gebhart/patrepeval huggingface dataset:
An interactive Landscape for Creativity and Innovation (1999)

We describe the i-LAND environment which constitutes an example of our vision of the workspaces of the future, in this case supporting cooperative work of dynamic teams with changing needs. i-LAND requires and provides new forms of human-computer interaction and new forms of computer-supported cooperative work. Its design is based on an integration of information and architectural spaces, implications of new work practices and an empirical requirements study informing our design. i-LAND consists of several ‘roomware’ components, i.e. computer-augmented objects integrating room elements with information technology. We present the current realization of i-LAND in terms of an interactive electronic wall, an interactive table, two computer-enhanced chairs, and two “bridges” for the Passage-mechanism. This is complemented by the description of the creativity support application and the technological infrastructure. The paper is accompanied by a video figure in the CHI’99 video program.
BSA treatment to enhance enzymatic hydrolysis of cellulose in lignin containing substrates (2006)

Cellulase and bovine serum albumin (BSA) were added to Avicel cellulose and solids containing 56% cellulose and 28% lignin from dilute sulfuric acid pretreatment of corn stover. Little BSA was adsorbed on Avicel cellulose, while pretreated corn stover solids adsorbed considerable amounts of this protein. On the other hand, cellulase was highly adsorbed on both substrates. Adding a 1% concentration of BSA to dilute acid pretreated corn stover prior to enzyme addition at 15 FPU/g cellulose enhanced filter paper activity in solution by about a factor of 2 and beta-glucosidase activity in solution by about a factor of 14. Overall, these results suggested that BSA treatment reduced adsorption of cellulase and particularly beta-glucosidase on lignin. Of particular note, BSA treatment of pretreated corn stover solids prior to enzymatic hydrolysis increased 72 h glucose yields from about 82% to about 92% at a cellulase loading of 15 FPU/g cellulose or achieved about the same yield at a loading of 7.5 FPU/g cellulose. Similar improvements were also observed for enzymatic hydrolysis of ammonia fiber explosion (AFEX) pretreated corn stover and Douglas fir treated by SO(2) steam explosion and for simultaneous saccharification and fermentation (SSF) of BSA pretreated corn stover. In addition, BSA treatment prior to hydrolysis reduced the need for beta-glucosidase supplementation of SSF. The results are consistent with non-specific competitive, irreversible adsorption of BSA on lignin and identify promising strategies to reduce enzyme requirements for cellulose hydrolysis.
Algorithms for macromolecular dynamics and constraint dynamics (1977)

The application of the computer simulation method of molecular dynamics to macromolecules is investigated. The protein trypsin inhibitor (BPTI), consisting of 454 united atoms, is used as an example. Different algorithms for integrating the equations of motion are compared, both theoretically and in practice. It is examined to what extent the chain structure of a macromolecule allows a reduction of the computational effort by the introduction of constraints in the dynamics of the chain. A calculational scheme is proposed, by which constraints can be incorporated in predictor-corrector algorithms. The optimum choice of an algorithm depends on the desired accuracy of the solution and on the character of the forces acting on the molecule, viz. whether these are noisy or not. For nonconstraint dynamics a Gear predictor-corrector algorithm yields the best results, whereas for constraint dynamics the Gear and Verlet algorithms produce comparable results. The application of bond-length constraints reduces the required computer time by a factor of 3. The inclusion of bondangle constraints is not recommended.
NF-kappa B-mediated chromatin reconfiguration and transcriptional activation of the HIV-1 enhancer in vitro. (1996)

NF-kappa B is a potent inducible transcription factor that regulates many genes in activated T cells. In this report we examined the ability of different subunits of NF-kappa B to enhance HIV-1 transcription in vitro with chromatin templates. We find that the p65 subunit of NF-kappa B is a strong transcriptional activator of nucleosome-assembled HIV-1 DNA, whereas p50 does not activate transcription, and that p65 activates transcription synergistically with Sp1 and distal HIV-1 enhancer-binding factors (LEF-1, Ets-1, and TFE-3). These effects were observed with chromatin, but not with nonchromatin templates. Furthermore, binding of either p50 or p65 with Sp1 induces rearrangement of the chromatin to a structure that resembles the one reported previously for integrated HIV-1 proviral DNA in vivo. These results suggest that p50 and Sp1 contribute to the establishment of the nucleosomal arrangement of the uninduced provirus in resting T cells, and that p65 activates transcription by recruitment of the RNA polymerase II transcriptional machinery to the chromatin-repressed basal promoter.
Extended Scope of Dirhodium(II)-Catalysed Enantioselective Intramolecular 1,3-Dipolar Cycloadditions of Carbonyl Ylides with Alkene and Alkyne Dipolarophiles (2002)

Catalytic enantioselective tandem carbonyl ylide formation-intramolecular 1,3-dipolar cycloaddition reactions of 2-diazo-3,6-diketoesters show promising scope in terms of asymmetric induction as the tethered alkene/alkyne dipolarophile component is varied.
Introduction to Physics in Modern Medicine (2002)

The medical applications of physics are not typically covered in introductory physics courses. Introduction to Physics in Modern Medicine fills that gap by explaining the physical principles behind technologies such as surgical lasers or computed tomography (CT or CAT) scanners. Each chapter includes a short explanation of the scientific background, making this book highly accessible to those without an advanced knowledge of physics. It is intended for medicine and health studies students who need an elementary background in physics, but it also serves well as a non-mathematical introduction to applied physics for undergraduate students in physics, engineering, and other disciplines.
Polyisobutylene‐based segmented polyureas. I. Synthesis of hydrolytically and oxidatively stable polyureas (2008)

Abstract Novel segmented polyurea elastomers containing soft polyisobutylene (PIB) segments were synthesized and characterized. The key ingredient, primary amine‐telechelic PIB oligomers (NH 2 ‐PIB‐NH 2 ) with number average molecular weights of 2500 and 6200 g/mol were synthesized. PIB‐based polyureas were prepared by using various aliphatic diisocyanates and diamine chain extenders with hard segment contents between 9.5 and 46.5% by weight. All copolymers displayed microphase morphologies as determined by dynamic mechanical analysis. Tensile strengths of nonchain‐extended and chain‐extended polyureas showed a linear dependence on the urea hard segment content. PIB‐based polyureas prepared with NH 2 ‐PIB‐NH 2 of M n = 2500 g/mol, 4,4′‐methylendbis(cyclohexylisocyantate), and 1,6‐diaminohexane containing 45% hard segment exhibited 19.5 MPa tensile strength which rose to 23 MPa upon annealing at 150 °C for 12 h. With increasing hard segment content, elongation at break decreased from ∼ 450% to a plateau of 110%. The hydrolytic and oxidative stability of PIB‐based polyureas were unprecedented. Although commercial “oxidatively resistant” thermoplastic polyurethanes degraded severely upon exposure to boiling water or concentrated nitric acid, the experimental polyureas survived without much degradation in properties. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 38–48, 2009
Shogaols from Zingiber officinale Protect IMR32 Human Neuroblastoma and Normal Human Umbilical Vein Endothelial Cells from β-Amyloid(25 - 35) Insult (2002)

From the rhizome of Zingiber officinale L. (Zingiberaceae), four shogaols that protect IMR32 human neuroblastoma and normal human umbilical vein endothelial cells from beta-amyloid(25 - 35) insult at EC50 = 4.5 - 81 microM were isolated. The efficacy of cell protection from beta-amyloid(25 - 35) insult by these shogaols was shown to improve as the length of the side chain increases.
Molecular cloning, nucleotide sequencing, and expression of the Bacillus subtilis (natto) IAM1212 alpha-amylase gene, which encodes an alpha-amylase structurally similar to but enzymatically distinct from that of B. subtilis 2633 (1990)

An alpha-amylase gene of Bacillus subtilis (natto) IAM1212 was cloned in a lambda EMBL3 bacteriophage vector, and the nucleotide sequence was determined. An open reading frame encoding the alpha-amylase (AMY1212) consists of 1,431 base pairs and contains 477 amino acid residues, which is the same in size as the alpha-amylase (AMY2633) of B. subtilis 2633, an alpha-amylase-hyperproducing strain, and smaller than that of B. subtilis 168, Marburg strain. The amino acid sequence of AMY1212 is different from that of AMY2633 at five residues. Enzymatic properties of these two alpha-amylases were examined by introducing the cloned genes into an alpha-amylase-deficient strain, B. subtilis M15. It was revealed that products of soluble starch hydrolyzed by AMY1212 are maltose and maltotriose, while those of AMY2633 are glucose and maltose. From the detailed analyses with oligosaccharides as substrates, it was concluded that the difference in hydrolysis products of the two similar alpha-amylases should be ascribed to the different activity hydrolyzing low-molecular-weight substrates, especially maltotriose; AMY1212 slowly hydrolyzes maltotetraose and cannot hydrolyze maltotriose, while AMY2633 efficiently hydrolyzes maltotetraose and maltotriose. Further analyses with chimeric alpha-amylase molecules constructed from the cloned genes revealed that only one amino acid substitution is responsible for the differences in hydrolysis products.
Inflammatory Cytokine Regulation of Fas-mediated Apoptosis in Thyroid Follicular Cells (1999)

The occurrence of apoptosis in thyroid follicular cells induced by Fas activation has been a subject of much debate. This is due, in part, to the fact that no physiologically relevant treatment conditions have been reported to cause rapid and extensive Fas-mediated apoptosis in thyroid cells, whereas treatment with the protein synthesis inhibitor cycloheximide prior to Fas activation allows for massive cell death. This indicates that the Fas signaling pathway is present but that its function is blocked in the overwhelming majority of cultured thyroid cells. To reconcile the conflicting reports, we set out to identify physiologically relevant conditions in which rapid, massive thyroid cell apoptosis in response to Fas activation could be demonstrated. We determined that susceptibility to Fas-activated apoptosis could be influenced by certain combinations of inflammatory cytokines. Although no single cytokine was effective, pretreatment of thyroid cells with the combination of gamma-interferon and either tumor necrosis factor-alpha or interleukin 1beta allowed for massive Fas-mediated apoptosis. Susceptibility to Fas-induced death correlated with an increase in expression of a tunicamycin-inhibitable high molecular weight form of Fas but not with aggregate expression of Fas.
A Clinical Trial of Vena Caval Filters in the Prevention of Pulmonary Embolism in Patients with Proximal Deep-Vein Thrombosis (1998)

In high-risk patients with proximal deep-vein thrombosis, the initial beneficial effect of vena caval filters for the prevention of pulmonary embolism was counterbalanced by an excess of recurrent deep-vein thrombosis, without any difference in mortality. Our data also confirmed that low-molecular-weight heparin was as effective and safe as unfractionated heparin for the prevention of pulmonary embolism.
Efficient Organic Electrophosphorescent White‐Light‐Emitting Device with a Triple Doped Emissive Layer (2004)

An organic electrophosphorescent white‐light‐emitting device (see Figure) containing green, red, and blue emitters doped into a 9 nm thick wide‐bandgap material is shown to attain a maximum forward viewing power efficiency of (26±3) lm W –1 . The high power efficiency is attributed to the efficient confinement of excitons and charge within the emissive layer, a thin emissive layer, and highly efficient blue electrophosphorescent dopant.
Cryptococcal Meningitis and AIDS (1993)

Dr. William G. Powderly provides a comprehensive review of the state of our knowledge regarding cryptococcal infection in persons with infection due to human immunodeficiency virus type 1. The introduction of fluconazole and itraconazole increased insight into prognostic factors affecting these patients. The need to suppress this fungal infection in individuals with impaired immunity has greatly altered the management of cryptococcal meningitis; therapy for this condition was established by the landmark study conducted by the Mycosis Study Group in 1979 (Bennett JE, Dismukes WE, Duma RJ, et al. A comparison of amphotericin B alone and combined with flucytosine in treatment of cryptococcal meningitis. N Engl J Med 1979;301:126-31). In this AIDS commentary Dr. Powderly clearly outlines the progress made through clinical investigations and the problems that remain to be resolved.
DNA double-strand breaks measured in individual cells subjected to gel electrophoresis. (1991)

Microscopic examination of individual mammalian cells embedded in agarose, subjected to electrophoresis, and stained with a fluorescent DNA-binding dye provides a novel way of measuring DNA damage and more importantly, of assessing heterogeneity in DNA damage within a mixed population of cells. With this method, DNA double-strand breaks can be detected in populations of cells exposed to X-ray doses as low as 5 Gy. The radiation dose-response relationship for initial formation of double-strand breaks was identical for cell lines irradiated in G1, regardless of their sensitivity to killing by ionizing radiation. However, for cells irradiated in S phase, DNA migration was significantly reduced. For Chinese hamster V79 cells, Chinese hamster ovary cells, WiDr human colon carcinoma cells, and L5178Y-R mouse lymphoblastoid cells, S-phase DNA appeared to be about 3 times less sensitive to X-ray damage than DNA from other phases of the cell cycle. However, for the very radiosensitive L5178Y-S cells, the migration of replicating DNA was reduced only slightly. For Chinese hamster V79 and Chinese hamster ovary cells, damage was repaired at a similar rate in all cells of the population, and 85% of the breaks were rejoined within 2 h after irradiation. The radiosensitive L5178Y-S cells repaired damage more slowly than V79 or Chinese hamster ovary cells; 2 h after exposure to 50 Gy, approximately 50% of the damage was still present.
Viral Persistence in Neurons Explained by Lack of Major Histocompatibility Class I Expression (1991)

Viruses frequently persist in neurons, suggesting that these cells can evade immune surveillance. In a mouse model, 5 × 10 6 cytotoxic T lymphocytes (CTLs), specific for lymphocytic choriomeningitis virus (LCMV), did not lyse infected neurons or cause immunopathologic injury. In contrast, intracerebral injection of less than 10 3 CTL caused disease and death when viral antigens were expressed on leptomeningial and choroid plexus cells of the nervous system. The neuronal cell line OBL21 expresses little or no major histocompatibility (MHC) class I surface glycoproteins and when infected with LCMV, resisted lysis by virus-specific CTLs. Expression of MHC heavy chain messenger RNA was limited, but β 2 -microglobulin messenger RNA and protein was made normally. OBL21 cells were made sensitive to CTL lysis by transfection with a fusion gene encoding another MHC class I molecule. Hence, neuronal cells probably evade immune surveillance by failing to express MHC class I molecules.
Review of methodological developments in laser Doppler flowmetry (2008)

Laser Doppler flowmetry is a non-invasive method of measuring microcirculatory blood flow in tissue. In this review the technique is discussed in detail. The theoretical and experimental developments to improve the technique are reviewed. The limitations of the method are elaborated upon, and the research done so far to overcome these limitations is critically assessed.
A versatile transgenic allele for mouse overexpression studies (2015)

For the analysis of gene function in vivo, gene overexpression in the mouse provides an alternative to loss-of-function knock-out approaches and can help reveal phenotypes where compensatory mechanisms are at play. Furthermore, when multiple lines overexpressing a gene-of-interest at varying levels are studied, the consequences of differences in gene dosage can be explored. Despite these advantages, inherent shortcomings in the methodologies used for the generation of gain-of-function transgenic mouse models have limited their application to functional gene analysis, and the necessity for multiple lines comes at a significant animal and financial cost. The targeting of transgenic overexpression constructs at single copy into neutral genomic loci is the preferred method for the generation of such models, which avoids the unpredictable outcomes associated with conventional random integration. However, despite the increased reliability that targeted transgenic methodologies provide, only one expression level results, as defined by the promoter used. Here, we report a new versatile overexpression allele, the promoter-switch allele, which couples PhiC31 integrase-targeted transgenesis with Flp recombinase promoter switching and Cre recombinase activation. These recombination switches allow the conversion of different overexpression alleles, combining the advantages of transgenic targeting with tunable transgene expression. With this approach, phenotype severity can be correlated with transgene expression in a single mouse model, providing a cost-effective solution amenable to systematic gain-of-function studies.
Treatment of Anemia Progression via Magnetite and Folate NanoparticlesIn Vivo (2014)

Iron deficiency anemia is a major global public health problem. Food fortification with iron (Fe) can be an effective strategy to control iron deficiency. An iron oxide nanoparticle (NP) is a new physical and chemical property form. These properties (small particle size, unique physical properties) make nanoiron a great scientific interest especially in the treatment of anemia. The study aimed to reduce anemia by nanoparticles (NPs). Forty-eight adult female Sprague-Dewily rats were divided into four groups (12 rats each). Group A represented a negative control. Other groups were fed standard diet iron free and three time of require zinc to reach anemic. Group B fed standard diet with ferrous sulfate until the improvement of the situation of anemia or for 8 weeks. Groups C and D were divided into three subgroups; each subgroup was fed a dose from magnetite or folate coated magnetite NPs. Results showed that symptoms of loss of appetite and severe lethargy demonstrate that magnetite and folate-coated magnetite nanoparticles have serious toxicological effects in vivo . Some doses from NPs improve blood picture during 2 weeks but change in histopathology examinations were occur in some groups within 2 weeks. Nanoparticles were considered the toxicological hazards especially the size of less than 54 nm.
Characterization of enzymatically synthesized structured lipids containing eicosapentaenoic, docosahexaenoic, and caprylic acids (1998)

Abstract Structured lipids (SL) containing n‐3 polyunsaturated (eicosapentaenoic or docosahexaenoic) and mediumchain (caprylic) fatty acids were synthesized in gram quantities and characterized. Tricaprylin was mixed with n‐3‐rich polyunsaturated fatty acids in a 1:2 molar ratio and transesterified by incubating at 55°C in hexane with SP 435 lipase (10% by wt of total substrates) in a 125‐mL Erlenmeyer flask as the bioreactor. After several batches of reaction, the products were pooled and hexane was evaporated. Short‐path distillation was used for purification of synthesized SL. The distillation conditions were 1.1 Torr and 170°C at a feed flow rate of 3 mL/min. Up to 240 g of SL was isolated and deacidified by alkaline extraction or ethanol‐water solvents. The fatty acid profile, free fatty acid value, saponification number, iodine value, peroxide value, thiobarbituric acid, and conjugated diene contents were determined. Oxidation stability, with α‐tocopherol as antioxidant, and the oxidative stability index were also determined.
Techniques for single molecule sequencing (1997)

A method is described that demonstrates a new technique for rapid and high-throughput single molecule sequencing. This sequencing technique is based on the successive enzymatic degradation of fluorescently labeled single DNA molecules, and the detection and identification of the released monomer molecules according to their sequential order in a microstructured channel. The detection technique is evolved from confocal fluorescence microscopy, with two different laser sources to excite the individual mononucleotides that are either labeled with tetramethylrhodamine (TMR) or Cyanine5 (Cy5). The handling of DNA which is immobilized on carrier beads, and the detection of the cleaved monomers is performed in optically transparent and biochemically inert microstructures (glass or PMMA) with detection channels of 7 μ × 10 μm. The projected rate of sequencing is ≈100 bases min−1, dependent solely on the rate of the enzymatic DNA cleavage.
Graphene-Based Chemical Sensors (2012)

Pioneering research in 2004 by Geim and Novoselov (2010 Nobel Prize winners in Physics) of the University of Manchester led to the isolation of a monolayer graphene sheet. Graphene is a single-atom-thick sheet of sp(2) hybridized carbon atoms that are packed in a hexagonal honeycomb crystalline structure. Graphene is the fundamental building block of all sp(2) carbon materials including single-walled carbon nanotubes, mutliwalled carbon nanotubes, and graphite and is therefore interesting from the fundamental standpoint as well as for practical applications. One of the most promising applications of graphene that has emerged so far is its utilization as an ultrasensitive chemical or gas sensor. In this article, we review some of the significant work performed with graphene and its derivatives for gas detection and provide a perspective on the challenges that need to be overcome to enable commercially viable graphene chemical sensor technologies.