gebhart/patrepeval huggingface dataset:
Temperature-dependent Chaperone Activity and Structural Properties of Human αA- and αB-crystallins (2000)

The chaperone activity and biophysical properties of recombinant human alphaA- and alphaB-crystallins were studied by light scattering and spectroscopic methods. While the chaperone function of alphaA-crystallin markedly improves with an increase in temperature, the activity of alphaB homopolymer appears to change very little upon heating. Compared with alphaB-crystallin, the alphaA-homopolymer is markedly less active at low temperatures, but becomes a more active species at high temperatures. At physiologically relevant temperatures, the alphaB homopolymer appears to be modestly (two times or less) more potent chaperone than alphaA homopolymer. In contrast to very similar thermotropic changes in the secondary structure of both homopolymers, alphaA- and alphaB-crystallins markedly differ with respect to the temperature-dependent surface hydrophobicity profiles. Upon heating, alphaA-crystallin undergoes a conformational transition resulting in the exposure of additional hydrophobic sites, whereas no such transition occurs for alphaB-crystallin. The correlation between temperature-dependent changes in the chaperone activity and hydrophobicity properties of the individual homopolymers supports the view that the chaperone activity of alpha-crystallin is dependent on the presence of surface-exposed hydrophobic patches. However, the present data also show that the surface hydrophobicity is not the sole determinant of the chaperone function of alpha-crystallin.
Combined compile-time and runtime-driven, pro-active data movement in software DSM systems (2004)

Scientific applications contain program sections that exhibit repetitive data accesses. This paper proposes combined compile-time/runtime data reference analysis techniques that exploit repetitive data access behavior in both regular and irregular program sections. We present a new compiler algorithm to detect such repetitive data references and an API to an underlying software distributed shared memory (software DSM) system to orchestrate the learning and pro-active reuse of communication patterns. We evaluate the combined compile-time/runtime system on a selection of OpenMP applications, exhibiting both regular and irregular data reference patterns, resulting in average performance improvement of 28.1% on 8 processors.
Optimization of rotor performance in hover using a free wake analysis (1991)

The aim of this research was to demonstrate that a free wake hover performance prediction code could be coupled to a numerical optimization algorithm. The hover code, dubbed EHPIC (evaluation of hover performance using influence coefficients), uses a quasilinear wake relaxation to solve for the rotor performance and is well suited to optimization applications
TRB3 Inhibits the Transcriptional Activation of Stress-regulated Genes by a Negative Feedback on the ATF4 Pathway (2007)

The integrated stress response (ISR) is defined as a highly conserved response to several stresses that converge to the induction of the activating transcription factor 4 (ATF4). Because an uncontrolled response may have deleterious effects, cells have elaborated several negative feedback loops that attenuate the ISR. In the present study, we describe how induction of the human homolog of Drosophila tribbles (TRB3) attenuates the ISR by a negative feedback mechanism. To investigate the role of TRB3 in the control of the ISR, we used the regulation of gene expression by amino acid limitation as a model. The enhanced production of ATF4 upon amino acid starvation results in the induction of a large number of target genes like CHOP (CAAT/enhancer-binding protein-homologous protein), asparagine synthetase (ASNS), or TRB3. We demonstrate that TRB3 overexpression inhibits the transcriptional induction of CHOP and ASNS whereas TRB3 silencing induces the expression of these genes both under normal and stressed conditions. In addition, transcriptional profiling experiments show that TRB3 affects the expression of many ISR-regulated genes. Our results also suggest that TRB3 and ATF4 belong to the same protein complex bound to the sequence involved in the ATF4-dependent regulation of gene expression by amino acid limitation. Collectively, our data identify TRB3 as a negative feedback regulator of the ATF4-dependent transcription and participates to the fine regulation of the ISR.
NEDL1, a Novel Ubiquitin-protein Isopeptide Ligase for Dishevelled-1, Targets Mutant Superoxide Dismutase-1 (2004)

Approximately 20% of familial amyotrophic lateral sclerosis (FALS) arises from germ-line mutations in the superoxide dismutase-1 (SOD1) gene. However, the molecular mechanisms underlying the process have been elusive. Here, we show that a neuronal homologous to E6AP carboxyl terminus (HECT)-type ubiquitin-protein isopeptide ligase (NEDL1) physically binds translocon-associated protein-delta and also binds and ubiquitinates mutant (but not wild-type) SOD1 proportionately to the disease severity caused by that particular mutant. Immunohistochemically, NEDL1 is present in the central region of the Lewy body-like hyaline inclusions in the spinal cord ventral horn motor neurons of both FALS patients and mutant SOD1 transgenic mice. Two-hybrid screening for the physiological targets of NEDL1 has identified Dishevelled-1, one of the key transducers in the Wnt signaling pathway. Mutant SOD1 also interacted with Dishevelled-1 in the presence of NEDL1 and caused its dysfunction. Thus, our results suggest that an adverse interaction among misfolded SOD1, NEDL1, translocon-associated protein-delta, and Dishevelled-1 forms a ubiquitinated protein complex that is included in potentially cytotoxic protein aggregates and that mutually affects their functions, leading to motor neuron death in FALS.
Recent Advances in Indazole-Containing Derivatives: Synthesis and Biological Perspectives (2018)

Indazole-containing derivatives represent one of the most important heterocycles in drug molecules. Diversely substituted indazole derivatives bear a variety of functional groups and display versatile biological activities; hence, they have gained considerable attention in the field of medicinal chemistry. This review aims to summarize the recent advances in various methods for the synthesis of indazole derivatives. The current developments in the biological activities of indazole-based compounds are also presented.
A simple re‐evaluation of the hammett ϱσ relation (1959)

Abstract Starting from ten selected σ values, a large number of ϱ values is calculated; these ϱ values in their turn serve to calculate other σ values. The results prove that the concept of “duality of σ constants” is erroneous. In those cases in which a substituent enters into mesomeric para interaction with the reaction centre, a multiplicity of (exalted) σ values is observed; this holds for +M as well as for −M substituents. In the absence of mesomeric para interaction σ values are reasonably constant; the mean of such σ values (σ n ) is listed. It is demonstrated that σ values are, in general, not suitable for judging mesomeric para interactions, and should be replaced by the (free) energy difference term involving not only the exaltation of σ, but ϱ and T as well. Several important applications of this concept are discussed, illustrating the way in which the ϱσ relationship can be most profitably used for mechanistic and predictive purposes.
A simulation model fusing space and agent for indoor dynamic fire evacuation analysis (2016)

Research on indoor fire emergency evacuations is crucial for hazard mitigation purposes, and dynamic indoor environments examined in this field demand a flexible solution. Current approaches separately address spatial and human elements of evacuations, producing superficial evacuation analysis results. In this paper, we employ a hierarchical structure to efficiently organize indoor accessible space and combine it with agents to simulate the indoor evacuation process. Thus, analysis functions from both accessible space and agent perspectives may be fused to thoroughly investigate simulation results. The experiment shows that this simulation model can be used to efficiently analyze evacuation characteristics of buildings for fire emergencies.
Preparation of 1-<sup>14</sup>C Labelled Tributyltin Acetate and Dibutyltin Dichloride (1977)

Abstract 1-14C Bu3 SnOAc and 1-14C Bu2 SnCl2 have been synthesized in high yield, by a multistep synthesis, starting from 1-14C BuBr.
Regenerating Heart Valves (2011)

Valvular heart disease is a significant cause of morbidity and mortality worldwide. Current options for surgical heart valve replacement are associated with several major disadvantages as clinically available valve prostheses represent nonviable structures and lack the potential to grow, repair, and remodel. Heart valve tissue engineering represents a promising scientific concept to overcome these limitations, aiming at the fabrication of living autologous heart valves with a thromboresistant surface and a viable interstitium with repair and remodeling capabilities. Following the in vitro tissue engineering concept, autologous cells are harvested and seeded onto three-dimensional matrices followed by biomimetic conditioning enabling the development of neo-heart valve tissue. Here, we review the concept of both in vitro and in vivo heart valve tissue engineering, focusing in particular on different synthetic scaffold materials and available cell sources for the fabrication of living autologous heart valve substitutes.
Summary of a distributed control algorithm for a dynamically reconfigurable array architecture (2003)

An array architecture composed of two hyperplanes is described. The execution plane is constructed using polymorphic processing elements and a programmable, switch-controlled, reconfigurable interconnection network. The control of the processing plane is accomplished by using a smaller hyperplane composed of small processing elements and a two-dimensional mesh interconnection scheme. The control plane cells have the capability of determining from a single seed the global configuration of the array, and of determining the size of the fault-free area surrounding each cell. Once the size of this area is determined, the size necessary for the executing algorithm can be determined, and the state pattern generated in an area with sufficient size. Reconfiguration elements in the control plane make it possible to have local reconfiguration around faulty cells, and to increase the fault-free area adjacent to a cell by isolating faulty cells. The discussion is limited to the local reconfiguration algorithm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The value of magnetic stimulation in the diagnosis of radiculopathies (1993)

We studied 42 patients with cervical and lumbar radiculopathies using magnetic stimulation. Prolonged latencies following magnetic stimulation of the brain, the paravertebral spinal nerve, or both, showed a highly significant correlation with muscle weakness in clinical testing (24 of 26 patients with weakness had pathological motor evoked potentials) as well as with spontaneous activity of the target muscles in needle electromyography (24 of 25 subjects). The determination of both the central and the peripheral motor conduction time was found to be essential in patients with radiculopathies, because different patterns of latency changes correlated with different morphological results in computed tomography: in patients diagnosed as having a lateral compression of the nerve root the peripheral nerve latency was delayed; whereas, in patients with more medially localized herniations, a prolonged central motor latency was the most frequent finding. This study posits that combined magnetic stimulation of the brain and nerve root is an effective and painless technique for the noninvasive evaluation of nerve root function.
The demographics of web search (2010)

How does the web search behavior of "rich" and "poor" people differ? Do men and women tend to click on difffferent results for the same query? What are some queries almost exclusively issued by African Americans? These are some of the questions we address in this study.
Evolutionary History of “Early-Diverging” Eukaryotes: The Excavate Taxon Carpediemonas is a Close Relative of Giardia1 (2002)

Diplomonads, such as Giardia, and their close relatives retortamonads have been proposed as early-branching eukaryotes that diverged before the acquisition-retention of mitochondria, and they have become key organisms in attempts to understand the evolution of eukaryotic cells. In this phylogenetic study we focus on a series of eukaryotes suggested to be relatives of diplomonads on morphological grounds, the "excavate taxa". Phylogenies of small subunit ribosomal RNA (SSU rRNA) genes, alpha-tubulin, beta-tubulin, and combined alpha- + beta-tubulin all scatter the various excavate taxa across the diversity of eukaryotes. But all phylogenies place the excavate taxon Carpediemonas as the closest relative of diplomonads (and, where data are available, retortamonads). This novel relationship is recovered across phylogenetic methods and across various taxon-deletion experiments. Statistical support is strongest under maximum-likelihood (ML) (when among-site rate variation is modeled) and when the most divergent diplomonad sequences are excluded, suggesting a true relationship rather than an artifact of long-branch attraction. When all diplomonads are excluded, our ML SSU rRNA tree actually places retortamonads and Carpediemonas away from the base of the eukaryotes. The branches separating excavate taxa are mostly not well supported (especially in analyses of SSU rRNA data). Statistical tests of the SSU rRNA data, including an "expected likelihood weights" approach, do not reject trees where excavate taxa are constrained to be a clade (with or without parabasalids and Euglenozoa). Although diplomonads and retortamonads lack any mitochondria-like organelle, Carpediemonas contains double membrane-bounded structures physically resembling hydrogenosomes. The phylogenetic position of Carpediemonas suggests that it will be valuable in interpreting the evolutionary significance of many molecular and cellular peculiarities of diplomonads.
Design strategies for controlling damping in micromechanical and nanomechanical resonators (2014)

Damping is a critical design parameter for miniaturized mechanical resonators used in microelectromechanical systems (MEMS), nanoelectromechanical systems (NEMS), optomechanical systems, and atomic force microscopy for a large and diverse set of applications ranging from sensing, timing, and signal processing to precision measurements for fundamental studies of materials science and quantum mechanics. This paper presents an overview of recent advances in damping from the viewpoint of device design. The primary goal is to collect and organize methods, tools, and techniques for the rational and effective control of linear damping in miniaturized mechanical resonators. After reviewing some fundamental links between dynamics and dissipation for systems with small linear damping, we explore the space of design and operating parameters for micromechanical and nanomechanical resonators; classify the mechanisms of dissipation into fluid–structure interactions (viscous damping, squeezed-film damping, and acoustic radiation), boundary damping (stress-wave radiation, microsliding, and viscoelasticity), and material damping (thermoelastic damping, dissipation mediated by phonons and electrons, and internal friction due to crystallographic defects); discuss strategies for minimizing each source using a combination of models for dissipation and measurements of material properties; and formulate design principles for low-loss micromechanical and nanomechanical resonators.
Distribution of paraoxon hydrolytic activity in the serum of patients after myocardial infarction. (1986)

Abstract The activity of paraoxonase in serum was found to be bimodally distributed, both in a control group and in a group of patients who had suffered myocardial infarction. Activity in the myocardial infarct group was significantly lower than in the control group. Low paraoxonase activity in serum may provide an indication of susceptibility to the development of coronary heart disease.
Microbial Degradation of Steroids to Hexahydroindanone Derivatives (1980)

Journal Article Microbial Degradation of Steroids to Hexahydroindanone Derivatives Get access Tsuyoshi Nakamatsu, Tsuyoshi Nakamatsu Department of Agricultural Chemistry, University of Tokyo Present Address: Central Research Laboratories of Ajinomoto Co., Kawasaki, Japan Search for other works by this author on: Oxford Academic Google Scholar Teruhiko Beppu, Teruhiko Beppu Department of Agricultural Chemistry, University of Tokyo Search for other works by this author on: Oxford Academic Google Scholar Kei Arima Kei Arima Department of Agricultural Chemistry, University of Tokyo Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 44, Issue 7, 1 July 1980, Pages 1469–1474, https://doi.org/10.1080/00021369.1980.10864160 Published: 01 July 1980 Article history Received: 31 August 1979 Published: 01 July 1980
CD19 as a therapeutic target in a spontaneous autoimmune polyneuropathy (2013)

Spontaneous autoimmune polyneuropathy (SAP) in B7-2 knock-out non-obese diabetic (NOD) mice is mediated by myelin protein zero (P0)-reactive T helper type 1 (Th1) cells. In this study, we investigated the role of B cells in SAP, focusing on CD19 as a potential therapeutic target. We found that P0-specific plasmablasts and B cells were increased in spleens of SAP mice compared to wild-type NOD mice. Depletion of B cells and plasmablasts with anti-CD19 monoclonal antibody (mAb) led to attenuation of disease severity when administered at 5 months of age. This was accompanied by decreased serum immunoglobulin (Ig)G and IgM levels, depletion of P0-specific plasmablasts and B cells, down-regulation/internalization of surface CD19 and increased frequency of CD4(+) regulatory T cells in spleens. We conclude that B cells are crucial to the pathogenesis of SAP, and that CD19 is a promising B cell target for the development of disease-modifying agents in autoimmune neuropathies.
Drought stress and carbon uptake in an Amazon forest measured with spaceborne imaging spectroscopy (2004)

Amazônia contains vast stores of carbon in high-diversity ecosystems, yet this region undergoes major changes in precipitation affecting land use, carbon dynamics, and climate. The extent and structural complexity of Amazon forests impedes ground studies of ecosystem functions such as net primary production (NPP), water cycling, and carbon sequestration. Traditional modeling and remote-sensing approaches are not well suited to tropical forest studies, because (i) biophysical mechanisms determining drought effects on canopy water and carbon dynamics are poorly known, and (ii) remote-sensing metrics of canopy greenness may be insensitive to small changes in leaf area accompanying drought. New spaceborne imaging spectroscopy may detect drought stress in tropical forests, helping to monitor forest physiology and constrain carbon models. We combined a forest drought experiment in Amazônia with spaceborne imaging spectrometer measurements of this area. With field data on rainfall, soil water, and leaf and canopy responses, we tested whether spaceborne hyperspectral observations quantify differences in canopy water and NPP resulting from drought stress. We found that hyperspectral metrics of canopy water content and light-use efficiency are highly sensitive to drought. Using these observations, forest NPP was estimated with greater sensitivity to drought conditions than with traditional combinations of modeling, remote-sensing, and field measurements. Spaceborne imaging spectroscopy will increase the accuracy of ecological studies in humid tropical forests.
Complexation of Doxorubicin with <i>β</i> and <i>γ</i>-Cyclodextrins (1992)

The binding of β and γ-cyclodextrins with the anti-cancer drug doxorubicin has been examined with the use of fluorescence and absorbance spectroscopy, circular dichroism measurements, and proton NMR spectroscopy. The stoichiometry of the complexes formed and their apparent formation constants have been estimated with the use of various approaches. The stoichiometrics for both the β-cyclodextrin-doxorubicin complex and the γ-cyclodextrin-doxorubicin complex have been determined to be predominantly 1:1. The strength of the interaction of the drug with γ-cyclodextrin is stronger than that with β-cyclodextrin. The effect of varying the pH on the calculated formation constants of the complexes has also been investigated.
Wing box transonic-flutter suppression using piezoelectric self-sensing actuators attached to skin (2010)

The main objective of this research is to study the capability of piezoelectric (PZT) self-sensing actuators to suppress the transonic wing box flutter, which is a flow–structure interaction phenomenon. The unsteady general frequency modified transonic small disturbance (TSD) equation is used to model the transonic flow about the wing. The wing box structure and piezoelectric actuators are modeled using the equivalent plate method, which is based on the first order shear deformation plate theory (FSDPT). The piezoelectric actuators are bonded to the skin. The optimal electromechanical coupling conditions between the piezoelectric actuators and the wing are collected from previous work. Three main different control strategies, a linear quadratic Gaussian (LQG) which combines the linear quadratic regulator (LQR) with the Kalman filter estimator (KFE), an optimal static output feedback (SOF), and a classic feedback controller (CFC), are studied and compared. The optimum actuator and sensor locations are determined using the norm of feedback control gains (NFCG) and norm of Kalman filter estimator gains (NKFEG) respectively. A genetic algorithm (GA) optimization technique is used to calculate the controller and estimator parameters to achieve a target response.
The potential of optical coherence tomography in the engineering of living tissue (2004)

The better repair of human tissue is an urgent medical goal and in order to achieve a safe outcome there is a parallel need for sensitive, non-invasive methods of assessing the quality of the engineered tissues and organs prior to surgical implantation. Optical coherence tomography (OCT) can potentially fulfil this role. The current status of OCT as an advanced imaging tool in clinical medicine, developmental biology and material science is reviewed and the parallels to the engineering of living tissue and organs are discussed. Preliminary data are also presented for a tissue engineering bioreactor with in situ OCT imaging. The data suggest that OCT can be utilized as a real time, non-destructive, non-invasive tool to critically monitor the morphology of tissue-engineered constructs during their fabrication and growth.
RGC Sensitivity to Mild Systemic Hypoxia (2006)

Inner neuroretinal function remained unchanged during increased blood O2 and carbon dioxide levels known to alter retinal blood flow, but it was altered during decreased blood O2 levels. Overall, these results indicate that the generators of P50 are resistant to systemic hyperoxia, hypercapnia/hyperoxia, and hypoxia. They further indicate that the generators of N95, namely the retinal ganglion cells, are particularly sensitive to transient, mild systemic hypoxia.