gebhart/patrepeval huggingface dataset:
Regulators of the anaphylatoxin C5a (2000)

The complement system comprises a network of serum proteins that are important in host defence. Activation of complement occurs following antigen-antibody interactions or in response to certain foreign surfaces, and this leads to the formation of a number of complement factors, including C5a. C5a is a protein of 74 amino acids, and is a potent inflammatory mediator and immunomodulator, which is proposed to be a major pathogenic factor in numerous immuno-inflammatory diseases. Many research groups have attempted to develop agents principally to block C5a, or in some cases, to reproduce its activities. Agents blocking C5a should have anti-inflammatory activities, and agents mimicking C5a might possibly be developed as immune adjuvants. This review summarises relevant patent applications for this area that have appeared mostly over the last decade, and scientific publications will be incorporated as background where appropriate. A recent comprehensive scientific review on therapeutic efforts to inhibit the complement system is highly recommended for background reading [1].
The autonomic ether: emerging electrophysiologic associations. (2012)

As a result of large, multicenter trials supporting ICDs for prevention of sudden cardiac arrest, there has been an exponential increase in ICD device therapy. Cardiologists and general practitioners are increasingly faced with the challenge to evaluate and troubleshoot device problems. In this review, we provide an overview of basic ICD function and malfunction and show examples of common ICD problems and troubleshooting.
Binocular interactions in random chromatic changes at isoluminance (2006)

To examine the type of chromatic interactions at isoluminance in the phenomenon of binocular vision, I have determined simple visual reaction times (VRT) under three observational conditions (monocular left, monocular right, and binocular) for different chromatic stimuli along random color axes at isoluminance (simultaneous L-, M-, and S-cone variations). Upper and lower boundaries of probability summation as well as the binocular capacity coefficient were estimated with observed distributions of reaction times. The results were not consistent with the notion of independent chromatic channels between eyes, suggesting the existence of excitatory and inhibitory binocular interactions at suprathreshold isoluminance conditions.
High-speed query processing over high-speed networks (2015)

Modern database clusters entail two levels of networks: connecting CPUs and NUMA regions inside a single server in the small and multiple servers in the large. The huge performance gap between these two types of networks used to slow down distributed query processing to such an extent that a cluster of machines actually performed worse than a single many-core server. The increased main-memory capacity of the cluster remained the sole benefit of such a scale-out. The economic viability of high-speed interconnects such as InfiniBand has narrowed this performance gap considerably. However, InfiniBand's higher network bandwidth alone does not improve query performance as expected when the distributed query engine is left unchanged. The scalability of distributed query processing is impaired by TCP overheads, switch contention due to uncoordinated communication, and load imbalances resulting from the inflexibility of the classic exchange operator model. This paper presents the blueprint for a distributed query engine that addresses these problems by considering both levels of networks holistically. It consists of two parts: First, hybrid parallelism that distinguishes local and distributed parallelism for better scalability in both the number of cores as well as servers. Second, a novel communication multiplexer tailored for analytical database workloads using remote direct memory access (RDMA) and low-latency network scheduling for high-speed communication with almost no CPU overhead. An extensive evaluation within the HyPer database system using the TPC-H benchmark shows that our holistic approach indeed enables high-speed query processing over high-speed networks.
<i>Pc</i>MYB1, a novel plant protein containing a DNA‐binding domain with one MYB repeat, interacts <i>in vivo</i> with a light‐regulatory promoter unit (1997)

Light regulatory unit 1 (LRU1) is necessary for and sufficient to mediate light-dependent activation of the chalcone synthase (CHS) minimal promoter in Petroselinum crispum. This composite promoter unit consists of at least two distinct cis-acting elements, designated ACECHS and MRECHS, both of which are required for light induction. The ACGT-containing element ACECHS interacts with common plant regulatory factors (CPRFs) which belong to the basic region/leucine zipper (bZIP) class of transcription factors. Here, we demonstrate that MRECHS, originally identified as an in vivo DNA footprint, is a MYB recognition element. This element possesses a functional core that is essential for light responsiveness and is specifically recognized by two distantly related MYB-like proteins: MYB305 and the novel factor MYB1 from P. crispum. PcMYB1 was identified by both its specific binding to MRECHS in vitro and recognition of MRECHS in vivo. The deduced amino acid sequence revealed that PcMYB1 contains only one MYB-like repeat. This portion of the protein constitutes the DNA-binding domain. Mutational analysis of PcMYB1 in combination with sequence comparison suggests the presence of a helix-turn-helix structure containing a recognition helix that is sufficient for sequence-specific binding. The structure of this distinct MYB-like DNA-binding domain appears to be conserved in proteins from all three eukaryotic phyla.
Subcellular distribution and characteristics of ciprofibroyl-CoA synthetase in rat liver. Its possible identity with long-chain acyl-CoA synthetase (1992)

The subcellular distribution and characteristics of ciprofibroyl-CoA synthetase were studied in rat liver and compared with those of long-chain acyl-CoA synthetase (palmitate as substrate) which, as already known, is distributed among mitochondria, microsomes and peroxisomes. Upon differential centrifugation, the subcellular distribution of ciprofibroyl-CoA synthetase followed closely that of palmitoyl-CoA synthetase and was specifically inactivated in the mitochondrial fraction by freezing and thawing, a behaviour already described for palmitoyl-CoA synthetase. Both enzyme activities were found to co-purify through several steps from rat liver microsomes. By using a partially purified enzyme, the activation of ciprofibrate to its acyl-CoA ester followed Michaelis-Menten kinetics with an apparent Km of 0.63 +/- 0.1 mM. Ciprofibroyl-CoA synthetase was competitively inhibited by 25 and 50 microM-palmitic acid. Higher concentrations of the fatty acid resulted in a mixed type of inhibition. Conversely, ciprofibrate up to 0.5 mM was found to inhibit competitively palmitoyl-CoA synthetase, whereas higher concentrations also resulted in a mixed inhibition. The highest activity of ciprofibroyl-CoA synthetase was found in fat and liver homogenates. The distribution of the enzyme in different rat tissues was similar to that of palmitoyl-CoA synthetase. The present results suggest that long-chain acyl-CoA synthetase and ciprofibroyl-CoA synthetase activities reside in identical or closely related proteins.
Graphene-coated materials using silica particles as a framework for highly efficient removal of aromatic pollutants in water (2015)

The substantial aggregation of pristine graphene nanosheets decreases its powerful adsorption capacity and diminishes its practical applications. To overcome this shortcoming, graphene-coated materials (GCMs) were prepared by loading graphene onto silica nanoparticles (SiO2). With the support of SiO2, the stacked interlamination of graphene was held open to expose the powerful adsorption sites in the interlayers. The adsorption of phenanthrene, a model aromatic pollutant, onto the loaded graphene nanosheets increased up to 100 fold compared with pristine graphene at the same level. The adsorption of GCMs increased with the loading amount of the graphene nanosheets and dramatically decreased with the introduction of oxygen-containing groups in the graphene nanosheets. The highly hydrophobic effect and the strong π-π stacking interactions of the exposed graphene nanosheets contributed to their superior adsorption of GCMs. An unusual GCM peak adsorption coefficient (Kd) was observed with the increase in sorbate concentration. The sorbate concentration at peak Kd shifted to lower values for the reduced graphene oxide and graphene relative to the graphene oxide. Therefore, the replacement of water nanodroplets attached to the graphene nanosheets through weak non-hydrogen bonding with phenanthrene molecules via strong π-π stacking interactions is hypothesized to be an additional adsorption mechanism for GCMs.
Stabilization of small unilamellar liposomes: polymerization of surfactants in phospholipid vesicles (1983)

Cosonication of a styrene-containing surfactant H2CCHC6H4NHCO[CH2]10N+(C16H33)Me2Br–(1) with dipalmitoylphosphatidylcholine (DPPC) leads to mixed DPPC–(1) 300 Å diameter unilamellar vesicles which subsequent to photopolymerization maintain their morphologies for months; conversely, nonpolymerized vesicles undergo spontaneous growth to 700 Å diameter vesicles.
Automated Reference Region Extraction and Population-Based Input Function for Brain [<sup>11</sup>C]TMSX PET Image Analyses (2014)

[(11)C]TMSX ([7-N-methyl-(11)C]-(E)-8-(3,4,5-trimethoxystyryl)-1,3,7-trimethylxanthine) is a selective adenosine A2A receptor (A2AR) radioligand. In the central nervous system (CNS), A2AR are linked to dopamine D2 receptor function in striatum, but they are also important modulators of inflammation. The golden standard for kinetic modeling of brain [(11)C]TMSX positron emission tomography (PET) is to obtain arterial input function via arterial blood sampling. However, this method is laborious, prone to errors and unpleasant for study subjects. The aim of this work was to evaluate alternative input function acquisition methods for brain [(11)C]TMSX PET imaging. First, a noninvasive, automated method for the extraction of gray matter reference region using supervised clustering (SCgm) was developed. Second, a method for obtaining a population-based arterial input function (PBIF) was implemented. These methods were created using data from 28 study subjects (7 healthy controls, 12 multiple sclerosis patients, and 9 patients with Parkinson's disease). The results with PBIF correlated well with original plasma input, and the SCgm yielded similar results compared with cerebellum as a reference region. The clustering method for extracting reference region and the population-based approach for acquiring input for dynamic [(11)C]TMSX brain PET image analyses appear to be feasible and robust methods, that can be applied in patients with CNS pathology.
A 6.5 GHz-11.5 GHz source using a grid amplifier with a twist reflector (1993)

The authors have constructed and tested an oscillator using a grid amplifier with external feedback from a twist reflector. The twist reflector serves two functions; it changes the output polarization to match the input, and its position sets the feedback phase. This permits a wider tuning range than has been possible with previous grid oscillators. The source could be continuously tuned from 8.2 GHz to 11.0 GHz by moving the twist reflector. By moving the polarizer and mirror in the twist reflector independently, a 1.8-to-1 frequency range from 6.5 GHz to 11.5 GHz was achieved. The peak effective radiated power was 6.3 W at 9.9 GHz.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Quantitative assessment of circumduction, hip hiking, and forefoot contact gait using Lissajous figures (2012)

Itoh N, Kagaya H, Saitoh E, Ohtsuka K, Yamada J, Tanikawa H, Tanabe S, Itoh N, Aoki T, Kanada Y. Quantitative assessment of circumduction, hip hiking, and forefoot contact gait using Lissajous figures. Jpn J Compr Rehabil Sci 2012; 3: 78-84.Objective: To quantitatively assess gait abnormalities using Lissajous figures obtained from three-dimensional motion analysis of treadmill gait, with the goal of applying the findings to the treatment of gait disorders.Methods: Thirty-nine healthy subjects and 30 hemiplegic patients were studied. Treadmill gait analysis was conducted using a three-dimensional motion analysis system. Using the Lissajous figures obtained from the gait analysis, quantitative indexes were developed for three gait abnormalities: circumduction, hip hiking, and forefoot contact. The indexes were validated through comparison with observational assessment by physiotherapists with expertise in gait analysis. Results: The values obtained for all the indexes were significantly higher in hemiplegic patients compared to healthy subjects (p < 0.001). Correlation analysis was conducted between the index values and observational scores for each gait abnormality, yielding Spearman’s rank correlation coefficients of -0.82 for circumduction, -0.64 for hip hiking, and -0.84 for forefoot contact (p < 0.001).Conclusion: We successfully developed objective quantitative indexes for gait abnormalities, which were not influenced by rater bias.
The Folylpolyglutamate Synthetase Plastidial Isoform Is Required for Postembryonic Root Development in Arabidopsis     (2011)

A recessive Arabidopsis (Arabidopsis thaliana) mutant with short primary roots and root hairs was identified from a forward genetic screen. The disrupted gene in the mutant encoded the plastidial isoform of folylpolyglutamate synthetase (FPGS), previously designated as AtDFB, an enzyme that catalyzes the addition of glutamate residues to the folate molecule to form folylpolyglutamates. The short primary root of atdfb was associated with a disorganized quiescent center, dissipated auxin gradient in the root cap, bundled actin cytoskeleton, and reduced cell division and expansion. The accumulation of monoglutamylated forms of some folate classes in atdfb was consistent with impaired FPGS function. The observed cellular defects in roots of atdfb underscore the essential role of folylpolyglutamates in the highly compartmentalized one-carbon transfer reactions (C1 metabolism) that lead to the biosynthesis of compounds required for metabolically active cells found in the growing root apex. Indeed, metabolic profiling uncovered a depletion of several amino acids and nucleotides in atdfb indicative of broad alterations in metabolism. Methionine and purines, which are synthesized de novo in plastids via C1 enzymatic reactions, were particularly depleted. The root growth and quiescent center defects of atdfb were rescued by exogenous application of 5-formyl-tetrahydrofolate, a stable folate that was readily converted to metabolically active folates. Collectively, our results indicate that AtDFB is the predominant FPGS isoform that generates polyglutamylated folate cofactors to support C1 metabolism required for meristem maintenance and cell expansion during postembryonic root development in Arabidopsis.
Inflammation Causes Mood Changes Through Alterations in Subgenual Cingulate Activity and Mesolimbic Connectivity (2009)

Inflammation-associated mood deterioration is reflected in changes in sACC activity and functional connectivity during evoked responses to emotional stimuli. Peripheral cytokines modulate this mood-dependent sACC connectivity, suggesting a common pathophysiological basis for major depressive disorder and sickness-associated mood change and depression.
The use of Bayes and causal modelling in decision making, uncertainty and risk (2011)

The most sophisticated commonly used methods of risk assessment (used especially in the financial sector) involve building statistical models from historical data. Yet such approaches are inadequate when risks are rare or novel because there is insufficient relevant data. Less sophisticated commonly used methods of risk assessment, such as risk registers, make better use of expert judgement but fail to provide adequate quantification of risk. Neither the data-driven nor the risk register approaches are able to model dependencies between different risk factors. Causal probabilistic models (called Bayesian networks) that are based on Bayesian inference provide a potential solution to all of these problems. Such models can capture the complex interdependencies between risk factors and can effectively combine data with expert judgement. The resulting models provide rigorous risk quantification as well as genuine decision support for risk management. 1.
Pulmonary fibrosis: rate of disease progression as a trigger for referral for lung transplantation (2007)

Patients with pulmonary fibrosis who died awaiting transplantation had similar disease severity at assessment as those who achieved transplantation. However, the interval between symptom onset and transplant referral was significantly shorter in those who died while on the waiting list, suggesting they had more rapidly progressive disease. The rate of disease progression appears to be a more sensitive indicator for transplantation referral than any single physiological measure of disease severity and should act as an important trigger for early transplant referral.
Ontological Insecurity and Reflective Processes (1977)

Abstract Strong support was found for the ontological model as it was interpreted and according to the procedures used. Reflective subjects are more likely to show anxiety than non-reflective subjects, and anxiety is less likely to be located at those points upon which reflection is deployed than at those points devoid of reflection. Reflective subjects are also more likely to show indications of dissatisfaction than non-reflective subjects; anxious subjects are also more likely to show signs of dissatisfaction than those who are non-anxious. A subanalysis helps to disassociate effects attributable to reflection from effects attributable to dissatisfaction. The "main" effect of reflection on anxiety is that, regardless of whether dissatisfaction is or is not indicated, reflective subjects are more likely to show anxiety than non-reflective subjects. However, the significantly greater likelihood of observing anxiety among dissatisfied reflective than satisfied reflective subjects is indicative of the degree to which dissatisfaction is a source of anxiety beyond that attributable to reflection alone. The higher likelihood of finding anxiety among reflective subjects, independent of the presence or absence of dissatisfaction, is of considerable importance in interpreting the portion of the ontological model bearing uon the regulation of anxiety according
Diagnosis of prostate carcinoma using multicompression strain imaging: data acquisition and first in vivo results (2002)

We present a new system for the acquisition of ultrasonic multicompression strain images of the human prostate in vivo. A mechanical force applied to the tip of an ultrasonic transrectal probe is measured continuously and ultrasonic RF-images are acquired consecutively at specified levels of tissue compression. An iterative phase-zero estimation method is used to obtain time delay estimates and the corresponding strain images from the acquired image sequence. We present phantom measurements as well as first in vivo results which are in good agreement to histological findings. Lateral tissue motion artifacts are corrected by a novel local companding method.
Estrogen Up-regulates Apolipoprotein E (ApoE) Gene Expression by Increasing ApoE mRNA in the Translating Pool via the Estrogen Receptor α-Mediated Pathway (1997)

The antiatherogenic property of estrogens is mediated via at least two mechanisms: first by affecting plasma lipoprotein profiles, and second by affecting the components of the vessel wall. Raising plasma apolipoprotein E (apoE) in mice protects them against diet-induced atherosclerosis (Shimano, H., Yamada, N., Katsuki, M., Gotoda, T., Harada, K., Murase, T., Fukuzawa, C., Takaku, F., and Yazaka, Y. (1992) <i>Proc. Natl. Acad. Sci. U. S. A.</i> 89, 1750–1754). It is possible that estrogen may be antiatherogenic at least in part by increasing plasma apoE levels. Therefore, we studied the regulation of apoE by estrogen. A survey of 15 inbred strains of mice showed that some mouse strains responded to injections or subcutaneously implanted pellets of estradiol by raising their apoB and apoE levels and some did not. We performed detailed studies in two "responder" strains, C57L and C57BL, and two "non-responder" strains, C3H and BALBc. Responders increased their plasma apoE levels 2.5-fold. Non-responders' levels were altered ±10%. In the responders the distribution of apoE among the plasma lipoproteins shifted from high density lipoprotein toward the apoB-containing lipoprotein fractions. In nonresponders the shift was toward high density lipoprotein. Hepatic apoE mRNA levels and relative rates of apoE mRNA transcription were unchanged in all strains, suggesting that apoE regulation occurred at posttranscriptional loci. Therefore, we measured apoE synthesis in fresh liver slices and on isolated hepatic polysomes. Two-fold increases were noted but only in responders accompanied by selective 1.5-fold increases in polysomal apoE mRNA levels. Similar increases in apoE synthesis were also observed in castrated C57BL mice given either physiological or pharmacological replacement doses of estradiol, but not testosterone, suggesting that the effect of estradiol was specific on the distribution of apoE mRNA in the translationally active polysomal pool. Next, we examined whether the effects of estrogen on apoE translation were mediated by estrogen receptors (ER). ER-α knock-out mice and their wild-type littermates were administered estradiol. As expected, apoE levels and hepatic apoE synthesis increased more than 2-fold in the wild-type littermates, but only 20% increases in the plasma apoE and hepatic synthesis were observed in the ER knock-out mice. Hepatic apoE mRNA levels did not change in either the wild-type or the ER knock-out mice. Thus, estradiol up-regulates apoE gene expression by increasing levels of apoE mRNA in the polysomal translating pool. Furthermore, the increased polysomal recruitment of apoE mRNA is largely mediated by estrogen receptors.
Regularized high-resolution image reconstruction considering inaccurate motion information (2007)

One of the major issues in recovering a high-resolution image from a sequence of low-resolution observations is the accuracy of the motion information. In most of the work in the literature, the motion information is assumed to be known with high accuracy. This is very often not the case, and therefore the accuracy of high-resolution image reconstruction suffers substantially, since it greatly depends on the motion information. To address these issues in this paper, we propose a high-resolution image reconstruction algorithm that reduces the distortion in the reconstructed high-resolution image due to the inaccuracy of the estimated motion. Towards this task, we analyze the reconstruction noise generated by the inaccurate motion information. Based on this analysis, we propose a new regularization functional and derive a sufficient condition for the convergence of the resulting iterative reconstruction algorithm. The proposed algorithm requires no prior information about the original image or the inaccuracy of the motion information. Experimental results illustrate the benefit of the proposed method when compared to conventional high-resolution image reconstruction methods in terms of both objective measurements and subjective evaluation.