gebhart/patrepeval huggingface dataset:
Endoxylanases in Durum Wheat Semolina Processing:  Solubilization of Arabinoxylans, Action of Endogenous Inhibitors, and Effects on Rheological Properties (2000)

Endoxylanases seriously affect the rheological properties of durum wheat (Triticum durum Desf.) semolina spaghetti doughs prepared with, and as evaluated, by the farinograph. Under the experimental conditions, control doughs (34.9% moisture content) made from two semolinas (semA and semB) yielded a maximal consistency of 525 and 517 farinograph units (FU), with, respectively, 19.4 and 16.4% of the total level of arabinoxylans (TOT-AX) being water-extractable (WE-AX). When 75.4 Somogyi units/50 g of semolina of the endoxylanases from Trichoderma viride (XTV), rumen microorganisms (XRM), Bacillus subtilis (XBS), and Aspergillus niger (XAN) were used, the maximal consistencies at 34.9% moisture decreased for semA to 467, 436, 448, and 417 FU, respectively. This was accompanied by increased WE-AX contents of 60.8, 71.2, 70.7, and 73.0%, respectively. Similar results were observed for semB. By reducing the total water content of doughs, it was possible to recover the maximal consistency of the original doughs. Both the decrease in maximal consistency and the amount of water to be omitted were significantly related to the decrease in molecular weight (MW) of the WE-AX and the percentage of WE-AX solubilized as a result of the enzymic action. At the same time, it was clear that endogenous endoxylanase inhibitors were present in the durum wheat semolinas and that they inhibited the endoxylanases used to different degrees. Part of the differences in effects between the different endoxylanases (decrease in maximal consistency, amount of AX solubilized, MWs of the WE-AX, and amount of water that could be omitted) could be ascribed to the differences in inhibition of the endoxylanases by endogenous inhibitors.
Endocrine and Pharmacological Suppressors of Bone Turnover Protect against Osteopenia in Ovariectomized Rats* (1989)

This study was designed to test the hypothesis that endocrine and pharmacological suppressors of bone turnover prevent the development of osteopenia during estrogen deficiency. Sham-operated control and ovariectomized (OVX) rats were treated intermittently with vehicle alone, estrogen, or the diphosphonate compounds etidronate disodium (EHDP) and NE-58095 [2-(3-pyridinyl)2-hydroxyethylidene-1,1-bisphosphonate disodium] for 35 or 70 days after surgery. Their proximal tibiae were processed undecalcified for quantitative bone histomorphometry. Vehicle-treated OVX rats were characterized by decreased cancellous bone volume and 3- to 4-fold increases in osteoblast surface, osteoclast surface, bone formation rate, and bone resorption rate. Treatment of OVX rats with estrogen and NE-58095 provided complete protection against bone loss and significantly depressed all of the above indices of bone turnover. OVX rats treated with EHDP exhibited at least partial protection against bone loss and decreased bone turnover. EHDP induced a mild mineralization defect, as indicated by a prolonged mineralization lag time at the tibial endocortical surface. The new diphosphonate compound NE-58095 did not impair bone mineralization. Our results indicate that endocrine and pharmacological suppressors of bone turnover prevent the development of osteopenia during the early stages of estrogen deficiency. If confirmed by clinical trials in humans, diphosphonate compounds may prove to be an alternative to estrogen for the prevention of postmenopausal bone loss.
The Duration of Nuclear Extracellular Signal-Regulated Kinase 1 and 2 Signaling during Cell Cycle Reentry Distinguishes Proliferation from Apoptosis in Response to Asbestos (2004)

Abstract Asbestos exposure causes activation of extracellular signal-regulated kinases 1 and 2 (ERK1/2) in lung epithelial cells, the targets of asbestos-associated lung carcinomas. The functional significance of ERK1/2 activation in pulmonary epithelial and mesothelial cells is unclear. Using serum-stimulated mouse alveolar type II epithelial cells as a model for cell cycle reentry, we show that the duration of phospho-ERK1/2 in the nucleus determines cell fate in response to crocidolite asbestos. In response to 10% serum, a proliferative stimulus, phosphorylated ERK1/2 initially accumulated in the nucleus, and reduction of nuclear phospho-ERK1/2 after 2 to 4 hours was followed by expression of cyclin D1 and S-phase entry. Low levels of asbestos (&amp;lt;0.5 μg/cm2) promoted S-phase entry in low (2%) serum through an epidermal growth factor receptor-dependent pathway but did not promote cell cycle progression or induce apoptosis in the presence of high (10%) serum-containing medium. Higher levels of asbestos (1.0 to 5.0 μg/cm2) prolonged the localization of phospho-ERK1/2 in the nucleus in the presence of high serum, impeded S-phase entry, and induced apoptosis in a dose-dependent manner. Immunofluorescence microscopy indicated that the duration of signaling by phospho-ERK1/2 in the nucleus was predictive of cell fate at any concentration of asbestos. After 8 hours of exposure, cells with nuclear phospho-ERK1/2 also were positive for nuclear localization of apoptosis-inducing factor (AIF), an early event in apoptosis. In contrast, asbestos-exposed cells that displayed cytoplasmic phospho-ERK1/2 at 8 hours expressed cyclin D1 and proceeded to S phase. Our studies show that prolonged localization of phospho-ERK1/2 in the nucleus is incompatible with expression of cyclin D1 and is predictive of asbestos-associated cell death by AIF, thereby providing an approach for determining cell fate in asbestos-induced tumorigenesis.
Thin film transistors for foldable displays (2002)

We report the first amorphous silicon thin film transistors (TFTs) on flexible, ultra-thin substrates of 25 /spl mu/m thick stainless steel foil. The transistors remain operational under convex or concave bending down to 2.5 mm radius of curvature. The goal of our work is a transistor backplane circuit that can be folded, for use in active matrices in highly rugged and portable applications such as foldable intelligent maps. Our results suggest that such foldable backplane circuits are feasible.
Interaction of Palladium/Hydrogen and Palladium/Deuterium to Measure the Excess Energy per Atom for Each Isotope (1997)

A search for the products of fusion reactions that could be triggered by sparking in hydrogen isotopes produced a negative result with no signatures above background being found. Very significant excess energy production in both hydrogen/palladium and deuterium/palladium systems is reported. The conditions of occurrence for this excess energy production are discussed, and the formation of a tightly bound state of the hydrogen (deuterium) atom is put forward to explain the results.
Activation of the Aspergillus PacC transcription factor in response to alkaline ambient pH requires proteolysis of the carboxy-terminal moiety. (1995)

Extremes of pH are an occupational hazard for many microorganisms. In addition to efficient pH homeostasis, survival effectively requires a regulatory system tailoring the syntheses of molecules functioning beyond the cell boundaries (permeases, secreted enzymes, and exported metabolites) to the pH of the growth environment. Our previous work established that the zinc finger PacC transcription factor mediates such pH regulation in the fungus Aspergillus nidulans in response to a signal provided by the products of the six pal genes at alkaline ambient pH. In the presence of this signal, PacC becomes functional, activating transcription of genes expressed at alkaline pH and preventing transcription of genes expressed at acidic pH. Here we detect two forms of PacC in extracts, both forming specific retardation complexes with a PacC-binding site. Under acidic growth conditions or in acidity-mimicking pal mutants (defective in ambient pH signal transduction), the full-length form of PacC predominates. Under alkaline growth conditions or in alkalinity-mimicking pacCc mutants (independent of the ambient pH signal), a proteolysed version containing the amino-terminal approximately 40% of the protein predominates. This specifically cleaved shorter version is clearly functional, both as an activator for alkaline-expressed genes and as a repressor for acid-expressed genes, but the full-length form of PacC must be inactive. Thus, PacC proteolysis is an essential and pH-sensitive step in the regulation of gene expression by ambient pH. Carboxy-terminal truncations, resulting in a gain-of-function (pacCc) phenotype, bypass the requirement for the pal signal transduction pathway for conversion of the full-length to the proteolyzed functional form.
Parallel Scan-Like Testing and Fault Diagnosis Techniques for Digital Microfluidic Biochips (2007)

Dependability is an important attribute for microfluidic biochips that are used for safety-critical applications such as point-of-care health assessment, air-quality monitoring, and food-safety testing. Therefore, these devices must be adequately tested after manufacture and during bioassay operations. Moreover, since disposable biochips are being targeted for a highly competitive and low-cost market segment, test and diagnosis methods should be inexpensive, quick, and effective. We propose a cost-effective testing methodology referred to as "parallel scan-like test", and a rapid diagnosis method based on test outcomes, for droplet-based microfluidic devices. The proposed method allows testing using parallel droplet pathways in both on-line and off-line scenarios. The diagnosis outcome can be used to reconfigure a droplet-based biochip such that faults can be easily avoided, thereby enhancing chip yield and defect tolerance. We evaluate the proposed test and diagnosis methods using complexity analysis as well as experiments using a fabricated biochip.
General Synthesis of Compound Semiconductor Nanowires (2000)

A broad range of multicomponent semiconductor nanowires (see also cover) has been synthesized using laser-assisted catalytic growth (LCG). Nanowires of binary group III–V materials, ternary III–V materials, binary II–VI compounds, and binary SiGe alloys have been prepared in bulk quantities as high-purity (> 90 %) single crystals. The nanowires have diameters varying from three to tens of nanometers, and lengths extending to tens of micrometers. The synthesis of this wide range of technologically important semiconductor nanowires can be extended to many other materials and opens up significant opportunities in nanoscale science and technology.
Tumor Targeting by Surface-Modified Protein Microspheres (2006)

Protein microspheres have been used in the fields of biomedical imaging and drug delivery, but surface modification for cell targeting has been problematic. We have for the first time used an electrostatic adhesion approach to adhere arginine-glutamic acid-aspartic acid (RGD) containing peptides to the surface of protein microspheres for the purpose of targeting these vesicles to tumor cells. RGD sequences are recognized by integrin membrane receptors, which are overexpressed in various tumors. We have succeeded in modifying the surface of serum albumin core-shell microspheres, which have a fluorescent nonaqueous core by using several polylysine peptides containing the RGD sequence. Fluorescence microscopy reveals that these modified microspheres are selectively bound and taken up by HT29 human colon cancer cells in vitro.
Genes Encoding Farnesyl Cysteine Carboxyl Methyltransferase in Schizosaccharomyces pombe and Xenopus laevis (1997)

The mam4 mutation of Schizosaccharomyces pombe causes mating deficiency in h- cells but not in h+ cells. h- cells defective in mam4 do not secrete active mating pheromone M-factor. We cloned mam4 by complementation. The mam4 gene encodes a protein of 236 amino acids, with several potential membrane-spanning domains, which is 44% identical with farnesyl cysteine carboxyl methyltransferase encoded by STE14 and required for the modification of a-factor in Saccharomyces cerevisiae. Analysis of membrane fractions revealed that mam4 is responsible for the methyltransferase activity in S. pombe. Cells defective in mam4 produced farnesylated but unmethylated cysteine and small peptides but no intact M-factor. These observations strongly suggest that the mam4 gene product is farnesyl cysteine carboxyl methyltransferase that modifies M-factor. Furthermore, transcomplementation of S. pombe mam4 allowed us to isolate an apparent homolog of mam4 from Xenopus laevis (Xmam4). In addition to its sequence similarity to S. pombe mam4, the product of Xmam4 was shown to have a farnesyl cysteine carboxyl methyltransferase activity in S. pombe cells. The isolation of a vertebrate gene encoding farnesyl cysteine carboxyl methyltransferase opens the way to in-depth studies of the role of methylation in a large body of proteins, including Ras superfamily proteins.
Efficacy of Etanercept for Wear Debris-Induced Osteolysis (2001)

A major limitation of total joint arthroplasty is that up to 20% of patients require revision surgery to correct prosthetic loosening. Aseptic loosening is believed to result from the phagocytosis of wear debris particles by macrophages, which secrete proinflammatory cytokines that stimulate osteolysis. Tumor necrosis factor alpha (TNF-alpha) has been shown to be one of the prominent cytokines in this cascade and to be involved critically in the generation of particle-induced osteolysis. Etanercept is a soluble inhibitor of TNF-alpha, which is widely used for the treatment of rheumatoid arthritis. Here, we show this agent's ability to prevent wear debris-induced osteolysis. In vitro we show that Etanercept can inhibit directly osteoclastic bone resorption in a bone wafer pit assay, as well as cytokine production from titanium (Ti)-stimulated macrophages. Using a quantitative in vivo model of wear debris-induced osteolysis, we show that Etanercept prevents bone resorption and osteoclastogenesis. In mice treated with Etanercept at the time of osteolysis induction, bone resorption and osteoclast numbers were reduced to background levels in both normal and human TNF-alpha (hTNF-alpha) transgenic mice. In an effort to evaluate its effect on established osteolysis, Etanercept was administered 5 days after Ti implantation, and we observed that further osteolysis was prevented. These data support the concept that TNF-alpha is involved critically in osteoclastogenesis and bone resorption during periprosthetic osteolysis and suggest that soluble TNF-alpha inhibitors may be useful as therapeutic agents for the treatment of prosthetic loosening in humans.
Production of poly(D‐3‐hydroxybutyrate) from CO2, H2, and O2 by high cell density autotrophic cultivation of Alcaligenes eutrophus (1995)

Hydrogen-oxidizing bacterium, Alcaligenes eutrophus autotrophically produces biodegradable plastic material, poly(D-3-hydroxybutyrate), P(3HB), from carbon dioxide, hydrogen, and oxygen. In autotrophic cultivation of the microorganism, it is essential to eliminate possible occurrence of gas explosions from the fermentation process. We developed a bench-plant scale, recycled-gas, closed-circuit culture system equipped with several safety features to perform autotrophic cultivation of A. eutrophus by maintaining the oxygen concentration in the substrate gas phase below the lower limit for a gas explosion (6.9%). The culture vessel utilized a baskettype agitator, resulting in a K(L) a value of 2970 h(-1). Oxygen gas was also directly fed to the fermentor separately from the other gases. As a result, 91.3 g . dm(-3) of the cells and 61.9 g . dm(-3) of P(3HB) were obtained after 40 h of cultivation under this oxygen-limited condition. The results compared favorably with those reported for mass production of P(3HB) by heterotrophic fermentation. (c) 1995 John Wiley & Sons, Inc.
Nanomolar concentrations of nitric oxide reversibly inhibit synaptosomal respiration by competing with oxygen at cytochrome oxidase (1994)

Nitric oxide (NO) reversibly inhibited oxygen consumption of brain synaptosomes. Inhibition was reversible, occurred at the level of cytochrome oxidase, and was apparently competitive with oxygen, with half-inhibition by 270 nM NO at oxygen concentrations around 145 microM and by 60 nM at around 30 microM O2. Isolated cytochrome oxidase was inhibited by similar levels of NO. These levels of NO are within the measured physiological and pathological range for a number of tissues and conditions, suggesting that NO inhibition of cytochrome oxidase and the competition with oxygen may occur in vivo.
Carbon Nanotube‐Based Biosensor (2003)

Carbon nanotubes, compounded into plastic to create bulk electrodes , form the basis of a novel sensor for biological assays. The nanotubes function as both a solid phase and working electrode for generation of electrochemiluminescence, the detection method used in this system. The Figure shows a scanning electron microscopy image of a composite used for an immunoassay. The bright spots in the image are 10 nm diameter gold colloids covalently attached to antibodies. The inset shows a region of a composite with no gold colloids.
Adsorption and Oxidation of Phenolic Compounds by Iron and Manganese Oxides (1987)

Abstract The adsorption and oxidation of catechol and hydroquinone by Fe and Mn oxides has been investigated by Fourier transform infrared spectroscopic (FTIR) analysis of the adsorbed molecules and by the measurement of O 2 consumption by aqueous suspensions of these oxides. Evidence for direct coordination of catechol and salicylate to surface Fe 3+ on iron oxides was obtained by FTIR. The promotion of catechol and hydroquinone oxidation by Fe and Mn oxides was confirmed by measured rates of O 2 consumption and by the appearance of Fe 2+ and Mn 2+ in the solutions. However, only trace levels of soluble Fe 2+ were detected, suggesting that oxidation by Fe(III) oxides was catalytic in that electron transfer between the phenols and Fe 3+ generated Fe 2+ , which was rapidly reoxidized by O 2 . Other adsorbates introduced into these oxide/phenol systems, such as acetate, phosphate, and Cu 2+ , diminished O 2 consumption rates, but the effect was generally attributable to a Iowered pH that inhibited oxidation. A model of surface oxidation by Mn and Fe is presented in which coordination of the organic at the surface is a prerequisite to electron transfer. Oxidation of organics can proceed with or without the uptake of O 2 , depending largely on pH, which determines the rate of reoxidation of the reduced metal ions by O 2 . The results emphasize the difficulty in interpreting the effects that chemical buffers have on oxidation reactions at oxide surfaces.
Effect of Prophylactic Brimonidine or Bleeding Complications and Flap Adherence After Laser in situ Keratomileusis (2002)

This study suggests that brimonidine administered before LASIK may significantly reduce subconjunctival hemorrhage and reduce the amount of hyperemia.
Spatially localized one-dimensional porous silicon photonic crystals (2008)

The authors report a straightforward method to achieve spatially localized photonic band-gap structures in porous silicon. This photonic band-gap lithography technique consists of local photo-oxidation followed by exposure to methanol solvent. Reflectance measurements show that the oxidized porous silicon regions maintain their photonic band structure with only a slight blueshift while there is significant spectral degradation in the nonoxidized regions. Fourier transform infrared spectroscopy and scanning electron microscopy were performed to investigate this phenomenon. The significant spectral change in the nonoxidized regions is attributed to chemical modification of the porous silicon.
New Directions in Polyvanadate Chemistry: From Cages and Clusters to Baskets, Belts, Bowls, and Barrels (1992)

As fragments of the V2O5 layer structure (shown right; spheres for bridging O atoms are large and shaded, for terminal O atoms large and open, and for V atoms small and open) the recently prepared, novel polyvanadate structures mentioned in the title are reported and systematized. In contrast to the classical polyoxoanions of the Keggin and Schlemper type, these “more open” structures contain easily accessible vanadium centers with free coordination sites. Examples of the anticipated host–guest chemistry have already been reported.
Large homogeneous mono-/bi-layer graphene on 6H–SiC(0 0 0 1) and buffer layer elimination (2010)

In this paper we discuss and review results of recent studies of epitaxial growth of graphene on silicon carbide. The presentation is focused on high quality, large and uniform layer graphene growth on the SiC(0 0 0 1) surface and the results of using different growth techniques and parameters are compared. This is an important subject because access to high-quality graphene sheets on a suitable substrate plays a crucial role for future electronics applications involving patterning. Different techniques used to characterize the graphene grown are summarized. We moreover show that atomic hydrogen exposures can convert a monolayer graphene sample on SiC(0 0 0 1) to bi-layer graphene without the carbon buffer layer. Thus, a new process to prepare large, homogeneous stable bi-layer graphene sheets on SiC(0 0 0 1) is presented. The process is shown to be reversible and should be very attractive for various applications, including hydrogen storage.
Purification, Cloning, and Expression of a Novel Salivary Anticomplement Protein from the Tick, Ixodes scapularis (2000)

The alternative pathway of complement is an important defense against pathogens and in tick rejection reactions. The tick Ixodes scapularis is able to feed repeatedly on its natural host and has a salivary anticomplement activity that presumably facilitates feeding. In this study, we purified and then obtained the amino-terminal sequence of the I. scapularis salivary anticomplement (Isac). We found a full-length clone coding for Isac by random screening of a salivary gland cDNA library. Expressing Isac cDNA in COS cells reproduced the activity found in tick saliva, namely, inhibition of rabbit erythrocyte lysis by human serum in the presence of Mg(2+) and EGTA, inhibition of C3b binding to agarose in the presence of Mg(2+) and EGTA, and acceleration of factor Bb uncoupling from the C3 convertase generated by the alternative pathway. Recombinant Isac had no effect on the recalcification time of human platelet-poor plasma or in the classical complement pathway, indicating that it is a specific inhibitor similar to the regulators of complement activation of the alternative pathway such as factor H. Isac, however, has no similarity to any protein in the GenBank(TM) data base, indicating that it is a novel and relatively small (18.5 kDa) anticomplement molecule.
NK cell activation through the NKG2D ligand MULT-1 is selectively prevented by the glycoprotein encoded by mouse cytomegalovirus gene m145 (2005)

The NK cell-activating receptor NKG2D interacts with three different cellular ligands, all of which are regulated by mouse cytomegalovirus (MCMV). We set out to define the viral gene product regulating murine UL16-binding protein-like transcript (MULT)-1, a newly described NKG2D ligand. We show that MCMV infection strongly induces MULT-1 gene expression, but surface expression of this glycoprotein is nevertheless completely abolished by the virus. Screening a panel of MCMV deletion mutants defined the gene m145 as the viral regulator of MULT-1. The MCMV m145-encoded glycoprotein turned out to be necessary and sufficient to regulate MULT-1 by preventing plasma membrane residence of MULT-1. The importance of MULT-1 in NK cell regulation in vivo was confirmed by the attenuating effect of the m145 deletion that was lifted after NK cell depletion. Our findings underline the significance of escaping MULT-1/NKG2D signaling for viral survival and maintenance.