gebhart/patrepeval huggingface dataset:
Investigating the Role of the Arabidopsis Homologue of the Human G3BP in RNA Metabolism, Cellular Stress Responses and Innate Immunity (2018)

Mitogen-activated protein kinases (MAPKs) belong to the most conserved signaling pathways and are found in all eukaryotes, including humans where they play important roles in various diseases and cancer. Stimulation of this signal transduction pathway by microbe-associated molecular patterns (MAMP) results in a multitude of events to regulate innate immune responses in Arabidopsis thaliana stimulating large-scale changes in gene expression. Starting from a phosphoproteomic screen in Arabidopsis thaliana wild type and mpk3, mpk4 and mpk6 mutants following microbe-associated molecular pattern (MAMP) treatment, several novel chromatin-associated proteins were identified that are differentially phosphorylated by stress-induced protein kinases. Arabidopsis Ras GTPase-activating protein SH3-domain-binding protein (AtG3BP-1) is a downstream putative substrate of the MAMP-stimulated MAPK pathway that is phosphorylated by MPK3, 4 and 6 in in vitro kinase assays. AtG3BP1 belongs to a highly conserved family of RNA-binding proteins in eukaryotes that link kinase receptormediated signaling to RNA metabolism. Here, we report the characterization of the Arabidopsis homolog of human G3BP1 in plant innate immunity. AtG3BP1 negatively regulates plant immunity and defense immune responses. Atg3bp1 mutant lines show constitutive stomata closure, expression of a number of key defense marker genes, and accumulate salicylic acid but not jasmonic acid. Furthermore, Atg3bp1 plants exhibit enhanced resistance to the biotrophic pathogen Pseudomonas syringae pv. tomato. Pathogen resistance was mediated by stomatal and apoplastic immunity in Atg3bp1. More generally, our data reinforce that AtG3BP1 is a key mediator of plant defense responses and transient expression of AtG3BP1 delivered striking disease resistance in the absence of yield penalty, highlighting a potential application of this gene in crop protection.
Central Hyperexcitability in Chronic Musculoskeletal Pain: A Conceptual Breakthrough with Multiple Clinical Implications (2002)

Recent investigations of dysfunctional pain processing in the central nervous system have contributed much knowledge about the development of chronic musculoskeletal pain. Many common chronic musculoskeletal pain syndromes - including regional myofascial pain syndromes, whiplash pain syndromes, refractory work-related neck-shoulder pain, certain types of chronic low back pain, fibromyalgia and others - may essentially be explained by abnormalities in central pain modulation. The growing awareness of dysfunctional central pain modulation may be a conceptual breakthrough leading to a better understanding of common chronic pain disorders. A new paradigm will have multiple clinical implications, including re-evaluation of clinical practice routines and rehabilitation methods, and will focus on controversial issues of medicolegal concern. The concept of dysfunctional central pain processing will also necessitate a mechanism-based classification of pain for the selection of individual treatment and rehabilitation programs for subgroups of patients with chronic musculoskeletal pain due to different pathophysiological mechanisms.
Midtarsal Arthrodesis in the Treatment of Charcot Midfoot Arthropathy (2009)

Open reduction and arthrodesis with use of multiple axially placed intramedullary screws for the surgical correction of neuropathic midfoot collapse provides a reliable stable construct to achieve and maintain correction of the deformity.
Fast near-field acoustic imaging with separable arrays (2011)

Acoustic imaging is a computationally intensive and ill-conditioned inverse problem, which involves estimating high resolution source distributions with large microphone arrays. We have recently shown how to significantly accelerate acoustic imaging under a far-field approximation using fast transforms. This paper generalizes our previous work to obtain computationally efficient and accurate transforms for near-field imaging with separable arrays. We show that under a suitable permutation, the imaging transform can be made nearly separable, even when modeling strong near-field effects. We exploit this quasi-separability to obtain a computationally efficient and accurate low-rank representation, allowing the design of fast transforms for near-field operation with arbitrary focal surfaces and arbitrary accuracy. We combine these transforms with calibration matrices, which compensate non-separable characteristics and allow one to quickly reshape focal surfaces without having to recompute the optimal transforms.
Photochemical formation of colloidal metals (1987)

Colloidal silver and gold have been formed by irradiation of AgClO4 and HAuCl4 solutions with 253.7 nm light in the presence of protective agents such as sodium dodecylsulphate, sodium alginate and colloidal silica. Absorption maxima of colloidal silver and gold have been observed at 390–420 and 540–560 nm, respectively. Colloidal metals have been purified by dialysis and their amounts analysed quantitatively. The quantum yields of metal deposition are 0.053–0.15 for colloidal silver and 0.030–0.039 for colloidal gold. The quantum yield is increased several times by the use of protective agents, with the exception of a AgClO4–sodium alginate solution.
Observation of stripe-direction dependence of threshold current density for AlGaInP laser diodes with CuPt-type natural superlattice in Ga0.5In0.5P active layer (1992)

An anisotropy for threshold current densities for AlGaInP laser diodes with CuPt-type natural superlattice (NSL) in a Ga0.5In0.5P active layer, grown on a (001) GaAs substrate, was observed, for the first time. Threshold current densities (Jth) for laser diodes with stripes in the [1̄10] and [110] direction were 1.35 and 2.10 kA/cm2, respectively. The lasers with a weak NSL formation in the active layer showed a very small anisotropy in Jth. Stripe direction dependence of electroluminescence (EL) polarization properties were also observed for lasers with well-developed NSL. The anisotropies in Jth and EL polarization properties are attributed to the existence of the NSL in the active layer and the appearance asymmetry previously observed in the NSL.
Designing Ionic Conductors: The Interplay between Structural Phenomena and Interfaces in Thiophosphate-Based Solid-State Batteries (2018)

Elucidating the underlying structural principles that govern ionic transport in thiophosphate solid electrolytes will enable the discovery of novel ionic conductors. Additionally, improving the properties of ionic conductors and exacting control over interfacial reactions and interphase stabilities are critical to the advancement of solid-state batteries. In this perspective, we focus on two major aspects at the foundation of solid-state battery development. First, we address the typical static structural requirements for achieving high ionic conductivities within thiophosphates, which is then extended to how a dynamic lattice and local structural effects can influence ionic transport. Furthermore, we provide an overview of some of the challenges that are currently hindering the progress of solid-state battery research, with particular attention being paid to interfacial instabilities and mechanochemical effects. We hope that this perspective provides a unique outlook on ionic conduction in thiophosphates toward the design of future solid electrolytes and highlights the importance of interfacial chemistry in the optimization of solid-state battery devices.
Neural network based image coding quality prediction (2002)

Developments in digital image coding tend to involve more and more complex algorithms, and require therefore an increasing amount of computation. To improve the overall system performance, some schemes apply different coding algorithms to separate parts of an image according to the content of this subimage. Such schemes are referred to as dynamic coding schemes. Applying the best suited coding algorithm to a part of an image will lead to an improved coding quality, but implies an algorithm selection phase. Current selection methods require the computation of the reconstructed image after coding and decoding with all the selected algorithms in order to choose the best method. Some other schemes use ways of pruning the search in the algorithm space. Both approaches suffer from a heavy computational load. Furthermore, the computational complexity is increased even more if the parameters have to be adjusted for a given algorithm during the search. This paper describes a way to predict the coding quality of a region of the input image for any given coding method. The system will then be able to select the best suited coding algorithm for each region according to the predicted quality. This prediction scheme has low complexity, and also enables the adjustment of algorithm specific parameters during the search.
A Randomized, Double‐Blind, Placebo‐Controlled Study of Breath Powered Nasal Delivery of Sumatriptan Powder ( <scp>AVP</scp> ‐825) in the Treatment of Acute Migraine (The <scp>TARGET</scp> Study) (2014)

Targeted delivery of a low-dose of sumatriptan powder via a novel, closed-palate, Breath Powered, intranasal device (AVP-825) provided fast relief of moderate or severe migraine headache in adults that reached statistical significance over placebo by 30 minutes. The treatment was well tolerated with a low incidence of systemic AEs.
Signal Transduction of Hyaluronic Acid−Peptide Conjugate for Formyl Peptide Receptor Like 1 Receptor (2008)

Agonistic and antagonistic peptides for formyl peptide receptor like 1 (FPRL1) receptor have been investigated as novel drug candidates for inflammatory diseases such as sepsis, asthma, and rheumatoid arthritis. In this work, a novel protocol for the synthesis of hyaluronic acid (HA)-peptide (CWRYMVm) conjugate for FPRL1 receptor was successfully developed for further clinical applications of peptide drugs. Aminoethyl methacrylated HA (HAAEMA) was synthesized by the coupling reaction of tetrabutyl ammonium salt of HA (HA-TBA) and AEMA using benzotriazol-1-yloxy-tris(dimethylamino) phosphonium hexafluorophosphate (BOP) in dimethyl sulfoxide (DMSO). Then, HA-AEMA was conjugated with CWRYMVm in water via Michael addition reaction between methacrylate group of HA-AEMA and thiol group in cysteine. The formation of HA-peptide conjugate was confirmed by 1H NMR and gel permeation chromatography (GPC). The average number of conjugated peptide molecules could be controlled from 5 to 23 per single HA chain. The HA-peptide conjugate showed serum stability longer than four days. In Vitro signal transduction activity of the HA-peptide conjugate for FPRL1 receptor was confirmed from the elevated levels of phospho-extracellular signal-regulated kinase (pERK) and calcium ion in FPRL1 overexpressing RBL-2H3 cells. The partially decreased biological activity of HA-peptide conjugates by the steric hindrance of HA was recovered after its degradation by hyaluronidase treatment.
UDP-Sugar Pyrophosphorylase: A New Old Mechanism for Sugar Activation   (2011)

Recent developments in studies on properties and functions of UDP-sugar pyrophosphorylase (USPase) in metabolism are presented. The protein was characterized from plants and protozoans (Leishmania, ...
Unusually stable β‐sheet formation in an ionic self‐complementary oligopeptide (1994)

A 16-residue amphiphilic oligopeptide (EAK16) with every other residue alanine and also containing glutamic acid and lysine (Ac-NH-AEAEAKAKAEAEAKAK-CONH2) is able to form an unusually stable beta-sheet structure. The beta-sheet structure is stable at very low concentrations in water and at high temperatures. Various pH changes at 1.5, 3, 7, and 11 had little effect on the stability of the beta-sheet structure. The beta-sheet structure was not altered significantly even in the presence of 0.1% SDS, 7 molar guanidine hydrochloride, or 8 molar urea. One of the structural characteristics of the EAK16 is its ionic self-complementarity in that ionic bonds and hydrogen bonds between Glu and Lys can form readily between two oligopeptide beta-sheet structures. This structural feature is probably one of the factors that promotes its extreme stability. This is the first example of such an extended ionic self-complementarity in a protein structure. EAK16 and its related peptides may have applications as useful biomaterials. It also offers a good model for studying the mechanism of beta-sheet formation. Because the oligopeptide can self-assemble to form a membranous structure, it may have relevance to origin of life research.
A New Algorithm to Optimize Maximal Information Coefficient (2016)

The maximal information coefficient (MIC) captures dependences between paired variables, including both functional and non-functional relationships. In this paper, we develop a new method, ChiMIC, to calculate the MIC values. The ChiMIC algorithm uses the chi-square test to terminate grid optimization and then removes the restriction of maximal grid size limitation of original ApproxMaxMI algorithm. Computational experiments show that ChiMIC algorithm can maintain same MIC values for noiseless functional relationships, but gives much smaller MIC values for independent variables. For noise functional relationship, the ChiMIC algorithm can reach the optimal partition much faster. Furthermore, the MCN values based on MIC calculated by ChiMIC can capture the complexity of functional relationships in a better way, and the statistical powers of MIC calculated by ChiMIC are higher than those calculated by ApproxMaxMI. Moreover, the computational costs of ChiMIC are much less than those of ApproxMaxMI. We apply the MIC values tofeature selection and obtain better classification accuracy using features selected by the MIC values from ChiMIC.
ChemInform Abstract: Ruthenium‐Catalyzed Direct Arylations Through C—H Bond Cleavages (2011)

Abstract Review: 93 refs.
Measurement of Cardiac Output in Man by Dye Dilution Curves Using Simultaneous Ear Oximeter and Whole Blood Cuvette Techniques (1961)

In 10 subjects, dye dilution curves were performed on 31 occasions by intravenous in jection of Coomassie blue dye. The curves were recorded by a conventional whole blood cuvette technique using arterial blood with drawn from the brachial artery, and by an ear oximetric technique. Comparison was made of the time contponents of the two curves and of the cardiac output values derived from them. The differences in time components were frequently considerable. It was con cluded that the ear curves were thus unsuit able for estimation of indices such as the "central blood volume." By contrast there was no systematic difference between the car diac output values computed by the two methods. The standard deviation of the differ ences between the two methods was 11.7 per cent of the average cardiac index observed. It was concluded that the ear oximetric tech nique employed offered a satisfactory method of studying the cardiac output in man.
Active perception and recognition learning system based on Actor‐Q architecture (2002)

Abstract This paper proposes the Actor‐Q architecture, which is a combination of Q‐Learning and Actor‐Critic architecture, as well as the active perception and recognition learning system based on that architecture. In Actor‐Q architecture, the system output is divided into the “action,” which is a discrete value as intention, and the “motion,” which is a continuous‐valued vector. As the first step, the “action” is determined from Q ‐values. If the “action” is accompanied with a “motion,” the “motion” is executed according to the corresponding Actor output. Q ‐value is learned by Q‐learning, and Actor is trained with the Q ‐value corresponding to that “action” on behalf of the Critic output. In this study, the action is defined as the decision of the sensor motion or the recognition of the respective pattern. Q ‐value is assigned to each of those. When the sensor motion is selected, the sensor is moved according to the Actor output. When recognition is selected, the recognition result that the presented pattern is the one corresponding to the selected Q ‐value is output. The Q ‐value is learned, using the reinforcement signal representing the true/false of the result. Both Q ‐value computing module and Actor are composed of neural networks, with the visual sensor signals as input. By this architecture, the following three problems of the conventional active perception and recognition learning system are dissolved. (1) The sensor can be trapped in a local maximum of the recognition evaluation. (2) It is necessary that the recognition output should be evaluated for each time‐step, and the reinforcement signal with a continuous value should be provided. (3) The system cannot decide by itself the timing to output the recognition result. The above effect was verified by some simulations, using the visual sensor with nonuniform sensor cells. © 2002 Wiley Periodicals, Inc. Syst Comp Jpn, 33(14): 12–22, 2002; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/scj.10207
Gaze manipulation for one-to-one teleconferencing (2003)

A new algorithm is proposed for novel view generation in one-to-one teleconferencing applications. Given the video streams acquired by two cameras placed on either side of a computer monitor, the proposed algorithm synthesizes images from a virtual camera in arbitrary position (typically located within the monitor) to facilitate eye contact. Our technique is based on an improved, dynamic-programming, stereo algorithm for efficient novel-view generation. The two main contributions are: i) a new type of three-plane graph for dense-stereo dynamic-programming, that encourages correct occlusion labeling; ii) a compact geometric derivation for novel-view synthesis by direct projection of the minimum-cost surface. Furthermore, we present a novel algorithm for the temporal maintenance of a background model to enhance the rendering of occlusions and reduce temporal artefacts (flicker); and a cost aggregation algorithm that acts directly on our three-dimensional matching cost space. Examples are given that demonstrate the robustness of the new algorithm to spatial and temporal artefacts for long stereo video streams. These include demonstrations of synthesis of cyclopean views of extended conversational sequences. We further demonstrate synthesis from a freely translating virtual camera.
Marginating neutrophils are reversibly adherent to normal lung endothelium. (1991)

Neutrophils have been implicated in the pathogenesis of several inflammatory lung disorders including asthma, emphysema, and adult respiratory distress syndrome. The precursors of these destructive cells are thought to be marginating neutrophils that, although intravascular, remain intimately associated with endothelium, resisting the shearing forces of flowing blood. The purposes of this study were (1) to examine a method for quantitating marginating lung neutrophils, (2) to assess the adherence of marginating neutrophils to normal lung endothelium, and (3) to determine the reversibility of neutrophil-endothelial cell adherence. Rats were anesthetized and ventilated, and their lungs were exposed through a median sternotomy. The left lung was tied off with blood in situ and the right lung was perfused intraarterially with colloid for 2 minutes. In separate experiments, both left and right lungs were perfused intraarterially with colloid for 25 minutes. Myeloperoxidase, a neutrophil granule enzyme, was related to lung neutrophils. Dithionite-sensitive optical density (DSOD) was related to lung hemoglobin. Marginating lung neutrophils were quantitated by measuring the peroxidase activity of normal blood-perfused lung (myeloperoxidase assay) and subtracting from it the fraction of activity corresponding to the lung blood content (DSOD). The marginating neutrophil pool was identified by 2.1 units myeloperoxidase (5 x 10(6) neutrophils) per gm wet lung. Although the marginating pool was depleted by 54% during 2 minutes of lung colloid perfusion, lung erythrocytes (DSOD) were decreased by a significantly greater 93% (p less than 0.05). Lungs perfused with colloid for 25 minutes had negligible remaining myeloperoxidase activity. We conclude that (1) marginating lung neutrophils can be quantitated with the myeloperoxidase and DSOD assays, (2) marginating neutrophils are relatively adherent to normal lung endothelium compared with intravascular erythrocytes, and (3) the adherence of marginating neutrophils is fully reversible.
Metabolic control and its analysis. Additional relationships between elasticities and control coefficients (1985)

Existing theorems from the analysis of metabolic control have been taken and embedded in a simple matrix algebra procedure for calculating the flux control coefficients of enzymes (formerly known as sensitivities) in a metabolic pathway from their kinetic properties (their elasticities). New theorems governing the flux control coefficients of branched pathways and substrate cycles have been derived to allow the procedure to be applied to complex pathway configurations. Modifications to the elasticity terms used in the equations have been theoretically justified so that the method remains valid for pathways with conserved metabolites (for example, the adenine nucleotide pool or the intermediates of a catalytic cycle such as the tricarboxylic acid cycle) or with pools of metabolites kept very near to equilibrium by very rapid reactions. The matrix equations generated using these theorems and relationships may be solved algebraically or numerically. Algebraic solutions have been used to determine the factors responsible for the degree of amplification of flux control coefficients by substrate cycles and to show that it is possible to derive expressions for the elasticities of a group of enzymes.
Phenotype and genotype in polycystic ovary syndrome (2001)

Polycystic ovary syndrome (PCOS) is a common disorder in premenopausal women and is characterized by hyperandrogenic chronic anovulation. The cause is unknown. PCOS is associated with significant insulin resistance as well as with defects in insulin secretion. These abnormalities place these women at substantial risk for developing type 2 diabetes mellitus. A defect in insulin-mediated receptor autophosphorylation has been found in a substantial proportion of PCOS women. Both PCOS and the insulin resistance that accompanies it appear to have major genetic components. Family studies of PCOS have supported this, although they suffer from incomplete phenotyping of probands and first-degree relatives. The phenotype in males and nonreproductive age females is uncertain. Despite the shortcomings of the family studies of PCOS, they have consistently indicated familial clustering and suggested that the mode of inheritance is dominant. Our initial studies of 50 families of PCOS probands indicate that 24% of sisters are affected with PCOS. There also appears to be an intermediate phenotype of sisters with regular menstrual cycles who are hyperandrogenic per se (22% of sisters). Additionally, there appears to be a major familial defect, with 50% of first-degree relatives having glucose intolerance (impaired glucose tolerance by oral glucose tolerance test or type 2 diabetes mellitus). These findings suggest that hyperandrogenism in females and glucose intolerance may be genetic traits in PCOS kindreds. Systematic phenotyping will allow assignment of affected status for eventual linkage analysis.