gebhart/patrepeval huggingface dataset:
LAT Is Required for Tyrosine Phosphorylation of Phospholipase Cγ2 and Platelet Activation by the Collagen Receptor GPVI (1999)

In the present study, we have addressed the role of the linker for activation of T cells (LAT) in the regulation of phospholipase Cgamma2 (PLCgamma2) by the platelet collagen receptor glycoprotein VI (GPVI). LAT is tyrosine phosphorylated in human platelets heavily in response to collagen, collagen-related peptide (CRP), and FcgammaRIIA cross-linking but only weakly in response to the G-protein-receptor-coupled agonist thrombin. LAT tyrosine phosphorylation is abolished in CRP-stimulated Syk-deficient mouse platelets, whereas it is not altered in SLP-76-deficient mice or Btk-deficient X-linked agammaglobulinemia (XLA) human platelets. Using mice engineered to lack the adapter LAT, we showed that tyrosine phosphorylation of Syk and Btk in response to CRP was maintained in LAT-deficient platelets whereas phosphorylation of SLP-76 was slightly impaired. In contrast, tyrosine phosphorylation of PLCgamma2 was substantially reduced in LAT-deficient platelets but was not completely inhibited. The reduction in phosphorylation of PLCgamma2 was associated with marked inhibition of formation of phosphatidic acid, a metabolite of 1,2-diacylglycerol, phosphorylation of pleckstrin, a substrate of protein kinase C, and expression of P-selectin in response to CRP, whereas these parameters were not altered in response to thrombin. Activation of the fibrinogen receptor integrin alpha(IIb)beta(3) in response to CRP was also reduced in LAT-deficient platelets but was not completely inhibited. These results demonstrate that LAT tyrosine phosphorylation occurs downstream of Syk and is independent of the adapter SLP-76, and they establish a major role for LAT in the phosphorylation and activation of PLCgamma2, leading to downstream responses such as alpha-granule secretion and activation of integrin alpha(IIb)beta(3). The results further demonstrate that the major pathway of tyrosine phosphorylation of SLP-76 is independent of LAT and that there is a minor, LAT-independent pathway of tyrosine phosphorylation of PLCgamma2. We propose a model in which LAT and SLP-76 are required for PLCgamma2 phosphorylation but are regulated through independent pathways downstream of Syk.
A Highly Efficient Asymmetric Synthesis of Vernakalant (2014)

A novel synthesis of vernakalant is described. Using inexpensive and readily available reagents, the key transformations involve (1) an efficient zinc-amine-promoted etherification, (2) a highly stereoselective enzyme-catalyzed dynamic asymmetric transamination to set up the two contiguous chiral centers in the cyclohexane ring, and (3) a pyrrolidine ring formation via alkyl-B(OH)2-catalyzed amidation and subsequent imide reduction.
Lavender Oil-Potent Anxiolytic Properties via Modulating Voltage Dependent Calcium Channels (2013)

Recent clinical data support the clinical use of oral lavender oil in patients suffering from subsyndromal anxiety. We identified the molecular mechanism of action that will alter the perception of lavender oil as a nonspecific ingredient of aromatherapy to a potent anxiolytic inhibiting voltage dependent calcium channels (VOCCs) as highly selective drug target. In contrast to previous publications where exorbitant high concentrations were used, the effects of lavender oil in behavioral, biochemical, and electrophysiological experiments were investigated in physiological concentrations in the nanomolar range, which correlate to a single dosage of 80 mg/d in humans that was used in clinical trials. We show for the first time that lavender oil bears some similarities with the established anxiolytic pregabalin. Lavender oil inhibits VOCCs in synaptosomes, primary hippocampal neurons and stably overexpressing cell lines in the same range such as pregabalin. Interestingly, Silexan does not primarily bind to P/Q type calcium channels such as pregabalin and does not interact with the binding site of pregabalin, the α2δ subunit of VOCCs. Lavender oil reduces non-selectively the calcium influx through several different types of VOCCs such as the N-type, P/Q-type and T-type VOCCs. In the hippocampus, one brain region important for anxiety disorders, we show that inhibition by lavender oil is mainly mediated via N-type and P/Q-type VOCCs. Taken together, we provide a pharmacological and molecular rationale for the clinical use of the oral application of lavender oil in patients suffering from anxiety.
Supporting multimedia information presentation in a distributed, heterogeneous environment (2002)

A design overview of a distributed object-oriented system is given which supports the distributed processing of multimedia information with special regard to information presentation in an environment of heterogeneous networks and workstations. Essential features of the system are an object model designed for the handling of multimedia information and the adaptation of presentation and transport of multimedia information to the capabilities and available resources of the workstations and underlying networks. This adaptation is done by a distributed support layer. Using environment information, this layer makes an information presentation and transport service available to the applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The Complete Amino Acid Sequence of Bovine Serum Amyloid Protein A (SAA) and of Subspecies of the Tissue‐Deposited Amyloid Fibril Protein A (1992)

Bovine serum amyloid A (SAA) was isolated from the acute phase high density lipoprotein (HDL) fraction of a cow suffering from acute mastitis. The elucidated primary structure revealed a protein consisting of 112 amino acid residues. Compared with SAA proteins from other species, the bovine protein was shown to have an insertion of nine amino acid residues between positions 69 and 70. No microheterogeneity could be observed in the protein. Amyloid fibrils extracted from the kidneys were found to contain at least three subspecies of protein AA, consisting of 68, 81 and about 110 amino acid residues. The amino acid sequences established for the protein AA subspecies revealed no microheterogeneity, and were identical to that elucidated for protein SAA.
Statistical Interior Tomography (2011)

This paper presents a statistical interior tomography (SIT) approach making use of compressed sensing (CS) theory. With the projection data modeled by the Poisson distribution, an objective function with a total variation (TV) regularization term is formulated in the maximization of a posteriori (MAP) framework to solve the interior problem. An alternating minimization method is used to optimize the objective function with an initial image from the direct inversion of the truncated Hilbert transform. The proposed SIT approach is extensively evaluated with both numerical and real datasets. The results demonstrate that SIT is robust with respect to data noise and down-sampling, and has better resolution and less bias than its deterministic counterpart in the case of low count data.
Hierarchical Order Parameters for Macromolecular Assembly Simulations. 1. Construction and Dynamical Properties of Order Parameters (2012)

Macromolecular assemblies often display a hierarchical organization of macromolecules or their sub-assemblies. To model this, we have formulated a space warping method that enables capturing overall macromolecular structure and dynamics via a set of coarse-grained order parameters (OPs). This article is the first of two describing the construction and computational implementation of an additional class of OPs that has built into them the hierarchical architecture of macromolecular assemblies. To accomplish this, first, the system is divided into subsystems, each of which is described via a representative set of OPs. Then, a global set of variables is constructed from these subsystem-centered OPs to capture overall system organization. Dynamical properties of the resulting OPs are compared to those of our previous nonhierarchical ones, and implied conceptual and computational advantages are discussed for a 100ns, 2 million atom solvated Human Papillomavirus-like particle simulation. In the second article, the hierarchical OPs are shown to enable a multiscale analysis that starts with the N-atom Liouville equation and yields rigorous Langevin equations of stochastic OP dynamics. The latter is demonstrated via a force-field based simulation algorithm that probes key structural transition pathways, simultaneously accounting for all-atom details and overall structure.
Circulating complement breakdown products in patients with rheumatoid arthritis. Correlation between plasma C3d, circulating immune complexes, and clinical activity. (1977)

Quantitative determination of the small C3 breakdown product, C3d, was used to investigate complement activation in 45 plasma samples from 30 patients with rheumatoid arthritis (RA). The mean plasma C3e level in these samples (3.0 +/- 1.3 mg/100 ml) was significantly increased (P less than 0.001) as compared to patients with degenerative joint disease (0.9 +/- 0.4 mg/100 ml) and healthy blood donors (0.8 +/- 0.5 mg/100 ml). C3d levels were increased by more than s SD in 79% of RA samples. Plasma C3d levels were compared with C3d concentrations in synovial fluid. In most RA patients, the C3d levels were higher in synovial fluid than in plasma. A very significant correlation between plasma C3d levels and circulating immune complexes, as measured by determination of Clq binding activity (Clq BA), was observed (P less than 0.001). C3d levels were more elevated in RA patients with extra-articular disease manifestations (3.8 +/- 1.2 mg/100 ml) as compared to patients with joint disease alone (2.2 +/- 1.0 mg/100 ml). C3d levels and Clq BA were also significantly correlated (P less than 0.001) with the RA disease activity expressed by an index derived from sedimentation rate, joint score, and duration of morning stiffness. A close relationship between C3d levels, Clq BA, and the clinical activity further appeared during follow-up studies. The present observations suggest that a parallel but rather independent activation of the complement system may be induced by immune complexes in circulating blood and in the joint spaces during the course of rheumatoid arthritis.
Large-Pose Face Alignment via CNN-Based Dense 3D Model Fitting (2016)

Large-pose face alignment is a very challenging problem in computer vision, which is used as a prerequisite for many important vision tasks, e.g, face recognition and 3D face reconstruction. Recently, there have been a few attempts to solve this problem, but still more research is needed to achieve highly accurate results. In this paper, we propose a face alignment method for large-pose face images, by combining the powerful cascaded CNN regressor method and 3DMM. We formulate the face alignment as a 3DMM fitting problem, where the camera projection matrix and 3D shape parameters are estimated by a cascade of CNN-based regressors. The dense 3D shape allows us to design pose-invariant appearance features for effective CNN learning. Extensive experiments are conducted on the challenging databases (AFLW and AFW), with comparison to the state of the art.
RNA binding mediates neurotoxicity in the transgenic Drosophila model of TDP-43 proteinopathy (2013)

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder characterized by progressive and selective loss of motor neurons. The discovery of mutations in the gene encoding an RNA-binding protein, TAR DNA-binding protein of 43 kD (TDP-43), in familial ALS, strongly implicated abnormalities in RNA processing in the pathogenesis of ALS, although the mechanisms whereby TDP-43 leads to neurodegeneration remain elusive. To clarify the mechanism of degeneration caused by TDP-43, we generated transgenic Drosophila melanogaster expressing a series of systematically modified human TDP-43 genes in the retinal photoreceptor neurons. Overexpression of wild-type TDP-43 resulted in vacuolar degeneration of the photoreceptor neurons associated with thinning of the retina, which was significantly exacerbated by mutations of TDP-43 linked to familial ALS or disrupting its nuclear localization signal (NLS). Remarkably, these degenerative phenotypes were completely normalized by addition of a mutation or deletion of the RNA recognition motif that abolishes the RNA binding ability of TDP-43. Altogether, our results suggest that RNA binding is key to the neurodegeneration caused by overexpression of TDP-43, and that abnormalities in RNA processing may be crucial to the pathogenesis of TDP-43 proteinopathy.
Reliability-Based Iterative Decoding Algorithm for LDPC Codes With Low Variable-Node Degree (2014)

In this letter, a new reliability-based iterative majority-logic decoding (RBI-MLGD) algorithm that computes the extrinsic information of previous iterations of the variable node is proposed. This decoding algorithm is called historical-extrinsic reliability-based iterative decoder (HE-RBID) and improves the bit-error-rate performance of the previous RBI-MLGD. HE-RBID is particularly interesting for codes with a low degree of variable node, where traditional RBI-MLGD algorithms do not provide a good behavior. HE-RBID ensures a good performance without searching for the minimum at the check node and only by exchanging 1-bit messages between variable and check nodes.
Twin-screw extruder development for the ITER pellet injection system (2009)

The ITER pellet injection system is comprised of devices to form and accelerate pellets, and will be connected to inner wall guide tubes for fueling, and outer wall guide tubes for ELM pacing. An extruder will provide a stream of solid hydrogen isotopes to a secondary section, where pellets are cut and accelerated with a gas gun into the plasma. The ITER pellet injection system is required to provide a plasma fueling rate of 120 Pa-m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> /s (900 mbar-L/s) and durations of up to 3000 s. The fueling pellets will be injected at a rate up to 10 Hz and pellets used to trigger ELMs will be injected at higher rates up to 20 Hz. A twin-screw extruder for the ITER pellet injection system is under development at the Oak Ridge National Laboratory. A one-fifth ITER scale prototype has been built and has demonstrated the production of a continuous solid deuterium extrusion. The 27 mm diameter, inter-meshed, counter-rotating extruder screws are rotated at a rate up to ~5 rpm. Deuterium gas is pre-cooled and liquefied and solidified in separate extruder barrels. The pre-cooler consists of a deuterium gas filled copper coil suspended in a separate stainless steel vessel containing liquid nitrogen. The liquefier is comprised of a copper barrel connected to a Cryomech AL330 cryocooler, which has a machined helical groove surrounded by a copper jacket, through which the pre-cooled deuterium condenses. The lower extruder barrel is connected to a Cryomech GB-37 cryocooler to solidify the deuterium (at ¿15 K) before it is forced through the extruder die. The die forms the extrusion to a 3 mm × 4 mm rectangular cross section. Design improvements have been made to improve the pre-cooler and liquefier heat exchangers, and to limit the loss of extrusion through gaps in the screws. This paper will describe the design improvements for the next iteration of the extruder prototype.
Enhancing Cross-Device Interaction Scripting with Interactive Illustrations (2016)

Cross-device interactions involve input and output on multiple computing devices. Implementing and reasoning about interactions that cover multiple devices with a diversity of form factors and capabilities can be complex. To assist developers in programming cross-device interactions, we created DemoScript, a technique that automatically analyzes a cross-device interaction program while it is being written. DemoScript visually illustrates the step-by-step execution of a selected portion or the entire program with a novel, automatically generated cross-device storyboard visualization. In addition to helping developers understand the behavior of the program, DemoScript also allows developers to revise their program by interactively manipulating the cross-device storyboard. We evaluated DemoScript with 8 professional programmers and found that DemoScript significantly improved development efficiency by helping developers interpret and manage cross-device interaction; it also encourages testing to think through the script in a development process.
A Food Freshness Sensor Using the Multistate Response from Analyte-Induced Aggregation of a Cross-Reactive Poly(thiophene) (2007)

A single cross-reactive conjugated polymer generates a multidimensional response capable of identifying and differentiating between 22 structurally similar and biologically relevant amines with 97% accuracy in a highly competitive aqueous environment. Statistical analysis on an array of wavelengths was used to assess the viability of this approach. In a separate investigation, the multidimensional response from a single cross-responsive poly(thiophene) has been analyzed using a different ratiometric method to quantify the amount of biogenic amine present in a fish matrix, thereby evaluating the quality of the food.
Chemical liquid phase deposition of thin aluminum oxide films (2004)

Abstract Thin aluminum oxide films were deposited by a new and simple physicochemical method called chemical liquid phase deposition (CLD) on semiconductor materials. Aluminum sulfate with crystallized water and sodium bicarbonate were used as precursors for film growth, and the control of the system's pH value played an important role in this experiment. The growth rate is 12 nm/h with the deposition at [Al 2 (SO 4 )] =0.0837 mol·L −1 , [NaHCO 3 ] = 0.214 mol·L −1 , 15 °C Post‐growth annealing not only densifies and purifies the films, but results in film crystallization as well. Excellent quality of Al 2 O 3 films in this work is supported by electron dispersion spectroscopy. Fourier transform infrared spectrum, X‐ray diffraction spectrum and scanning electron microscopy photograph.
Molecular cloning of the epidermal growth factor-stimulated protein kinase p56 KKIAMRE. (1996)

A 56 kDa protein kinase was molecularly cloned from human fetal brain. This protein kinase (p56 KKIAMRE) shares homology with p42 KKIALRE (Meyerson et al., 1992) and is related to the proline-directed protein kinase group of signal transducing enzymes. The p56 KKIAMRE and p42 KKIALRE protein kinases exhibit mutually exclusive expression in reproductive tissues; p56 KKIAMRE in testis and p42 KKIALRE in ovary. p56 KKIAMRE and p42 KKIALRE may therefore contribute to signal transduction within these highly differentiated tissues. p56 KKIAMRE and p42 KKIALRE are activated by treatment of cells with epidermal growth factor (EGF). Although p56 KKIAMRE and p42 KKIALRE contain the MAP kinase dual phosphorylation motif Thr-Xaa-Tyr (Thr-Asp-Tyr), phosphorylation on Thr and Tyr within this motif is not required for EGF-stimulated protein kinase activity.
CrO<sub>2</sub>predicted as a half-metallic ferromagnet (1986)

The band structure of chromium dioxide, which is an important material because of its magnetic properties, has been calculated with the augmented spherical wave method by performing self-consistent spin-polarised calculations. The majority-spin electrons are metallic, whereas the minority-spin electrons are semiconducting. A new class of half-metallic ferromagnets is found in the rutile structure.
Under the following conditions (2010)

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Planning in information space for a quadrotor helicopter in a GPS-denied environment (2008)

This paper describes a motion planning algorithm for a quadrotor helicopter flying autonomously without GPS. Without accurate global positioning, the vehicle’s ability to localize itself varies across the environment, since different environmental features provide different degrees of localization. If the vehicle plans a path without regard to how well it can localize itself along that path, it runs the risk of becoming lost. We use the Belief Roadmap (BRM) algorithm [1], an information-space extension of the Probabilistic Roadmap algorithm, to plan vehicle trajectories that incorporate sensing. We show that the original BRM can be extended to use the Unscented Kalman Filter (UKF), and describe a sampling algorithm that minimizes the number of samples required to find a good path. Finally, we demonstrate the BRM path-planning algorithm on the helicopter, navigating in an indoor environment with a laser range-finder.
Demand management: A demonstration of the comparison of price and due date negotiation strategies using simulation (1996)

This dissertation considers the problem of demand management in a firm where a firm's historical delivery service level reputation influences the number of quotation requests from its potential customers. There is also a trade-off between net price and due date for each job for both the customer and the firm. The demand manager can bargain with the customer over price and a promised due date. Bargaining finishes with the customer either agreeing to a price and delivery date, or refusing the firm's bid and placing the order elsewhere. The firm's objective is to maximize its long term net revenue. The firm's demand management negotiation strategy guides this bidding process. This research demonstrates the use of simulation to test different negotiation strategies for different market and company conditions. A demand management negotiation strategy consists of several parts: the due date estimation method, the bargaining approach, the minimum target price rates, and the uncertainty allowance used in generating the firm's proposed due dates. This simulation models a job shop model of five workstations with random routing and operation processing times. This demonstration first develops sixteen scenarios to test different demand management negotiation strategies. This investigation compares finite scheduling based due date estimation methods, as well as the more traditional parameter based methods. The results illustrate that such a comparison can give useful guidelines. The preferred due date estimation methods for this evaluation are the classical methods which use parameters. The results show that the most common method, using the customer's first due date, is inferior to other methods. Full negotiation over both price and due date is the preferred bargaining approach. The research concludes that firms should carefully evaluate their negotiation strategies, as using the wrong due date estimation method, bargaining approach, target price rates, or uncertainty allowance will affect revenue. The dissertation shows that simulation can be used to evaluate negotiation strategies easily.