gebhart/patrepeval huggingface dataset:
Impaired B and T Cell Antigen Receptor Signaling in p110δ PI 3-Kinase Mutant Mice (2002)

Class IA phosphoinositide 3-kinases (PI3Ks) are a family of p85/p110 heterodimeric lipid kinases that generate second messenger signals downstream of tyrosine kinases, thereby controlling cell metabolism, growth, proliferation, differentiation, motility, and survival. Mammals express three class IA catalytic subunits: p110alpha, p110beta, and p110delta. It is unclear to what extent these p110 isoforms have overlapping or distinct biological roles. Mice expressing a catalytically inactive form of p110delta (p110delta(D910A)) were generated by gene targeting. Antigen receptor signaling in B and T cells was impaired and immune responses in vivo were attenuated in p110delta mutant mice. They also developed inflammatory bowel disease. These results reveal a selective role for p110delta in immunity.
TAK, an HIV Tat-associated kinase, is a member of the cyclin-dependent family of protein kinases and is induced by activation of peripheral blood lymphocytes and differentiation of promonocytic cell lines (1997)

We have previously identified a cellular protein kinase activity termed TAK that specifically associates with the HIV types 1 and 2 Tat proteins. TAK hyperphosphorylates the carboxyl-terminal domain of the large subunit of RNA polymerase II in vitro in a manner believed to activate transcription [Herrmann, C. H. & Rice, A. P. (1995) J. Virol. 69, 1612-1620]. We show here that the catalytic subunit of TAK is a known human kinase previously named PITALRE, which is a member of the cyclin-dependent family of proteins. We also show that TAK activity is elevated upon activation of peripheral blood mononuclear cells and peripheral blood lymphocytes and upon differentiation of U1 and U937 promonocytic cell lines to macrophages. Therefore, in HIV-infected individuals TAK may be induced in T cells following activation and in macrophages following differentiation, thus contributing to high levels of viral transcription and the escape from latency of transcriptionally silent proviruses.
Anti-Inflammatory Activity of Immunoglobulin G Resulting from Fc Sialylation (2006)

Immunoglobulin G (IgG) mediates pro- and anti-inflammatory activities through the engagement of its Fc fragment (Fc) with distinct Fcg receptors (FcgRs). One class of Fc-FcgR interactions generates pro-inflammatory effects of immune complexes and cytotoxic antibodies. In contrast, therapeutic intravenous gamma globulin and its Fc fragments are anti-inflammatory. We show here that these distinct properties of the IgG Fc result from differential sialylation of the Fc core polysaccharide. IgG acquires anti-inflammatory properties upon Fc sialylation, which is reduced upon the induction of an antigen-specific immune response. This differential sialylation may provide a switch from innate anti-inflammatory activity in the steady state to generating adaptive pro-inflammatory effects upon antigenic challenge.
Effect of Exogenous Lipase on Dough Lipids During Mixing of Wheat Flours (1998)

ABSTRACT In control dough, endogenous wheat lipase was inactive, because the triacylglycerol (TAG), 1,2‐diacylglycerol (DAG 1,2 ), and 1,3‐diacylglycerol (DAG 1,3 ) fractions of nonpolar lipids were not affected by mixing. Conversely, the free fatty acid (FFA) and monoacylglycerol (MAG) fractions decreased, mainly due to the oxidation of polyunsaturated fatty acids (PUFA) catalyzed by wheat lipoxygenase. Addition of exogenous lipase to flour (15 lipase units [LU] per gram of dry matter) resulted in substantial modification of nonpolar lipids during dough mixing. Due to the 1,3 specificity of the lipase used in this experiment, the TAG and DAG 1,3 fractions decreased, whereas the MAG and FFA fractions increased. The DAG 1,2 fraction increased at the beginning of mixing and decreased after 40 min of mixing. Moreover, part of the PUFA released by lipase activity was oxidized by wheat lipoxygenase, resulting in major losses of PUFA. Conversely, the net content of the saturated and monounsaturated fatty acids (SMUFA) remained constant, because the free SMUFA content increased primarily at the expense of the esterified forms. For a constant mixing time of 20 min, increasing the amount of lipase added to dough (from 2.5 to 25 LU/g of dry matter) resulted in a linear decrease in the TAG fraction and a linear increase in the SMUFA content in the FFA fraction. At the same time, the PUFA content of the FFA fraction increased only for additions of lipase to flour of &gt;5 LU/g of dry matter, due to partial oxidation by wheat lipoxygenase.
Marine Magnetic Data Holdings of World Data Center-a for Marine Geology and Geophysics (1992)

The World Data Center-A for Marine Geology and Geophysics is co-located with the Marine Geology & Geophysical Data Center, Boulder, CO. Fifteen million digital marine magnetic trackline measurements are managed within the GEOphysical DAta System (GEODAS). The bulk of these data were collected with proton precision magnetometers under Transit Satellite navigational control. Along-track sampling averages about 1 sample per kilometer, while spatial density, a function of ship's track and survey pattern, range from 4 to 0.02 data points/sq. km. In the near future, the entire geophysical data set will be available on CD-ROM. The Marine Geology and Geophysics Division (World Data Center-A for MGG), of the National Geophysical Data Center, handles a broad spectrum of marine geophysical data, including measurements of bathymetry, magnetics, gravity, seismic reflection subbottom profiles, and side-scan images acquired by ships throughout the world's oceans. Digital data encompass the first three, while the latter two are in analog form, recorded on 35mm microfilm. The marine geophysical digital trackline data are contained in the GEODAS data base which includes 11.6 million nautical miles of cruise trackline coverage contributed by more than 70 organizations worldwide. The inventory includes data from 3206 cruises with 33 million digital records and indexing to 5.3 million track miles of analog data on microfilm.
Epidermal devices for noninvasive, precise, and continuous mapping of macrovascular and microvascular blood flow (2015)

Continuous monitoring of variations in blood flow is vital in assessing the status of microvascular and macrovascular beds for a wide range of clinical and research scenarios. Although a variety of techniques exist, most require complete immobilization of the subject, thereby limiting their utility to hospital or clinical settings. Those that can be rendered in wearable formats suffer from limited accuracy, motion artifacts, and other shortcomings that follow from an inability to achieve intimate, noninvasive mechanical linkage of sensors with the surface of the skin. We introduce an ultrathin, soft, skin-conforming sensor technology that offers advanced capabilities in continuous and precise blood flow mapping. Systematic work establishes a set of experimental procedures and theoretical models for quantitative measurements and guidelines in design and operation. Experimental studies on human subjects, including validation with measurements performed using state-of-the-art clinical techniques, demonstrate sensitive and accurate assessment of both macrovascular and microvascular flow under a range of physiological conditions. Refined operational modes eliminate long-term drifts and reduce power consumption, thereby providing steps toward the use of this technology for continuous monitoring during daily activities.
ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems (2010)

ToppCluster is a web server application that leverages a powerful enrichment analysis and underlying data environment for comparative analyses of multiple gene lists. It generates heatmaps or connectivity networks that reveal functional features shared or specific to multiple gene lists. ToppCluster uses hypergeometric tests to obtain list-specific feature enrichment P-values for currently 17 categories of annotations of human-ortholog genes, and provides user-selectable cutoffs and multiple testing correction methods to control false discovery. Each nameable gene list represents a column input to a resulting matrix whose rows are overrepresented features, and individual cells per-list P-values and corresponding genes per feature. ToppCluster provides users with choices of tabular outputs, hierarchical clustering and heatmap generation, or the ability to interactively select features from the functional enrichment matrix to be transformed into XGMML or GEXF network format documents for use in Cytoscape or Gephi applications, respectively. Here, as example, we demonstrate the ability of ToppCluster to enable identification of list-specific phenotypic and regulatory element features (both cis-elements and 3'UTR microRNA binding sites) among tissue-specific gene lists. ToppCluster's functionalities enable the identification of specialized biological functions and regulatory networks and systems biology-based dissection of biological states. ToppCluster can be accessed freely at http://toppcluster.cchmc.org.
Assessment of the p wave dispersion and duration in elite women basketball players. (2010)

P wave dispersion was increased in elite woman basketball players as compared with healthy sedentary subjects. P wave dispersion was correlated with heart rate, body height, body weight and body surface area.
STRUCTURE AND ASSEMBLY OF COATED VESICLES (1987)

CHARACTERISTICS OF THE COAT PROTEINS AND THEIR ASSEMBLy 52 Clathrin and Cages 52 Accessory Proteins and Reconstitution oJCoats 54 STRUCTURE OF CAGES AND COATS 55 Packing oj Clathrin to Form the Polyhedral Lattice 55 Three· Dimensional Structure oj the Cage... ..... ...... ..... .... .... 56 Three-Dimensional Structure oj the Coat .... ....... ...... 58 RECEPTORS IN COATED PITS AND VESICLES ••.••••.•• 61 Packing Considerations 61 The Cytoplasmic Portion oj Receptors 63 STRUCTURE AND FUNCTION 64
KIF5B‐RET fusions in Chinese patients with non–small cell lung cancer (2013)

KIF5B-RET fusions were quite rare, with a prevalence of approximately 1.5% in Chinese patients with NSCLC, and they were a little more common in patients with adenocarcinoma than in those with squamous carcinoma (1.73% vs 0.84%). In addition, KIF5B-RET fusions also existed in patients with low-grade malignant neuroendocrine tumors.
Reduced expression of the murine p85α subunit of phosphoinositide 3-kinase improves insulin signaling and ameliorates diabetes (2002)

A critical component of insulin action is the enzyme phosphoinositide (PI) 3-kinase.The major regulatory subunits of PI 3-kinase, p85 and its splice variants, are encoded by the Pik3r1 gene.Heterozygous disruption of Pik3r1 improves insulin signaling and glucose homeostasis in normal mice and mice made insulin-resistant by heterozygous deletion of the Insulin receptor and/or insulin receptor substrate-1 (IRS1) genes.Reduced expression of p85 modulates the molecular balance between this protein, the p110 catalytic subunit of PI 3-kinase, and the IRS proteins.Thus, despite the decrease in p85, PI 3-kinase activation is normal, insulin-stimulated Akt activity is increased, and glucose tolerance and insulin sensitivity are improved.Furthermore, Pik3r1 heterozygosity protects mice with genetic insulin resistance from developing diabetes.These data suggest that regulation of p85 levels may provide a novel therapeutic target for the treatment of type 2 diabetes.
Cholesterol Modification of Hedgehog Signaling Proteins in Animal Development (1996)

Hedgehog (Hh) proteins comprise a family of secreted signaling molecules essential for patterning a variety of structures in animal embryogenesis. During biosynthesis, Hh undergoes an autocleavage reaction, mediated by its carboxyl-terminal domain, that produces a lipid-modified amino-terminal fragment responsible for all known Hh signaling activity. Here it is reported that cholesterol is the lipophilic moiety covalently attached to the amino-terminal signaling domain during autoprocessing and that the carboxyl-terminal domain acts as an intramolecular cholesterol transferase. This use of cholesterol to modify embryonic signaling proteins may account for some of the effects of perturbed cholesterol biosynthesis on animal development.
Anatomic verification of a novel method for precise intrascalar localization of cochlear implant electrodes in adult temporal bones using clinically available computed tomography (2010)

We have anatomically validated this automated method for predicting the intrascalar location of CI arrays using CT. Using this algorithm and pre- and postintervention CT, rapid feedback regarding implant location and expected audiologic outcomes could be obtained in clinical settings.
Inhibition of Flavivirus Infections by Antisense Oligomers Specifically Suppressing Viral Translation and RNA Replication (2005)

RNA elements within flavivirus genomes are potential targets for antiviral therapy. A panel of phosphorodiamidate morpholino oligomers (PMOs), whose sequences are complementary to RNA elements located in the 5'- and 3'-termini of the West Nile (WN) virus genome, were designed to anneal to important cis-acting elements and potentially to inhibit WN infection. A novel Arg-rich peptide was conjugated to each PMO for efficient cellular delivery. These PMOs exhibited various degrees of antiviral activity upon incubation with a WN virus luciferase-replicon-containing cell line. Among them, PMOs targeting the 5'-terminal 20 nucleotides (5'End) or targeting the 3'-terminal element involved in a potential genome cyclizing interaction (3'CSI) exhibited the greatest potency. When cells infected with an epidemic strain of WN virus were treated with the 5'End or 3'CSI PMO, virus titers were reduced by approximately 5 to 6 logs at a 5 muM concentration without apparent cytotoxicity. The 3'CSI PMO also inhibited mosquito-borne flaviviruses other than WN virus, and the antiviral potency correlated with the conservation of the targeted 3'CSI sequences of specific viruses. Mode-of-action analyses showed that the 5'End and 3'CSI PMOs suppressed viral infection through two distinct mechanisms. The 5'End PMO inhibited viral translation, whereas the 3'CSI PMO did not significantly affect viral translation but suppressed RNA replication. The results suggest that antisense PMO-mediated blocking of cis-acting elements of flavivirus genomes can potentially be developed into an anti-flavivirus therapy. In addition, we report that although a full-length WN virus containing a luciferase reporter (engineered at the 3' untranslated region of the genome) is not stable, an early passage of this reporting virus can be used to screen for inhibitors against any step of the virus life cycle.
Cytoplasmic Inclusion Bodies in Escherichia coli Producing Biosynthetic Human Insulin Proteins (1982)

Escherichia coli that has been genetically manipulated by recombinant DNA technology to synthesize human insulin polypeptides (A chain, B chain, or proinsulin) contains prominent cytoplasmic inclusion bodies. The amount of inclusion product within the cells corresponds to the quantity of chimeric protein formed by the bacteria. At peak production, the inclusion bodies may occupy as much as 20 percent of the Escherichia coli cellular volume.
Robust biological nitrogen fixation in a model grass–bacterial association (2015)

Nitrogen-fixing rhizobacteria can promote plant growth; however, it is controversial whether biological nitrogen fixation (BNF) from associative interaction contributes to growth promotion. The roots of Setaria viridis, a model C4 grass, were effectively colonized by bacterial inoculants resulting in a significant enhancement of growth. Nitrogen-13 tracer studies provided direct evidence for tracer uptake by the host plant and incorporation into protein. Indeed, plants showed robust growth under nitrogen-limiting conditions when inoculated with an ammonium-excreting strain of Azospirillum brasilense. (11)C-labeling experiments showed that patterns in central carbon metabolism and resource allocation exhibited by nitrogen-starved plants were largely reversed by bacterial inoculation, such that they resembled plants grown under nitrogen-sufficient conditions. Adoption of S. viridis as a model should promote research into the mechanisms of associative nitrogen fixation with the ultimate goal of greater adoption of BNF for sustainable crop production.
Messenger RNA vaccine based on recombinant MS2 virus‐like particles against prostate cancer (2013)

Prostate cancer (PCa) is the most diagnosed cancer in the western male population with high mortality. Recently, alternative approaches based on immunotherapy including mRNA vaccines for PCa have shown therapeutic promise. However, for mRNA vaccine, several disadvantages such as the instability of mRNA, the high cost of gold particles, the limited production scale for mRNA-transfected dendritic cells in vitro, limit their development. Herein, recombinant bacteriophage MS2 virus-like particles (VLPs), which based on the interaction of a 19-nucleotide RNA aptamer and the coat protein of bacteriophage MS2, successfully addressed these questions, in which target mRNA was packaged by MS2 capsid. MS2 VLP-based mRNA vaccines were easily prepared by recombinant protein technology, nontoxic and RNase-resistant. We show the packaged mRNA was translated into protein as early as 12 hr after phagocytosed by macrophages. Moreover, MS2 VLP-based mRNA vaccines induced strong humoral and cellular immune responses, especially antigen-specific cytotoxic T-lymphocyte (CTL) and balanced Th1/Th2 responses without upregulation of CD4(+) regulatory T cells, and protected C57BL/6 mice against PCa completely. As a therapeutic vaccine, MS2 VLP-based mRNA vaccines delayed tumor growth. Our results provide proof of concept on the efficacy and safety of MS2 VLP-based mRNA vaccine, which provides a new delivery approach for mRNA vaccine and implies important clinical value for the prevention and therapy of PCa.
Chimpanzee adenovirus CV-68 adapted as a gene delivery vector interacts with the coxsackievirus and adenovirus receptor (2002)

A replication-defective form of chimpanzee adenovirus type 68 (C68) has been developed to circumvent problems posed by widespread preexisting immunity to common human adenovirus vectors. To investigate the determinants of C68 tropism, its interaction with the coxsackievirus and adenovirus receptor (CAR) was studied. Although CHO cells were resistant to transduction by C68 as well as by adenovirus type 5 (Ad5), CHO cells expressing either human or murine CAR were transduced readily. C68 transduction, like Ad5 transduction, was blocked when cells were exposed to anti-CAR antibody or when virus was exposed to a soluble form of the CAR extracellular domain. These results indicate that gene delivery by C68 occurs by a CAR-dependent mechanism.
Maximum mipmaps for fast, accurate, and scalable dynamic height field rendering (2008)

This paper presents a GPU-based, fast, and accurate dynamic height field rendering technique that scales well to large scale height fields. Current real-time rendering algorithms for dynamic height fields employ approximate ray-height field intersection methods, whereas accurate algorithms require pre-computation in the order of seconds to minutes and are thus not suitable for dynamic height field rendering. We alleviate this problem by using maximum mipmaps, a hierarchical data structure supporting accurate and efficient rendering while simultaneously lowering the pre-computation costs to negligible levels. Furthermore, maximum mipmaps allow for view-dependent level-of-detail rendering. In combination with hierarchical ray-stepping this results in an efficient intersection algorithm for large scale height fields.
Force output of cat motor units stimulated with trains of linearly varying frequency (1989)

1. A relation between stimulation frequency and muscle force is usually determined with stimulus trains of constant frequency and described as a single-valued sigmoid curve. This relationship fails to explain a number of features of rate coding. 2. Single motor units were isolated in medial gastrocnemius or soleus muscles of cats deeply anesthetized with pentobarbital sodium. Motor units were classified as fast or slow. Each unit was stimulated with a train whose frequency varied linearly from less than 3 pulses per second (pps) to 20% above the unit's fusion frequency and back to about 3 pps with a period of 5 s. 3. All motor units showed a marked hysteresis during frequency-varying stimulation. A greater force was produced when frequency was decreasing than when it was increasing. The force output of each unit remained nearly maximal as stimulus frequency declined from its maximum to about one-half of the unit's fusion frequency; force rapidly declined with further decreases in frequency. The force-frequency relation could change with each trial as frequency increased but was highly reproducible when frequency decreased. This suggested a strategy by which central nervous system (CNS) control could maximize the force at any discharge rate and produce a predictable force-frequency relation. 4. Posttetanic potentiation, motor unit slowing, and a preload which causes a motor unit to operate on the negatively sloping portion of the length-tension curve may each contribute to the observed hysteresis under certain circumstances. None can explain why hysteresis was consistently seen in all motor units. A time-dependent rate of tension development and decay together with a catchlike property can account for all of the properties of hysteresis and appeared to be the primary cause of hysteresis in fully potentiated motor units.
Vector-mediated delivery of 125I-labeled beta-amyloid peptide A beta 1-40 through the blood-brain barrier and binding to Alzheimer disease amyloid of the A beta 1-40/vector complex. (1995)

The brain amyloid of Alzheimer disease (AD) may potentially be imaged in patients with AD by using neuroimaging technology and a radiolabeled form of the 40-residue beta-amyloid peptide A beta 1-40 that is enabled to undergo transport through the brain capillary endothelial wall, which makes up the blood-brain barrier (BBB) in vivo. Transport of 125I-labeled A beta 1-40 (125I-A beta 1-40) through the BBB was found to be negligible by experiments with both an intravenous injection technique and an internal carotid artery perfusion method in anesthetized rats. In addition, 125I-A beta 1-40 was rapidly metabolized after either intravenous injection or internal carotid artery perfusion. BBB transport was increased and peripheral metabolism was decreased by conjugation of monobiotinylated 125I-A beta 1-40 to a vector-mediated drug delivery system, which consisted of a conjugate of streptavidin (SA) and the OX26 monoclonal antibody to the rat transferrin receptor, which undergoes receptor-mediated transcytosis through the BBB. The brain uptake, expressed as percent of injected dose delivered per gram of brain, of the 125I,bio-A beta 1-40/SA-OX26 conjugate was 0.15 +/- 0.01, a level that is 2-fold greater than the brain uptake of morphine. The binding of the 125I,bio-A beta 1-40/SA-OX26 conjugate to the amyloid of AD brain was demonstrated by both film and emulsion autoradiography performed on frozen sections of AD brain. Binding of the 125I,bio-A beta 1-40/SA-OX26 conjugate to the amyloid of AD brain was completely inhibited by high concentrations of unlabeled A beta 1-40. In conclusion, these studies show that BBB transport and access to amyloid within brain may be achieved by conjugation of A beta 1-40 to a vector-mediated BBB drug delivery system.