gebhart/patrepeval huggingface dataset:
A fifth member of the mammalian G-protein beta-subunit family. Expression in brain and activation of the beta 2 isotype of phospholipase C. (1994)

The beta-subunits of the heterotrimeric GTP-binding proteins (G-proteins) are important regulators of G-protein alpha-subunits as well as of certain signal transduction receptors and effectors. We have identified a fifth member of the G-protein beta-subunit family, G beta 5, by molecular cloning. Sequence analysis of recombinant clones revealed an open reading frame of 1,059 base pairs, potentially encoding a protein of 353 amino acids having 53% identity to previously identified G beta-subunit proteins. Northern blot analysis of poly(A)-selected mRNA prepared from different mouse tissues demonstrated that G beta 5 is predominantly expressed in adult brain as two transcripts of 2.3 and 1.75 kilobases. A G beta 5-specific antiserum detected a band of 39.3 kilodaltons on immunoblots of crude membrane proteins isolated from normal mouse brain but not from other tissues. Using a transient cotransfection assay, we showed that a plasmid construct expressing the G beta 5 open reading frame, when coexpressed with different G-protein gamma (G gamma)-subunits, can stimulate the activity of the beta 2 isoform of phosphoinositide-specific phospholipase C (PLC beta 2). The stimulation of PLC beta 2 was most pronounced when G beta 5 was co-expressed with G gamma 2, although activation was observed when G beta 5 was cotransfected with either G gamma 1, G gamma 3, G gamma 5, or G gamma cone. These results prove that G beta 5 can functionally associate with G gamma proteins and is therefore a bona fide member of the G beta protein family. The rather low level of identity between G beta 5 and the other mammalian G beta-subunits may shed light on structural/sequence elements necessary for G beta protein function.
Mouse/Human Chimeric Me1-14 Antibody: Genomic Cloning of the Variable Region Genes, Linkage to Human Constant Region Genes, Expression, and Characterization (1994)

Murine monoclonal antibody Me1-14, which recognizes an epitope on chondroitin proteoglycan sulfate expressed in malignant glioma and melanoma, has been used for radioimmunolocalization and therapy both in animal models and in patients. Here, we report the generation, characterization, and in vivo biodistribution of mouse/human chimeric Me1-14. Rearranged immunoglobulin genes from the Me1-14 hybridoma were identified by Southern blot analysis. Putative rearranged light- and heavy-chain genes were cloned from Lambda-ZapII Me1-14 genomic libraries and sequenced for nucleotide analysis. One of the putative heavy-chain Eco RI fragments (3.5 kb) had all the features of an intact variable region, including a functional leader sequence, in-frame V-D and D-J junctions, and cysteines 22 and 92. The deduced amino acid sequence from the heavy-chain variable region gene showed considerable homology with the invariant protein sequence of the mouse heavy-chain subgroup IIIB. Like the heavy-chain gene, one of the putative rearranged kappa-chain Hind III fragments (4 kb) had all of the characteristics of the functional variable region, and the deduced amino acid sequence showed homology to the invariant sequence of kappa-chain group V. The variable region genes for heavy- and light-chains were linked to human constant region exons in the expression vectors at the unique sites and cotransfected into mouse SP2/0 cells. The production level of chimeric Me1-14 from ascites in the highest expressing transfectoma was 1.8 mg/ml. The chimeric Me1-14 antibody exhibited the same specificity and similar affinity as that of parent Me1-14. Direct comparison of radioiodinated chimeric and murine Me1-14 in paired-label biodistribution analysis in subcutaneous xenograft-bearing mice showed higher tumor-to-normal organ ratios for chimeric Me1-14 IgG2, suggesting that this chimeric Me1-14 may be potentially useful in vivo for diagnostic and therapeutic purposes in patients.
Automation of ocean model performance metrics (2009)

A system to rapidly and automatically assess the performance of numerical ocean modeling systems was developed by the U.S. Naval Research Laboratory (NRL). This includes the calculation of quantitative, objective metrics of the accuracy of ocean forecasts. We will present results from this system, including metrics of surface and subsurface analysis and forecast fields. This work supports the U.S. Naval Oceanographic Office (NAVOCEANO), which provides oceanographic products in response to requests for environmental support for Navy operations. The development of a comprehensive automated system that provides model performance information is expected to increase the consistency of results, reduce errors, and reduce time required to generate oceanographie products.
Hierarchical data structures and algorithms for computer graphics. II. Applications (1988)

For pt.I see ibid., vol.8, no.3, p.48-68, May (1988). Advanced applications for preliminary display methods are focused on, with emphasis on the octree. Topics include use of the quadtree as a basis for hidden-surface algorithms, parallel and perspective projection methods to display a collection of objects represented by an octree, and the use of octrees to facilitate such image-rendering techniques as ray tracing and radiosity.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Gene therapy for Duchenne muscular dystrophy (2015)

Of the many approaches being pursued to treat DMD and BMD, gene therapy based on AAV-mediated delivery of microdystrophin is the most direct and promising method to treat the cause of the disorder. The major challenges to this approach are ensuring that microdystrophin can be delivered safely and efficiently without eliciting an immune response.
INT-131, a PPARgamma agonist for the treatment of type 2 diabetes. (2009)

INT-131, a novel, non-thiazolidinedione (TZD), selective peroxisome proliferator-activated receptor (PPAR)gamma modulator, is in development by InteKrin Therapeutics Inc for the treatment of type 2 diabetes mellitus (non-insulin dependent diabetes). The concept of selective modulation involves targeting and activating specific genes to minimize side effects while maintaining therapeutic benefits. In vitro, INT-131 attenuated adipogenic properties, indicating moderate PPARgamma activation/cofactor recruitment compared with the full agonistic properties of TZD compounds. INT-131 also compared favorably with TZDs in 6-month toxicity studies in rats and monkeys, exhibiting no increases in body or organ weights, and no relevant observations of edema or other fluid retention, which has been associated with congestive heart failure in TZDs. In phase I and II clinical trials, INT-131 was well tolerated, without any serious adverse events or reports of fluid retention. Antidiabetic efficacy was comparable with TZDs and was moderately greater than for other new, oral antidiabetic drugs, although only fasting plasma glucose levels were recorded. INT-131 appears to be a promising new PPARgamma agonist with potent antidiabetic actions and a favorable side effect profile; however, additional, extensive clinical investigation is required to justify the non-inferiority of this compound to TZDs and other oral antidiabetic drugs.
Management of the internal carotid artery during carotid body tumor surgery (1995)

Patients with carotid body tumors require accurate preoperative assessment of vessel involvement and the probable impact of interrupting blood flow through the internal carotid artery. Recent developments in imaging, methods of measuring cerebral blood flow, balloon occlusion testing, and techniques to maintain vascular flow when a graft is required have improved the surgeon's ability to completely resect these tumors with reduced complications. We discuss these methods with respect to our review of 20 carotid body tumors in 18 patients. Twenty-five percent of patients were misdiagnosed, and in four patients injury to the vessel wall required appropriate surgical intervention.
Delineation of hypoxia in canine myocardium using PET and copper(II)-diacetyl-bis(N(4)-methylthiosemicarbazone). (2002)

*Cu-ATSM PET has shown quantitative selective uptake in hypoxic myocardium within 20 min of tracer administration in 3 canine models of hypoxia.
Passion: Optimized I/O for Parallel Applications (1996)

We have implemented Passion on Intel's Paragon, Touchstone Delta, and iPSC/860 systems, and on the IBM SP system. We have also made it publicly available through the World Wide Web (http://www.cat.syr.edu/passion.html). We are in the process of porting the library to other machines and extending its functionality.
Changes of microsphere density with time in myocardial infarcts in dogs (1980)

The density of microspheres injected before occlusion of a coronary artery, in the infarcted region [I], was compared with that of healthy, normal myocardium [N], from the same dog. The [I]/[N] ratio was measured at different days after infarction up to 2 weeks. The ratio was below unity before the ninth day and above that thereafter. The changes in microspheres density can be explained on the basis of microsphere loss from necrotic tissue and changes in infarct mass.
Alert confidence fusion in intrusion detection systems with extended Dempster-Shafer theory (2005)

Accurate identification of misuse is a key factor in determining appropriate ways to protect systems. Modern intrusion detection systems often use alerts from different sources such as hosts and sub-networks to determine whether and how to respond to an attack. However, alerts from different locations should not be treated equally. We propose improving and assessing alert accuracy by incorporating an algorithm based on the exponentially weighted Dempster-Shafer (D-S) Theory of Evidence. Our approach uses D-S theory to combine beliefs in certain hypotheses under conditions of uncertainty and ignorance, and allows quantitative measurement of the belief and plausibility in our detection results. Our initial evaluations on the DARPA IDS evaluation data set show that our alert fusion algorithm can improve alert quality over those from Hidden Colored Petri-Net (HCPN) based alert correlation components installed at the demilitarized zone (DMZ) and inside network sites. Due to alert confidence fusion in our example, the detection rate rises from 75% to 93.8%, without adversely affecting the false positive rate.
Highly Sensitive in Vitro Selections for DNA-Linked Synthetic Small Molecules with Protein Binding Affinity and Specificity (2003)

We have developed in vitro selections for DNA-linked synthetic small molecules with protein binding affinity and specificity. These selections require only generally accessible equipment, offer high degrees of enrichment of active molecules from mixtures of predominantly inactive species, can be applied to a variety of unrelated proteins, and require approximately 108-fold less material than existing synthetic molecule screening methods. Iterating these selections multiplies the net enrichment of active molecules, enabling enormous overall enrichment factors exceeding 106 to be achieved. Further, the selections can be adapted to select for binding specificity in addition to binding affinity. The application of methods described in this work may play a key role in the discovery of desired molecules from DNA-templated synthetic libraries.
Increased metabolic activity in the septum and habenula during stress is linked to subsequent expression of learned helplessness behavior (2014)

Uncontrollable stress can have a profound effect on an organism's ability to respond effectively to future stressful situations. Behavior subsequent to uncontrollable stress can vary greatly between individuals, falling on a spectrum between healthy resilience and maladaptive learned helplessness. It is unclear whether dysfunctional brain activity during uncontrollable stress is associated with vulnerability to learned helplessness; therefore, we measured metabolic activity during uncontrollable stress that correlated with ensuing inability to escape future stressors. We took advantage of small animal positron emission tomography (PET) and 2-deoxy-2[(18)F]fluoro-D-glucose ((18)FDG) to probe in vivo metabolic activity in wild type Sprague Dawley rats during uncontrollable, inescapable, unpredictable foot-shock stress, and subsequently tested the animals response to controllable, escapable, predictable foot-shock stress. When we correlated metabolic activity during the uncontrollable stress with consequent behavioral outcomes, we found that the degree to which animals failed to escape the foot-shock correlated with increased metabolic activity in the lateral septum and habenula. When used a seed region, metabolic activity in the habenula correlated with activity in the lateral septum, hypothalamus, medial thalamus, mammillary nuclei, ventral tegmental area, central gray, interpeduncular nuclei, periaqueductal gray, dorsal raphe, and rostromedial tegmental nucleus, caudal linear raphe, and subiculum transition area. Furthermore, the lateral septum correlated with metabolic activity in the preoptic area, medial thalamus, habenula, interpeduncular nuclei, periaqueductal gray, dorsal raphe, and caudal linear raphe. Together, our data suggest a group of brain regions involved in sensitivity to uncontrollable stress involving the lateral septum and habenula.
Depletion/enhancement CMOS for a lower power family of three-valued logic circuits (1985)

A new family of ternary logic circuits that uses both depletion and enhancement types of complementary metal-oxide semiconductor (CMOS) transistors is presented. These circuits use two power supplies, each below the transistor's threshold voltages, and do not include resistors. Circuit designs of basic ternary operators (inverters, NAND, NOR) are described. These basic ternary operators can be used as building blocks in the VLSI implementation of three-valued digital systems. An example of the design of a ternary full adder using this family of logic circuits is also presented.
Poseidon: An Efficient Communication Architecture for Distributed Deep\n Learning on GPU Clusters (2017)

Deep learning models can take weeks to train on a single GPU-equipped\nmachine, necessitating scaling out DL training to a GPU-cluster. However,\ncurrent distributed DL implementations can scale poorly due to substantial\nparameter synchronization over the network, because the high throughput of GPUs\nallows more data batches to be processed per unit time than CPUs, leading to\nmore frequent network synchronization. We present Poseidon, an efficient\ncommunication architecture for distributed DL on GPUs. Poseidon exploits the\nlayered model structures in DL programs to overlap communication and\ncomputation, reducing bursty network communication. Moreover, Poseidon uses a\nhybrid communication scheme that optimizes the number of bytes required to\nsynchronize each layer, according to layer properties and the number of\nmachines. We show that Poseidon is applicable to different DL frameworks by\nplugging Poseidon into Caffe and TensorFlow. We show that Poseidon enables\nCaffe and TensorFlow to achieve 15.5x speed-up on 16 single-GPU machines, even\nwith limited bandwidth (10GbE) and the challenging VGG19-22K network for image\nclassification. Moreover, Poseidon-enabled TensorFlow achieves 31.5x speed-up\nwith 32 single-GPU machines on Inception-V3, a 50% improvement over the\nopen-source TensorFlow (20x speed-up).\n
The selective Trk inhibitor AZ623 inhibits brain‐derived neurotrophic factor–mediated neuroblastoma cell proliferation and signaling and is synergistic with topotecan (2010)

AZ623 is a novel selective Trk inhibitor that inhibits BDNF-mediated signaling and neuroblastoma cell proliferation. AZ623 treatment inhibits the growth of human neuroblastoma xenograft tumors, and treatment with AZ623 combined with topotecan results in the prolonged inhibition of tumor regrowth. On the basis of these results, further preclinical development is warranted.
Serum Uric Acid and Risk of Cardiovascular Mortality: A Prospective Long-Term Study of 83 683 Austrian Men (2007)

Our study demonstrates for the first time in a large prospective male cohort that SUA is independently related to mortality from CHF and stroke. Although increased SUA is not necessarily a causal risk factor, our results suggest the clinical importance of monitoring and intervention based on the presence of an increased SUA concentration, especially because SUA is routinely measured.
Magnetic Resonance Imaging of Blood and Clots In Vitro (1990)

The effects of variations in blood clot composition on magnetic relaxation rates and magnetic resonance (MR) image have been characterized in vitro. Both 1/T1 and 1/T2 were found to be linear functions of hematocrit for blood and clot, with increases in hematocrit resulting in progressive decreases in image signal intensity. Clot formation in fully oxygenated samples produced no change in relaxation rates or MR images compared with unclotted blood, but clot retraction was associated with a significant increase in 1/T2 that resulted in a decreased signal. Retraction resulted in a heterogenous image with appearance of a hypointense peripheral rim; differences in the method of clot preparation resulted in significant image inhomogeneity. The pattern of fibrinolysis was found to depend on the type of plasminogen activator used and its site of initial application. Injection of tissue plasminogen activator into the clot resulted in lysis, primarily in the clot interior, whereas placing the enzyme in the surrounding serum caused degradation from the outside of the clot. Both observations are consistent with the high binding affinity of tissue plasminogen activator for fibrin. By comparison, streptokinase, with low fibrin binding affinity, dissolved thrombi in a peripheral pattern whether injected into the thrombus or introduced in the serum. These findings identify several variables of clot composition and structure that influence MR images of thrombi and should be considered in their interpretation.
Simulation and Software Radio for Mobile Communications (2002)

Introduction. General Definition of Simulation Tools, Performance Evaluation for Digital Modulation Techniques. Orthogonal Frequency Division Multiplexing (OFDM) Transmission System. Code Division Multiplexing (CDM) Transmission System. Cellular Telecommunication System. Packet Telecommunications System. Software Radio Communication System.
Serum gelatinase B, TIMP-1 and TIMP-2 levels in multiple sclerosis (1999)

Metalloproteinases have been implicated in the pathogenesis of multiple sclerosis. We report longitudinal serum levels of gelatinase B and of the tissue inhibitors of matrix metalloproteinases (TIMP), TIMP-1 and TIMP-2, in 21 patients with relapsing multiple sclerosis. Patients had monthly clinical and gadolinium-enhanced MRI follow-up for 10 months. Longitudinal samples in nine healthy controls and cross-sectional samples from 12 patients with inflammatory CNS disease and 15 patients with other neurological diseases were used for comparison. Average serum gelatinase B, TIMP-1 and TIMP-2 levels were significantly higher in multiple sclerosis patients and those with other neurological diseases than in healthy controls. In the patients with multiple sclerosis, gelatinase B levels were significantly higher during clinical relapse compared with periods of clinical stability. Multiple sclerosis patients with high mean serum gelatinase B levels had significantly more T1-weighted gadolinium-enhancing MRI lesions than those with mean levels within the control range. TIMP-1 levels were not different during relapse and between relapses. There was a trend for TIMP-2 levels to be lower during relapse compared with non-relapse periods. For similar levels of serum gelatinase B, associated TIMP-1 levels were significantly lower and TIMP-2 levels significantly higher in multiple sclerosis patients compared with the inflammatory CNS control group. We propose that an abnormality in the inhibitory response to metalloproteinases may play an aetiological role in the chronicity of multiple sclerosis.
Sialylation of Group B Streptococcal Capsular Polysaccharide Is Mediated by<i>cpsK</i>and Is Required for Optimal Capsule Polymerization and Expression (2005)

Several bacterial pathogens have evolved the means to escape immune detection by mimicking host cell surface carbohydrates that are crucial for self/non-self recognition. Sialic acid, a terminal residue on these carbohydrates, inhibits activation of the alternate pathway of complement by recruiting the immune modulating molecule factors H, I, and iC3b. Sialylation of capsular polysaccharide (CPS) is important for virulence of group B streptococci (GBS), a significant human pathogen. We previously reported that cpsK, a gene within the cps locus of type III GBS, could complement a sialyltransferase deficient lst mutant of Haemophilus ducreyi, implicating its role in sialylation of the GBS capsule. To explore the function of cpsK in GBS capsule production, we created a mutant in cpsK. Immunoblot analysis and enzyme-linked immunosorbent assay using anti-type III CPS antisera demonstrated that the mutant CPS did not contain sialic acid. This was confirmed by high-performance liquid chromatography after mild acid hydrolysis of the CPS. Although increased CPS chain length was seen for this strain, CPS production was <20% of the parental isolate. An episomal cpsK copy restored synthesis of sialo-CPS to wild-type levels. These data support our hypothesis that cpsK encodes the GBS CPS sialyltransferase and provide further evidence that lack of CPS oligosaccharide sialylation reduces the amount of CPS expressed on the cell surface. These observations also imply that one or more of the components involved in synthesis or transport of oligosaccharide repeating units requires a sialo-oligosaccharide for complete activity.
An Interferon-γ-binding Protein of Novel Structure Encoded by the Fowlpox Virus (2003)

Poxviruses have evolved various strategies to counteract the host immune response, one of which is based on the expression of soluble cytokine receptors. Using various biological assays, we detected a chicken interferon-gamma (chIFN-gamma)-neutralizing activity in supernatants of fowlpox virus (FPV)-infected cells that could be destroyed by trypsin treatment. Secreted viral proteins were purified by affinity chromatography using matrix-immobilized chIFN-gamma, followed by two-dimensional gel electrophoresis. Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) analysis indicated that the viral IFN-gamma-binding protein in question was encoded by the FPV gene 016. The chicken IFN-gamma binding and neutralizing activity of the recombinant FPV016 protein was confirmed using supernatants of cells infected with a recombinant vaccinia virus that lacked its own IFN-gamma-binding protein but instead expressed the FPV016 gene. The FPV016 gene product also neutralized the activity of duck and human IFN-gamma but failed to neutralize the activity of mouse and rat IFN-gamma. Unlike previously known cellular and poxviral IFN-gamma receptors, which all contain fibronectin type III domains, the IFN-gamma-binding protein of FPV contains an immunoglobulin domain. Remarkably, it exhibits no significant homology to any known viral or cellular protein. Because IFN-gamma receptors of birds have not yet been characterized at the molecular level, the possibility remains that FPV016 represents a hijacked chicken gene and that avian and mammalian IFN-gamma receptors have fundamentally different primary structures.