gebhart/patrepeval huggingface dataset:
Structure from function: screening structural models with functional data. (1994)

Structural constraints derived from different antibody epitopes on human growth hormone (hGH) were used to screen three-dimensional models of hGH that were generated by computer algorithms. Previously, alanine-scanning mutagenesis defined the residues that modulate binding to 21 different monoclonal antibodies to hGH. These functional epitopes were composed of 4-14 side chains whose alpha-carbons clustered within 4-23 A. Distance and topographic constraints for these functional epitopes were virtually the same as constraints derived from known x-ray structures of protein-antigen complexes. The constraints were used to evaluate about 1400 models of hGH that were computer-generated by a secondary-structure prediction and packing algorithm. On average each functional epitope reduced the number of models in the pool by a factor of 2, so that 8 monoclonal antibodies could reduce the number of possible models to < 10. The average root-mean-square deviation of alpha-carbon coordinates between the x-ray structure and either the pool of starting models or final models ranged from 13 to 16 A or 4 to 7 A, respectively, depending on the pool of starting models and the level of constraints imposed. All of the final models had the correct folding topography, and the best model was within 3.8 A root-mean-square deviation of the x-ray coordinates. This model was as close as it could have been because the models were built by using ideal helices and those in the x-ray structure are not. Our studies suggest that epitope mapping data can effectively screen structural models and, when coupled to predictive algorithms, can help to generate low-resolution models of a protein.
Adsorption of Microorganisms to Sand Diatomaceous Earth Particles Coated With Metallic Hydroxides (1996)

Particles of diatomaceous earth and sand were coated with metallic hydroxides. The coating increased the concentration of metals associated with the particles, their zeta potential, and their ability to adsorb microorganisms in water. The maximum adsorption of microorganisms was achieved using particles coated with a combination of ferric hydroxide and aluminum hydroxide.
Use of a multiseparation fiber optic probe for the optical diagnosis of breast cancer (2005)

We explore the effects of the illumination and collection geometry on optical spectroscopic diagnosis of breast cancer. Fluorescence and diffuse reflectance spectroscopy in the UV-visible spectral range are made with a multiseparation probe at three illumination-collection separations of 735, 980, and 1225 microm, respectively, from 13 malignant and 34 nonmalignant breast tissues. Statistical analysis is carried out on two types of data inputs: (1) the fluorescence and diffuse reflectance spectra recorded at each of the three illumination-collection separations and (2) the integrated fluorescence (at each excitation wavelength) or diffuse reflectance over the entire spectrum at all three illumination-collection separations. The results show that using the integrated fluorescence intensities recorded at a single excitation wavelength at all three illumination-collection separations can discriminate malignant from nonmalignant breast tissues with similar classification accuracy to that using spectral data measured at several excitation wavelengths with a single illumination-collection separation. These findings have significant implications with respect to the design of an optical system for breast cancer diagnosis. Examining the intensity attenuation at a single wavelength rather than spectral intensities at multiple wavelengths can significantly reduce the measurement and data processing time in a clinical setting as well as the cost and complexity of the optical system.
Effect of Simvastatin on Cetuximab Resistance in Human Colorectal Cancer With KRAS Mutations (2011)

Simvastatin may overcome cetuximab resistance in colon cancer cells with KRAS mutations by modulating BRAF activity and inducing apoptosis.
The entD Gene of the Escherichia coli K12 Enterobactin Gene Cluster (1989)

The Escherichia coli entD gene encodes a product necessary for the synthesis of the iron-chelating and transport molecule enterobactin (Ent); cells harbouring entD mutations fail to grow in iron-deficient environments. For unknown reasons, it has not been possible to identify the entD product. The nucleotide sequence of the entD region has now been determined. An open reading frame extending in the same direction as the adjacent fepA gene and capable of encoding an approximately 24 kDa polypeptide was found; it contained a high percentage of rare codons and two possible translational start sites. Complementation data suggested that EntD proteins truncated at the carboxy terminus retain some activity. Two REP sequences were present upstream of entD and an IS186 sequence was observed downstream. RNA dot-blot hybridizations demonstrated that entD is transcribed from the strand predicted by the sequencing results. An entD-lacZ recombinant plasmid was constructed and shown to express low amounts of a fusion protein of the anticipated size (approximately 125 kDa). The evidence suggests a number of possible explanations for difficulties in detecting the entD product. Sequence data indicate that if entD has its own promoter, it is weak; the REP sequences suggest that entD mRNA may be destabilized; and translation may be slow because of the frequency of rare codons and a possible unusual start codon (UUG). The data are also consistent with previous evidence that the entD product is unstable.
A 32-channel modular bi-directional neural interface system with embedded DSP for closed-loop operation (2014)

A prototype bi-directional neural interface system is presented with closed-loop and embedded DSP capabilities. The system includes 32-electrode stimulation capability, eight multiplexed low-noise low-power bio-potential sensing channels with on-chip digital FFT, and a Cortex M3-based microcontroller for implementing closed-loop algorithms. The stimulation subsystem can provide a maximum stimulation current of 12mA with approximately 3% accuracy per channel. The sensing subsystem uses a fully differential chopping amplifier achieving a noise floor <;100nV/rtHz with approximately 1μA current from 2V supply. A 13bit continuous-time sigma-delta ADC is used to sample the amplifier output at the rate of 33kHz. The ADC consumes approximately 100nA while achieving an ENOB of 12b with a 250Hz date rate. A hardware implementation of a cached-FFT is included in the sensing IC to perform spectral analysis of the bio-potential signal. The resulting multiple spectral signatures can be selectively sent to the microcontroller allowing for algorithmic control of the stimulator system. The system partition was designed to minimize overall computational power while providing user flexibility. The sensing performance of the prototype has been demonstrated with 2-D cursor control in a non-human primate brain machine interface (BMI) model using 20 features simultaneously.
Natural Competence in Thermoanaerobacter and Thermoanaerobacterium Species (2010)

Low-G+C thermophilic obligate anaerobes in the class Clostridia are considered among the bacteria most resistant to genetic engineering due to the difficulty of introducing foreign DNA, thus limiting the ability to study and exploit their native hydrolytic and fermentative capabilities. Here, we report evidence of natural genetic competence in 13 Thermoanaerobacter and Thermoanaerobacterium strains previously believed to be difficult to transform or genetically recalcitrant. In Thermoanaerobacterium saccharolyticum JW/SL-YS485, natural competence-mediated DNA incorporation occurs during the exponential growth phase with both replicating plasmid and homologous recombination-based integration, and circular or linear DNA. In T. saccharolyticum, disruptions of genes similar to comEA, comEC, and a type IV pilus (T4P) gene operon result in strains unable to incorporate further DNA, suggesting that natural competence occurs via a conserved Gram-positive mechanism. The relative ease of employing natural competence for gene transfer should foster genetic engineering in these industrially relevant organisms, and understanding the mechanisms underlying natural competence may be useful in increasing the applicability of genetic tools to difficult-to-transform organisms.
Variable expression of immunoreactive surface proteins of Propionibacterium acnes (2006)

Despite accumulating data implicating Propionibacterium acnes in a variety of diseases, its precise role in infection remains to be determined. P. acnes antigen-specific CD4(+) T cells are present in early inflamed acne lesions and may be involved in the inflammatory response; however, little is known about the specific antigens involved. In this study, B cell and T cell antigens from P. acnes expression libraries were cloned and evaluated and the four predominant proteins identified were investigated. Two of these antigens share some homology with an M-like protein of Streptococcus equi and have dermatan-sulphate-binding activity (PA-25957 and 5541). The remaining two antigens, PA-21693 and 4687, are similar to the product of the Corynebacterium diphtheriae htaA gene from the hmu ABC transport locus, although only one of these (PA-21693) is encoded within an hmu-like operon and conserved amongst a range of clinical isolates. All four proteins contain an LPXTG motif, although only PA-21693 contains a characteristic sortase-sorting signal. Variation in the expression of PA-4687, 25957 and 5541 is evident amongst clinical isolates and is generated both by frameshifts associated with the putative signal peptide and by variable numbers of repeat regions toward the carboxy-terminus, potentially generating heterogeneity of molecular mass and antigenic variation. In addition, in the case of PA-25957, a frameshift in a C-rich region at the extreme carboxy-terminus eliminates the LPXTG motif in some isolates. For the dermatan-sulphate-binding PA-25957, IgG1 antibody in serum from acne-positive donors was shown to be specific for the amino-terminal region of the protein, which also contains a CD4(+) T cell epitope. In contrast, serum from acne-negative donors shows an IgG2 and IgG3 antibody subclass response to the carboxy-terminal region. These data have implications for the potential role of P. acnes in inflammatory acne and other diseases.
Defective Export of a Periplasmic Enzyme Disrupts Regulation of Fatty Acid Synthesis (1995)

Escherichia coli thioesterase I (TesA) encoded by the tesA gene is located in the cellular periplasm. The tesA gene was modified by deletion of the leader sequence such that the mature enzyme was instead localized to the cellular cytosol. Production of thioesterase I in the cytosol results in striking changes in the pattern of E. coli lipid synthesis. In contrast to normal E. coli cells, cells producing cytosolic TesA synthesize large amounts of free fatty acid at all stages of growth. Moreover, cultures of the cytosolic TesA-producing strain continue lipid synthesis (as free fatty acid) in stationary phase whereas lipid synthesis is normally strongly inhibited in such cultures. Surprisingly, production of cytosolic thioesterase I gave only modest inhibition of membrane phospholipid synthesis. These results demonstrate that internalization of a normally secreted enzyme can disrupt normal cellular regulatory mechanisms.
Changes of physicochemical indicators during mastitis and the effects of milk ejection on their sensitivity (2004)

We examined the relationship between physicochemical indicators and somatic cells in the milk of dairy cows during experimentally induced mastitis and their significance as indicators for use in controlling udder health. We were concerned particularly with the effect of alveolar milk ejection on the sensitivity of these indicators. In Expt 1, Escherichia coli lipopolysaccharide (Esch. coli LPS) was injected into the left rear quarter to induce an inflammatory reaction in one quarter in each of six cows. The contralateral control quarter was injected with a solution of NaCl (9 g/l). Nine milk samples were taken from both quarters until 60 h after injection. In Expt 2, repeated milk samples were taken every 20 s from one quarter during a 120-s teat stimulation in 20 cows with different somatic cell counts (SCC). Quarters were clustered for low (<5.0 log cells/ml), mid (5.0-5.7 log cells/ml) and high (>5.7 log cells/ml) SCC of the sample taken at t=0 s. Samples were analysed for SCC, electrical conductivity (EC) and Na+ and Cl- concentrations. During the experimental inflammation SCC, EC, Na+ and Cl- peaked at 12 h from LPS administration and values in treated quarters (T) at this time were elevated to 7900, 157, 501 and 169% of the values in untreated quarters, respectively. In Expt 2, SCC, EC, Na+ and Cl- in high SCC quarters were 2520, 121, 283 and 141% of low SCC quarters at the start of stimulation (t=0 s), respectively. Highly significant (P<0.001) differences in EC, Na+ and Cl- between high and low SCC quarters disappeared owing to the onset of alveolar milk ejection 100 s after the first contact with the teat. In conclusion, SCC in cows' milk provided the strongest amplitude in the case of an intramammary inflammation. EC, Na+ or Cl- were useful tools only if the measurements were performed in cisternal milk before the start of alveolar milk ejection.
Antiangiogenesis signals by endostatin (2001)

Endostatin is a potent endogenous angiogenesis inhibitor that induces regression of tumors in mice. Neither an extracellular receptor for endostatin nor intracellular signals that result in the regression of tumor vascular beds have been identified. We demonstrate that endostatin, but not angiostatin, at comparable concentrations to those used in in vivo animal trials, rapidly down-regulates many genes in exponentially growing endothelial cells. These include immediate early response genes, cell cycle-related genes, and genes regulating apoptosis inhibitors, mitogen-activated protein kinases, focal adhesion kinase, G-protein-coupled receptors mediating endothelial growth, a mitogenic factor, adhesion molecules, and cell structure components. Suppression of both apoptosis inhibitors and cell proliferation genes may have a limited contribution to the antiangiogenesis process because endostatin induces neither apoptosis nor growth inhibition, unless studied under reduced serum conditions. In contrast, the antimigratory effect of endostatin was rapid and potent even under serum-supplemented conditions. Endostatin caused gene suppression and migration arrest exclusively in endothelial cells, most profoundly in microvascular endothelial cells. The c-myc null fibroblasts obtained by targeted homologous recombination showed an attenuated migration rate compared with isogenic parental cells, whereas the introduction of the c-myc gene into endothelial cells abrogated the antimigratory effect of endostatin. Inhibition of E-box-driven transcription by overexpressing max or mad suppressed endothelial migration. Thus, rapid down-regulation of genes by endostatin neither restores proliferating endothelial cells to their resting states nor induces apoptosis; rather, it potently inhibits endothelial cell migration partly via suppression of c-myc expression.
Pyridoxamine, an Inhibitor of Advanced Glycation Reactions, Also Inhibits Advanced Lipoxidation Reactions (2000)

Maillard or browning reactions lead to formation of advanced glycation end products (AGEs) on protein and contribute to the increase in chemical modification of proteins during aging and in diabetes. AGE inhibitors such as aminoguanidine and pyridoxamine (PM) have proven effective in animal model and clinical studies as inhibitors of AGE formation and development of diabetic complications. We report here that PM also inhibits the chemical modification of proteins during lipid peroxidation (lipoxidation) reactions in vitro, and we show that it traps reactive intermediates formed during lipid peroxidation. In reactions of arachidonate with the model protein RNase, PM prevented modification of lysine residues and formation of the advanced lipoxidation end products (ALEs) N(epsilon)-(carboxymethyl)lysine, N(epsilon)-(carboxyethyl)lysine, malondialdehyde-lysine, and 4-hydroxynonenal-lysine. PM also inhibited lysine modification and formation of ALEs during copper-catalyzed oxidation of low density lipoprotein. Hexanoic acid amide and nonanedioic acid monoamide derivatives of PM were identified as major products formed during oxidation of linoleic acid in the presence of PM. We propose a mechanism for formation of these products from the 9- and 13-oxo-decadienoic acid intermediates formed during peroxidation of linoleic acid. PM, as a potent inhibitor of both AGE and ALE formation, may prove useful for limiting the increased chemical modification of tissue proteins and associated pathology in aging and chronic diseases, including both diabetes and atherosclerosis.
Use of the Polymerase Chain Reaction to Detect Legionella DNA in Urine and Serum Samples from Patients with Pneumonia (1996)

Legionella pneumonia can be difficult to diagnose. Existing laboratory tests for detecting Legionella species lack sensitivity or provide only a retrospective diagnosis. We used the polymerase chain reaction (PCR) with primers that amplify a 104-base pair segment of the coding region of the 5S tRNA gene to detect Legionella DNA in urine and serum samples from patients with pneumonia. Stored urine and serum samples from patients enrolled in two prospective studies of pneumonia were tested. Legionella DNA was detected in urine and/or serum samples from 18 (64%) of 28 patients with legionella pneumonia diagnosed by conventional tests, but it was not detected in urine or serum samples from 24 patients with pneumonia due to other organisms. The sensitivity of PCR improved to 73% if testing was restricted to samples taken within 4 days of the onset of symptoms. Detection of Legionella DNA in urine and serum promises to be a valuable tool for the rapid diagnosis of legionella pneumonia.
Semisynthetic Hydrophilic Polyals (2005)

Non-bioadhesive, fully biodegradable soluble polymers would be very instrumental in advanced biomedical applications, such as gene and drug delivery and tissue engineering. However, rational development of such materials is hindered by the complexity of macromolecule interactions with biological milieu. The prevalence of carbohydrates in naturally occurring interface structures suggests an alternative, biomimetic approach. Interface carbohydrates, regardless of their biological function, have common non-signaling substructures (e.g., acetal and ketal groups, secondary and primary alcohols). We hypothesized that hydrophilic polymers (polyals) consisting of acyclic units built of non-signaling carbohydrate substructures would be highly biocompatible and non-bioadhesive, while intrachain acetal or ketal groups would enable nonenzymatic biodegradation upon uptake by cells. Acyclic hydrophilic polyals can be prepared via either polymerization of suitable monomers or lateral cleavage of cyclic polyals (e.g., polysaccharides). In this study, model polyals were produced via lateral cleavage of polyaldoses and polyketoses. Best results were achieved using dextran B-512 as a precursor. The resultant poly[hydroxymethylethylene hydroxymethylformal], in agreement with the hypothesis, demonstrated excellent biological properties and technological flexibility. Materials of this type can potentially have several applications in pharmacology and bioengineering.
Enhanced Differentiation of Three-Gene-Reprogrammed Induced Pluripotent Stem Cells into Adipocytes via Adenoviral-Mediated PGC-1α Overexpression (2011)

Induced pluripotent stem cells formed by the introduction of only three factors, Oct4/Sox2/Klf4 (3-gene iPSCs), may provide a safer option for stem cell-based therapy than iPSCs conventionally introduced with four-gene iPSCs. Peroxisome proliferator-activated receptor gamma coactivator-1α (PGC-1α) plays an important role during brown fat development. However, the potential roles of PGC-1α in regulating mitochondrial biogenesis and the differentiation of iPSCs are still unclear. Here, we investigated the effects of adenovirus-mediated PGC-1α overexpression in 3-gene iPSCs. PGC-1α overexpression resulted in increased mitochondrial mass, reactive oxygen species production, and oxygen consumption. Microarray-based bioinformatics showed that the gene expression pattern of PGC-1α-overexpressing 3-gene iPSCs resembled the expression pattern observed in adipocytes. Furthermore, PGC-1α overexpression enhanced adipogenic differentiation and the expression of several brown fat markers, including uncoupling protein-1, cytochrome C, and nuclear respiratory factor-1, whereas it inhibited the expression of the white fat marker uncoupling protein-2. Furthermore, PGC-1α overexpression significantly suppressed osteogenic differentiation. These data demonstrate that PGC-1α directs the differentiation of 3-gene iPSCs into adipocyte-like cells with features of brown fat cells. This may provide a therapeutic strategy for the treatment of mitochondrial disorders and obesity.
An Enzymatic Method for Glucose Determination in Body Fluids (1958)

Abstract 1. Details are given for the qualitative detection of glucose in urine and for its quantitative determination in urine and blood filtrates by an enzymatic procedure. 2. The method, which is highly specific, is based upon the release of hydrogen peroxide from glucose during its oxidation by glucose oxidase. The peroxide is detected by a suitable indicator in the presence of horseradish root peroxidase. 3. The results yielded by the new procedures have been compared with those obtained by other accepted methods.
Olefin Metathesis. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
eNOS Knockout Mice with Advanced Diabetic Nephropathy Have Less Benefit from Renin-Angiotensin Blockade than from Aldosterone Receptor Antagonists (2009)

While blockade of the renin angiotensin system (RAS) is beneficial in treating many patients with diabetic nephropathy, some patients show a poor response. We hypothesized that the poor response of RAS blockade is attributed to inability to stimulate endothelial nitric oxide. Recently, we reported that diabetic eNOS knockout (KO) mice develop advanced diabetic nephropathy similar to human disease. Here, we tested the hypothesis that blockade of the RAS would be less beneficial in this model than in diabetic wild-type mice. Both enalapril and telmisartan were less effective at reducing renal injury in diabetic eNOSKO mice compared with diabetic wild-type mice. Blood pressure was only transiently reduced by these treatments in diabetic eNOSKO mice and later returned to levels similar to that of untreated diabetic eNOSKO mice. Serum aldosterone tended to be paradoxically higher with enalapril or telmisartan in diabetic eNOSKO mice, whereas these treatments tended to lower aldosterone in diabetic wild-type mice. The pathogenic role of aldosterone was demonstrated by the evidence that spironolactone significantly reduced blood pressure and prevented renal injury. In addition, a higher dose of enalapril also failed to prevent hypertension and renal injury in diabetic eNOSKO mice. In conclusion, an impaired endothelial NO response could lessen the benefit of RAS inhibition in diabetic renal disease. Aldosterone blockade may provide superior protection in this setting.