gebhart/patrepeval huggingface dataset:
Antigenic surface of the bee venom allergen phospholipase A2. Structural functional analysis of human IgG4 antibodies reveals potential role in protection. (1994)

In the human immune response to the main bee venom allergen phospholipase A2 (PLA2), Abs of the IgG4 isotype are associated with protection. The antigenic sites of PLA2 that are recognized by two mAb of this isotype have been analyzed at the molecular level. The interaction of PLA2 with these two Abs has previously been shown to depend on the conformation of the Ag and to be sensitive to lysine modifications. Therefore, genetically engineered Ag displaying single point mutations of lysine residues were generated. Nine out of twelve surface-exposed lysine residues were substituted by glutamate or glutamine, and the effect of individual mutations on mAb binding was analyzed in the context of the folded Ag. Substitution of lysine at position 25 with either glutamate or glutamine completely abrogates binding to both mAb. All other mutants do not show a difference in binding when compared with wild-type Ag. Probing of sera from bee keepers with lysine 25 mutants reveals that a significant proportion of serum Abs of the IgG4 isotype display specificity for this epitope, suggesting that this represents a major B cell-antigenic site in hyperimmune individuals. We further found that both mAbs inhibit the catalytic activity of PLA2, a property that may account for the protective role of IgG4 Abs in hyperimmune individuals.
Mechanism of Action and Preclinical Antitumor Activity of the Novel Hypoxia-Activated DNA Cross-Linking Agent PR-104 (2007)

PR-104 is a novel hypoxia-activated DNA cross-linking agent with marked activity against human tumor xenografts, both as monotherapy and combined with radiotherapy and chemotherapy.
Cardiorenal Syndrome Type 5: Clinical Presentation, Pathophysiology and Management Strategies from the Eleventh Consensus Conference of the Acute Dialysis Quality Initiative (ADQI) (2013)

Cardiorenal syndrome type 5 (CRS-5) includes conditions where there is a simultaneous involvement of the heart and kidney from a systemic disorder. Given the wide spectrum of diseases that contribute to CRS-5, several pathophysiological mechanisms are invoked representing the response of the heart and kidney to the contributing disorder that is ongoing. The nature, duration and the underlying condition of the heart and kidney strongly influence the clinical course of CRS-5. In this paper we discuss the pathophysiology of CRS-5 in the setting of sepsis as a model system for CRS-5 providing a brief overview of strategies for monitoring and therapeutic intervention. We offer a framework for reference for considering other disorders leading to CRS-5 where the development of cardiac and renal dysfunction is more insidious.
Highly Selective Decarbonylation of 5‐(Hydroxymethyl)furfural in the Presence of Compressed Carbon Dioxide (2011)

Weniger ist mehr: Die kombinierte Entwicklung und Optimierung von Katalysatoren und Reaktionsbedingungen (Iridium/Phosphan-Katalysator in Gegenwart von verdichtetem Kohlendioxid) führte zur hochselektiven Decarbonylierung von 5-(Hydroxymethyl)furfural (HMF) zu Furfurylalkohol (FFA). Die anschließende Hydrierung über Ruthenium-Nanopartikeln (RuNPs) lieferte Tetrahydrofurfurylalkohol (THFA), ein mögliches Lösungsmittel für die Decarbonylierung (siehe Schema).
AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models (2011)

Small Angle X-ray Scattering (SAXS) techniques are becoming more and more useful for structural biologists and biochemists, thanks to better access to dedicated synchrotron beamlines, better detectors and the relative easiness of sample preparation. The ability to compute the theoretical SAXS profile of a given structural model, and to compare this profile with the measured scattering intensity, yields crucial structural informations about the macromolecule under study and/or its complexes in solution. An important contribution to the profile, besides the macromolecule itself and its solvent-excluded volume, is the excess density due to the hydration layer. AquaSAXS takes advantage of recently developed methods, such as AquaSol, that give the equilibrium solvent density map around macromolecules, to compute an accurate SAXS/WAXS profile of a given structure and to compare it to the experimental one. Here, we describe the interface architecture and capabilities of the AquaSAXS web server (http://lorentz.dynstr.pasteur.fr/aquasaxs.php).
A Characterization of Vanadate Interactions with the (Na,K)-ATPase (1978)

The interaction of vanadium in the +5 oxidation state (vanadate) with purified dog kidney Na+ and K+-stim- ulated adenosine trlphosphatase [(Na,K)-ATPase] has been studied using equilibrium binding, steady state kinetics, and measurements of relaxation kinetics. Van- adate binds to one high affinity site (Kl = 4 no) and one low afinity site (Kz = 0.5
Template Assembled Synthetic Proteins (TASP) as Functional Mimetics of Proteins (1996)

The bare essentials of a functional protein are all that are retained when the structural domain of a native protein is replaced by a synthetic template molecule (see picture below). New strategies for the synthesis of this novel type of template-assembled synthetic peptide (TASP) provide functional mimetics of receptors and antibodies.
A Simple Method for In Vivo Measurement of Implant Rod Three-Dimensional Geometry During Scoliosis Surgery (2012)

Scoliosis is defined as a spinal pathology characterized as a three-dimensional deformity of the spine combined with vertebral rotation. Treatment for severe scoliosis is achieved when the scoliotic spine is surgically corrected and fixed using implanted rods and screws. Several studies performed biomechanical modeling and corrective forces measurements of scoliosis correction. These studies were able to predict the clinical outcome and measured the corrective forces acting on screws, however, they were not able to measure the intraoperative three-dimensional geometry of the spinal rod. In effect, the results of biomechanical modeling might not be so realistic and the corrective forces during the surgical correction procedure were intra-operatively difficult to measure. Projective geometry has been shown to be successful in the reconstruction of a three-dimensional structure using a series of images obtained from different views. In this study, we propose a new method to measure the three-dimensional geometry of an implant rod using two cameras. The reconstruction method requires only a few parameters, the included angle θ between the two cameras, the actual length of the rod in mm, and the location of points for curve fitting. The implant rod utilized in spine surgery was used to evaluate the accuracy of the current method. The three-dimensional geometry of the rod was measured from the image obtained by a scanner and compared to the proposed method using two cameras. The mean error in the reconstruction measurements ranged from 0.32 to 0.45 mm. The method presented here demonstrated the possibility of intra-operatively measuring the three-dimensional geometry of spinal rod. The proposed method could be used in surgical procedures to better understand the biomechanics of scoliosis correction through real-time measurement of three-dimensional implant rod geometry in vivo.
Pulsed-Laser Plasmon-assisted Nanoscale Photothermal Energy Transfer in Fluid (2012)

We present an analysis of photothermal phenomena associated with nanosecond-pulsed, laser-illuminated metallic nanoparticles in aqueous solutions. We use computational electromagnetic and fluid analysis to predict energy conversion at plasmon resonance, heat transfer and bubble generation.
Engineered Production of Hapalindole Alkaloids in the Cyanobacterium Synechococcus sp. UTEX 2973 (2019)

Cyanobacteria produce numerous valuable bioactive secondary metabolites (natural products) including alkaloids, isoprenoids, nonribosomal peptides, and polyketides. However, the genomic organization of the biosynthetic gene clusters, complex gene expression patterns, and low compound yields synthesized by the native producers currently limits access to the vast majority of these valuable molecules for detailed studies. Molecular cloning and expression of such clusters in heterotrophic hosts is often precarious owing to genetic and biochemical incompatibilities. Production of such biomolecules in photoautotrophic hosts analogous to the native producers is an attractive alternative that has been under-explored. Here, we describe engineering of the fast-growing cyanobacterium <i>Synechococcus elongatus</i> UTEX 2973 to produce key compounds of the hapalindole family of indole-isonitrile alkaloids. Engineering of the 42-kbp "<i>fam</i>" hapalindole pathway from the cyanobacterium <i>Fischerella ambigua</i> UTEX 1903 into S2973 was accomplished by rationally reconstructing six to seven core biosynthetic genes into synthetic operons. The resulting <i>Synechococcus</i> strains afforded controllable production of indole-isonitrile biosynthetic intermediates and hapalindoles H and 12-<i>epi</i>-hapalindole U at a titer of 0.75-3 mg/L. Exchanging genes encoding <i>fam</i> cyclase enzymes in the synthetic operons was employed to control the stereochemistry of the resulting product. Establishing a robust expression system provides a facile route to scalable levels of similar natural and new forms of bioactive hapalindole derivatives and its structural relatives (e.g., fischerindoles, welwitindolinones). Moreover, this versatile expression system represents a promising tool for exploring other functional characteristics of orphan gene products that mediate the remarkable biosynthesis of this important family of natural products.
A TDMA Energy Consumption Model for WSN Radio Selection in On-Board Aerospace Systems (2018)

Wireless sensor applications in the aerospace industry often require specific sampling rates, are latency bound and energy-budget constrained at the same time. Wireless transceiver technologies offer a wide range of data rates at various energy consumption levels. A broad range of MAC protocols were designed to handle the various trade-offs between throughput, energy, and latency. Moreover, the protocols and transceivers have to be carefully selected according to the application requirements. This paper provides a mathematical model to calculate both the power consumption and data delivery latency for nodes within a WSN, to select the optimal solution given specific application requirements. A proof-of-concept implementation and evaluation with commercial hardware demonstrates its effectiveness.
Narrowband and Pure Violet Organic Emitter with a Full Width at Half Maximum of 14 nm and y Color Coordinate of Below 0.02 (2020)

Violet organic light-emitting diodes (OLEDs) with a very narrow emission spectrum with a full width at half maximum of 14 nm and y color coordinate of 0.02 are developed using a indolo[3,2,1-jk]carbazole-derived pure violet emitter. The violet emitter, 2,5,13,16-tetra-tert-butylindolo[3,2,1-jk]-indolo[1',2',3':1,7]indolo[2,3-b]carbazole (tDIDCz), is designed to have a very rigid molecular structure driven by the multiresonance-type core structure through the alternating carbon and nitrogen atoms. The violet emitter is decorated with t-butyl groups to prevent intermolecular aggregation and packing, which allow pure violet emission without excimer emission. The violet OLEDs derived from the tDIDCz emitter show a violet color coordinate of (0.164, 0.018) with a narrow emission spectrum and a full width at half maximum of 14 nm (105 meV). The external quantum efficiency of the pure violet OLEDs is 3.3%. This is the first work reporting pure violet emission without any ultraviolet emission below 380 nm and blue emission above 450 nm by showing a very narrow emission spectrum.
Intrarenal dopamine acts at the dopamine-1 receptor to control renal function (1988)

Exogenous dopamine increases renal blood flow and produces diuresis and natriuresis in mammalian species. Dopamine is produced intrarenally and dopamine-1 receptors have been demonstrated within the kidney. However, the role of intrarenal dopamine in the control of renal function is unknown. We studied the renal effects of a specific dopamine-1 antagonist, SCH 23390 (SCH, MW 398, Schering-Plough, Bloomfield, New Jersey, USA) infused into the renal artery of uninephrectomized conscious dogs (n = 5) in metabolic balance at a sodium intake of 40 mmol/day. The infusion of SCH at 0.01 pmol/kg per min did not change the urinary flow rate or urinary sodium excretion. Significant dose-dependent reductions in urine volume, urinary sodium excretion and fractional excretion of sodium were observed with intrarenal SCH administration at 0.1, 5.0 and 10 pmol/kg per min. Rebound diuresis and natriuresis occurred after cessation of SCH administration. There were no changes in renal haemodynamic function, systemic plasma renin activity (PRA), plasma aldosterone concentration or mean arterial pressure during intrarenal SCH administration. These results demonstrate for the first time that intrarenal dopamine controls renal function physiologically by acting at the renal dopamine-1 receptors.
ChemInform Abstract: New Monoterpene Glycosides and Phenolic Compounds from Distylium racemosum and Their Inhibitory Activity Against Ribonuclease H. (2011)

Abstract The novel monoterpene glycosides distyloside A (I) and B (II) and the new megastigmane glucoside iso‐dihydrodendranthemoside A (III) are isolated from twigs and leaves of Distylium racemosum together with five known phenolic compounds.
Evidence for a Retro-Diels−Alder Reaction on a Single Crystalline Surface:  Butadienes on Ge(100) (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTEvidence for a Retro-Diels−Alder Reaction on a Single Crystalline Surface: Butadienes on Ge(100)Andrew V. Teplyakov, Pratik Lal, Yétundé A. Noah, and Stacey F. BentView Author Information Department of Chemistry, New York University New York, New York 10003 Cite this: J. Am. Chem. Soc. 1998, 120, 29, 7377–7378Publication Date (Web):July 10, 1998Publication History Received22 January 1998Published online10 July 1998Published inissue 1 July 1998https://pubs.acs.org/doi/10.1021/ja980243fhttps://doi.org/10.1021/ja980243frapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views334Altmetric-Citations56LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Adducts,Chemical reactions,Hydrocarbons,Organic reactions,Surface analysis Get e-Alerts
A dynamic BRDF display (2011)

Traditional computer displays are designed to be invariant to illumination and viewing conditions. However, this is not what the real world behaves like. Real materials reflect the surrounding light in a characteristic way that depends on the angles of illumination and observation.
3D Air-Ground Channel Model Reconstruction Based on the Experimental Data and Q-D Method (2020)

This paper proposes to use the Q-D (Quasi-Deterministic) method for reconstructing the angular and frequency characteristics of the 3D Air-to-Ground (A-G) channel from the available experimental data. This method allows to expand the applicability of tapped delay line (TDL) channel models for performance investigation of the aviation radio systems with directional antennas and multi-element antenna arrays. The developed 3D A-G channel models also give opportunity to take into account Doppler spread impact on the communication system performance.
Rapid Enrichment and Isolation of Polyphosphate-Accumulating Organisms Through 4’6-Diamidino-2-Phenylindole (DAPI) Staining With Fluorescence-Activated Cell Sorting (FACS) (2020)

Screening for bacteria with abilities to accumulate valuable intracellular compounds from an environmental community is difficult and requires strategic methods. Combining the experimental procedure for phenotyping living cells in a microbial community with the cell recovery necessary for further cultivation will allow for an efficient initial screening process. In this study, we developed a strategy for the isolation of polyphosphate-accumulating organisms (PAOs) by combining (i) nontoxic fluorescence staining of polyphosphate granules in viable microbial cells and (ii) fluorescence-activated cell sorting (FACS) for the rapid detection and collection of target cells. To implement this screening approach, cells from wastewater sludge samples were stained with 4'6-diamidino-2-phenylindole (DAPI) to target cells with high polyphosphate (polyP) accumulation. We found a staining procedure (10 μg/ml of DAPI for 30 min) that can visualize polyP granules while maintaining viability for the majority of the cells (>60%). The polyP positive cells were recovered by FACS, purified by colony isolation and phylogenetically identified by 16S rRNA gene sequencing. Follow-up analysis confirmed that these isolates accumulate polyP, indicating that DAPI can be implemented in staining living cells and FACS can effectively and rapidly screen and isolate individual cells from a complex microbial community.
Limits of Extramobile and Intramobile Motion of Cylindrical Developable Mechanisms (2020)

Abstract Mechanisms that can both deploy and perform desired tasks offer a multifunctional advantage over traditional mechanisms. Developable mechanisms (DMs) are devices capable of conforming to a predetermined developable surface and deploying from that surface to achieve specific motions. This paper presents new terminology that defines motion of developable mechanisms while interior and exterior to a developable surface. The limits of motion are identified using defined conditions, and it is shown that the more difficult of these conditions may be treated as a non-factor during the design of cylindrical developable mechanisms given certain assumptions.
Systems biology in drug safety assessment: Use of a recalibrated hund-rudy model to predict the effect of novel drug compounds on action potential duration (2010)

Emerging practice in drug safety assessment delivers relatively early data on the potency of compounds at a range of cardiac ion channels, but there is little consensus on how to use this data to understand human risk, particularly when a compound modifies a range of mutually compensatory electrophysiological processes. In-silico physiological modelling of the processes involved offers a method to achieve this understanding but the models in the literature are not yet widely validated in the presence of a range of pharmacological profiles. We have used a model of canine ventricular myocytes and retrained it to data from a series of action potential (AP) recordings on isolated canine myocytes. By representing inter-animal variability by using an ensemble of parameters sets, we are able to evaluate the likely impact of novel compounds on a series of virtual dogs.
Modeling neuronal consequences of autism-associated gene regulatory variants with human induced pluripotent stem cells (2020)

Genetic factors contribute to the development of autism spectrum disorder (ASD), and although non-protein-coding regions of the genome are being increasingly implicated in ASD, the functional consequences of these variants remain largely uncharacterized. Induced pluripotent stem cells (iPSCs) enable the production of personalized neurons that are genetically matched to people with ASD and can therefore be used to directly test the effects of genomic variation on neuronal gene expression, synapse function, and connectivity. The combined use of human pluripotent stem cells with genome editing to introduce or correct specific variants has proved to be a powerful approach for exploring the functional consequences of ASD-associated variants in protein-coding genes and, more recently, long non-coding RNAs (lncRNAs). Here, we review recent studies that implicate lncRNAs, other non-coding mutations, and regulatory variants in ASD susceptibility. We also discuss experimental design considerations for using iPSCs and genome editing to study the role of the non-protein-coding genome in ASD.
Hypoxia (2001)

Abstract The dependence of many cells on aerobic respiration as an obligatory energy source requires a variety of responses to oxygen lack or hypoxia.
Engineered Cementitious Composites: An Innovative Concrete for Durable Structure (2009)

This paper reviews recent research on the durability properties of Engineered Cementitious Composites (ECC), a special type of high-performance fiber reinforced cementitious composites designed with micromechanical principles, under various environmental and mechanical loads. The durability subjects include (a) ECC cracking and transport properties (permeability, absorption and diffusion), (b) corrosion resistance (c) freeze-thaw and salt scaling resistance, (d) performance under hot and humid environment, and (e) performance under high alkaline environment. The research results indicate that due to intrinsic self-control tight crack width and high tensile strain capacity, many durability challenges confronting concrete can be overcome by using ECC. The enhanced performances of ECC under mechanical and environmental loads are expected to contribute substantially to improving civil infrastructure sustainability by reducing the amount of repair and maintenance during the service life of the structure.
BCR/ABL induces expression of vascular endothelial growth factor and its transcriptional activator, hypoxia inducible factor-1α, through a pathway involving phosphoinositide 3-kinase and the mammalian target of rapamycin (2002)

Recent data suggest that vascular endothelial growth factor (VEGF), a cytokine involved in autocrine growth of tumor cells and tumor angiogenesis, is up-regulated and plays a potential role in myelogenous leukemias. In chronic myelogenous leukemia (CML), VEGF is expressed at high levels in the bone marrow and peripheral blood. We show here that the CML-associated oncogene BCR/ABL induces VEGF gene expression in growth factor-dependent Ba/F3 cells. Whereas starved cells were found to contain only baseline levels of VEGF mRNA, Ba/F3 cells induced to express BCR/ABL exhibited substantial amounts of VEGF mRNA. BCR/ABL also induced VEGF promoter activity and increased VEGF protein levels in Ba/F3 cells. Moreover, BCR/ABL was found to promote the expression of functionally active hypoxia-inducible factor-1 (HIF-1), a major transcriptional regulator of VEGF gene expression. BCR/ABL-induced VEGF gene expression was counteracted by the phosphoinositide 3-kinase (PI3-kinase) inhibitor LY294002 and rapamycin, an antagonist of mammalian target of rapamycin (mTOR), but not by inhibition of the mitogen-activated protein kinase pathway. Similarly, BCR/ABL-dependent HIF-1alpha expression was inhibited by the addition of LY294002 and rapamycin. Together, our data show that BCR/ABL induces VEGF- and HIF-1alpha gene expression through a pathway involving PI3-kinase and mTOR. BCR/ABL-induced VEGF expression may contribute to the pathogenesis and increased angiogenesis in CML.