gebhart/patrepeval huggingface dataset:
De Novo Expression of Killer Immunoglobulin-Like Receptors and Signaling Proteins Regulates the Cytotoxic Function of CD4 T Cells in Acute Coronary Syndromes (2003)

The inflammatory infiltrate in atherosclerotic plaque is composed of T cells and macrophages. CD4+ T cells with a unique phenotype, CD4+CD28null, are preferentially recruited into culprit lesions. These T cells are distinct from classic CD4+CD28+ T cells in gene expression and function, including their ability to mediate cytolysis. In this study, we have investigated the regulation of CD4+CD28null T-cell cytolytic function. In patients with acute coronary syndromes (ACS), CD4+CD28null T cells express killer immunoglobulin-like receptors (KIRs). KIRs encompass a polymorphic family of receptors that recognize HLA class I molecules and have been implicated in self-tolerance. CD4+CD28null T-cell clones from patients with ACS and age-matched controls were compared for their KIR-expression profile. T-cell clones derived from the patients expressed a broader spectrum of KIRs (P<0.001) with preference for the stimulatory variant, CD158j. Additionally, CD4+ T-cell clones from patients but not those from controls acquired de novo expression of the DAP12 molecule, an adapter chain that transmits CD158j-derived signals. Cumulative expression of CD158j and DAP12 endowed cytolytic competence on CD4+CD28null T cells, allowing them to kill in the absence of T-cell receptor triggering. Our data demonstrate that CD4+CD28null T cells in ACS are characterized by a unique gene expression profile. Consequently, these T cells acquire cytolytic capability that can bypass the need for T-cell receptor triggering and, thus, impose a threat to self-tolerance.
Thyroid hormone signaling is highly heterogeneous during pre- and postnatal brain development (2004)

We have generated transgenic reporter mice to analyze the spatio-temporal distribution of thyroid hormone signaling during mouse brain development. The reporter system, utilizing a chimeric yeast Gal4 DNA-binding domain-thyroid hormone alpha ligand-binding domain fusion protein to drive lacZ expression, revealed that thyroid hormone signaling starts in the midbrain roof several days before the onset of thyroid gland function, and that it remains highly heterogeneous in the central nervous system throughout pre- and postnatal development. We speculate that this heterogeneity might provide neural cells with positional information during development.
Energy expenditure and fluid production in hyperbaric He-O2 environments using doubly labeled water. (1994)

Energy expenditure (EE), carbon dioxide production (rCO2), water turnover (rH2O), and urine production (UP) were measured to determine nutrient requirements of U.S. Navy divers during saturation dives. Parameters were measured in a normal surface environment (n = 10) and in 0.56 MPa (n = 9) and 3.17 MPa (n = 11) helium-oxygen environments. Daily EE, rCO2, and rH2O were measured with the doubly labeled water method for 10-14 days in each environment. Daily UP was determined by 24-h urine collection for 5- to 10-day periods in each environment. Divers consumed a mixed diet composed of 30% calories from fat, 15% protein, and 55% carbohydrate. Both EE and rCO2 increased significantly relative to surface conditions at 0.56 MPa (13 +/- 4% and 11 +/- 4%) and 3.17 MPa (14 +/- 4% and 11 +/- 3%), but there was no difference between dives. Water turnover was not significantly affected by the hyperbaric environment. UP was significantly greater than surface conditions at 0.56 MPa (53 +/- 19%) but not at 3.17 MPa (38 +/- 18%). Increased EE is attributed to thermal stress caused by the helium-oxygen environment. Increased UP may have been caused by decreased evaporative water loss.
Improved contrast in inverted selective plane illumination microscopy of thick tissues using confocal detection and structured illumination (2017)

Inverted selective plane illumination microscopy (iSPIM) enables fast, large field-of-view, long term imaging with compatibility with conventional sample mounting. However, the imaging quality can be deteriorated in thick tissues due to sample scattering. Three strategies have been adopted in this paper to optimize the imaging performance of iSPIM on thick tissue imaging: electronic confocal slit detection (eCSD), structured illumination (SI) and the two combined. We compared the image contrast when using SPIM, confocal SPIM (using eCSD alone), SI SPIM (using SI alone) or confocal-SI SPIM (combining both methods) on images of gelatin phantom and highly-scattering fluorescently-stained human tissue. We demonstrate that all the three methods showed remarkable contrast enhancement on both samples compared to iSPIM alone, and SI SPIM and the combined confocal-SI mode outperformed confocal SPIM in contrast enhancement. Moreover, the use of SI at high pattern frequencies outperformed confocal SPIM in terms of optical sectioning capability. However, image signal-to-noise ratio (SNR) was decreased at high pattern frequencies when imaging scattering samples with SI SPIM. By combining eCSD with SI to reduce background signal and noise, the superior optical sectioning performance of SI could be achieved while also maintaining high image SNR.
A Rapid Technique for the Estimation of Polynucleotide Adenylyltransferase and Ribonucleic Acid Polymerase in Plant Tissues (1975)

Nucleic acid-dependent polynucleotide adenylytransferase (EC 2.7.7.19) and ribonucleic acid polymerase (EC 2.7.7.6) have been partially purified from maize tissues (Zea mays L.) utilizing ammonium sulfate precipitation and batch diethylaminoethylcellulose chromatography. The technique is applicable to the simultaneous processing of up to eight samples of plant tissue and affords a rapid and reproducible means of assaying these two enzymes from small quantities of kernels or seedlings. The kinetic characteristics of the partially purified enzymes resemble those from more extensively purified preparations.
Immunosuppressive effects of mouse seminal plasma components <i>in vivo</i> and <i>in vitro</i>. (1982)

Mouse seminal plasma (SP), a mixture of aqueous extracts of prostate, seminal vesicle, and epididymis, exerts potent immunosuppressive effects in vivo. The SP mixture completely suppressed both primary and secondary humoral immune responses in mice to low immunizing doses of antigen (bovine serum albumin or washed epididymal sperm), and also significantly suppressed the antibody response to high doses of immunizing antigen. The humoral immune response to epididymal sperm was also suppressed when sperm were incubated in SP and then washed before immunization and when SP was administered at a secondary site (i. p.) at the time of sperm immunization (subcutaneous). When SP components were tested individually in in vitro assays, all of them (prostate, seminal vesicle, and epididymis) suppressed mitogen-induced lymphocyte transformation. Prostatic fluid also inhibited complement-mediated hemolysis in a standard immune hemolytic assay. These data indicate that potent immunosuppressive factors are present at several locations within the male reproductive tract; these factors may serve to protect sperm from immunologic damage and prevent sensitization of females to sperm antigens after insemination.
Active peptides from the carboxyl‐terminal globular domain of laminin α2 and <i>Drosophila</i> α chains (1996)

The laminin alpha1 chain carboxyl-terminal globular domain (G domain) contains multiple biological activities. Recently, we identified five cell binding sequences from the G domain by screening with overlapping 12-mer peptides encompassing the entire domain. The structures of these five sequences in the alpha1 chain are conserved in the corresponding regions of the different laminin alpha chains. Here we characterize the adhesion activities of the corresponding peptide segments from both the mouse laminin alpha2 chain and Drosophila laminin alpha chain using peptide-coated plastic plates and peptide-conjugated Sepharose beads. Using several cell lines, the laminin alpha2 chain peptides showed cell attachment and/or spreading activities with cell type specificities. Cell spreading on MG-10 was inhibited by integrin antibodies. Four of the Drosophila laminin peptides showed cell attachment activities. These results suggest that biologically active regions in the G domain are conserved in the laminin alpha1 and alpha2 chains, and that these regions in laminin play an important role in cell surface receptor interactions.
Methods for molecular surveillance of influenza (2010)

Molecular-based techniques for detecting influenza viruses have become an integral component of human and animal surveillance programs in the last two decades. The recent pandemic of the swine-origin influenza A virus (H1N1) and the continuing circulation of highly pathogenic avian influenza A virus (H5N1) further stress the need for rapid and accurate identification and subtyping of influenza viruses for surveillance, outbreak management, diagnosis and treatment. There has been remarkable progress on the detection and molecular characterization of influenza virus infections in clinical, mammalian, domestic poultry and wild bird samples in recent years. The application of these techniques, including reverse transcriptase-PCR, real-time PCR, microarrays and other nucleic acid sequencing-based amplifications, have greatly enhanced the capability for surveillance and characterization of influenza viruses.
Global navigation satellite system inanintegrated air traffic management constellation (1997)

Enhanced surveillance, communications and navigation are the primary functions needed for an advanced air traffic management (ATM). To provide ATM globally, including areas not covered by terrestrial systems, the advantages of satellite technology must be exploited. In a previous work, a novel architecture based on low-elevation orbit satellites was described and evaluated. The satellite constellation is designed to supply the surveillance and data link capabilities equivalent to an advanced secondary surveillance radar mode S, as well as to provide satellite communication and navigation functions. Such a co-operative independent surveillance integrating navigation and communication (CISINC) is fully compliant with the communication, navigation and surveillance/air traffic management concept endorsed by the ICAO in 1991. The space-based implementation of CISINC is called ATM-Star. The paper treats the navigation component of ATM-Star called GNSS-LEO, which is compatible with today's GPS receivers and aims to be a solution for the Global Navigation Satellite System Phase 2.
Somatic embryogenesis and plantlet regeneration from embryos isolated from stored seeds of <i>Picea glauca</i> (1990)

White spruce (Picea glauca) embryogenic callus was obtained using 3- to 11-year-old seeds as a source of zygotic embryos. They were cultured on half-strength Litvay's medium supplemented with 10 μM 2,4-dichlorophenoxyacetic acid, 5 μM benzylaminopurine, 1 g/L casein hydrolysate, 500 mg/L glutamine, and 1% sucrose. The frequency of induction of embryogenic callus was significantly improved by incubation at 25 °C and by a 4-h imbibition of the seeds. The yield of embryogenic callus was significantly affected by the geographic provenance of the seeds and by their number of years in storage. A significant correlation was also found between the yield of embryogénie callus and the percentage of germination of the seedlot used. Even after 11 years of storage, 40% of the zygotic embryos could produce an embryogenic callus when dissected from seeds with a high germination rate. Somatic embryos were matured after transfer onto an embryo development medium composed of the same medium but including 6% sucrose, 1 μM 2,4-dichlorophenoxyacetic acid, and 5 μM kinetin. The somatic embryos developed further under in vitro conditions and were then transplanted into soil. The somatic embryoderived plantlets established in the greenhouse were similar to control plantlets obtained from germinated seeds. Mature embryos from stored seeds were shown to constitute a valuable source for white spruce somatic embryogenesis.
Efficient large-scale production and concentration of HIV-1-based lentiviral vectors for use in vivo (2003)

The aim of this study was to develop an efficient method for packaging and concentrating lentiviral vectors that consistently yields high-titer virus on a scale suitable for in vivo applications. Transient cotransfection of 293T packaging cells with DNA plasmids encoding lentiviral vector components was optimized using SuperFect, an activated dendrimer-based transfection reagent. The use of SuperFect allowed reproducible and efficient production of high-titer lentiviral vector at concentrations greater than 1 x 10(7) transducing units per ml (TU/ml) and required less than one-third of the total amount of DNA used in traditional calcium phosphate transfection methods. Viral titers were further increased using a novel concentration protocol that yielded an average final titer of 1.4 x 10(10) TU/ml. Lentiviruses produced using these methods exhibited efficient transduction of central nervous system and peripheral tissues in vivo. The method is reproducible and can be scaled up to facilitate the use of these vectors in animal studies.
Binarity in Cool Asymptotic Giant Branch Stars: A<i>GALEX</i>Search for Ultraviolet Excesses (2008)

The search for binarity in AGB stars is of critical importance for our understanding of how planetary nebulae acquire the dazzling variety of aspherical shapes which characterizes this class. However, detecting binary companions in such stars has been severely hampered due to their extreme luminosities and pulsations. We have carried out a small imaging survey of AGB stars in ultraviolet light (using GALEX), where these cool objects are very faint, in order to search for hotter companions. We report the discovery of significant far-ultraviolet excesses toward nine of these stars. The far-ultraviolet excess most likely results either directly from the presence of a hot binary companion or indirectly from a hot accretion disk around the companion.
Collectins and their role in lung immunity (2003)

The collectins are a small family of secreted glycoproteins that contain C-type lectin domains and collagenous regions. They have an important function in innate immunity, recognizing and binding to microorganisms via sugar arrays on the microbial surface. Their function is to enhance adhesion and phagocytosis of microorganisms by agglutination and opsonization. In the lung, two members of the collectin family, surfactant proteins A and D, are major protein constituents of surfactant. Another collectin, mannan-binding lectin, is also present in the upper airways and buccal cavity and may protect against respiratory infections. Recent work has shown that collectins have roles in resistance to allergy and in the control of apoptosis and clearance of apoptotic macrophage in the lung.
The therapeutic efficacy of human adipose tissue‐derived mesenchymal stem cells on experimental autoimmune hearing loss in mice (2011)

Autoimmune inner ear disease is characterized by progressive, bilateral although asymmetric, sensorineural hearing loss. Patients with autoimmune inner ear disease had higher frequencies of interferon-γ-producing T cells than did control subjects tested. Human adipose-derived mesenchymal stem cells (hASCs) were recently found to suppress effector T cells and inflammatory responses and therefore have beneficial effects in various autoimmune diseases. The aim of this study was to examine the immunosuppressive activity of hASCs on autoreactive T cells from the experimental autoimmune hearing loss (EAHL) murine model. Female BALB/c mice underwent β-tubulin immunization to develop EAHL; mice with EAHL were given hASCs or PBS intraperitoneally once a week for 6 consecutive weeks. Auditory brainstem responses were examined over time. The T helper type 1 (Th1)/Th17-mediated autoreactive responses were examined by determining the proliferative response and cytokine profile of splenocytes stimulated with β-tubulin. The frequency of regulatory T (Treg) cells and their suppressive capacity on autoreactive T cells were also determined. Systemic infusion of hASCs significantly improved hearing function and protected hair cells in established EAHL. The hASCs decreased the proliferation of antigen-specific Th1/Th17 cells and induced the production of anti-inflammatory cytokine interleukin-10 in splenocytes. They also induced the generation of antigen-specific CD4(+) CD25(+) Foxp3(+) Treg cells with the capacity to suppress autoantigen-specific T-cell responses. The experiment demonstrated that hASCs are one of the important regulators of immune tolerance with the capacity to suppress effector T cells and to induce the generation of antigen-specific Treg cells.
Defining the blueprint of the cancer genome (2008)

It is widely accepted that cancer is a disease caused by accumulation of mutations in specific genes. These tumor-specific mutations provide clues to the cellular processes underlying tumorigenesis and have proven useful for diagnostic and therapeutic purposes. To date, however, only a small fraction of genes has been analyzed and the number and type of alterations responsible for the development of common tumor types are unknown. The determination of the human genome sequence coupled with improvements in sequencing and bioinformatic approaches have made it possible to examine the cancer cell genome in a comprehensive and unbiased manner. Systematic sequencing studies have been performed on gene families involved in signal transduction in several tumor types, and have now been extended to include the majority of protein-coding genes in breast and colorectal cancers. These analyses have identified new genes and pathways that had not been linked previously to human cancer. One example has been the discovery of genetic alterations in the PIK3CA gene encoding p110alpha phosphatidylinositol 3-kinase and in related pathway genes in >30% of colon and breast cancers. These mutational analyses provide a window into the genetic landscape of human cancer, indicate new targets for personalized diagnostic and therapeutic intervention, and suggest lessons for future large-scale genomic analyses in human tumors.
Phrenic nerve stimulation in normal subjects and in patients with diaphragmatic weakness. (1987)

Phrenic nerve stimulation is often considered to be difficult and unreliable. The time taken for the phrenic nerves to be located and adequately stimulated was measured in 110 subjects, aged 21-89 years, 26 of whom had diaphragmatic weakness; and phrenic nerve conduction time was recorded in 76 of these individuals. Each phrenic nerve was stimulated transcutaneously in the neck with square wave impulses 0.1 ms in duration at 1 Hz and 80-160 volts while diaphragmatic muscle action potentials were recorded with surface electrodes. The time taken to locate either phrenic nerve ranged from two seconds to 22 minutes (median 10s). Both nerves were located in 83 of the 84 control subjects (99%) and in 21 of the 26 patients with diaphragmatic weakness (81%). Mean (SD) phrenic nerve conduction time in the control subjects was 6.94 (0.77) ms on the right and 6.61 (0.77) ms on the left. A weak relationship was found between conduction time and the subjects' age and height. Four out of 24 patients with diaphragmatic weakness had a prolonged phrenic nerve conduction time. Transcutaneous stimulation of the phrenic nerves was not a time consuming procedure, and it was well tolerated, reproducible, and successful in 95% of subjects.
Initial experience related to the use of the Cosman-Roberts-Wells stereotactic instrument (1990)

Initial experience with a new arc-radius design of stereotactic frame that interfaced with the existing components of the Brown-Roberts-Wells instrument is reported. Over a 6-month period, 32 procedures were performed on 23 males and nine female patients (mean age 32 years); these included 27 stereotactic biopsy procedures, two stereotactic implantations of cyst catheter reservoirs, two ventriculoscopic aspirations of third ventricular colloid cysts, and one stereotactic aspiration of a craniopharyngioma. In all cases successful targeting was achieved and verified by postoperative computerized tomography. There were no operation-related complications. This new frame offers rapid and accurate targeting and is a useful adjunct to the stereotactic armamentarium.
Distributed Coupling of Dual-Modes in a Circular Resonator and Low-Profile Dielectric Disk Resonator BPF (1999)

this paper, the coupling is calculated by distributed coupling concept and is compared with an experiment and FD-TD analysis result. The method of frequency tuning of each mode is also discussed.
Text-based crude oil price forecasting: A deep learning approach (2018)

This study proposes a new, novel crude oil price forecasting method based on online media text mining, with the aim of capturing the more immediate market antecedents of price fluctuations. Specifically, this is an early attempt to apply deep learning techniques to crude oil forecasting, and to extract hidden patterns within online news media using a convolutional neural network (CNN). While the news-text sentiment features and the features extracted by the CNN model reveal significant relationships with the price change, they need to be grouped according to their topics in the price forecasting in order to obtain a greater forecasting accuracy. This study further proposes a feature grouping method based on the Latent Dirichlet Allocation (LDA) topic model for distinguishing effects from various online news topics. Optimized input variable combination is constructed using lag order selection and feature selection methods. Our empirical results suggest that the proposed topic-sentiment synthesis forecasting models perform better than the older benchmark models. In addition, text features and financial features are shown to be complementary in producing more accurate crude oil price forecasts.
City Mobility Model with Google Earth Visualization (2007)

Mobile Ad Hoc Networks are flexible, self configuring networks that do not need a fixed infrastructure. When these nets are simulated, mobility models can be used to specify node movements. The work in this thesis focuses on designing an extension of the random trip mobility model on a city section from EPFL (Swiss federal institute of technology). Road data is extracted from the census TIGER database, displayed in Google Earth and used as input for the model. This model produces output that can be used in the open source network simulator ns-2. We created utilities that take output from a database of US counties, the TIGER database, and convert it to KML. KML is an XML based format used by Google Earth to store geographical data, so that it can be viewed in Google Earth. This data will then be used as input to the modified mobility model and finally run through the ns-2 simulator. We present some NAM traces, a network animator that will show node movements over time. We managed to complete most of the goals we set out, apart from being able to modify node positions in Google Earth. This was skipped because the model we modified had an initialization phase that made node positions random regardless of initial position. We were also asked to add the ability to set stationary nodes in Google Earth; this was not added due to time constraints.