gebhart/patrepeval huggingface dataset:
Site-Directed Mutagenesis of a Catalytic Antibody: An Arginine and a Histidine Residue Play Key Roles (1994)

Individual residues important for ligand binding and catalytic activity were identified by computer modeling and investigated by site-directed mutagenesis for catalytic antibody 43C9, which accelerates amide hydrolysis by a factor of 10(6). On the basis of a computer model, Tyr L32, His L91, Arg L96, His H35, and Tyr H95 were chosen for replacement by site-directed mutagenesis. To facilitate these studies, an expression system was developed in which properly folded 43C9 single-chain antibody was secreted from an engineered Escherichia coli host. Substitution of His L91 by Gln produced a mutant with no catalytic activity, but whose affinities for ligands were nearly the same as those of the wild-type, identifying His L91 as the nucleophile that forms the acyl intermediate implicated by previous kinetic studies. Arg L96 is also critical for catalytic activity and appears to function as a oxyanion hole for the tetrahedral transition states. Two substitutions for His H35 resulted in mutant proteins with no catalytic activity as well as altered affinities for ligands, indicating an important structural role for this residue. Substitutions for Tyr L32 and Tyr H95 were made in an attempt to improve the catalytic efficiency of 43C9. The results of these mutations allow us to propose a mechanism for 43C9-catalyzed hydrolysis: Substrate binding to 43C9 orients the scissile carbonyl group adjacent to both the His L91 and Arg L96 side chains. The imidazole of His L91 acts as a nucleophile, forming an acyl-antibody intermediate that breaks down by hydroxide attack to afford the products and regenerate the catalyst.
Origins and Pathways of Cerebrovascular Vasoactive Intestinal Polypeptide-Positive Nerves in Rat (1988)

In order to clarify the origins and pathways of vasoactive intestinal polypeptide (VIP)-containing nerve fibers in cerebral blood vessels of rat, denervation experiments and retrograde axonal tracing methods (true blue) were used. Numerous VIP-positive nerve cells were recognized in the sphenopalatine ganglion and in a mini-ganglion (internal carotid mini-ganglion) located on the internal carotid artery in the carotid canal, where the parasympathetic greater superficial petrosal nerve is joined by the sympathetic fibers from the internal carotid nerve, to form the Vidian nerve. VIP fiber bridges in the greater deep petrosal nerve and the internal carotid nerve reached the wall of the internal carotid artery. Two weeks after bilateral removal of the sphenopalatine ganglion or sectioning of the structures in the ethmoidal foramen, VIP fibers in the anterior part of the circle of Willis completely disappeared. Very few remained in the middle cerebral artery, the posterior cerebral artery, and rostral two-thirds of the basilar artery, whereas they remained in the caudal one-third of the basilar artery, the vertebral artery, and intracranial and carotid canal segments of the internal carotid artery. One week after application of true blue to the middle cerebral artery, dye accumulated in the ganglion cells in the sphenopalatine, otic and internal carotid mini-ganglion; some of the cells were positive for VIP. The results show that the VIP nerves in rat cerebral blood vessels originate: (a) in the sphenopalatine, and otic ganglion to innervate the circle of Willis and its branches from anterior and caudally and (b) from the internal carotid mini-ganglion to innervate the internal carotid artery at the level of the carotid canal and to some extent its intracranial extensions.
Input Attenuation Functions Improve Servomechanism Performance (1971)

The advent of numerically controlled point-to-point industrial equipment has provided a suitable set of conditions for input attenuation functions to improve the performance of linear servomechanisms. The replacement of a random input by a programmed sequence of events allows the output to have essentially dead beat transient response. The elimination of overshoot and a substantial reduction of settling time, allows a numerical instruction to be completed in less time than normally required. The additional control circuitry is simple, inexpensive, and should not impair the reliability.
Interleukin-6, Secreted by Human Ovarian Carcinoma Cells, Is a Potent Proangiogenic Cytokine (2005)

Angiogenesis, a key rate-limiting step in the growth and dissemination of malignant tumors, is regulated by the balance between positive and negative effectors. Recent studies indicate that the pleiotropic cytokine interleukin-6 (IL-6) may contribute to the vascularization of some tumors by disrupting the equilibrium between positive and negative angiogenic regulatory molecules. We determined whether IL-6 participates in the angiogenesis observed during the progression of ovarian carcinoma. We measured IL-6 production by human ovarian cancer cell lines in vitro and in vivo. Not all cell lines secreted IL-6 in vitro; however, when the cell lines were implanted into the peritoneal cavity of female nude mice, every line secreted IL-6. Most human ovarian carcinoma cell lines tested secreted significant levels of the soluble IL-6 receptor (sIL-6R). Endothelial cell lines established from the ovary and mesentery of female H-2K(b)-tsA58 mice were tested for response to IL-6. Both endothelial cell lines expressed the IL-6R and their stimulation with the exogenous ligand significantly enhanced cell migration and activated the downstream signaling molecule signal transducers and activators of transcription 3. Dual immunohistochemical staining for IL-6R and CD31 revealed IL-6R expression on human endothelial cells within normal ovary and carcinoma specimens. Gelfoam sponges containing 0.4% agarose and IL-6 or basic fibroblast growth factor and implanted into the subcutis of BALB/c mice were vascularized to the same extent. Collectively, the data indicate that ovarian tumor cells secreted IL-6, a highly angiogenic cytokine that supports progression of disease.
Genetic control of levels of murine kidney glucuronidase mRNA in response to androgen. (1983)

A cis-acting genetic element, designated Gus-r, regulates the androgen-induced rates of murine glucuronidase (EC 3.2.1.31) synthesis in kidney tubule cells and is tightly linked to the glucuronidase structural gene, Gus-s. To investigate the molecular mechanism underlying this regulation, we have cloned a glucuronidase-specific cDNA sequence in plasmid pBR322. This cloned DNA has been utilized as a probe in blot hybridization analyses to determine whether the control of androgen responsiveness of kidney glucuronidase synthesis by Gus-r is exerted over the level or the translatability of glucuronidase mRNA. Three important observations emerged from these studies: (i) glucuronidase mRNA exists as a single size class of approximately 2,800 nucleotides; (ii) androgen stimulation of glucuronidase synthesis is directly related to the level of glucuronidase mRNA; and (iii) strain differences in levels of kidney glucuronidase mRNA accumulated in response to androgen are controlled by alleles of Gus-r. Thus, Gus-r regulates the androgen responsiveness of glucuronidase synthesis by controlling the amount of glucuronidase mRNA available for translation and is a cis-acting genetic element that regulates the hormonal responsiveness of a specific mRNA.
The Effects of Cytokines on Suppression of Lymphocyte Proliferation by Dexamethasone (2009)

Treatment failure occurs in up to 30% of patients treated with steroids for inflammatory diseases. The aim of this study was to explore the potential role of 21 cytokines in steroid-resistant inflammatory disease and to develop methods to restore steroid sensitivity through cytokine manipulation. The dexamethasone inhibition of lymphocyte proliferation assay correlates with the outcome of steroid therapy in ulcerative colitis (UC) and other inflammatory diseases. Using this assay, PBMC production of 21 cytokines, assayed by cytokine bead array, was correlated with percentage of suppression of proliferation by 10(-6) M dexamethasone (Imax) in 26 healthy volunteers. Effects of the addition of exogenous cytokines to induce steroid resistance in PBMCs from healthy volunteers and cytokine blockade to improve steroid sensitivity in PBMCs from patients with steroid-resistant UC were then explored. Production of IL-1alpha, IL-10, IL-17, IFN-gamma, G-CSF, GM-CSF, TNF-alpha, and IFN-inducible protein 10 (IP-10) correlated significantly with in vitro steroid sensitivity; however, only IL-2 and TNF-alpha reduced steroid sensitivity when added exogenously. Addition of IL-10 enhanced steroid suppression. Immunoneutralization or receptor blockade of IL-2, but not TNF-alpha, IFN-gamma, IL-4, IL-17, or IP-10 increased steroid sensitivity in cells from steroid-resistant UC patients. Neutralization of IL-10 reduced steroid sensitivity. Of the large panel of cytokines studied, IL-2 appears to have the greatest antagonistic effect on the antiproliferative effect of steroids. These data suggest that IL-2 inhibition in vivo may improve the response to steroids in steroid-resistant individuals.
<title>X-ray holography for VLSI using synthetic bilevel holograms</title> (1997)

The gains are pointed out of the potential replacement of the usual patterned transmission x-ray mask, in consideration of high-resolution proximity lithography for VLSI, by a diffraction element, or bilevel in-line hologram, to be projected under near-field conditions using synchrotron radiation. The hologram can be configured to correct for diffraction blurring due to projection, and be designed for pre-determined gaps between mask and wafer. The adjustment of experimental parameters can account for the waveguide effects that arise from mask elements with small features which are several hundred x-ray wavelengths thick.It is shown that the hologram, for projection printing at the 50nm feature size, at mask to wafer gaps of 10micrometers or greater, can be fabricated in a similar fashion to a high-resolution mask. The calculation of the hologram is computationally intensive, but a database of calculated features is envisaged.
Nutritional Support to Prevent and Treat Multiple Organ Failure (1996)

Enteral nutrition (EN) has several advantages over parenteral nutrition (PN) for postoperative/posttrauma patients. Modern technologies for tube-feeding have made early EN possible. Jejunal tube-feeding has advantages over gastric tube-feeding: faster metabolic recovery, less vomiting, and less risk of regurgitation and aspiration. Immediate or early EN stimulates the splanchnic and hepatic circulations, improves mucosal blood flow, prevents intramucosal acidosis and permeability disturbances, and eliminates the need for stress ulcer prophylaxis. Saliva containing important antimicrobial substances and gastric acidity are important in sepsis prevention. Chewing, saliva, and gastric acidity support gastric nitric oxide (NO) release, important for mucosal blood flow, gastrointestinal (GI) motility, mucus formation, and bacteriostasis. An oral supply of NO-donating substances and chewing of nitrate-rich food, such as lettuce or spinach, can be useful. Oral and mucosa-protective lipids are recommended. H2 blockers and saliva-inhibiting drugs are avoided. Immediate EN should be given, starting with 25 ml/hr and increasing to 100 ml/hr over 24 to 48 hours. For the immunocompromised patient special attention should be given to the purity of water. Bottled water can contain bacteria such as Pseudomonas. Food antioxidants such as glutathione, vitamin E, and beta-carotenes are important. Ingredients for the colonic mucosa are important. Approximately 10% of caloric need is satisfied by so-called colonic food (prebiotics), fermented at the level of the colonic mucosa to produce colonic mucosa nutrients and to prevent gut origin sepsis. More than 10 g of fiber per day is recommended. The fermenting flora (probiotic flora) is deranged owing to disease or antibiotic treatment, and resupply of flora is important. A new concept of ecoimmune nutrition is presented for enteral supply of mucosa-reconditioning ingredients: new surfactants, pseudomucus, fiber, amino acids such as arginine, and mucosa-adhering Lactobacillus plantarum 299.
Individual Pd nanowire hydrogen sensors fabricated by electron-beam lithography (2009)

We report on the hydrogen gas (H2) sensing performance of lithographically patterned Pd nanowires as a function of the nanowire thickness and H2 concentration. A combination of electron-beam lithography and a lift-off process has been utilized to fabricate four-terminal devices based on individual Pd nanowires with width w = 300 nm, length l = 10 microm, and thickness t = 20-400 nm from continuous Pd films. The variation of the resistance and sensitivity at 20 000 ppm H2 of Pd nanowires was found to be much lager than at 10 000 ppm H2, which can be explained by an alpha-beta phase transition occurring at 20 000 ppm H2. This is confirmed by the observation of hysteresis behavior in the resistance versus H2 concentration for Pd thin films. The response time was found to decrease with decreasing thickness regardless of H2 concentration due to a higher surface-to-volume ratio and a higher clamping effect. A single Pd nanowire with t = 100 nm was found to successfully detect H2 at a detection limit of 20 ppm. Our results suggest that lithographically patterned Pd nanowires can be used as hydrogen gas sensors to quantitatively detect H2 over a wide range of concentrations.
Semen parameters, including WHO and strict criteria morphology, in a fertile and subfertile population: an effort towards standardization of in-vivo thresholds (2001)

In this study, the semen analysis results of a fertile population were compared with those from a subfertile population, in order to establish normal cut-off values for the standard semen parameters with the aid of receiver operating characteristic (ROC) curve analysis. The fertile group comprised healthy males (n 107) without any history of fertility problems, the partners of whom had had a spontaneous pregnancy within one year of unprotected intercourse and were pregnant at the time of the male's inclusion into the study. A total of 103 males from couples attending the infertility clinic, and with an initial sperm count of <2010 6 /ml were recruited to form the subfertile population. The best discriminating parameter between the two populations was sperm morphology evaluated according to WHO criteria at a cut-off point of 31% normal spermatozoa. The other cut-off values were at 8% for the acrosome index, 45% for motility, and 4% normal spermatozoa for strict criteria. Recalculating the ROC curve cut-off values based on an assumed 50% prevalence of subfertility in an assisted reproductive setting, the cut-off points were reduced to 21% and 3% normal spermatozoa for WHO and strict criteria respectively. For motility, the new cut-off value was at 20% motile spermatozoa, for motility quality at 3.5 (on a scale of 1-6), the acrosome index at 3% normal acrosomes, and the teratozoospermia index at 2.09.
Cyclosporin-mediated inhibition of bovine calcineurin by cyclophilins A and B. (1992)

The Ca(2+)- and calmodulin-dependent protein phosphatase calcineurin is inhibited by the immunosuppressant drug cyclosporin A in the presence of cyclophilin A or B. Of the two isoforms, cyclophilin B is more potent by a factor of 2-5 when either the phosphoprotein [32P]casein or the [32P]phosphoserine [Ser(32P)] form of the 19-residue bovine cardiac cAMP-dependent protein kinase regulatory subunit peptide RII, [Ser(32P)15]RII, is used as substrate. With [Ser(32P15]RII as substrate, the concentrations of the cyclosporin A.cyclophilin A and cyclosporin A.cyclophilin B complexes, which cause 50% inhibition of calcineurin activity, are 120 and 50 nM, respectively. Lowering the concentration of calcineurin 80% with [32P]casein as substrate lowered the apparent inhibition constant for each complex even further; 50% inhibition of calcineurin was observed at 40 nM for cyclosporin A.cyclophilin A, whereas it was less than 10 nM for cyclosporin A.cyclophilin B. In all inhibition assays with [32P]casein or [Ser(32P)15]RII, the concentration of calcineurin required for measurable phosphatase activity is such that these complexes behave as tight-binding inhibitors of calcineurin, and steady-state kinetics cannot be used to assess inhibition patterns or Ki values. Limited trypsinization of calcineurin produces a fragment that is still inhibited, indicating that the interaction of cyclosporin.cyclophilin with calcineurin does not require either calmodulin or Ca2+.
Characterization of the Carbohydrate Fragments Obtained from Saccharomyces cerevisiae Mannan by Alkaline Degradation (1974)

Abstract Mild alkaline degradation of Saccharomyces cerevisiae X2180 wild type mannan, under conditions that effect β elimination of the substituted serine and threonine residues, releases mannose, mannobiose, mannotriose, and mannotetraose. Methylation analysis demonstrated that these fragments have the same structures as those that are obtained by acetolysis of the polysaccharide component of the yeast mannan. Similar treatment of a mutant mannan that lacks the mannotetraose unit in the polysaccharide component produced only mannose, mannobiose, and mannotriose. Thus, the single mutation alters both the tetrasaccharide units in the polysaccharide component of the mannan and those that are attached to serine and threonine. Because these studies were carried out on the total cell wall mannan, rather than a single molecular species, we cannot say that both the polysaccharide chains and the shorter oligosaccharides linked to serine and threonine are present in the same molecule. Strong alkaline degradation in the presence of sodium borotritide of the mannan residue recovered from the β elimination reaction yielded a protein-free polysaccharide that gave radioactive N-acetylglucosaminitol on acetolysis. Thus, the mannose-containing polysaccharide of the mannan is attached to glucosamine, and it is probable that the linkage to protein is through a di-N-acetylchitobiose to asparagine as in many other glycoproteins. The mannan isolated from the wild type and mutant strains of S. cerevisiae by procedures that avoid exposure to alkali had a molecular weight of 133,000. On treatment with 0.1 n sodium hydroxide at room temperature, the molecular weight was reduced to about 40,000. These conditions could saponify acyl ester bonds but are unlikely to break phosphodiester linkages or any other linkages except those of the oligosaccharides attached to serine and threonine.
Telomere dynamics and telomerase activation in tumor progression: prospects for prognosis and therapy. (1995)

Eukaryotic telomeres provide a reservoir of redundancy to compensate for incomplete replication of chromosome ends. In multicellular eukaryotes, they are eroded by a varying number of base pairs at every cell division. When telomere repeats are critically shortened, DNA damage response pathways involving p53 (and in some cell types retinoblastoma protein) are invoked, leading to "M1 senescence" in normal cells; cancer cells, which frequently lack normal p53 and RB functions, often develop chromosomal instability leading to telomeric associations, ring chromosomes, and breakage-fusion-bridge cycles. These consequences of telomere erosion exert selection pressure for activation of the ribonucleoprotein enzyme telomerase, which adds new telomeric repeats at chromosome ends, and in vertebrates normally is active only in the germ line and the early embryo. Somatic cells that reactivate telomerase in vitro or in vivo become immortal. Telomerase activity has been found in many advanced and metastatic human cancers, suggesting that telomerase-dependent M2 immortalization may contribute to metastatic potential. When mammalian telomerases are isolated and their genes cloned and sequenced, the localization of telomerase expression in tumors may provide prognostic indicators of metastatic potential. The abrogation of telomerase function by pharmacological inhibition, genetic disruption, or repression of gene expression is a potential avenue of antimetastatic therapy.
Studies on cell adhesion and recognition. I. Extent and specificity of cell adhesion triggered by carbohydrate-reactive proteins (glycosidases and lectins) and by fibronectin. (1981)

The extent and the specificity of the initial cell attachment induced by various proteins coated on plastic surfaces have been studied with the following results: (a) Cell adhesion on the surfaces coated with sialidase and beta-galactosidase was as strong as on concanavalin A and limulus lectin-coated surfaces and the reactions were strongly inhibited by glycosidase inhibitors or by competitive substrates. The adhesion on sialidase was inhibited by 2-deoxy-2,3-dehydro-N-acetylneuraminic acid and by polysialoganglioside (GT1b) at low concentration (0.05-0.1 mM). The cell adhesion on beta-galactosidase coat was inhibited by 1,4-D-galactonolactone and beta-methylgalactoside but not by alpha-methylgalactoside. Thus, the initiation of cell adhesion on glycosidase surfaces could be mediated through the interactions of the specific binding sites of the enzyme surface with the cell surface substrates under physiological conditions. (b) Cell adhesion on various lectins could be blocked by various competing monosaccharides at the concentrations similar to the inhibitory concentrations for binding of lectins from solution to the cells. (c) Cell adhesion on fibronectin surfaces as well as on gelatin-coated surfaces was equally inhibited by GT1b at relatively high concentrations (0.25-0.5 mM). Lower concentrations of GT1b (0.05-0.1 mM) inhibited the cell adhesion on surfaces of Limulus lectin and sialidase. It is suggested that the cell adhesion mediated by fibronectin is based on yet unknown interactions in contrast to a specific cell adhesion through glycosidases and lectins.
Near-infrared spectroscopy measurement of the pulsatile component of cerebral blood flow and volume from arterial oscillations (2007)

We describe a near-infrared spectroscopy (NIRS) method to noninvasively measure relative changes in the pulsate components of cerebral blood flow (pCBF) and volume (pCBV) from the shape of heartbeat oscillations. We present a model that is used and data to show the feasibility of the method. We use a continuous-wave NIRS system to measure the arterial oscillations originating in the brains of piglets. Changes in the animals' CBF are induced by adding CO(2) to the breathing gas. To study the influence of scalp on our measurements, comparative, invasive measurements are performed on one side of the head simultaneously with noninvasive measurements on the other side. We also did comparative measurements of CBF using a laser Doppler system to validate the results of our method. The results indicate that for sufficient source-detector separation, the signal contribution of the scalp is minimal and the measurements are representative of the cerebral hemodynamics. Moreover, good correlation between the results of the laser Doppler system and the NIRS system indicate that the presented method is capable of measuring relative changes in CBF. Preliminary results show the potential of this NIRS method to measure pCBF and pCBV relative changes in neonatal pigs.