gebhart/patrepeval huggingface dataset:
A Potentially Valuable Advance in the Synthesis of Carbohydrate-Based Anticancer Vaccines through Extended Cycloaddition Chemistry (2006)

An advance in the long-term problem of joining complex oligosaccharides to polypeptides and even proteins is described herein. The key method involves equipping the oligosaccharide sector with an azide and the polypeptide with pendant alkynyl functionality. The two sectors are joined through a "click-like" cycloaddition. The method encompasses oligosaccharide constructs with several azide linkages which undergo concurrent cycloaddition to peptide-based acetylenes. This technology could well prove to be useful in the construction of fully synthetic vaccines.
A ferroelectric transparent thin-film transistor (1996)

Operation is demonstrated of a field-effect transistor made of transparant oxidic thin films, showing an intrinsic memory function due to the usage of a ferroelectric insulator. The device consists of a high mobility Sb-doped n-type SnO2 semiconductor layer, PbZr0.2Ti0.8O3 as a ferroelectric insulator, and SrRuO3 as a gate electrode, each layer prepared by pulsed laser deposition. The hysteresis behavior of the channel conductance is studied. Using gate voltage pulses of 100 μs duration and a pulse height of ±3 V, a change of a factor of two in the remnant conductance is achieved. The dependence of the conductance on the polarity of the gate pulse proves that the memory effect is driven by the ferroelectric polarization. The influence of charge trapping is also observed and discussed.
Production of natural killer cell stimulatory factor (interleukin 12) by peripheral blood mononuclear cells. (1992)

Natural killer cell stimulatory factor (NKSF), or interleukin 12 (IL-12), is a 70-kD heterodimeric cytokine composed of two covalently linked chains, p40 and p35. NKSF/IL-12 has multiple effects on T and NK cells and was originally identified and purified from the supernatant fluid of Epstein-Barr virus (EBV)-transformed human B lymphoblastoid cell lines. We have produced a panel of monoclonal antibodies against both chains of NKSF/IL-12. Some of these antibodies have neutralizing activity, and several combinations of them have been used to establish sensitive radioimmunoassays detecting the free p40 chain, the free p35 chain, or the p70 heterodimer. Using these reagents, we have determined that most EBV-transformed human B lymphoblastoid cell lines constitutively produce low levels of the p70 heterodimer and an excess of the free p40 chain, whereas Burkitt lymphoma-derived, T, myeloid, and many solid tumor-derived cell lines produce neither. Production of both p40 and p70 is increased several-fold upon stimulation of the EBV-transformed cell lines with phorbol diesters. The ability of supernatant fluids from unstimulated and phorbol diester-stimulated cell lines to induce interferon gamma (IFN-gamma) production from T and NK cells, one of the effects of NKSF/IL-12, parallels the levels of production of the p70 heterodimer, known to be the biologically active form of NKSF/IL-12. Staphylococcus aureus Cowan I strain (SAC) and other stimuli induce accumulation of p40 mRNA and production of both p40 and p70 by peripheral blood mononuclear cells (PBMC). The producer cells appear to include both adherent cells and nonadherent lymphocytes, possibly B cells. The supernatant fluids from SAC-stimulated PBMC mediate the typical functions of NKSF/IL-12 (i.e., IFN-gamma induction, mitogenic effects on T/NK blasts, enhancement of NK cell cytotoxicity) at concentrations of p70 similar to those at which recombinant NKSF/IL-12 mediates the same functions. Moreover, these activities are significantly inhibited by anti-NKSF/IL-12 antibodies. The neutralizing anti-NKSF/IL-12 antibodies also inhibit 85% of the IFN-gamma production in response to SAC, an NKSF/IL-12 inducer, and approximately 50% of the IFN-gamma production in response to non-NKSF/IL-12-inducers such as IL-2, phytohemagglutinin, and anti-CD3 antibodies. These results indicate that induced or constitutively produced NKSF/IL-12 has a major role in facilitating IFN-gamma production by peripheral blood lymphocytes.(ABSTRACT TRUNCATED AT 400 WORDS)
Selective epitaxial growth techniques to integrate high-quality germanium on silicon (2011)

High-quality Ge-on-Si heterostructures have been actively pursued for many advanced applications, including near-infrared photodetectors, high-mobility field effect transistors, and virtual substrates for integrating III-V multijunction solar cells. However, growing epitaxial Ge on Si poses many engineering challenges, ranging from lattice mismatch, to thermal expansion coefficient mismatch, to non-planar morphological evolution. The lattice mismatch between Ge and Si often leads to a high density of threading dislocations. These dislocations, if not reduced, propagate through the subsequently grown GaAs layer, deteriorating its quality. To overcome these engineering challenges, we have developed three different approaches based on molecular beam epitaxy to significantly reduce, manage, or eliminate the defects in Ge films grown on Si. The first approach involves the nucleation of Ge islands within nanoscale windows in a thin layer of chemically grown SiO2 and successive island coalescence over the SiO2 to form a continuous film. Nanoscale contact areas between Ge and Si effectively relieve the lattice mismatch stress between Ge/Si so that dislocations do not nucleate. We observe that annealing the nucleated islands prior to full coalescence also leads to Ge films that are free of defects, along with significant improvement in GaAs integrated on Ge. The second approach involves trapping dislocations in Ge between high aspect ratio walls of SiO2. Defects form during coalescence of Ge from adjacent channels and at the corners of the SiO2 walls due to stress resulting from differences in thermal expansion coefficients of Ge, Si, and SiO2. The third approach involves filling etch pits, which reveal dislocations, with SiO2 and subsequent Ge growth over SiO2. The filling prevents dislocations in the lower Ge layer from propagating into the upper Ge layer. The third method reduces the defect density from 2.8 × 108 cm-2 to 9.1 × 10 6 cm-2, and is proven to be the most effective at reducing the defects in epitaxial growth of Ge on Si. We expect that our engineering approaches may finally resolve a longstanding engineering challenge in heteroepitaxy, finally providing the cost reduction needed for widespread commercialization of multijunction solar cells, light-emitting diodes, and high-mobility transistors on Si substrates.
Cancer-linked targets modulated by curcumin. (2012)

In spite of major advances in oncology, the World Health Organization predicts that cancer incidence will double within the next two decades. Although it is well understood that cancer is a hyperproliferative disorder mediated through dysregulation of multiple cell signaling pathways, most cancer drug development remains focused on modulation of specific targets, mostly one at a time, with agents referred to as "targeted therapies," "smart drugs," or "magic bullets." How many cancer targets there are is not known, and how many targets must be attacked to control cancer growth is not well understood. Although more than 90% of cancer-linked deaths are due to metastasis of the tumor to vital organs, most drug targeting is focused on killing the primary tumor. Besides lacking specificity, the targeted drugs induce toxicity and side effects that sometimes are greater problems than the disease itself. Furthermore, the cost of some of these drugs is so high that most people cannot afford them. The present report describes the potential anticancer properties of curcumin, a component of the Indian spice turmeric (Curcuma longa), known for its safety and low cost. Curcumin can selectively modulate multiple cell signaling pathways linked to inflammation and to survival, growth, invasion, angiogenesis, and metastasis of cancer cells. More clinical trials of curcumin are needed to prove its usefulness in the cancer setting.
Experimental and Computational Assessment of Conditionally Essential Genes inEscherichia coli (2006)

Genome-wide gene essentiality data sets are becoming available for Escherichia coli, but these data sets have yet to be analyzed in the context of a genome scale model. Here, we present an integrative model-driven analysis of the Keio E. coli mutant collection screened in this study on glycerol-supplemented minimal medium. Out of 3,888 single-deletion mutants tested, 119 mutants were unable to grow on glycerol minimal medium. These conditionally essential genes were then evaluated using a genome scale metabolic and transcriptional-regulatory model of E. coli, and it was found that the model made the correct prediction in approximately 91% of the cases. The discrepancies between model predictions and experimental results were analyzed in detail to indicate where model improvements could be made or where the current literature lacks an explanation for the observed phenotypes. The identified set of essential genes and their model-based analysis indicates that our current understanding of the roles these essential genes play is relatively clear and complete. Furthermore, by analyzing the data set in terms of metabolic subsystems across multiple genomes, we can project which metabolic pathways are likely to play equally important roles in other organisms. Overall, this work establishes a paradigm that will drive model enhancement while simultaneously generating hypotheses that will ultimately lead to a better understanding of the organism.
Ultra rigid cross-bridged tetraazamacrocycles as ligands—the challenge and the solution (1998)

The challenge to metal ion binding that is represented by the proton-sponge nature of two-carbon cross-bridged tetraazamacrocycles has been overcome and a general method developed for the synthesis of their transiton, and other, metal complexes; these ultra-rigid ligands form complexes having remarkable kinetic stabilities.
DNA vaccines: are they still just a powerful tool for the future? (2007)

Vaccination is historically one of the most successful strategies for the prevention of infectious diseases. For safety reasons, modern vaccinology tends toward the usage of inactivated or attenuated microorganisms and uses predominantly subunit vaccines. The antigens need to be clearly defined, pure, stable, appropriately composed, and properly presented to the immune system of the host. Differing ratios of various proportions between specific CD4+ and CD8+ T cell responses are essential for conferring the required protection in the case of individual vaccines. To stimulate both CD4+ and CD8+ T cells, the antigens must be processed and presented to both antigen-presentation pathways, MHC I and MHC II. Protein antigens delivered by vaccination are processed as extracellular antigens. However, extracellularly delivered antigen can be directed towards intracellular presentation pathways in conjugation with molecules involved in antigen cross-presentation, e.g. heat shock proteins, or by genomic-DNA vaccination. In this overview, current knowledge of the host immune response to DNA vaccines is summarized in the introduction. The subsequent sections discuss techniques for enhancing DNA vaccine efficacy, such as DNA delivery to specific tissues, delivery of DNA to the cell cytoplasm or nucleus, and enhancement of the immune response using molecular adjuvants. Finally, the prospects of DNA vaccination and ongoing clinical trials with various DNA vaccines are discussed.
Cell Wall Architecture of the Elongating Maize Coleoptile (2001)

The primary walls of grasses are composed of cellulose microfibrils, glucuronoarabinoxylans (GAXs), and mixed-linkage beta-glucans, together with smaller amounts of xyloglucans, glucomannans, pectins, and a network of polyphenolic substances. Chemical imaging by Fourier transform infrared microspectroscopy revealed large differences in the distributions of many chemical species between different tissues of the maize (Zea mays) coleoptile. This was confirmed by chemical analyses of isolated outer epidermal tissues compared with mesophyll-enriched preparations. Glucomannans and esterified uronic acids were more abundant in the epidermis, whereas beta-glucans were more abundant in the mesophyll cells. The localization of beta-glucan was confirmed by immunocytochemistry in the electron microscope and quantitative biochemical assays. We used field emission scanning electron microscopy, infrared microspectroscopy, and biochemical characterization of sequentially extracted polymers to further characterize the cell wall architecture of the epidermis. Oxidation of the phenolic network followed by dilute NaOH extraction widened the pores of the wall substantially and permitted observation by scanning electron microscopy of up to six distinct microfibrillar lamellae. Sequential chemical extraction of specific polysaccharides together with enzymic digestion of beta-glucans allowed us to distinguish two distinct domains in the grass primary wall. First, a beta-glucan-enriched domain, coextensive with GAXs of low degrees of arabinosyl substitution and glucomannans, is tightly associated around microfibrils. Second, a GAX that is more highly substituted with arabinosyl residues and additional glucomannan provides an interstitial domain that interconnects the beta-glucan-coated microfibrils. Implications for current models that attempt to explain the biochemical and biophysical mechanism of wall loosening during cell growth are discussed.
Prodrugs of anthracyclines for chemotherapy via enzyme-monoclonal antibody conjugates. (1994)

New prodrugs of daunorubicin, 1c, 1e and 2c, including a galactopyranosyl residue linked to the N-3' of the daunosaminyl moiety through substituted o- or p-benzyloxycarbonyl groups were synthesized. Their low cytotoxicity and high stability in plasma fulfil the conditions for antibody-directed enzyme prodrug therapy (ADEPT). Enzymatic hydrolysis using alpha-D-galactosidase gives rise to daunorubicin by subsequent self-elimination of the spacers. However, elimination clearly depends on the aromatic substitution pattern, as demonstrated especially by comparison with non-substituted analogues.
Beta-amyloid secretases and beta-amloid degrading enzyme expression in lens. (2003)

BACE, BACE2, Nicastrin and NEP are expressed primarily in elongating peripheral fiber cells, overlapping with Notch, Presenilin, and AbetaPP protein distribution in lens, consistent with their role in regulating Notch and AbetaPP ectodomain shedding in lens. Lens expression of beta- and gamma-secretases together with NEP suggests these proteins may also regulate Abeta turnover in the lens. The presence of Abeta processing and degrading proteases in lens provides further evidence that Alzheimer-related cell biology is fundamentally involved in lens development, and provides additional evidence that mechanisms of Alzheimer pathophysiology can contribute to lens degeneration, suggesting further that therapeutics targeting Abeta proteases may be applicable to lens degenerative disease.
The porphyrin pigmentation of subspecies of Bacteroides melaninogenicus (1979)

Various subspecies of Bacteroides melaninogenicus differ in their pigmentation. Subsp. asaccharolyticus produces protohaem almost exclusively, subsp. intermedicus both protohaem and a smaller proportion of protoporphyrin, and subsp. melaninogenicus mainly protoporphyrin with a trace of protohaem. As a consequence young colonies can be differentiated by their red fluorescence in u.v. light (365nm): subsp. asaccharolyticus does not fluoresce, subsp. intermedicus shows a limited fluorescence, and subsp. melaninogenicus shows a bright fluorescence. The pigments were isolated as the dimethyl esters of protohaemin and of protoporphyrin and identified by electronic spectroscopy, mass spectrometry and comparisons by t.l.c. Incorporation of delta-aminolaevulinate into these pigments was not detected, nor was porphobilinogen formation observed. Subsp. melaninogenicus grown in the presence of [14C]protohaemin formed [14C]protoporphyrin. This appears to represent a novel biological demetallation.
The Formation of Higher Alcohols in the Fermentation of Amino Acids by Yeast (1965)

1.Itwasconfirmed that washedyeastcellsproducedisobutanolandisoamylalcoholfrom pyruvic acid or α-ketoisovaleric acid. 2. These results strengthen the reliability of the postulated scheme of the formation of these two alcohols from puruvic acid proposed by us. 3. Effect of aeration, pH and leucine and ammonium chloride added in the fermenting medium on the formation of isobutanol and isoamyl alcohol was examined.
Cloning and functional expression of a human orthologue of rat vanilloid receptor-1 (2000)

Capsaicin, resiniferatoxin, protons or heat have been shown to activate an ion channel, termed the rat vanilloid receptor-1 (rVR1), originally isolated by expression cloning for a capsaicin sensitive phenotype. Here we describe the cloning of a human vanilloid receptor-1 (hVR1) cDNA containing a 2517 bp open reading frame that encodes a protein with 92% homology to the rat vanilloid receptor-1. Oocytes or mammalian cells expressing this cDNA respond to capsaicin, pH and temperature by generating inward membrane currents. Mammalian cells transfected with human VR1 respond to capsaicin with an increase in intracellular calcium. The human VR1 has a chromosomal location of 17p13 and is expressed in human dorsal root ganglia and also at low levels throughout a wide range of CNS and peripheral tissues. Together the sequence homology, similar expression profile and functional properties confirm that the cloned cDNA represents the human orthologue of rat VR1.
The application and future development of a MEMS SiVS/spl reg/ for commercial and military inertial products (2003)

BAE Systems has been developing Coriolis vibratory gyros for over 15 years. The latest gyro to emerge from this development uses a silicon MEMS sensor, SiVSG/spl reg/. This is an evolutionary development from earlier ceramic cylinder and metal ring VSGs, produced by BAE Systems. SiVSG/spl reg/ is being mass-produced for the commercial and automotive rate sensor market. SiVSG/spl reg/'s immunity to vibration and shock has enabled its application in advanced braking systems on automobiles. BAE Systems has now leveraged the high volumes from the automotive and commercial market to introduce next generation, low cost gyro products into the military and aerospace sectors. BAE Systems is using these SiVSG/spl reg/ as the basis of a family of single-axis rate sensors (SiVSG/spl reg/) and Inertial Measurement Units (SiIMU/spl trade/) that are aimed at defense and aerospace applications. The robust structure of the gyro has allowed it to survive and operate after a 23,000g gun-launch shock. Variants of SiJMU/spl trade/ have been selected for a number of guided missile programs such as the UK Vertical Launch Seawolf Missile system and the US Navy Extended Range Guided Munition (ERGM). This paper describes the performance of SiVSG/spl reg/ technology as applied to SiIMU/spl trade/. Future technology and product development strategy is outlined. The development of a digital gyro drive circuit is described, and its implementation in both a rate integrating gyro (SiRIG/spl trade/) and a variable rate range gyro (SiVRG/spl reg/) for high roll rate platforms. Current and projected performance of SiIMU/spl trade/ is presented, together with the strategy for integration with GPS.
Increased Growth of the Microalga Chlorella vulgaris when Coimmobilized and Cocultured in Alginate Beads with the Plant-Growth-Promoting Bacterium Azospirillum brasilense (2000)

Coimmobilization of the freshwater microalga Chlorella vulgaris and the plant-growth-promoting bacterium Azospirillum brasilense in small alginate beads resulted in a significantly increased growth of the microalga. Dry and fresh weight, total number of cells, size of the microalgal clusters (colonies) within the bead, number of microalgal cells per cluster, and the levels of microalgal pigments significantly increased. Light microscopy revealed that both microorganisms colonized the same cavities inside the beads, though the microalgae tended to concentrate in the more aerated periphery while the bacteria colonized the entire bead. The effect of indole-3-acetic acid addition to microalgal culture prior to immobilization of microorganisms in alginate beads partially imitated the effect of A. brasilense. We propose that coimmobilization of microalgae and plant-growth-promoting bacteria is an effective means of increasing microalgal populations within confined environments.
Base-Pair Resolution DNA Methylation Sequencing Reveals Profoundly Divergent Epigenetic Landscapes in Acute Myeloid Leukemia (2012)

We have developed an enhanced form of reduced representation bisulfite sequencing with extended genomic coverage, which resulted in greater capture of DNA methylation information of regions lying outside of traditional CpG islands. Applying this method to primary human bone marrow specimens from patients with Acute Myelogeneous Leukemia (AML), we demonstrated that genetically distinct AML subtypes display diametrically opposed DNA methylation patterns. As compared to normal controls, we observed widespread hypermethylation in IDH mutant AMLs, preferentially targeting promoter regions and CpG islands neighboring the transcription start sites of genes. In contrast, AMLs harboring translocations affecting the MLL gene displayed extensive loss of methylation of an almost mutually exclusive set of CpGs, which instead affected introns and distal intergenic CpG islands and shores. When analyzed in conjunction with gene expression profiles, it became apparent that these specific patterns of DNA methylation result in differing roles in gene expression regulation. However, despite this subtype-specific DNA methylation patterning, a much smaller set of CpG sites are consistently affected in both AML subtypes. Most CpG sites in this common core of aberrantly methylated CpGs were hypermethylated in both AML subtypes. Therefore, aberrant DNA methylation patterns in AML do not occur in a stereotypical manner but rather are highly specific and associated with specific driving genetic lesions.
Alleviation of Fatty Liver in Dairy Cows with 14-Day Intravenous Infusions of Glucagon (1999)

Twenty multiparous cows were fed additional concentrate during the final 30 d prepartum to cause susceptibility to fatty liver. From 14 to 42 d postpartum, all cows were subjected to a protocol to induce fatty liver and ketosis. To test glucagon as a treatment for fatty liver, either glucagon at 10 mg/d or excipient was infused via the jugular vein from 21 to 35 d postpartum. All cows had fatty liver at 14 d postpartum and became ketonemic and hypoglycemic during the induction of ketosis. Glucagon increased plasma glucose to 142% of that of controls throughout the 14-d treatment. The hypoinsulinemia present in cows with fatty liver was not affected by glucagon. Plasma beta-hydroxybutyrate and nonesterified fatty acids were decreased by glucagon. At 6 d postpartum, liver triacylglycerol averaged 12.9% of liver (wet weight basis). Glucagon had decreased triacylglycerol content of livers by 71% at d 35. Glycogen was 1.0% of the wet weight of livers at 6 d in milk, but it was decreased by glucagon to 0.5% at 2 d after glucagon began. Glycogen then increased in cows treated with glucagon until at 38 d in milk liver glycogen was 3.7% versus 1.6% in controls. Our results document that glucagon decreases the degree of fatty liver in early lactation dairy cows, which also decreases the incidence of ketosis after alleviation of fatty liver.
4 × 4 free-space optical switching using real-time binary phase-only holograms generated by a liquid-crystal display (1991)

Experimental 4 × 4 free-space optical switching is successfully demonstrated by real-time binary phase-only holograms. The real-time holograms are generated by a twisted nematic liquid-crystal display, which is a binary phase-only modulator. This holographic free-space switching is applicable to optical interconnections and photonic switching systems.