gebhart/patrepeval huggingface dataset:
Ensemble Docking into Flexible Active Sites. Critical Evaluation of FlexE against JNK-3 and β-Secretase (2006)

One of the main complicating factors in structure-based drug design is the conformational rearrangement of the receptor upon ligand binding implicating protein flexibility as a crucial component in virtual screening. The FlexE approach allows flexibility through discrete alternative conformations of varying parts of the protein taken from structures having similar backbone traces. Here the performance of FlexE was tested against that of FlexX and FlexX-Pharm, by carrying out virtual screening experiments on two sets of structurally distinct complexes, for the enzymes beta-secretase (BACE), and c-jun N-terminal kinase 3 (JNK-3). A large number of incompatible instances occurred between structural elements of the proteins thus loop movements could not be studied in JNK-3 as well as in BACE. The investigation of the side-chain flexibility revealed that at the most FlexE could achieve the enrichment yielded by FlexX in JNK-3 but not in BACE. Although limited side-chain variations (e.g. different protonation states) can be treated by FlexE, docking into protein ensembles remains a practical tool that decreases the average run time for a ligand.
A Practical Parallel Synthesis of 2‐Substituted Indolizines. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Chaining direct memory access data transfer operations for compute nodes in a parallel computer (2023)

Methods, systems, and products are disclosed for chaining DMA data transfer operations for compute nodes in a parallel computer that include: receiving, by an origin DMA engine on an origin node in an origin injection FIFO buffer for the origin DMA engine, a RGET data descriptor specifying a DMA transfer operation data descriptor on the origin node and a second RGET data descriptor on the origin node, the second RGET data descriptor specifying a target RGET data descriptor on the target node, the target RGET data descriptor specifying an additional DMA transfer operation data descriptor on the origin node; creating, by the origin DMA engine, an RGET packet in dependence upon the RGET data descriptor, the RGET packet containing the DMA transfer operation data descriptor and the second RGET data descriptor; and transferring, by the origin DMA engine to a target DMA engine on the target node, the RGET packet.
Memory Warps for Long-Term Online Video Representations and Anticipation (2019)

We propose a novel memory-based online video representation that is efficient, accurate and predictive. This is in contrast to prior works that often rely on computationally heavy 3D convolutions, ignore motion when aligning features over time, or operate in an off-line mode to utilize future frames. In particular, our memory (i) holds the feature representation, (ii) is spatially warped over time to compensate for observer and scene motions, (iii) can carry long-term information, and (iv) enables predicting feature representations in future frames. By exploring a variant that operates at multiple temporal scales, we efficiently learn across even longer time horizons. We apply our online framework to object detection in videos, obtaining a large 2.3 times speed-up and losing only 0.9% mAP on ImageNet-VID dataset, compared to prior works that even use future frames. Finally, we demonstrate the predictive property of our representation in two novel detection setups, where features are propagated over time to (i) significantly enhance a real-time detector by more than 10% mAP in a multi-threaded online setup and to (ii) anticipate objects in future frames.
Cell Death Triggered by the YUCCA-like Bs3 Protein Coincides with Accumulation of Salicylic Acid and Pipecolic Acid But Not of Indole-3-Acetic Acid (2019)

The pepper (<i>Capsicum annuum</i>) resistance gene <i>bacterial spot3</i> (<i>Bs3</i>) is transcriptionally activated by the matching <i>Xanthomonas euvesicatoria</i> transcription-activator-like effector (TALE) AvrBs3. AvrBs3-induced <i>Bs3</i> expression triggers a rapid and local cell death reaction, the hypersensitive response (HR). Bs3 is most closely related to plant flavin monooxygenases of the YUCCA (YUC) family, which catalyze the final step in auxin biosynthesis. Targeted mutagenesis of predicted NADPH- and FAD-cofactor sites resulted in Bs3 derivatives that no longer trigger HR, thereby suggesting that the enzymatic activity of Bs3 is crucial to Bs3-triggered HR. Domain swap experiments between pepper <i>Bs3</i> and Arabidopsis (<i>Arabidopsis thaliana</i>) <i>YUC8</i> uncovered functionally exchangeable and functionally distinct regions in both proteins, which is in agreement with a model whereby <i>Bs3</i> evolved from an ancestral <i>YUC</i> gene. Mass spectrometric measurements revealed that expression of <i>YUC</i>s, but not expression of <i>Bs3</i>, coincides with an increase in auxin levels, suggesting that Bs3 and YUCs, despite their sequence similarity, catalyze distinct enzymatic reactions. Finally, we found that expression of <i>Bs3</i> coincides with increased levels of the salicylic acid and pipecolic acid, two compounds that are involved in systemic acquired resistance.
Steroidal Affinity Labels of the Estrogen Receptor α. 4. Electrophilic 11β-Aryl Derivatives of Estradiol (2000)

Ten electrophilic estradiol 11beta-aryl derivatives were synthesized, with three different types of 11beta-substituent: (i) pOO(CH(2))(2)X (compounds: 6, X = OSO(2)CH(3); 7, X = I; 13, X = NHCOCH(2)Cl; 15, X = N(CH(3))COCH(2)Br; and 16, X = N(CH(3))COCH(2)Cl); (ii) pOO(CH(2))(5)X (compounds: 17, X = I; 20, X = NHCOCH(2)Br; and 22, X = N(CH(3))COCH(2)Br); and (iii) pOC(triple bond)CCH(2)X (compounds: 27, X = NHCOCH(2)Cl; and 29, X = N(CH(3))COCH(2)Cl). The range of their apparent affinity constants for binding the lamb uterine estrogen receptor alpha (ERalpha) was 3-40% that of estradiol. Six electrophiles, chloroacetamides 13, 16, 27, and 29, iodide 17, and bromoacetamide 20 (whose arm linking the electrophilic carbon to the 11beta-phenyl group includes at least six bonds), were able to irreversibly inhibit the binding of [(3)H]estradiol to ER (25-60% decrease in binding sites), with the following compound effectiveness order: 17 < 13 < 16 approximately 20 approximately 27 approximately 29. Mesylate 6, iodide 7 (whose linking arm includes only three bonds), and bromoacetamides 15 and 22 (which differ from 16 by the Cl to Br change and from 20 by the NH to NCH(3) change, respectively) were much less effective (<10% decrease in binding sites, if any). The fact that the inactivation of estradiol-binding sites by the six electrophiles was totally prevented by estradiol indicated that they were ER affinity labeling agents. When ER was modified by methyl methanethiosulfonate, an SH-specific reagent, the different compounds led to very contrasting results in ER affinity labeling. With modified ER, iodide 17 and chloroacetamides 27 and 29 were practically inactive, chloroacetamides 13 and 16 and bromoacetamide 20 were still active but less effective than on the native ER, whereas tertiary bromoacetamides 15 and 22, found to be practically inactive on native ER, became the most effective electrophiles ( approximately 45% and approximately 65% binding sites inactivated, respectively). The results indicate that in the steroid-filled hormone-binding pocket: (i) nucleophilic residues are localized on the beta-side but relatively remote from the steroid nucleus (distance from C-11 > "seven bonds"); (ii) relatively discrete changes in the electrophilic functionality, such as Cl to Br or NH to NCH(3) of haloacetamido compounds, can markedly modify the positioning of the electrophilic center which could no longer react with the nucleophilic residues; and (iii) cysteine residues (probably homologues of human ERalpha cysteine 381 and/or cysteine 530) are, at least partly, the covalent attachment sites of the electrophiles. Moreover, modification of cysteine residues by methyl methanethiosulfonate changes the structure of the hormone-binding pocket, whose labeling by the various electrophiles is profoundly altered.
Venomic Interrogation Reveals the Complexity of Conus striolatus Venom (2020)

Given the complexity of cone snail venoms, high throughput venomics approaches are required to fully investigate venom composition, envenomation strategies, and evolutionary trajectories. This study describes 158 conotoxins in the venom transcriptome of the little studied C. striolatus from the fish hunting clade Pionoconus. Despite similar gene superfamily distributions along the venom duct, only 18 common transcripts were identified between distal, central, and proximal venom duct transcriptomes. Proteomic analysis of the injected predatory venom collected from the same individual revealed an ~18-fold enhanced complexity at the proteomic level, consistent with complex post-translational modifications and variable venom peptide processing occurring in the venom duct. Overall, C. striolatus venom was dominated by M, O1, O2, and A gene superfamily conotoxins and conkunitzins, which are potential modulators of sodium, calcium, and potassium channels. Conkunitzins and gene superfamily A peptides dominated the proximal over the distal duct, the M and O1 gene superfamily peptides were distributed along the full length of the duct, while the O2 gene superfamily peptides dominated the distal duct. Interestingly, the predatory injected venom of C. striolatus was dominated by peptides from gene superfamilies M, O1, O2, A, and conkunitzins, suggesting the predatory venom of C. striolatus may arise at multiple sites along the venom duct.
Quantum dot resonant-fluorescence linewidth narrowing and enhanced intensity (2017)

We study the processes in a quantum dot and its surrounds under resonant excitation with the addition of weak non-resonant light. We observe a decrease in inhomogeneous emission linewidth, as well as previously observed enhancement of resonant fluorescence (RF). Scanning excitation and detection frequencies, we distinguish between homogeneous and inhomogeneous broadening. Monte Carlo simulations model the enhanced RF only if we include charge-carrier loss from the quantum dot induced by the resonant laser. The cause of the linewidth narrowing is predominantly independent of the enhanced RF.
Immunotypes of a Quaternary Site of HIV-1 Vulnerability and Their Recognition by Antibodies (2011)

HIV-1 is neutralized by a class of antibodies that preferentially recognize a site formed on the assembled viral spike. Such quaternary structure-specific antibodies have diverse neutralization breadths, with antibodies PG16 and PG9 able to neutralize 70 to 80% of circulating HIV-1 isolates while antibody 2909 is specific for strain SF162. We show that alteration between a rare lysine and a common N-linked glycan at position 160 of HIV-1 gp120 is primarily responsible for toggling between 2909 and PG16/PG9 neutralization sensitivity. Quaternary structure-specific antibodies appear to target antigenic variants of the same epitope, with neutralization breadth determined by the prevalence of recognized variants among circulating isolates.
Ventilatory Efficiency Is Reduced in People With Hypertension During Exercise (2023)

Background An elevated ventilatory efficiency slope during exercise (minute ventilation/volume of expired CO<sub>2</sub>; V<sub>E</sub>/VCO<sub>2</sub> slope) is a strong prognostic indicator in heart failure. It is elevated in people with heart failure with preserved ejection, many of whom have hypertension. However, whether the V<sub>E</sub>/VCO<sub>2</sub> slope is also elevated in people with primary hypertension versus normotensive individuals is unknown. We hypothesize that there is a spectrum of ventilatory inefficiency in cardiovascular disease, reflecting an increasingly abnormal physiological response to exercise. The aim of this study was to evaluate the V<sub>E</sub>/VCO<sub>2</sub> slope in patients with hypertension compared with age-, peak oxygen consumption-, and sex-matched healthy subjects. Methods and Results Ramped cardiovascular pulmonary exercise tests to peak oxygen consumption were completed on a bike ergometer in 55 patients with primary hypertension and 24 normotensive controls. The V<sub>E</sub>/VCO<sub>2</sub> slope was assessed from the onset of exercise to peak oxygen consumption. Data were compared using unpaired Student <i>t</i> test. Age (mean±SD, 66±6 versus 64±6 years; <i>P</i>=0.18), body mass index (25.4±3.5 versus 24±2.4 kg/m<sup>2</sup>; <i>P</i>=0.13), and peak oxygen consumption (23.2±6.6 versus 24±7.3 mL/min per kg; <i>P</i>=0.64) were similar between groups. The V<sub>E</sub>/VCO<sub>2</sub> slope was elevated in the hypertensive group versus controls (31.8±4.5 versus 28.4±3.4; <i>P</i>=0.002). Only 27% of the hypertensive group were classified as having a normal V<sub>E</sub>/VCO<sub>2</sub> slope (20-30) versus 71% in the control group. Conclusions Ventilatory efficiency is impaired people with hypertension without a diagnosis of heart failure versus normotensive individuals. Future research needs to establish whether those patients with hypertension with elevated V<sub>E</sub>/VCO<sub>2</sub> slopes are at risk of developing future heart failure.
The endothelial function in cardiac surgery. (2006)

Cardiac operations with cardiopulmonary bypass exerts many different actions which modify the natural function of endothelial cells. The main determinant is the activation of the coagulation system both through the intrinsic and extrinsic pathways, leading to an overwhelming thrombin formation. To counteract the coagulant effects of thrombin, heparin is used in large doses. As a result, the endothelium is asked to promote all its anticoagulant properties, basically through the AT release from the surface, the tissue factor pathway inhibitor release, and the activation of the protein C protein S system. At the end of cardiac operations, all these systems are depleted, and low levels of antithrombin, tissue factor pathway inhibitor, protein C are available for further anticoagulant effects. There is the evidence that levels of antithrombin activity below 50% at the end of cardiac operations with cardiopulmonary bypass are associated to bad outcomes in terms of surgical revision rate, thromboembolic events, and neurological events. Exogenous antithrombin administration has a well defined action in limiting thrombin formation during cardiac operations; however, we are still lacking an evidence-based information about the clinical impact of this and others possible preventive strategies based on exogenous administration of antithrombin before or during cardiac operations.
An Efficient Jacobian Reduction Method For Image Reconstruction Using Diffuse Optical Tomography (2008)

Image reconstruction using Diffuse Optical Tomography requires an accurate inverse model which is usually computationally expensive. We present a Jacobian reduction method which uses the magnitude of the sensitivity to reduce the Jacobian and reconstruct images without detriment to the final solution.
Characteristics of SiF4 Plasma Doping (PLAD) (2016)

SiF <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> PLAD has been systematically characterized and optimized. The correlations between the etching, deposition, retained F dose and profile as functions of the PLAD process variables including implant voltage, RF power, pressure, pulse duty cycle, and the diluting gases have been extensively investigated. It was found that PLAD process by using pure SiF <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> is in an etching or RIE regime, but can be adjusted to minimize the etching effect. It was found that diluting SiF <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> with different gases can significantly impact etching and deposition characteristics. The selectivity of etching and deposition behaviors on the different substrate materials such as poly-Si, silicon oxide, and silicon nitride have been explored. With the understanding of these behaviors, SiF <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> PLAD can be optimized for multiple precision doping and material modification applications.
C . elegans Vulval Induction (2002)

Abstract Study of Caenorhabditis elegans vulval development has improved our understanding of inductive signalling and pattern formation at the single cell level, and has led to the definition of signalling cascades. Studies of signal transduction during vulval development have led to the discovery of what is considered a universal signalling pathway from growth factor receptor to RAS to MAP kinase to the nucleus, and the discovery of the LIN‐12/Notch family of receptors that mediate lateral signalling.
General splicing factors SF2 and SC35 have equivalent activities in vitro, and both affect alternative 5' and 3' splice site selection. (1992)

The human pre-mRNA splicing factors SF2 and SC35 have similar electrophoretic mobilities, and both of them contain an N-terminal ribonucleoprotein (RNP)-type RNA-recognition motif and a C-terminal arginine/serine-rich domain. However, the two proteins are encoded by different genes and display only 31% amino acid sequence identity. Here we report a systematic comparison of the splicing activities of recombinant SF2 and SC35. We find that either protein can reconstitute the splicing activity of S100 extracts and of SC35-immunodepleted nuclear extracts. Previous studies revealed that SF2 influences alternative 5' splice site selection in vitro, by favoring proximal over distal 5' splice sites, and that the A1 protein of heterogeneous nuclear RNP counteracts this effect. We now show that SC35 has a similar effect on competing 5' splice sites and is also antagonized by A1 protein. In addition, we report that both SF2 and SC35 also favor the proximal site in a pre-mRNA containing duplicated 3' splice sites, but this effect is not modulated by A1. We conclude that SF2 and SC35 are distinct splicing factors, but they display indistinguishable splicing activities in vitro.
Some Cobalt(III) Complexes of Glycine (1966)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSome Cobalt(III) Complexes of GlycineM. Dale Alexander and Daryle H. BuschCite this: Inorg. Chem. 1966, 5, 9, 1590–1593Publication Date (Print):September 1, 1966Publication History Published online1 May 2002Published inissue 1 September 1966https://pubs.acs.org/doi/10.1021/ic50043a027https://doi.org/10.1021/ic50043a027research-articleACS PublicationsRequest reuse permissionsArticle Views460Altmetric-Citations13LEARN 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-Alertsclose Get e-Alerts
Effect of General Anaesthetics and Organic Solvents on α1–Adrenoceptors in the Myometrium (1985)

The alpha 1 selective radioligand 3H-prazosin was used to assay alpha 1 receptors in membranes prepared from the rabbit myometrium. 3H-Prazosin was found to bind to a single high affinity site in these membranes which was the presumed alpha 1 receptor. A series of general anaesthetics and organic solvents were tested for their ability to inhibit 3H-prazosin binding. The order of potency of the tested agents to inhibit the binding was: chloroform=halothane=trichloroethylene greater than carbon tetrachloride greater than dichloromethane. The depression of 3H-prazosin binding seemed to be induced on the alpha 1 receptor since non-specific radioligand binding was not affected as revealed by a saturation experiment with 3H-prazosin where halothane was used as inhibiting agent. Computer analysis of the latter experiment also showed that halothane depressed mainly the affinity of 3H-prazosin for the alpha 1 receptor. The ability of the general anaesthetics and organic solvents to inhibit contractions elicited by alpha 1 stimulation with phenylephrine in the rabbit uterus was also investigated. In these tests the order of potency for the inhibition of the contractile response was: carbon tetrachloride greater than or equal to halothane=chloroform greater than trichloroethylene greater than dichloromethane. The mechanism of action for alpha 1 receptor and myometrial depression is discussed.
Design of a High-Power Gaussian Pulse Transmitter for Sensing and Imaging of Buried Objects (2021)

This paper aims to investigate a high-power and low-cost monopulse transmitter circuit for underground and underwater sensing and imaging. The transmitter utilizes two Marx transistor-based pulse generators, a balun, and a Vivaldi antenna. A simple output network, including an inductor and Schottky diode, is employed to compensate for the ringing level and distortion and improve the pulse width. The ringing level of the developed circuit is around 6 percent. The output is a Gaussian pulse with pulse width and amplitude of 481 ps and 50 V, respectively. In order to have a high amplitude monopulse, an exact replica of this network in parallel is exploited. The outputs of the parallel circuits are subtracted through the balun to have a <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dc</i> -free monopulse with amplitude and pulse width of 26 V and 483 ps, respectively. The monopulse is radiated by a Vivaldi antenna toward a buried object. The image of the target is generated using the time-domain global back projection (TD-GBP) method. Three imaging experiments are conducted to verify the functionality of the designed sensor system. The reconstructed images and the reference images are shown high structural similarity indexes of 98.6%, 95.4%, and 97.6%.
Fourth-order interference effects at large distances (1992)

We present an experimental demonstration of a fourth-order interference effect first suggested by Franson [Phys. Rev. Lett. 62, 2205 (1989)], where pair photons are directed to two separated Mach-Zehnder interferometers. Apparent nonlocal control of the output ports in which coincident photons are detected can be demonstrated. We show that this effect is present when one of the photons has passed through 170 m of multimode optical fiber. Such a system could form the basis of an interception-proof communication system.