gebhart/patrepeval huggingface dataset:
Characterization of a Novel α1,2-Fucosyltransferase of Escherichia coli O128:B12 and Functional Investigation of Its Common Motif (2007)

The wbsJ gene from Escherichia coli O128:B12 encodes an alpha1,2-fucosyltransferase responsible for adding a fucose onto the galactose residue of the O-antigen repeating unit via an alpha1,2 linkage. The wbsJ gene was overexpressed in E. coli BL21 (DE3) as a fusion protein with glutathione S-transferase (GST) at its N-terminus. GST-WbsJ fusion protein was purified to homogeneity via GST affinity chromatography followed by size exclusion chromatography. The enzyme showed broad acceptor specificity with Galbeta1,3GalNAc (T antigen), Galbeta1,4Man and Galbeta1,4Glc (lactose) being better acceptors than Galbeta-O-Me and galactose. Galbeta1,4Fru (lactulose), a natural sugar, was furthermore found to be the best acceptor for GST-WbsJ with a reaction rate four times faster than that of lactose. Kinetic studies showed that GST-WbsJ has a higher affinity for lactose than lactulose with apparent Km values of 7.81 mM and 13.26 mM, respectively. However, the kcat/appKm value of lactose (6.36 M(-1) x min(-1)) is two times lower than that of lactulose (13.39 M(-1) x min(-1)). In addition, the alpha1,2-fucosyltransferase activity of GST-WbsJ was found to be independent of divalent metal ions such as Mn2+ or Mg2+. This activity was competitively inhibited by GDP with a Ki value of 1.41 mM. Site-directed mutagenesis and a GDP-bead binding assay were also performed to investigate the functions of the highly conserved motif H152xR154R155xD157. In contrast to alpha1,6-fucosyltransferases, none of the mutants of WbsJ within this motif exhibited a complete loss of enzyme activity. However, residues R154 and D157 were found to play critical roles in donor binding and enzyme activity. The results suggest that the common motif shared by both alpha1,2-fucosyltransferases and alpha1,6-fucosyltransferases have similar functions. Enzymatic synthesis of fucosylated sugars in milligram scale was successfully performed using Galbeta-O-Me and Galbeta1,4Glcbeta-N3 as acceptors.
Comparative efficacy of daptomycin, vancomycin, and cloxacillin for the treatment of Staphylococcus aureus endocarditis in rats and role of test conditions in this determination (1990)

The in vivo efficacy of daptomycin, a new cell wall-active anti-gram-positive-bacterial agent, was compared to those of cloxacillin and vancomycin in a rat model of Staphylococcus aureus endocarditis. Both methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA) strains were used. When therapy was initiated early (8 h) after infection, at the time when valvular bacterial counts were relatively low (approximately 10(6) CFU/g of vegetation), 3 days of therapy was found to be effective against the MSSA strains whatever the antibiotic regimen. In contrast, when the onset of therapy was delayed up to 15 h after infection, so that higher bacterial counts could develop on the valves (approximately 10(9) CFU/g of vegetation), a longer period of treatment (6 days) was required to cure infection. Under these conditions after 3 days of therapy, daptomycin was more effective than cloxacillin and vancomycin against the MSSA strains. Similarly, daptomycin showed a greater activity than vancomycin against the MRSA strain after 3 days of treatment, but after 6 days both antibiotics were equally effective. Decreasing doses of daptomycin showed decreasing activity: 10 mg/kg of body weight every 12 h (q12h) was better than 5 mg/kg q12h, whereas 5 mg/kg q24h (providing drug levels in blood detectable only during the first 12 h) failed to cure infection. In vitro, daptomycin was highly bactericidal at high concentrations (25 and 60 micrograms/ml, corresponding to peak levels in serum after doses of 5 and 10 mg/kg, respectively) and bacteriostatic at lower concentrations (0.5 to 2.5 micrograms/ml, corresponding to trough levels in serum). In conclusion, against low-bacterial-count S. aureus endocarditis, daptomycin showed an efficacy similar to those of vancomycin and cloxacillin. Against high-bacterial-count S. aureus endocarditis, daptomycin showed a higher bactericidal activity than cloxacillin (against the MSSA strains) and vancomycin (against both the MSSA and MRSA strains).
Mycosis fungoides – analysis of the duration of disease stages in patients who progress and the time point of high‐grade transformation (2007)

The course of progressing MF is chronic and advancing. The progression is initially slow and later accelerates. Important prognostic factors are the stage of disease and the presence of blast transformation. The prognosis is better in the early stage and when blast transformation is absent.
Evaluation of new rapid commercial enzyme immunoassay for detection of Cryptosporidium oocysts in untreated stool specimens (1995)

Sixty-six stool specimens were evaluated by the ProSpecTR Cryptosporidium rapid enzyme immunoassay (EIA) (Alexon, Sunnyvale, Calif.). Approximately 2 g of untreated stool suspended in buffer was filtered through membranes labelled with anti-Cryptosporidium-specific antigen antibody. Anti-Cryptosporidium-specific antigen antibody was labelled with biotin, horseradish peroxidase conjugated to streptavidin, and tetramethylbenzidine, and each labelled antibody was added in sequence to the membranes. Each membrane had a positive control and test area. EIA results were compared with those of the modified acid-fast procedure. Twenty-three specimens were positive by the initial acid-fast procedure and the EIA. Forty-two specimens were negative by the initial acid-fast test and the EIA. One specimen was negative by the initial acid-fast test and positive by the EIA (sensitivity, 100%; specificity, 98.5%). This technique is easy to use by comparison with the cumbersome, labor-intensive, and more subjective microscopic methods currently available, and its sensitivity equals that of current microscopic methods.
Structural Studies of Bombyx mori Silk Fibroin during Regeneration from Solutions and Wet Fiber Spinning (2005)

Regenerated silk fibroin materials show properties dependent on the methods used to process them. The molecular structures of B. mori silk fibroin both in solution and in solid states were studied and compared using X-ray diffraction, FTIR, and (13)C NMR spectroscopy. Some portion of fibroin protein molecules dissolved in formic acid already have a beta-sheet structure, whereas those dissolved in TFA have some helical conformation. Moreover, fibroin molecules were spontaneously assembled into an ordered structure as the acidic solvents were removed from the fibroin-acidic solvent systems. This may be responsible for the improved physical properties of regenerated fibroin materials from acidic solvents. Regenerated fibroin materials have shown poor mechanical properties and brittleness compared to their original form. These problems were technically solved by improving the fiber forming process according to a method reported here. The regenerated fibroin fibers showed much better mechanical properties compared to the native silk fiber and their physical and chemical properties were characterized by X-ray diffraction, solid state (13)C NMR spectroscopy, SinTech tensile testing, and SEM.
Inhibition of lipid synthesis by beta beta'-tetramethyl-substituted, C14-C22, alpha, omega-dicarboxylic acids in the rat in vivo. (1985)

beta beta'-Methyl-substituted alpha, omega-dicarboxylic acids (MEDICA) of C14-C18 chain length were found to inhibit liver lipid synthesis in the rat in vivo. Maximum inhibition was observed with MEDICA 16 amounting to a 50% decrease in fatty acid and cholesterol biosynthesis in the presence of 0.07 and 0.015% (w/w) of the drug in the diet, respectively. Inhibition of lipid biosynthesis by MEDICA 16 involved a reduction in cytosolic acetyl-CoA content, while the carbon flux from glucose to glycogen, protein, and carbon dioxide remained unaffected. Inhibition of lipogenesis by MEDICA 16 resulted in a 50% decrease in liver and carcass (but not brain) neutral lipid ester content at 0.25% (w/w) of the drug in the diet, as well as in a dose-dependent hypotriglyceridemic effect, with an up to 3-fold reduction in serum triacylglycerols. Inhibition of cholesterogenesis by MEDICA 16 resulted in a hypocholesterolemic effect, with 60 and 45% reductions in (very low density + low density lipoprotein) cholesterol and high density lipoprotein cholesterol, respectively.
The origin of high electrolyte–electrode interfacial resistances in lithium cells containing garnet type solid electrolytes (2014)

Dense LLZO (Al-substituted Li7La3Zr2O12) pellets were processed in controlled atmospheres to investigate the relationships between the surface chemistry and interfacial behavior in lithium cells. Laser induced breakdown spectroscopy (LIBS), scanning electron microscopy (SEM), X-ray diffraction (XRD), Raman spectroscopy, synchrotron X-ray photoelectron spectroscopy (XPS) and soft X-ray absorption spectroscopy (XAS) studies revealed that Li2CO3 was formed on the surface when LLZO pellets were exposed to air. The distribution and thickness of the Li2CO3 layer were estimated by a combination of bulk and surface sensitive techniques with various probing depths. First-principles thermodynamic calculations confirmed that LLZO has an energetic preference to form Li2CO3 in air. Exposure to air and the subsequent formation of Li2CO3 at the LLZO surface is the source of the high interfacial impedances observed in cells with lithium electrodes. Surface polishing can effectively remove Li2CO3 and dramatically improve the interfacial properties. Polished samples in lithium cells had an area specific resistance (ASR) of only 109 Ω cm(2) for the LLZO/Li interface, the lowest reported value for Al-substituted LLZO. Galvanostatic cycling results obtained from lithium symmetrical cells also suggest that the quality of the LLZO/lithium interface has a significant impact on the device lifetime.
视觉“驱动力”与电影叙事：在拉康、希区柯克和穆尔维作品中读解“凝视理论” (2009)

自20世纪90年代初期以来，“凝视理论”已形成一定规模，这很大程度上得益于劳拉·穆尔维1975年的论文《视觉快感与叙事电影》所产生的广泛影响。穆尔维关于“积极”男性凝视的父权制结构的命题的影响力，己远远超出阿尔弗雷德·希区柯克和好莱坞的女性主义电影批评，并延伸至电影和文化理论，以及知觉理论。穆尔维旨在用精神分析揭示好莱坞电影中的父权力量。
Thermal Decomposition and IR Spectra of Mg(II) Compounds with Caffeine (1999)

Thermogravimetry (TG), differential thermal analysis (DTA), and other analytical methods have been applied to the investigation of the thermal behaviour and structure of the com­ pounds Mg(ac)2(caf)2-3H20 (/) Mg(Clac)2(caf) • 2H 20 (II), Mg(Cl 2 ac) 2 (caf)- H 20 (III) and Mg(Cl 3 ac) 2 (caf) 2 -5H 20 (IV) (ac = СНзСОО, Clac = С1СН 2СОО, Cl2ac = ChCHCOO , Cl3ac = Cl 3CCOO~, and caf = caffeine). Thermal decomposition of these compounds is a multi­ stage process. The compositions of the complexes and the solid state intermediate and resultant products of thermolysis have been identified by means of elemental analysis and complexometric titration. The possible scheme of destruction of the complexes is suggested. Heating of the com­ pounds first results in a release of water molecules. In complexes /, II, and III the loss of the volatile ligand (caf) occurs (on the TG curves) in one step (- 2caf or - caf) and in complex IV in two steps (- caf, - caf). The final product of the thermal decomposition was MgO. The thermal stability of the complexes increases in the sequence: /, IV, II, III. Caffeine was coordinated to Mg(II) through the N(9) atom of its heterocyclic ring. IR data suggest a unidentate coordination of carboxylates to magnesium in complexes /—IV.
Massive cytogenetic heterogeneity in a pancreatic carcinoma: Fifty‐four karyotypically unrelated clones (1995)

Chromosome analysis after short-term culture revealed remarkable cytogenetic heterogeneity in a pancreatic carcinoma. The patient had no prior history of radio- or chemotherapy. A total of 54 aberrant, near-diploid, karyotypically unrelated clones were identified, three of which displayed clonal evolution. The abnormalities were unbalanced in 30% of the clones. From one to eight karyotypic anomalies per clone were found. Numerical changes were rare, whereas structural aberrations were numerous and diverse and included deletions, duplication, insertions, inversions, translocations, ring formation, and telomeric associations. All chromosomes except No. 15 were involved in structural rearrangements, chromosomes 1, 6, 7, 8, 11, and 12 being the most frequently affected. A similarly massive cytogenetic polyclonality has never been reported previously. Although the spectrum of epithelial neoplasms characterized by karyotypically unrelated clones is increasing, the pathogenetic role of this type of cytogenetic intratumor heterogeneity remains unknown.
Selective Protection against Conidia by Mononuclear and against Mycelia by Polymorphonuclear Phagocytes in Resistance to Aspergillus (1982)

By comparing natural immunity to Aspergillus fumigatus (AF) in vivo with the action of human or mouse phagocytes against AF in vitro, we delineated two sequential lines of defense against AF. The first line of defense was formed by macrophages and directed against spores. Macrophages prevented germination and killed spores in vitro and rapidly eradicated conidia in vivo, even in neutropenic and athymic mice. The second was the neutrophilic granulocyte (PMN), which protected against the hyphal form of AF. Human and mouse PMN killed mycelia in vitro. Normal, but not neutropenic mice, stopped hyphal growth, and eradicated mycelia. Either line of defense acting alone protected mice from high challenge doses. Natural immunity collapsed only when both the reticuloendothelial system and PMN were impaired. These findings are in keeping with the clinical observation that high doses of cortisone and neutropenia are the main risk factors for invasive aspergillosis. Cortisone inhibited the conidiacidal activity of mouse macrophages in vivo and of human or mouse mononuclear phagocytes in vitro. Cortisone damaged this first line of defense directly and not through the influence of T lymphocytes or other systems modifying macrophage function as shown in athymic mice and in vitro. In addition, daily high doses of cortisone in mice reduced the mobilization of PMN so that the second line of defense was also impaired. Thus, cortisone can break down natural resistance on its own. Myelosuppression rendered mice susceptible only when the first line of defense was overpowered by high challenge doses, by activated spores that cannot be killed by macrophages, or by cortisone suppression of the conidiacidal activity of macrophages. The host, thus, can call upon two independent phagocytic cell lines that form graded defense systems against aspergillus. These lines of defense function in the absence of a specific immune response, which seems superfluous in the control and elimination of this fungus.
Antisense-based cancer therapeutics: are we there yet? (2006)

Despite significant advances that have been made in recent years, there is still an urgent need for novel, more effective and less toxic therapeutics for human cancer. Among many new molecular therapeutics being explored for cancer therapy, antisense oligonucleotides are a promising nucleic acid-based approach, with numerous antisense agents being evaluated in preclinical studies and several anticancer antisense drugs in clinical trials. Although there are still a few problems facing the development of antisense strategies for cancer therapy, with progress made in chemical modifications, target selection and drug delivery systems, antisense oligonucleotides are emerging as a novel approach to cancer therapy used alone or in combination with conventional treatments such as chemotherapy and radiation therapy.
(4-[18F]Fluoro-3-iodobenzyl)guanidine, a Potential MIBG Analog for Positron Emission Tomography (1994)

The aims of this investigation were to develop a no-carrier-added (nca) synthesis of (4-[18F]-fluoro-3-iodobenzyl)guanidine ([18F]FIBG) and to evaluate its potential as an MIBG analogue useful for positron emission tomography. [18F]FIBG was prepared in four steps starting from 4-cyano-2-iodo-N,N,N-trimethylanilinium trifluoromethanesulfonate in 5% decay-corrected radiochemical yield in a total synthesis time of 130 min. The specific activity was more than 1500 Ci per mmol. In vitro binding studies showed that the percent binding of [18F]FIBG to SK-N-SH human neuroblastoma cells remained constant over a 3-log activity range and was similar to that of nca [131I]MIBG. Specific and high uptake of FIBG was also seen in mouse heart and adrenals. The in vitro and in vivo properties of [18F]FIBG suggest that this compound may be a useful positron-emitting analogue of MIBG.
Molecular determinants of FGF‐21 activity—synergy and cross‐talk with PPARγ signaling (2006)

Fibroblast growth factor (FGF)-21 is a novel regulator of insulin-independent glucose transport in 3T3-L1 adipocytes and has glucose and triglyceride lowering effects in rodent models of diabetes. The precise mechanisms whereby FGF-21 regulates metabolism remain to be determined. Here we describe the early signaling events triggered by FGF-21 treatment of 3T3-L1 adipocytes and reveal a functional interplay between FGF-21 and peroxisome proliferator-activated receptor gamma (PPARgamma) pathways that leads to a marked stimulation of glucose transport. While the early actions of FGF-21 on 3T3-L1 adipocytes involve rapid accumulation of intracellular calcium and phosphorylation of Akt, GSK-3, p70(S6K), SHP-2, MEK1/2, and Stat3, continuous treatment for 72 h induces an increase in PPARgamma protein expression. Moreover, chronic activation of the PPARgamma pathway in 3T3-L1 adipocytes with the PPARgamma agonist and anti-diabetic agent, rosiglitazone (BRL 49653), enhances FGF-21 action to induce tyrosine phosphorylation of FGF receptor-2. Strikingly, treatment of cells with FGF-21 and rosiglitazone in combination leads to a pronounced increase in expression of the GLUT1 glucose transporter and a marked synergy in stimulation of glucose transport. Together these results reveal a novel synergy between two regulators of glucose homeostasis, FGF-21 and PPARgamma, and further define FGF-21 mechanism of action.
The nanogranular origin of friction and cohesion in shale—A strength homogenization approach to interpretation of nanoindentation results (2010)

Abstract An inverse micromechanics approach allows interpretation of nanoindentation results to deliver cohesive‐frictional strength behavior of the porous clay binder phase in shale. A recently developed strength homogenization model, using the Linear Comparison Composite approach, considers porous clay as a granular material with a cohesive‐frictional solid phase. This strength homogenization model is employed in a Limit Analysis Solver to study indentation hardness responses and develop scaling relationships for indentation hardness with clay packing density. Using an inverse approach for nanoindentation on a variety of shale materials gives estimates of packing density distributions within each shale and demonstrates that there exists shale‐independent scaling relations of the cohesion and of the friction coefficient that vary with clay packing density. It is observed that the friction coefficient, which may be interpreted as a degree of pressure‐sensitivity in strength, tends to zero as clay packing density increases to one. In contrast, cohesion reaches its highest value as clay packing density increases to one. The physical origins of these phenomena are discussed, and related to fractal packing of these nanogranular materials. Copyright © 2010 John Wiley &amp; Sons, Ltd.
Ultrafast image transmission by optical time-to-two-dimensional-space-to-time-to-two-dimensional-space conversion (1999)

We propose an optical time-to-two-dimensional (2-D)-space-to-time-to-2-D-space conversion technique for ultrafast image transmission with ultrashort-pulse lasers. The proposed technique is based on the concepts of the time–space transform, the spatial time–frequency transform, and their inverses. We describe and analyze the proposed technique for ultrafast all-optical processors that can convert an input 2-D spatial object into a modulated ultrafast optical pulse sequence and can retrieve the original 2-D spatial image from the temporal signals transmitted through the optical fiber channel with ultrahigh bandwidth. To verify the proposed technique, we report preliminary experimental results.
Sound-resonance hydrogen sensor (2003)

A hydrogen sensor is reported in which a small piezoelectric-sound-resonance-cavity (PSRC) is used as the sensing element. Detection utilizes sound resonance and acoustic property differences between H2 and air as a sensing mechanism. Changes in H2 concentration result in a shift of the sound-resonance state of the PSRC. Preliminary experiments have demonstrated a sensitivity limit of 8 ppm, a fast response time ∼1.5 second, and detection capabilities over a broad concentration range 10−5&amp;lt;n&amp;lt;0.2.
Functional analysis of the Bunyamwera orthobunyavirus Gc glycoprotein (2009)

The virion glycoproteins Gn and Gc of Bunyamwera orthobunyavirus (family Bunyaviridae) are encoded by the M RNA genome segment and have roles in both viral attachment and membrane fusion. To investigate further the structure and function of the Gc protein in viral replication, we generated 12 mutants that contain truncations from the N terminus. The effects of these deletions were analysed with regard to Golgi targeting, low pH-dependent membrane fusion, infectious virus-like particle (VLP) formation and virus infectivity. Our results show that the N-terminal half (453 residues) of the Gc ectodomain (909 residues in total) is dispensable for Golgi trafficking and cell fusion. However, deletions in this region resulted in a significant reduction in VLP formation. Four mutant viruses that contained N-terminal deletions in their Gc proteins were rescued, and found to be attenuated to different degrees in BHK-21 cells. Taken together, our data indicate that the N-terminal half of the Gc ectodomain is dispensable for replication in cell culture, whereas the C-terminal half is required to mediate cell fusion. A model for the domain structure of the Gc ectodomain is proposed.
Query optimization in compressed database systems (2001)

Over the last decades, improvements in CPU speed have outpaced improvements in main memory and disk access rates by orders of magnitude, enabling the use of data compression techniques to improve the performance of database systems. Previous work describes the benefits of compression for numerical attributes, where data is stored in compressed format on disk. Despite the abundance of string-valued attributes in relational schemas there is little work on compression for string attributes in a database context. Moreover, none of the previous work suitably addresses the role of the query optimizer: During query execution, data is either eagerly decompressed when it is read into main memory, or data lazily stays compressed in main memory and is decompressed on demand only
An SRAM-programmable field-configurable memory (2002)

This paper describes the design and implementation of an SRAM-Programmable Field-Configurable Memory (FCM), which has the flexibility to form over two hundred different memory configurations, each with up to four individual memories. The prototype Field-Configurable Memory has four 1 Kb memory blocks, each of which can be configured into four different aspect ratios. It requires just 40 configuration bits and is only 38% larger and 46% slower than the ASIC memory upon which it is based. User memories implemented on this chip require from 16 to 23 times less area than if they were implemented on a Xilinx 4000 series memory architecture. Although this is a standalone FCM implementation, the design can be embedded as part of an FPGA.