gebhart/patrepeval huggingface dataset:
Reconciling schemas of disparate data sources (2001)

A data-integration system provides access to a multitude of data sources through a single mediated schema. A key bottleneck in building such systems has been the laborious manual construction of semantic mappings between the source schemas and the mediated schema. We describe LSD, a system that employs and extends current machine-learning techniques to semi-automatically find such mappings. LSD first asks the user to provide the semantic mappings for a small set of data sources, then uses these mappings together with the sources to train a set of learners. Each learner exploits a different type of information either in the source schemas or in their data. Once the learners have been trained, LSD finds semantic mappings for a new data source by applying the learners, then combining their predictions using a meta-learner. To further improve matching accuracy, we extend machine learning techniques so that LSD can incorporate domain constraints as an additional source of knowledge, and develop a novel learner that utilizes the structural information in XML documents. Our approach thus is distinguished in that it incorporates multiple types of knowledge. Importantly, its architecture is extensible to additional learners that may exploit new kinds of information. We describe a set of experiments on several real-world domains, and show that LSD proposes semantic mappings with a high degree of accuracy.
Neuronal Responses to Physiological Stress (2012)

Physiological stress can be defined as any external or internal condition that challenges the homeostasis of a cell or an organism. It can be divided into three different aspects: environmental stress, intrinsic developmental stress, and aging. Throughout life all living organisms are challenged by changes in the environment. Fluctuations in oxygen levels, temperature, and redox state for example, trigger molecular events that enable an organism to adapt, survive, and reproduce. In addition to external stressors, organisms experience stress associated with morphogenesis and changes in inner chemistry during normal development. For example, conditions such as intrinsic hypoxia and oxidative stress, due to an increase in tissue mass, have to be confronted by developing embryos in order to complete their development. Finally, organisms face the challenge of stochastic accumulation of molecular damage during aging that results in decline and eventual death. Studies have shown that the nervous system plays a pivotal role in responding to stress. Neurons not only receive and process information from the environment but also actively respond to various stresses to promote survival. These responses include changes in the expression of molecules such as transcription factors and microRNAs that regulate stress resistance and adaptation. Moreover, both intrinsic and extrinsic stresses have a tremendous impact on neuronal development and maintenance with implications in many diseases. Here, we review the responses of neurons to various physiological stressors at the molecular and cellular level.
Designs and experiments on infrared two-dimensional silicon photonic crystal slab devices (2012)

Photonic crystal (PhC) has offered a powerful means to mold the flow of light and manipulate light-matter interaction at subwavelength scale. Silicon has a large refraction index and low loss in infrared wavelengths, which makes it an important optical material. And silicon has been widely used for integrated photonics applications. In this paper, we have reviewed some recent theoretical and experimental works in our group on infrared two-dimensional (2D) air-bridged silicon PhC slab devices that are based on both band gap and band structure engineering. We have designed, fabricated, and characterized a series of PhC waveguides with novel geometries, PhC high-quality (high-Q) cavity, and channel drop filters utilizing resonant coupling between waveguide and cavity. These devices are aimed to construct a more flexible network of transport channel for infrared light at micrometer/nanometer scale. We have also explored the remarkable dispersion properties of PhCs by engineering the band structures to achieve negative refraction, self-collimation, superprism, and other anomalous dispersion behaviors of infrared light beam. Furthermore, we have designed and fabricated a PhC structure with negative refraction effect and used scanning near-field optical microscopy to observe the negative refraction beam. Finally, we have designed and realized a PhC structure that exhibits a self-collimation effect in a wide angle range and with a large bandwidth. Our works presented in this review show that PhCs have a strong power of controlling propagation of light at micrometer/nanometer scale and possess a great potential of applications in integrated photonic circuits.
A high-performance lateral bipolar transistor fabricated on SIMOX (1993)

Double-diffused, lateral n-p-n bipolar transistors were fabricated in a simple CMOS-like process using SIMOX silicon-on-insulator (SOI) substrates. Excellent device characteristics were achieved, with peak h/sub FE/=120, BV/sub CEO/=10 V, and peak f/sub t/=4.5 GHz. The f/sub t/ versus BV/sub CEO/ trade-off was studied as a function of n/sup -/ collector width. f/sub t/>25 GHz is predicted for this structure with an improved device layout and optimized basewidth. This process may be easily extended in order to fabricate complementary BJTs in a C-BiCMOS thin-film SOI technology.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Progress Toward an HIV Vaccine (2002)

The development of an HIV vaccine is proving to be an unprecedented challenge. The difficulty in creating this vaccine arises from the enormous genetic variation of the virus and the unusual importance of cytotoxic T lymphocytes (CTL) in controlling its spread. Whereas traditional vaccine strategies are unlikely to confer safe and effective HIV protection, novel strategies for eliciting CTL have provided substantial clinical benefits in nonhuman primate model systems. These vaccine strategies, including plasmid DNA and live recombinant vectors, are currently being evaluated in human clinical trials.
Inhibition of HIV-1 Replication in Alveolar Macrophages by Adenovirus Gene Transfer Vectors (2002)

To assess the hypothesis that infection of alveolar macrophages (AM) with adenovirus (Ad) gene transfer vectors might prevent subsequent human immunodeficiency virus (HIV)-1 replication in AM, AM isolated from normal volunteers were infected with increasing doses of first generation (E1(-)) Ad vectors, followed 72 h later by infection with HIV-1(JRFL), an R5/M-tropic strain that preferentially uses the CCR5 coreceptor. As a measure of HIV-1 replication, p24 Ag was quantified by enzyme-linked imunosorbent assay in supernatants on Days 4 to 14 after HIV-1infection. Pretreatment of the AM with an Ad vector resulted in a dose- and time-dependent suppression of subsequent HIV-1 replication. The Ad vector inhibition of HIV-1 replication was independent of the transgene in the Ad vector expression cassette and E4 genes in the Ad backbone. Moreover, it did not appear to be secondary to a soluble factor released by the AM, nor was it overridden by the concomitant transfer of the CCR5 or CXCR4 receptors to the AM before HIV-1 infection. These observations have implications regarding pulmonary host responses associated with HIV-1 infection, as well as possibly uncovering new therapeutic strategies against HIV-1 infection.
High capacity Na-storage and superior cyclability of nanocomposite Sb/C anode for Na-ion batteries (2012)

A Sb/C nanocomposite was synthesized and found to deliver a reversible 3 Na storage capacity of 610 mA h g(-1), a strong rate capability at a very high current of 2000 mA g(-1) and a long-term cycling stability with 94% capacity retention over 100 cycles, offering practical feasibility as a high capacity and cycling-stable anode for room temperature Na-ion batteries.
Purification of polynucleotide phosphorylase by affinity chromatography and some properties of the purified enzymes (1974)

A method is described for the preparation of p-aminophenyl oligo(dT)-Sepharose. This matrix has been used for the purification of polynucleotide phosphorylase from both E.coli and B.stearothermophilus. The effects of temperature and pH on the binding of the different enzymes to the matrix have been investigated. B.stearothermophilus isolated by affinity chromatography may be useful in selectively removing the polyA tract on the 3'-end of mRNA's.
Antigen-specific cancer immunotherapy using a GM-CSF secreting allogeneic tumor cell-based vaccine (2000)

Granulocyte-macrophage colony-stimulating factor (GM-CSF)-transduced autologous tumor cell-based vaccines are currently one of the major forms of cancer vaccines. However, the preparation of GM-CSF-transduced autologous tumor vaccines is time-consuming and technically challenging. In addition, the host antigen presenting cells, rather than the tumor vaccine cells themselves, present tumor-specific antigens and prime the host T cells. Therefore, we tested the efficacy of antigen-specific allogeneic tumor vaccines. We used human papillomavirus 16 (HPV-16) E7 protein as a model tumor antigen, which is associated with the development of most cervical carcinoma. B16, a C57BL/6 (H-2(b)) derived melanoma cell line, was genetically engineered to produce GM-CSF alone (B16GM), HPV-16 E7 alone (B16E7), or both (B16GME7). These vaccine cells were injected into BALB/c (H-2(d)) mice (10(6) cells/mouse). Two weeks later, mice were challenged with 10(5) live HPV-16 E7(+) BL-1 (H-2(d)) tumor cells and monitored for tumor progression twice weekly. To determine the effective cell population in the antitumor immunity elicited by B16GME7, we carried out in vivo antibody depletion experiments using CD4 and CD8 specific antibodies. In addition, as a measure of the immune responses produced by B16GME7, we performed an in vitro cytotoxic T lymphocyte assay using a standard chromium release method. We found that all of the mice vaccinated with B16GME7 remained tumor free 49 days post-BL-1 challenge. In contrast, mice vaccinated with B16GM and B16E7 did not show any tumor protection against a similar dose of BL-1 cells. Furthermore, the antitumor immunity produced by B16GME7 was dependent on both CD4 and CD8 T cells. In addition, E7-specific cytotoxic T lymphocyte activity could be readily demonstrated in mice immunized with B16GME7. These results suggest that allogeneic tumor cells transduced with GM-CSF and the tumor antigen, HPV-16 E7, cannot only generate an E7-specific cytotoxic T lymphocytes response in vitro, but can also elicit a potent antitumor immune response against an E7 expressing tumor in vivo.
The combination of low cytoplasmic and high nuclear expression of p27 predicts a better prognosis in high-grade astrocytoma. (2009)

A combination of low cytoplasmic and high nuclear expression of p27 predicts a better prognosis in high-grade astrocytomas and thus the subcellular localization of p27 expression is useful for predicting the prognosis for these patients.
Clinical Deterioration in Probable Alzheimer's Disease Correlates with Progressive Metabolic Impairment of Association Areas (1994)

Regional cerebral glucose metabolism (rCMRG1) measured by positron emission tomography of 18F-2-fluoro-2-deoxy-D-glucose was studied longitudinally (interval ranging from 6 to 27 months) in 25 patients with probable Alzheimer's disease (AD). A significant decline of rCMRG1 was noted in the whole brain (p = 0.02) which was most pronounced in the temporoparietal (p = 0.002), frontal (p = 0.01), superior parietal (p = 0.01) and occipital (p = 0.03) association cortex. A similar decline was also present in the thalamus (p = 0.04) but not in the primary visual and sensorimotor cortex, basal ganglia, cerebellum and brainstem. The changes of rCMRG1 in the temporoparietal, frontal and occipital association cortex were related to the change of the Mini Mental State Examination score (temporoparietal: r = 0.49, p = 0.01; frontal: r = 0.40, p = 0.05; occipital: r = 0.44, p = 0.03). The rate of clinical and metabolic decline was not related to age at onset, sex, family history or duration of disease. The results suggest that clinical deterioration and metabolic impairment in probable AD are closely related and dependent on progression of pathological changes in cortical association areas.
Stability of TEM β‐lactamase mutants hydrolyzing third generation cephalosporins (1995)

The stability properties of six natural mutants of the TEM-1 beta-lactamase have been studied. The glutamate to lysine substitution at positions 104 and 240 stabilize the enzyme. Conversely, the G238S mutant's decreased stability might reflect an altered conformation of the active site and thus be related to the modified substrate profile. The relative stability of the R164S and R164H mutants is explained by the formation of a hydrogen bond between these residues and Asp-179 conferring a somewhat different structure to the omega loop and thus also explaining the extended substrate profile of these mutants. The loss of stability of the R164H mutant with increasing pH values can be explained by the titration of a hydrogen bond between the N delta of His-164 and the O delta of Asp-179. The properties of the G238S + E104K double mutant which is the most active against third-generation cephalosporins result from a balance of destabilizing and stabilizing substitutions, and their effects seem to be additive. The behavior of the R164S + E240K mutant might be explained on the basis of a similar compensation phenomenon.
Protein engineering : principles and practice (1996)

Partial table of contents: Protein Conformation (F. Cohen & D. Hearst). Predicting the Conformation of Proteins from Sequence Data (S. Benner). Expression of Proteins in Bacteria (G. Georgiou). Expression of Heterologous Gene Products in Yeast (S. Pichuantes, et al.). Insect Cell Expression Technology (V. Luckow). Protein Expression in Xenopus Oocytes (M. Marino). Protein Engineering for Stability (S. Braxton). Structure--Function Relationships for Protein Design (C. Gibbs). Bacteriophage Display Libraries (J. Winter). Engineering Therapeutic Antibodies (R. Kelley). Site--Directed Drug Design (D. DeCamp, et al.). Index.
Evidence that the 90-kDa phosphoprotein associated with the untransformed L-cell glucocorticoid receptor is a murine heat shock protein. (1985)

Two phosphoproteins are adsorbed to protein-A-Sepharose when cytosol from 32P-labeled L-cells is incubated with a monoclonal antibody against the glucocorticoid receptor: one is a 98-100-kDa phosphoprotein that contains the steroid-binding site and the other is a 90-kDa nonsteroid-binding phosphoprotein that is associated with the untransformed, molybdate-stabilized receptor (Housley, P. R., Sanchez, E. R., Westphal, H.M., Beato, M., and Pratt, W.B. (1985) J. Biol. Chem. 260, in press). In this paper we show that the 90-kDa receptor-associated phosphoprotein is an abundant cytosolic protein that reacts with a monoclonal antibody that recognizes the 90-kDa phosphoprotein that binds steroid receptors in the chicken oviduct. The 90-kDa protein immunoadsorbed from L-cell cytosol with this antibody reacts on Western blots with rabbit antiserum prepared against the 89-kDa chicken heat shock protein. Immunoadsorption of molybdate-stabilized cytosol by antibodies against the glucocorticoid receptor results in the presence of a 90-kDa protein that interacts on Western blots with the antiserum against the chicken heat shock protein. The association between the 90-kDa protein and the receptor is only seen by this technique when molybdate is present to stabilize the complex; and when steroid-bound receptors are incubated at 25 degrees C to transform them to the DNA-binding state, the 90-kDa protein dissociates. These observations are consistent with the proposal that the untransformed glucocorticoid receptor in L-cells exists in a complex with the murine 90-kDa heat shock protein.
Immune complex transfer enzyme immunoassay that is more sensitive and specific than western blotting for detection of antibody immunoglobulin G to human immunodeficiency virus type 1 in serum with recombinant pol and gag proteins as antigens (1995)

Antibody immunoglobulin G (IgG) to human immunodeficiency virus type 1 (HIV-1) in serum was detected by ultrasensitive enzyme immunoassays (immune complex transfer enzyme immunoassays) with recombinant reverse transcriptase (rRT), p17 (rp17) and p24 (rp24) of HIV-1 as antigens and beta-D-galactosidase from Escherichia coli as the label. The immune complex, comprising 2,4-dinitrophenyl-bovine serum albumin-recombinant protein conjugate, antibody IgG to HIV-1, and recombinant protein-beta-D-galactosidase conjugate, was trapped on polystyrene beads coated with affinity-purified (anti-2,4-dinitrophenyl group) IgG, eluted with epsilon N-2,4-dinitrophenyl-L-lysine, and transferred to polystyrene beads coated with affinity-purified (anti-human IgG gamma-chain) IgG. Bound beta-D-galactosidase activity was assayed by fluorometry. The assays were highly reproducible with no serious serum interference, and they were much more sensitive than Western immunoblotting for the corresponding antigens. Signals with rRT, rp17, and rp24 for asymptomatic carriers were at least 56,000-, 680-, and 22-fold higher, respectively, than those for seronegative individuals, and neither indeterminate nor false-positive results were observed, whereas some serum samples were false negative or false positive by Western blotting for p17 and/or p24 antigen. In some cases, seroconversion was detected earlier than by conventional methods. Therefore, these assays are suggested to be more useful than conventional methods not only for the confirmation of antibody IgGs to RT, p17, and p24 of HIV-1 in serum but also for the detection of seroconversion.
Alpha-melanocyte-stimulating hormone stimulates oxytocin release from the dendrites of hypothalamic neurons while inhibiting oxytocin release from their terminals in the neurohypophysis. (2003)

The peptides alpha-melanocyte stimulating hormone (alpha-MSH) and oxytocin, when administered centrally, produce similar behavioral effects. alpha-MSH induces Fos expression in supraoptic oxytocin neurons, and alpha-MSH melanocortin-4 receptors (MC4Rs) are highly expressed in the supraoptic nucleus, suggesting that alpha-MSH and oxytocin actions are not independent. Here we investigated the effects of alpha-MSH on the activity of supraoptic neurons. We confirmed that alpha-MSH induces Fos expression in the supraoptic nucleus when injected centrally and demonstrated that alpha-MSH also stimulates Fos expression in the nucleus when applied locally by retrodialysis. Thus alpha-MSH-induced Fos expression is not associated with electrophysiological excitation of supraoptic neurons because central injection of alpha-MSH or selective MC4 receptor agonists inhibited the electrical activity of oxytocin neurons in the supraoptic nucleus recorded in vivo. Consistent with these observations, oxytocin secretion into the bloodstream decreased after central injection of alpha-MSH. However, MC4R ligands induced substantial release of oxytocin from dendrites in isolated supraoptic nuclei. Because dendritic oxytocin release can be triggered by changes in [Ca2+]i, we measured [Ca2+]i responses in isolated supraoptic neurons and found that MC4R ligands induce a transient [Ca2+]i increase in oxytocin neurons. This response was still observed in low extracellular Ca2+ concentration and probably reflects mobilization of [Ca2+]i from intracellular stores rather than entry via voltage-gated channels. Taken together, these results show for the first time that a peptide, here alpha-MSH, can induce differential regulation of dendritic release and systemic secretion of oxytocin, accompanied by dissociation of Fos expression and electrical activity.
An expandable single-IC digital filter/Correlator (2005)

The commercial success of single-integrated circuit multipliers and correlators has prompted the design of a new integrated circuit for video-speed digital convolution and correlation. This device is based on two concepts: 1.) the merging of delay and pipeline registers and 2.) "bit-slicing" the filter array in both the signal data word and coefficient dimensions. The device can update one coefficient per clock cycle. The result is an expandable "building block" which can be cascaded or paralleled to give the desired length, signal data word length, and coefficient data word length for any desired filter up to 20 MSPS.
Nucleotide Sequence of Bovine Papillomavirus Type 2 Late Region (1985)

The late region of bovine papillomavirus type 2 (BPV-2) DNA has been identified. The complete nucleotide sequence of the region was determined and revealed two large open reading frames. The DNA sequence results and the predicted amino acid sequence of putative polypeptides encoded by this region are presented. Comparative analysis of the BPV-2 late region and the corresponding area of BPV-1 was performed. This study demonstrates that identical genetic organization and considerable nucleotide sequence conservation exists between these two serotypes.
Acute ACTH regulation of adrenal corticosteroid biosynthesis. Rapid accumulation of a phosphoprotein. (1986)

Two-dimensional gel electrophoresis was used to monitor proteins synthesized in unstimulated control and in adrenocorticotropic hormone (ACTH)- or cAMP-stimulated rat adrenal cells. Four proteins, which have similar proteolytic peptide maps, have been identified. The two found primarily in unstimulated cells are referred to as pb and pa, where pb is the protein with more basic isoelectric point. Similarly, proteins ib and ia were detected only in stimulated cells. The synthesis of pb occurs only in unstimulated cells and that of ib only in stimulated cells. Protein ib accumulates with the same lag time, rate, and stimulant dose response as the increase in steroid hormone synthesis. Pulse-chase studies showed that protein ib is not produced from pb by a post-translational modification. Proteins pb and ib thus seem identical with proteins p and i previously identified in rat adrenal cortex and corpus luteum (Krueger, R.J., and Orme-Johnson, N. R. (1983) J. Biol. Chem. 258, 10159-10167, and Pon, L.A., and Orme-Johnson, N.R. (1986) J. Biol. Chem. 261, 6594-6599). The acidic forms, pa and ia, appear after a longer lag time and are produced at a slower rate than the basic forms. Pulse-chase studies showed that the disappearance of the basic form of each protein occurs concurrently with the appearance of the corresponding acidic form. Addition of [32P]orthophosphate to stimulated adrenal cells allowed direct demonstration that proteins ib and ia are phosphorylated. Moreover, alkaline phosphatase treatment of [35S]methionine-labeled, cAMP-stimulated adrenal cells caused a large decrease in the amounts of ib and ia and the appearance of proteins with the same two-dimensional electrophoretic mobilities as pb and pa. These observations suggest that protein ib may mediate stimulation of steroidogenesis, be produced by an ACTH- or cAMP-dependent, cotranslational phosphorylation of protein pb, and be lost by a cycloheximide-insensitive, post-translational conversion to ia.