gebhart/patrepeval huggingface dataset:
Tyr721 regulates specific binding of the CSF-1 receptor kinase insert to PI 3′-kinase SH2 domains: a model for SH2-mediated receptor-target interactions. (1992)

Efficient binding of active phosphatidylinositol (PI) 3'-kinase to the autophosphorylated macrophage colony stimulating factor receptor (CSF-1R) requires the noncatalytic kinase insert (KI) region of the receptor. To test whether this region could function independently to bind PI 3'-kinase, the isolated CSF-1R KI was expressed in Escherichia coli, and was inducibly phosphorylated on tyrosine. The tyrosine phosphorylated form of the CSF-1R KI bound PI 3'-kinase in vitro, whereas the unphosphorylated form had no binding activity. The p85 alpha subunit of PI 3'-kinase contains two Src homology (SH)2 domains, which are implicated in the interactions of signalling proteins with activated receptors. Bacterially expressed p85 alpha SH2 domains complexed in vitro with the tyrosine phosphorylated CSF-1R KI. Binding of the CSF-1R KI to PI 3'-kinase activity, and to the p85 alpha SH2 domains, required phosphorylation of Tyr721 within the KI domain, but was independent of phosphorylation at Tyr697 and Tyr706. Tyr721 was also critical for the association of activated CSF-1R with PI 3'-kinase in mammalian cells. Complex formation between the CSF-1R and PI 3'-kinase can therefore be reconstructed in vitro in a specific interaction involving the phosphorylated receptor KI and the SH2 domains of p85 alpha.
Complexity reduction of joint temporal-spatial bit allocation using R-D models for video streaming (2003)

The joint temporal-spatial bit allocation problem was examined in our previous work to achieve proper temporal-spatial quality tradeoff for low bit rate video coding. Both theoretical analysis and performance benchmark of several optimal/suboptimal algorithms were presented. However, the high computational complexities of these solutions prevent them from being used in practical applications. To solve this problem, rate-distortion (R-D) models are adopted in this work to reduce the complexity of the proposed rate control scheme. Different R-D models are applied to intra, inter and skipped frames, respectively, with consideration of both prediction and interpolation dependencies among successive frames. A look ahead window (LAW) structure is implemented, with buffer and delay constraints applied, for continuous and smooth video playback. The approximation errors of the proposed R-D models are very small, which results in small degradation of the compressed video quality, while the complexity of rate control is greatly reduced so that it is suitable for streaming applications. It is shown by experiments that the proposed rate control method can achieve better overall quality than the standard MPEG-4/TM7 rate control.
Gene Therapy 2000 (2000)

This article reviews 1) the use of gene transfer methods to genetically manipulate hematopoietic stem cell targets, 2) recent advances in technology that are addressing problems that have prevented widespread successful translation of gene transfer approaches for the cure of disease, and 3) recent regulatory issues related to human gene therapy trials. In Section I, Dr. Nienhuis describes the use of alternative viral envelopes and vector systems to improve efficiency of transduction of hematopoietic stem cells. Major limitations of stem cell transduction are related to low levels of viral receptors on the stem cells of large animal species and the low frequency of cycling stem cells in the bone marrow. Attempts to circumvent these limitations by exploiting non-oncoretroviral vectors and pseudotyping of Moloney vectors with alternative envelopes are discussed. In Section II, Dr. Hawley addresses new strategies to improve the expression of transgenes in cells derived from long-term reconstituting hematopoietic stem cells. Transgene silencing in transduced hematopoietic stem cells remains an obstacle to gene therapy for some gene sequences. New generations of retroviral backbones designed to both improve expression and reduce silencing in primary cells are explored. In Section III, Drs. Smith and Cornetta update regulatory issues related to human gene therapy trials. Increased scrutiny of human trials has led to changes in requirements and shifts in emphasis of existing regulations, which apply to human gene therapy trials. The current Food and Drug Administration's structure and regulations and the roles of the Recombinant DNA Advisory Committee of the NIH and other sponsors and partners in gene therapy trials are reviewed.
A Novel Electrochemical Microsensor for Nitric Oxide Based on Electropolymerized Film ofo-Aminobenzaldehyde-ethylene-diamine Nickel (1999)

A novel electrochemical microsensor for nitric oxide (NO) is described. The microsensor, which is based on an electropolymerized film ofo-aminobenzaldehyde-ethylene-diamine nickel [Ni(ABED)] and Nafion, shows a low detection limit, high selectivity and sensitivity to NO determination. The oxidation current (measured by differential pulse amperometric method) is linear with NO concentration ranging from 1.0×10−8to 1.0×10−6mol/L with a calculated detection limit, at a signal-to-noise ratio of three, equal to 5.0×10−9mol/L and a linear coefficient of 0.9921. Some endogenous electroactive substances in biological tissues, such as ascorbate, dopamine, 5-hydroxytryptamine, cysteine and nitrite do not interfere with NO determination at the concentrations higher than those in biological systems. The microsensor should be promising for in vivo measurement of NO. The mechanism of the response of the microsensor to NO is preliminary studied.
Analysis of regulation of phoB expression using a phoB-cat fusion (1983)

The phoB gene, which encodes a positive control factor for a number of phosphate-regulated genes in Escherichia coli, was cloned into multicopy plasmid pBR322. A phoB-cat fusion that expressed chloramphenicol transacetylase from the phoB promoter was constructed. Studies of the expression of the phoB-cat fusion showed that the pattern of regulation of the phoB gene was similar to that of the phoA gene, the structural gene for alkaline phosphatase. The phoB gene was derepressed under conditions of phosphate starvation, was constitutively expressed in a phoR background, and required the phoM gene product for expression in a phoR strain. Finally, a functional phoB product was required for its own synthesis. Our results indicate either that phoA gene expression responds directly to the concentration of the phoB gene product in cells or that the phoA and phoB controlling elements are quite similar.
Major histocompatibility complex class I‐restricted CD8+ T cells and class II‐restricted CD4+ T cells, respectively, mediate and regulate contact sensitivity to dinitrofluorobenzene (1995)

Contact sensitivity (CS) is a form of delayed-type hypersensitivity to haptens applied epicutaneously and is thought to be mediated, like classical delayed-type hypersensitivity responses, by CD4+ T helper-1 cells. The aim of this study was to identify the effector T cells involved in CS. We studied CS to the strongly sensitizing hapten dinitrofluorobenzene (DNFB) in mice rendered deficient by homologous recombination in either major histocompatibility complex (MHC) class I, MHC class II, or both, and which exhibited deficiencies in, respectively, CD8+, CD4+, or both, T cells. MHC class I single-deficient and MHC class I/class II double-deficient mice, both of which have a drastic reduction in the number of CD8+ T cells, were unable to mount a CS response to DNFB. In contrast, both MHC class II-deficient mice and normal mice treated with an anti-CD4 monoclonal antibody (mAb) developed exaggerated and persistent responses relative to heterozygous control littermates. Furthermore, anti-CD8 mAb depletion of class II-deficient mice totally abolished their ability to mount an inflammatory response to DNFB. Removal of residual CD4+ T cells in class II-deficient mice by anti-CD4 mAb treatment did not diminish the intensity of CS. These data clearly demonstrate that class I-restricted CD8+ T cells are sufficient for the induction of CS to DNFB, and further support the idea that MHC class II-restricted CD4+ T cells down-regulate this inflammatory response.
Tropospheric Air Pollution: Ozone, Airborne Toxics, Polycyclic Aromatic Hydrocarbons, and Particles (1997)

Tropospheric air pollution has impacts on scales ranging from local to global. Reactive intermediates in the oxidation of mixtures of volatile organic compounds (VOCs) and oxides of nitrogen (NOx) play central roles: the hydroxyl radical (OH), during the day; the nitrate radical (NO3), at night; and ozone (O3), which contributes during the day and night. Halogen atoms can also play a role during the day. Here the implications of the complex VOC-NOx chemistry for O3 control are discussed. In addition, OH, NO3, and O3 are shown to play a central role in the formation and fate of airborne toxic chemicals, mutagenic polycyclic aromatic hydrocarbons, and fine particles.
[Effect of intratracheally administered IL-12 recombinant adenovirus on ovalbumin induced bronchial hyresponsiveness in mouse model]. (2001)

Intratracheally administered Adm IL-12 inhibits ovalbumin induced airway hyperresponsiveness, which may be an effective approach in the management of antigen induced bronchial asthma.
Monoclonal antibody characterization of the C proteins of heterogeneous nuclear ribonucleoprotein complexes in vertebrate cells. (1984)

The C proteins (C1 and C2) are major constituents of the 40S subparticle of heterogeneous nuclear ribonucleoprotein complexes (hnRNPs) (Beyer, A.L., M.E. Christensen, B.W. Walker, and W.M. LeStourgeon, 1977, Cell, 11:127-138) and are two of the most prominent proteins that become cross-linked by ultraviolet light to heterogeneous nuclear RNA (hnRNA) in vivo. Studies are described here on the characterization of the C proteins in vertebrate cells using monoclonal and polyclonal antibodies. Monoclonal antibodies to genuine RNP proteins, including the C proteins, were obtained by immunizing mice with purified complexes of poly(A)+ hnRNA and poly(A)+ mRNA with their contacting proteins in vivo obtained by ultraviolet cross-linking the complexes in intact cells (Dreyfuss, G., Y.D. Choi, and S.A. Adam, 1984, Mol. Cell. Biol., 4:1104-1114). One of the monoclonal antibodies identified the C proteins in widely divergent species ranging from human to lizard. In all species examined, there were two C proteins in the molecular weight range of from 39,000 to 42,000 for C1, and from 40,000 to 45,000 for C2. The two C proteins were found to be highly related to each other; they were recognized by the same monoclonal antibodies and antibodies raised against purified C1 reacted also with C2. In avian, rodent, and human cells the C proteins were phosphorylated and were in contact with hnRNA in vivo. Immunofluorescence microscopy demonstrated that the C proteins are segregated to the nucleus. Within the nucleus the C proteins were not found in nucleoli and were not associated with chromatin as seen in cells in prophase. These findings demonstrate that C proteins with similar characteristics to those in humans are ubiquitous components of hnRNPs in vertebrates.
Water Soluble Acrylamidomethyl Propane Sulfonate (AMPS) Copolymer as an Enhanced Oil Recovery Chemical (2003)

A high molecular weight (>106) copolymer of N,N-dimethyl acrylamide with Na-2-acrylamido-2-methylpropanesulfonate (NNDAM-NaAMPS) was prepared and characterized. The efficacy of the copolymer as an enhanced oil recovery (EOR) chemical was studied. Core flood tests using 72−150 mesh size unconsolidated sand having a porosity of 42% were carried out at different brine concentrations and temperatures. Initially, a crude oil fraction (150−300 °C) and, finally, the crude itself were used as the oils to be recovered. The copolymer was brine compatible. After a water flood, about 5.6% original oil in place (OIP) could be recovered by injecting 2000 ppm polymer solution to the sand pack containing oil fraction and 5000 ppm NaCl brine. The polymer solution was found to be thermally stable at 120 °C at least for a period of 1 month. It was further confirmed that the residual oil recovery increased with the increase of temperature. About 11% of OIP could be recovered as additional oil by injecting a 2000 ppm polymer solution to the unconsolidated sand pack containing one of the Indian crude oils and brine consisting of mono- and bivalent metal ions at 90 °C.
Mutation of the Gene for I sK Associated With Both Jervell and Lange-Nielsen and Romano-Ward Forms of Long-QT Syndrome (1998)

These data provide strong evidence that KCNE1 mutations represent a fifth LQTS locus (LQT5). Further functional analysis, as well as the identification of more LQTS patients with KCNE1 mutations, will be important to confirm the role of IsK in LQTS.
Cancer Gene Therapy by Adenovirus-Mediated Gene Transfer (2001)

Cancer arises as a direct result of genetic mutations. It therefore stands to reason that cancer should be well suited for the correction through gene therapy. Recent advances in the understanding of the molecular pathogenesis of cancer and the rapid development of recombinant DNA technology have made cancer gene therapy feasible in the clinical setting. The current efforts for cancer gene therapy mainly focus on immunogene therapy, chemogene therapy, restoration of tumor suppressor gene function, and oncolytic virus therapy. Central to all these therapies is the development of efficient vectors for gene delivery--this remains a work in progress. These vectors can be classified as viral and non-viral vectors. This paper will concentrate on viral vectors because of their practical advantages over non-viral vectors. Of the viral vectors, by far the most important are the human adenoviruses as is reflected by the enormous data and literature accumulated by studies relating to animal tumor models and clinical trials. In this review, we examine the recent progress in adenovirus-mediated cancer gene therapy with regard to cytokine gene, tumor suppressor gene, chemogene, and oncolytic adenovirus. We also discuss the current limitations of the adenoviral vector system and how they may be circumvented in future developments relating to targeted gene delivery.
On the construction of some capacity-approaching coding schemes (2000)

This thesis proposes two constructive methods of approaching the Shannon limit very closely. Interestingly, these two methods operate in opposite regions, one has a block length of one and the other has a block length approaching infinity. The first approach is based on novel memoryless joint source-channel coding schemes. We first show some examples of sources and channels where no coding is optimal for all values of the signal-to-noise ratio (SNR). When the source bandwidth is greater than the channel bandwidth, joint coding schemes based on space-filling curves and other families of curves are proposed. For uniform sources and modulo channels, our coding scheme based on space-filling curves operates within 1.1 dB of Shannon’s rate-distortion bound. For Gaussian sources and additive white Gaussian noise (AWGN) channels, we can achieve within 0.9 dB of the rate-distortion bound. The second scheme is based on low-density parity-check (LDPC) codes. We first demonstrate that we can translate threshold values of an LDPC code between channels accurately using a simple mapping. We develop some models for density evolution
Turning the corner on therapeutic cancer vaccines (2019)

Recent advances in several areas are rekindling interest and enabling progress in the development of therapeutic cancer vaccines. These advances have been made in target selection, vaccine technology, and methods for reversing the immunosuppressive mechanisms exploited by cancers. Studies testing different tumor antigens have revealed target properties that yield high tumor versus normal cell specificity and adequate immunogenicity to affect clinical efficacy. A few tumor-associated antigens, normal host proteins that are abnormally expressed in cancer cells, have been demonstrated to serve as good targets for immunotherapies, although many do not possess the needed specificity or immunogenicity. Neoantigens, which arise from mutated proteins in cancer cells, are truly cancer-specific and can be highly immunogenic, though the vast majority are unique to each patient's cancer and thus require development of personalized therapies. Lessons from previous cancer vaccine expeditions are teaching us the type and magnitude of immune responses needed, as well as vaccine technologies that can achieve these responses. For example, we are learning which vaccine approaches elicit the potent, balanced, and durable CD4 plus CD8 T cell expansion necessary for clinical efficacy. Exploration of interactions between the immune system and cancer has elucidated the adaptations that enable cancer cells to suppress and evade immune attack. This has led to breakthroughs in the development of new drugs, and, subsequently, to opportunities to combine these with cancer vaccines and dramatically increase patient responses. Here we review this recent progress, highlighting key steps that are bringing the promise of therapeutic cancer vaccines within reach.
Implicit Memory: A Selective Review (1993)

The brain's default mode network consists of discrete, bilateral and symmetrical cortical areas, in the medial and lateral parietal, medial prefrontal, and medial and lateral temporal cortices of the human, nonhuman primate, cat, and rodent brains. Its ...Read More
The suppression of 5-lipoxygenation of arachidonic acid in human polymorphonuclear leucocytes by the 15-lipoxygenase product (15S)-hydroxy-(5Z,8Z,11Z,13E)-eicosatetraenoic acid: structure-activity relationship and mechanism of action (1996)

(15S)-Hydroxy-(5Z,8Z,11Z,13E)-eicosatetraenoic acid (15-HETE) suppresses in ionophore-A23187-stimulated human polymorphonuclear leucocytes (PMN) the conversion of exogenous arachidonic acid into leukotriene B(4) (LTB4) and (5S)-hydroxy-(6E,8Z,11Z,14Z)-eicosatetraenoic acid (5-HETE). However, contrary to earlier suggestions, 15-HETE is not a genuine 5-lipoxygenase inhibitor under these conditions, but rather suppresses the 5-lipoxygenation of arachidonic acid by switching-over of substrate utilization, as judged from a sizeable formation of labelled (5S,15S)-dihydroxy-(6E,8Z,11Z,13E)-eicosatetr aen oic acid (5,15-diHETE) from 15-[1(-14)C]HETE. Identical results were obtained with human recombinant 5-lipoxygenase. In PMN the formation of 5,15-diHETE is strongly stimulated by either hydroperoxypolyenoic fatty acids or arachidonic acid, suggesting a crucial role of the hydroperoxide tone of the cell. A comparison of a selection of hydroxypolyenoic fatty acids with respect to their capability of suppressing 5-lipoxygenation of arachidonic acid revealed that 15-mono-hydroxyeicosanoids throughout exhibit the highest inhibitory potencies, whereas the other HETEs, 5,15-diHETE as well as octadecanoids, are modest or poor inhibitors. The R and S enantiomers of 15-HETE do not differ from each other, excluding a receptor-like binding of the 15-hydroxy group.
Dynamic bandwidth allocation algorithm in ethernet passive optical networks (2003)

A dynamic bandwidth allocation algorithm in ethernet passive optical networks (EPON) is proposed. Specifically, an analytic model to estimate the proper allocation of the bandwidth in EPON is introduced. In particular, it is shown that the proper allocation of the bandwidth for the optical network units leads to improvement in the network&apos;s performance.
VIPase autoantibodies in Fas ‐defective mice and patients with autoimmune disease (2003)

The immunoregulatory neuropeptide vasoactive intestinal peptide (VIP) was cleaved by purified IgG from Fas-defective C3H/gld mice, lupus patients, and autoimmune thyroiditis patients. No VIPase activity was detected in IgG from control mice and humans. Kinetic analyses of VIPase IgG preparations suggested low-affinity recognition of VIP. Yet the VIPase activity was VIP selective, judged by lack of correlation with other protease activities expressed by the IgG and by noninterference of unrelated peptides in the activity. Recombinant Fv constructs selected from a human lupus phage show library displayed VIPase activity, confirming that the active site is located in the V domains. Inhibition of the VIPase activity by di-isopropylfluorophosphate suggested a serine protease-like mechanism of catalysis. Irreversible binding of a biotinyated phosphonate diester by the IgG and Fv preparations was observed, consistent with the presence of activated nucleophiles similar to those in enzymes capable of covalent catalysis. These observations show that VIP is a target for specific catalytic autoantibodies in autoimmune disease.
Advantage of radical oxidation for improving reliability of ultra-thin gate oxide (2002)

This paper focuses attention on the advantage of oxygen radical oxidation by a microwave-excited high-density Kr/O/sub 2/ plasma for improving the disadvantages of conventional thermal oxidation processes using H/sub 2/O and/or O/sub 2/ molecules, and demonstrates that the Kr/O/sub 2/ plasma oxidation process can improve the thickness variation on shallow-trench isolation and integrity of silicon oxide not only on the [100] surface but also on the [111] surface compared to those of conventional thermal oxidation processes.
SARS-CoV-2 detection in different respiratory sites: A systematic review and meta-analysis (2020)

This study was funded in part by the NIH grants U01AI106701 and by the Harvard University for AIDS Research (NIAID 5P30AI060354).
ST-segment, T-wave, and U-wave changes during myocardial ischemia and after myocardial infarction. (1986)

This review deals with the pathogenesis of ischemia-related abnormalities of ventricular repolarization. The most common repolarization abnormality during acute myocardial ischemia is the deviation of ST segment from the baseline due to diastolic and systolic currents of injury. The patterns of primary and reciprocal ST deviations during and after myocardial infarction are discussed. A very tall upright or a deeply inverted T wave, and shortened QT interval are transient phenomena followed by postischemic T wave abnormalities associated with QT lengthening. These changes are associated with lengthening of the ventricular action potentials at the border of infarction. Persistence of ST elevation after myocardial infarction is usually associated with ventricular dyskinesia. The differential diagnosis of this pattern and its possible mechanism are discussed. Also the mechanisms of ST alternans, T alternans and negative U waves, i.e. less common manifestations of myocardial ischemia are discussed. Studies of exercise-induced T wave normalization suggest that the behavior of primary T wave abnormalities after exercise does not alter the interpretation of the ischemic changes. T wave abnormalities are frequently non-specific but the post myocardial infarction T wave changes persist after administration of isoproterenol while various functional and neurogenic T wave abnormalities are corrected by isoproterenol.