gebhart/patrepeval huggingface dataset:
Alkali‐based AFEX pretreatment for the conversion of sugarcane bagasse and cane leaf residues to ethanol (2010)

Sugarcane is one of the major agricultural crops cultivated in tropical climate regions of the world. Each tonne of raw cane production is associated with the generation of 130 kg dry weight of bagasse after juice extraction and 250 kg dry weight of cane leaf residue postharvest. The annual world production of sugarcane is approximately 1.6 billion tones, generating 279 MMT tones of biomass residues (bagasse and cane leaf matter) that would be available for cellulosic ethanol production. Here, we investigated the production of cellulosic ethanol from sugar cane bagasse and sugar cane leaf residue using an alkaline pretreatment: ammonia fiber expansion (AFEX). The AFEX pretreatment improved the accessibility of cellulose and hemicelluloses to enzymes during hydrolysis by breaking down the ester linkages and other lignin carbohydrate complex (LCC) bonds and the sugar produced by this process is found to be highly fermentable. The maximum glucan conversion of AFEX pretreated bagasse and cane leaf residue by cellulases was approximately 85%. Supplementation with hemicellulases during enzymatic hydrolysis improved the xylan conversion up to 95-98%. Xylanase supplementation also contributed to a marginal improvement in the glucan conversion. AFEX-treated cane leaf residue was found to have a greater enzymatic digestibility compared to AFEX-treated bagasse. Co-fermentation of glucose and xylose, produced from high solid loading (6% glucan) hydrolysis of AFEX-treated bagasse and cane leaf residue, using the recombinant Saccharomyces cerevisiae (424A LNH-ST) produced 34-36 g/L of ethanol with 92% theoretical yield. These results demonstrate that AFEX pretreatment is a viable process for conversion of bagasse and cane leaf residue into cellulosic ethanol.
Apolipoprotein E-epsilon4 alleles in cerebral amyloid angiopathy and cerebrovascular pathology associated with Alzheimer's disease. (1996)

The presence of apolipoprotein E-epsilon4 (APOE-epsilon4) allele has been implicated as a risk factor for Alzheimer's disease (AD). We examined the frequencies of APOE-epsilon4 alleles in age-matched controls and subgroups of 190 AD subjects exhibited cerebral amyloid angiopathy (CAA) and other frequently associated lesions. CAA was evident in 96% of the AD subjects, which were divided into two groups, one bearing mild or no apparent CAA and the other with moderate to severe CAA. APOE-epsilon4 allele frequency (48%) in the latter advanced CAA group was six times higher than in those who exhibited mild CAA. In the advanced CAA subjects, the occurrence of an epsilon4 allele was increased by a factor of 17 (95% confidence interval, 7.56 to 38.9). This was despite the fact that neocortical amyloid-beta plaque densities in the two groups were similar and that all of the AD subjects had met the accepted neuropathological criteria. We also observed that the degree of CAA severity was greatest in the group of subjects with the epsilon4/epsilon4 genotype. The association between CAA and APOE-epsilon4 was further implicated in two non-AD subjects among neurological controls with severe CAA. These two subjects, both homozygous for the APOE-epsilon4 allele, were primarily diagnosed as having Creutzfeldt-Jakob disease and Pick's disease in the absence of significant neocortical amyloid deposition. Allele frequency comparisons between neurological control subjects with CAA and those without likewise accorded a strong relationship between the APOE-epsilon4 allele and the presence of CAA. More remarkably, the epsilon4 allele frequency was highly associated with AD subjects exhibiting lobar or intracerebral hemorrhage, all of whom had advanced CAA. We observed that 36% of the AD subjects had concomitant cerebrovascular pathology resulting from single infarcts, multiple microinfarcts, ischemic white matter lesions, or petechial hemorrhages. Although the difference in APOE genotype distribution between subjects with and without cerebrovascular lesions did not reach statistical significance, we did note that the frequency of the epsilon4 allele was significantly higher in subjects with such pathology as compared with those without. However, we found no evidence to suggest that the acquisition of an APOE-epsilon4 allele or one of the alleles, epsilon2 or epsilon3, was a factor in the occurrence of atherosclerosis localized in the basal surface arteries. Analyses of our sample also confirm that there was a lower frequency of the APOE-epsilon2 allele in AD subjects and that the frequency of the epsilon4 allele in AD subjects with concomitant diffuse Lewy body disease was intermediate between controls and AD subjects. Our results suggest that the APOE-epsilon4 allele is a significant factor in the development of CAA in AD and reveal the possibility that APOE is an independent factor in CAA and other vascular abnormalities associated with AD.
Staphyloxanthin Plays a Role in the Fitness of Staphylococcus aureus and Its Ability To Cope with Oxidative Stress (2006)

Staphyloxanthin is a membrane-bound carotenoid of Staphylococcus aureus. Here we studied the interaction of staphyloxanthin with reactive oxygen substances (ROS) and showed by comparative analysis of the wild type (WT) and an isogenic crtM mutant that the WT is more resistant to hydrogen peroxide, superoxide radical, hydroxyl radical, hypochloride, and neutrophil killing.
Effect of Alendronate on Risk of Fracture in Women With Low Bone Density but Without Vertebral Fractures<SUBTITLE>Results From the Fracture Intervention Trial</SUBTITLE> (1998)

In women with low BMD but without vertebral fractures, 4 years of alendronate safely increased BMD and decreased the risk of first vertebral deformity. Alendronate significantly reduced the risk of clinical fractures among women with osteoporosis but not among women with higher BMD.
Characteristics of optical duobinary signals in terabit/s capacity, high-spectral efficiency WDM systems (1998)

Optical duobinary signals have been applied to dense wavelength division multiplexing (WDM) systems with high-spectral efficiency to fully utilize a limited gain bandwidth of about 35 nm (4.4 THz) for an erbium-doped fiber amplifier (EDFA). These signals are one type of partial response signals and have narrower bandwidth than conventional intensity modulation (IM) signals. Thus, the use of these signals should make possible to attain ultradense WDM systems. In this paper, characteristics of optical duobinary and IM signals in ultradense WDM systems are compared through experimental evaluations at 20 Gb/s. High-spectral efficiency of 0.6 b/s/Hz was reached in this demonstration.
Effect of culture pH on erythropoietin production by Chinese hamster ovary cells grown in suspension at 32.5 and 37.0°C (2004)

To investigate the effect of culture pH in the range of 6.85-7.80 on cell growth and erythropoietin (EPO) production at 32.5 and 37.0 degrees C, serum-free suspension cultures of recombinant CHO cells (rCHO) were performed in a bioreactor with pH control. Lowering culture temperature from 37.0 to 32.5 degrees C suppressed cell growth, but cell viability remained high for a longer culture period. Regardless of culture temperature, the highest specific growth rate (mu) and maximum viable cell concentration were obtained at pH values of 7.00 and 7.20, respectively. Like mu, the specific consumption rates of glucose and glutamine decreased at 32.5 degrees C compared to 37.0 degrees C. In addition, they increased with increasing culture pH. Culture pH at 32.5 degrees C affected specific EPO productivity (q(EPO)) in a different fashion from that at 37 degrees C. At 37 degrees C, the q(EPO) was fairly constant in the pH range of 6.85-7.80, while at 32.5 degrees C, the q(EPO) was significantly influenced by culture pH. The highest q(EPO) was obtained at pH 7.00 and 32.5 degrees C, and its value was approximately 1.5-fold higher than that at pH 7.00 and 37.0 degrees C. The proportion of acidic EPO isoforms, which is a critical factor for high in vivo biological activity of EPO, was highest in the stationary phase of growth, regardless of culture temperature and pH. Although cell viability rapidly decreased in death phase at both 32.5 and 37.0 degrees C, the significant degradation of produced EPO, probably by the action of proteases released from lysed cells, was observed only at 37.0 degrees C. Taken together, through the optimization of culture temperature and pH, a 3-fold increase in maximum EPO concentration and a 1.4-fold increase in volumetric productivity were obtained at pH 7.00 and 32.5 degrees C when compared with those at 37.0 degrees C. These results demonstrate the importance of optimization of culture temperature and pH for enhancing EPO production in serum-free, suspension culture of rCHO cells.
Inhibition of Ca(2+)-dependent K+ transport and cell dehydration in sickle erythrocytes by clotrimazole and other imidazole derivatives. (1993)

We have investigated the interaction of clotrimazole (CLT) and related compounds with the erythroid Ca(2+)-activated K+ channel, a mediator of sickle cell dehydration. We measured K+ transport, membrane potential, and cell volume upon activation of this pathway in sickle erythrocytes. CLT blocked almost completely Ca(2+)-activated K+ transport in homozygous hemoglobin S cells, with IC50 values of 29 +/- 15 nM in isotonic 20 mM salt solution and 51 +/- 15 nM in normal saline (n = 3). The inhibition of K+ transport by CLT was caused by a specific interaction with the Ca(2+)-activated K+ channel of human red cells, since it displaced bound 125I-Charybdotoxin, a specific ligand of the Gardos channel, with an IC50 (12 +/- 4 nM in isotonic 20 mM) similar to the IC50 values for flux inhibition. When homozygous hemoglobin S cells were dehydrated by incubation in the presence of 100 microM CaCl2 and the ionophore A23187, or by exposure to cycles of oxygenation and deoxygenation, CLT effectively inhibited cell dehydration and K+ loss. The IC50 of CLT for inhibition of Ca(2+)-activated K+ transport in sickle cells is significantly lower than plasma concentrations of CLT achievable after nontoxic oral doses. We therefore propose that oral administration of CLT may prevent red cell dehydration in patients with sickle cell anemia.
IRIS at TREC-8 (1999)

We tested two relevance feedback models, an adaptive linear model and a probabilistic model, using massive feedback query expansion in TREC-5 (Sumner & Shaw, 1997), experimented with a three-valued scale of relevance and reduced feedback query expansion in TREC-6 (Sumner, Yang, Akers & Shaw, 1998), and examined the effectiveness of relevance feedback using a subcollection and the effect of system features in an interactive retrieval system called IRIS (Information Retrieval Interactive System) in TREC-7 (Yang, Maglaughlin, Mehol & Sumner, 1999). In TREC-8, we continued our exploration of relevance feedback approaches. Based on the result of our TREC-7 interactive experiment, which suggested relevance feedback using user-selected passages to be an effective alternative to conventional document feedback, our TREC-8 interactive experiment compared a passage feedback system and a document feedback system that were identical in all aspects except for the feedback mechanism. For the TREC-8 ad-hoc task, we merged results of pseudo-relevance feedback to subcollections as in TREC-7. Our results were consistent with that of TREC-7. The results of passage feedback, whose system log showed high level of searcher intervention, was superior to the document feedback results. As in TREC-7, our ad-hoc results showed high precision in top few documents, but performed poorly overall compared to results using the collection as a whole.
Amino acid sequence of the nonsecretory ribonuclease of human urine (1988)

The amino acid sequence of a nonsecretory ribonuclease isolated from human urine was determined except for the identity of the residue at position 7. Sequence information indicates that the ribonucleases of human liver and spleen and an eosinophil-derived neurotoxin are identical or very closely related gene products. The sequence is identical at about 30% of the amino acid positions with those of all of the secreted mammalian ribonucleases for which information is available. Identical residues include active-site residues histidine-12, histidine-119, and lysine-41, other residues known to be important for substrate binding and catalytic activity, and all eight half-cystine residues common to these enzymes. Major differences include a deletion of six residues in the (so-called) S-peptide loop, insertions of two, and nine residues, respectively, in three other external loops of the molecule, and an addition of three residues at the amino terminus. The sequence shows the human nonsecretory ribonuclease to belong to the same ribonuclease superfamily as the mammalian secretory ribonucleases, turtle pancreatic ribonuclease, and human angiogenin. Sequence data suggest that a gene duplication occurred in an ancient vertebrate ancestor; one branch led to the nonsecretory ribonuclease, while the other branch led to a second duplication, with one line leading to the secretory ribonucleases (in mammals) and the second line leading to pancreatic ribonuclease in turtle and an angiogenic factor in mammals (human angiogenin). The nonsecretory ribonuclease has five short carbohydrate chains attached via asparagine residues at the surface of the molecule; these chains may have been shortened by exoglycosidase action.(ABSTRACT TRUNCATED AT 250 WORDS)
Endocytosis of hyaluronic acid by rat liver endothelial cells. Evidence for receptor recycling (1989)

Hyaluronic acid (HA) is cleared from the blood by liver endothelial cells through receptor-mediated endocytosis [Eriksson, Fraser, Laurent, Pertoft & Smedsrod (1983) Exp. Cell Res. 144, 223-238]. We have measured the capacity of cultured rat liver endothelial cells to endocytose and degrade 125I-HA (Mr approximately 44,000) at 37 degrees C. Endocytosis was linear for 3 h and then reached a plateau. The rate of endocytosis was concentration-dependent and reached a maximum of 250 molecules/s per cell. Endocytosis of 125I-HA was inhibited more than 92% by a 150-fold excess of non-radiolabelled HA. HA, chondroitin sulphate and heparin effectively competed for endocytosis of 125I-HA, whereas glucuronic acid, N-acetylglucosamine, DNA, RNA, polygalacturonic acid and dextran did not compete. In the absence of cycloheximide, endothelial cells processed 13 times more 125I-HA in 6 h than their total (cell-surface and intracellular) specific HA-binding capacity. This result was not due to degradation and rapid replacement of receptors, because, even in the presence of cycloheximide, these cells processed 6 times more HA than their total receptor content in 6 h. Also, in the presence of cycloheximide, no decrease in 125I-HA-binding capacity was seen in cells processing or not processing HA for 6 h, indicating that receptors are not degraded after the endocytosis of HA. During endocytosis of HA at 37 degrees C, at least 65% of the intracellular HA receptors became occupied with HA within 30 min. This indicates that the intracellular HA receptors (75% of the total) function during continuous endocytosis. Hyperosmolarity inhibits endocytosis and receptor recycling in the asialoglycoprotein and low-density-lipoprotein receptor systems by disrupting the coated-pit pathway [Heuser & Anderson (1987) J. Cell Biol. 105, 230a; Oka & Weigel (1988) J. Cell. Biochem. 36, 169-183]. Hyperosmolarity inhibited 125I-HA endocytosis in liver endothelial cells by more than 90%, suggesting use of a coated-pit pathway by this HA receptor. We conclude that liver endothelial cell HA receptors are recycled during the continuous endocytosis and processing of HA.
Electrochemical Properties of (111)-Oriented n-Si Surfaces Derivatized with Covalently- Attached Alkyl Chains (1998)

The electrochemical properties of alkyl-terminated, (111)-oriented, n-type Si surfaces, prepared via a two-step halogenation/alkylation procedure, were analyzed in contact with CH3OH−1,1‘-dimethylferrocene+/0 (Me2Fc+/0) solutions. Current density−potential and differential capacitance−potential measurements of these surfaces in contact with CH3OH−Me2Fc+/0 indicated that the electrochemical properties of the alkyl-terminated surfaces were very similar to those of the H-terminated Si surface. The alkyl overlayers did not shift the Si band edges or induce significant surface recombination, but they did provide an additional electrical series resistance to charge transfer across the Si/liquid interface. The efficacy of alkyl overlayers in preventing photooxidation and photocorrosion of n-silicon surfaces was measured in contact with CH3OH−Me2Fc+/0 solutions to which a known amount of water had been added. Under these conditions, the alkyl-terminated surfaces consistently showed excellent current density−potential characteristics and displayed lower oxidation rates than the H-terminated surface, indicating that stability toward oxidation had been achieved without any significant compromise in the electrochemical qualities of the silicon surface.
NOTE On Active Contour Models and Balloons (1991)

puted, the maxima are extracted and then edges are linked together. Here we do it another way; we start with a continuous curve model and we try to localize it on the maxima of the gradient. We draw a simple curve close to the intended contours and let the action of the image forces push the curve the rest of the way. The final position corresponds to the equilibrium reached at the minimum of the model’s energy. The external forces are derived from the image data or imposed as constraints. Internal forces define the physical properties of the model. If this original idea is due to [l, 3, 41, our model presents the following interesting new features which can solve some of the problems encountered with the original snake method:
Heparanase Induces Endothelial Cell Migration via Protein Kinase B/Akt Activation (2004)

Heparanase is a mammalian endoglycosidase that degrades heparan sulfate (HS) at specific intra-chain sites. Blood-borne neutrophils, macrophages, mast cells, and platelets exhibit heparanase activity that is thought to be stored in specific granules. The degranulated heparanase is implicated in extravasation of metastatic tumor cells and activated cells of the immune system. Degranulation and heparanase release in response to an inflammatory stimulus or platelet activation would facilitate cellular extravasation directly, by altering the composition and structural integrity of the extracellular matrix, or indirectly, by releasing HS-bound proinflammatory cytokines and chemokines. We hypothesized that in addition to such indirect effect, the released heparanase may also locally affect and activate neighboring cells such as endothelial cells. Here, we provide evidence that addition of the 65-kDa latent heparanase to endothelial cells enhances Akt signaling. Heparanase-mediated Akt phosphorylation was independent of its enzymatic activity or the presence of cell membrane HS proteoglycans and was augmented by heparin. Moreover, addition of heparanase stimulated phosphatidylinositol 3-kinase-dependent endothelial cell migration and invasion. These results suggest, for the first time, that heparanase activates endothelial cells and elicits angiogenic responses directly. This effect appears to be mediated by as yet unidentified heparanase receptor.
MPI as an abstraction for software-hardware interaction for HPRCs (2008)

High performance reconfigurable computers (HPRCs) consist of one or more standard microprocessors tightly coupled with one or more reconfigurable FPGAs. HPRCs have been shown to provide good speedups and good cost/performance ratios, but not necessarily ease of use, leading to a slow acceptance of this technology. HPRCs introduce new design challenges, such as the lack of portability across platforms, incompatibilities with legacy code, users reluctant to change their code base, a prolonged learning curve, and the need for a system-level hardware/software co-design development flow. This paper presents the evolution and current work on TMD-MPI, which started as an MPI-based programming model for multiprocessor systems-on-chip implemented in FPGAs, and has now evolved to include multiple X86 processors. TMD-MPI is shown to address current design challenges in HPRC usage, suggesting that the MPI standard has enough syntax and semantics to program these new types of parallel architectures. Also presented is the TMD-MPI ecosystem, which consists of research projects and tools that are developed around TMD-MPI to further improve HPRC usability.
Modulation of the Triggering Receptor Expressed on the Myeloid Cell Type 1 Pathway in Murine Septic Shock (2006)

ABSTRACT The triggering receptor expressed on myeloid cell type 1 (TREM-1) is a cell surface molecule that has been identified on both human and murine polymorphonuclear neutrophils and mature monocytes. The activation of TREM-1 in the presence of microbial components amplifies the inflammatory response and may be responsible for the hyperresponsiveness observed during the initial stage of sepsis. To investigate the effect of the modulation of the TREM-1 pathway during experimental murine sepsis, we used analogue synthetic peptides derived from the extracellular moiety of TREM-1. The TREM-1 ligand was expressed on both peritoneal and peripheral neutrophils during experimental peritonitis in mice. The TREM-1 peptides inhibited the recognition by TREM-1 of its ligand and protected endotoxinic mice from death. In septic rats, the TREM-1 peptides improved the hemodynamic status, attenuated the development of lactic acidosis, modulated the production of such proinflammatory cytokines as tumor necrosis factor alpha and interleukin-1β, and improved survival. The protective effect of these peptides on arterial pressure could partly be explained by a decreased production of nitric oxide. These data suggest that in vivo modulation of TREM-1 might be a suitable therapeutic tool for the treatment of sepsis.
Expression and localization of PCSK9 in rat hepatic cells (2006)

Proprotein convertase subtilisin/kexin type 9 (PCSK9), recently cloned in several laboratories, including ours, causes a third form of autosomal dominant hypercholesterolemia. Its mechanism of action remains unclear. We studied the expression and subcellular localization of PCSK9 in fetal and adult rat tissues associated with cholesterol homeostasis using quantitative reverse transcriptase--PCR, Western blot analysis, subcellular fractionation, and confocal immunofluorescent microscopy. PCSK9 mRNA is most abundant in yolk sac and fetal liver, but the highest expression of the protein was found in differentiated hepatoma FAO-1 cell line, which also shows the highest expression of LDLR. In FAO-1 cells PCSK9 expression is downregulated by cholesterol and 25-hydroxycholesterol and upregulated in the absence of sterols following the same pattern of expression as HMG-CoA reductase, synthase, and LDLR. Subcellular fractionation, combined with Western blotting, showed that PCSK9 is localized in the ER and intermediate vesicular compartment of the cell but not in Golgi cisternae. The mature enzyme is secreted from the liver and hepatoma cells. Double labeling with antibodies to PCSK9 and LDLR or clathrin revealed some colocalization of PCSK9 with clathrin-coated vesicles and LDLR. In conclusion, our results show that PCSK9 is processed in the ER, and the mature convertase is secreted in the plasma.