.9/6.1. The amido ketones (R)‐ 8 /(S)‐ 9a‐c were employed in the synthesis of the secondary amines (R)‐ 16a‐c , (S)‐ 16a and for the preparation of (−)‐homolaudanosine (R)‐ 18 . By X‐ray crystallography the conformation of 1 in the crystal lattice was established and the preferred conformation of 1 in solution was elucidated by NOE experiments. Finally, the addition reaction of 7a to the iminium ion 21 derived from menthyl carbamate 20 was investigated, which reaction, however, proceeded only with insignificant asymmetric induction.