gebhart/patrepeval huggingface dataset:
Electrostatic contributions to protein stability and folding energy (2007)

The ability to predict the thermal stability of proteins based on their corresponding sequence is a problem of great fundamental and practical importance. Here we report an approach for calculating the electrostatic contribution to protein stability based on the use of the semimacroscopic protein dipole Langevin dipole (PDLD/S) in its linear response approximation version for self-energy with a dielectric constant, (epsilon(p)) and an effective dielectric for charge-charge interactions (epsilon(eff)). The method is applied to the test cases of ubiquitin, lipase, dihydrofolate reductase and cold shock proteins with series of epsilon(p) and epsilon(eff). It is found that the optimal values of these dielectric constants lead to very promising results, both for the relative stability and the absolute folding energy. Consideration of the specific values of the optimal dielectric constants leads to an exciting conceptual description of the reorganization effect during the folding process. Although this description should be examined by further microscopic studies, the practical use of the current approach seems to offer a powerful tool for protein design and for studies of the energetics of protein folding.
Nonsusceptibility artifacts due to metallic objects in MR imaging (1995)

The authors investigated eddy current artifacts due to metallic objects within the magnetic resonance imaging field. The problem was simplified by using a circular copper loop as a model for the more complex eddy current pathways present in a metallic implant. With this simple geometry, the authors show that radio-frequency (RF)-induced eddy currents in the metal produce a significant local artifact. However, no appreciable artifacts due to the switching magnetic field gradients were observed. A detailed quantitative analysis of the mechanism of RF-induced eddy current artifact due to the the copper loop was performed. The artifact was demonstrated experimentally to result from perturbations of the transmit and receive sensitivities of the RF coil. Theoretical calculations of these perturbations showed excellent agreement with experimental results. With an understanding of the artifact mechanism, methods for correcting the RF-induced eddy current artifact were applied.
Asymmetric epoxidation of electron-deficient olefins (2000)

In recent years, methods for the asymmetric epoxidation of electron-deficient olefins, particularly α,β-enones, have attracted widespread attention. A critical review is presented of these methods, which include epoxidations with chiral metal hydroperoxides, asymmetric phase-transfer methods, the use of polyamino acid catalysts and the use of chiral dioxiranes.
Active feedback lightwave receivers (1986)

This paper describes new p-i-n-FET lightwave receivers that achieve high sensitivity without signal integration, and dynamic ranges large enough that they cannot be saturated by present lightwave transmitters. IC versions can be realized inexpensively in standard fine-line NMOS, CMOS, or GaAs IC technologies, and thus are suitable for loop-plant, local-area-network, and data link applications, as well as long-haul transmission applications. These receivers also can readily be designed for bit-rates in excess of 1 Gbit/s for high-capacity systems. In addition, these receivers can be implemented on the same IC as other system functions, e.g., for single-chip lightwave regenerators and lightwave modems, and, eventually, for microprocessors with on-chip optical communications ports.
Antialias Filters and System Transient Response at High Sample Rates (2004)

Sample rates higher than 48 kHz allow freedom to tailor the audio response above 20 kHz in order to optimize the transient performance. A recording and reproduction chain may have pre- and postringing caused by brickwall band-limiting filters, but a single apodizing filter can substantially suppress the ringing and shorten the impulse response. The apodizing filter can be placed anywhere in the chain, but the mastering stage probably fits in best with current practice. The paper presents coefficients for a number of filters suitable for 96-kHz and 192-kHz sampled audio, and experimentation is encouraged. Some of the filters are symmetrical, but, taking into account the ear's sensitivity to preresponses, others have been optimized for a near-zero preresponse.
Synergistic antiproliferative activity of quercetin and cisplatin on ovarian cancer cell growth (1990)

It has been demonstrated that the flavonoid quercetin (3,3',4',5-7-pentahydroxyflavone) (Q) inhibits the growth of several cancer cell lines and that the antiproliferative activity of this substance is mediated by a so-called type II estrogen binding site (type II EBS). We investigated the effects of quercetin and cisplatin (CDDP) alone and in combination on the proliferation of the ovarian cancer cell line OVCA 433. Both drugs exhibited a dose-related growth inhibition in a range of concentrations between 0.01 and 2.5 microM and 0.01 and 2.5 micrograms/ml for Q and CDDP respectively. The combination of the two drugs resulted in a synergistic antiproliferative activity. Two other flavonoids tested, i.e., rutin (3-rhamnosylglucoside of quercetin) and hesperidin [7-b rutinoside of hesperetin (3'-5-3-hydroxy-4-methoxyflavone)] were ineffective both alone and in combination with CDDP. Since both rutin and hesperidin do not bind to type II EBS it can be hypothesized that Q synergizes with CDDP by acting through an interaction with these binding sites.
TorqueBAR (2003)

Kinesthetic feedback is a key mechanism by which people perceive object properties during their daily tasks - particularly inertial properties. For example, transporting a glass of water without spilling, or dynamically positioning a handheld tool such as a hammer, both require inertial kinesthetic feedback. We describe a prototype for a novel ungrounded haptic feedback device, the TorqueBAR, that exploits a kinesthetic awareness of dynamic inertia to simulate complex coupled motion as both a display and input device. As a user tilts the TorqueBAR to sense and control computer programmed stimuli, the TorqueBAR's centre-of-mass changes in real-time according to the user's actions. We evaluate the TorqueBAR using both quantitative and qualitative techniques, and we describe possible applications for the device such as video games and real-time robot navigation.
Inhibition of neutrophil elastase attenuates airway hyperresponsiveness and inflammation in a mouse model of secondary allergen challenge: neutrophil elastase inhibition attenuates allergic airway responses (2013)

These data indicate that neutrophil elastase plays an important role in the development of allergic airway inflammation and hyperresponsiveness, and would suggest that the neutrophil elastase inhibitor reduced AHR to inhaled methacholine indicating the potential for its use as a modulator of the immune/inflammatory response in both the neutrophil- and eosinophil-dominant phases of the response to secondary allergen challenge.
A proposal for a dynamic-response-evaluation method for torque transducers (1999)

A dynamic-response-evaluation method for torque transducers is proposed. In this method, dynamic torque is applied to the transducer being tested by using a rotating flywheel, via a frictional clutch. To realize the condition under which the angular impulse acting on the transducer is sufficiently equivalent to the change in angular momentum of the flywheel, the flywheel is supported by a pneumatic bearing with sufficiently small friction. The angular velocity of the flywheel is measured by means of a rotary-encoder system. The relative uncertainty in the measurement of the angular momentum acting on the transducer is estimated to be less than 10-3.
Bayesian Variable Selection for Nowcasting Economic Time Series (2013)

We consider the problem of short-term time series forecasting (nowcasting) when there are more possible predictors than observations. Our approach combines three Bayesian techniques: Kalman filtering, spike-and-slab regression, and model averaging. We illustrate this approach using search engine query data as predictors for consumer sentiment and gun sales.
Ischemic Preconditioning Upregulates Vascular Endothelial Growth Factor mRNA Expression and Neovascularization via Nuclear Translocation of Protein Kinase C ε in the Rat Ischemic Myocardium (2001)

Ischemic preconditioning (IP) exerts cardioprotection through protein kinase C (PKC) activation, whereas myocardial ischemia enhances vascular endothelial growth factor (VEGF) mRNA expression. However, the IP effect or the involvement of PKC on the VEGF expression is unknown in myocardial infarction. We investigated whether IP enhances VEGF gene expression and angiogenesis through PKC activation in the in vivo myocardial infarction model. Sprague-Dawley rats were assigned into the following 3 groups: the sham group; the IP group, which underwent 3 cycles of 3 minutes of ischemia and 5 minutes of reperfusion (IP procedure); and the non-IP group. The latter 2 groups were subsequently subjected to left anterior descending coronary artery occlusion. To examine the involvement of PKC, the PKC inhibitor chelerythrine (5 mg/kg) or bisindolylmaleimide (1 mg/kg) was injected intravenously before the IP procedures. PKCepsilon was translocated to the nucleus after 10 minutes of ischemia after the IP procedure but was not translocated in the non-IP and the sham groups. VEGF mRNA expression 3 hours after infarction was significantly higher in the IP group than in the non-IP and the sham groups. Capillary density in the infarction was significantly higher, whereas the infarct size was smaller in the IP group than in the non-IP group at 3 days of infarction. Chelerythrine but not bisindolylmaleimide blocked all of the IP effects on the nuclear translocation of PKCepsilon, enhancement of VEGF mRNA expression and angiogenesis, and infarct size limitation. These results show that IP may enhance VEGF gene expression and angiogenesis through nuclear translocation of PKCepsilon in the infarcted myocardium.
A stereoselective, Sm(ii)-mediated approach to decorated cis-hydrindanes: synthetic studies on faurinone and pleuromutilin (2011)

The cis-hydrindane motif is found in a number of natural products that display important biological activity. A flexible, stereoselective approach to the framework has been developed that features highly diastereoselective, SmI(2)-mediated cyclisations. The strategy has been exploited in the first synthesis of the proposed structure of faurinone and an approach to the skeleton of the antibacterial natural product, pleuromutilin.
Quantitative determination of fission products in irradiated fuel pins using nondestructive gamma scanning (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTQuantitative determination of fission products in irradiated fuel pins using nondestructive gamma scanningJ. R. Phillips, G. R. Waterbury, N. E. Vanderborgh, and T. K. MarshallCite this: Anal. Chem. 1975, 47, 1, 71–75Publication Date (Print):January 1, 1975Publication History Published online1 May 2002Published inissue 1 January 1975https://doi.org/10.1021/ac60351a022RIGHTS & PERMISSIONSArticle Views90Altmetric-Citations8LEARN 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 InReddit PDF (597 KB) Get e-Alertsclose Get e-Alerts
TESLA: Using microfluidics to thermally stabilize 3D stacked STT-RAM caches (2016)

In this work, we develop a 3D architecture that utilizes STT-RAM for the last level cache (LLC). 3D integration enables large LLCs to be stacked onto a die. However, 3D architectures suffer from higher operating temperatures due to increased power densities. The elevated temperatures can adversely impact the STT-RAM performance and reliability. The objective of this paper is to address the limits of integrating STT-RAM in 3D chip stacks from a thermal perspective and propose a novel stacking structure that minimizes heat-induced problems. Specifically, we analyze the system-level impact of increased temperatures and propose a novel technique to dynamically adjust the flow rate of the liquid interlayer cooling at run time to reduce the STT-RAM temperature and alleviate temperature-induced problems that cause the performance degradation and prevent overcooling the STT-RAM die and minimize the pump energy consumption. Evaluation results reveal that our approach achieves up to 19.1% performance improvement and 14.6% power reduction over an architecture that does not include an insulating layer.
X-ray scattering study on amorphous, polynuclear platinum uridine complexes (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTX-ray scattering study on amorphous, polynuclear platinum uridine complexesRitva Serimaa, Sakari Vahvaselka, Tarja Laitalainen, Timo Paakkari, and Anneli OksanenCite this: J. Am. Chem. Soc. 1993, 115, 22, 10036–10041Publication Date (Print):November 1, 1993Publication History Published online1 May 2002Published inissue 1 November 1993https://pubs.acs.org/doi/10.1021/ja00075a020https://doi.org/10.1021/ja00075a020research-articleACS PublicationsRequest reuse permissionsArticle Views79Altmetric-Citations5LEARN 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 (2)»Supporting Information Supporting Information Get e-Alerts
NMR relaxation measurements to quantify immiscible organic contaminants in sediments (2008)

Laboratory NMR relaxation time ( T 2 ) measurements at 2 MHz were used to quantify the amount of toluene and bis(2‐ethylhexyl)phthalate (BEHP) in the presence of water in sand‐clay mixtures. NMR measurements were made on water, toluene, or BEHP in each sand‐clay mixture to understand the role of clay and iron content on the T 2 of each fluid; we then made NMR measurements on mixtures of water and the contaminants in each sand‐clay mixture. Our ability to resolve the NMR response of the contaminant from that of water and to quantify the amount of the contaminant varied significantly with the clay and iron content of the sand‐clay mixtures. Detection limits as low as 3% contaminant (i.e., percent of the pore fluid, by weight) were observed in some sand‐clay mixtures. Our results suggest that NMR measurements could quantify toluene if some clay is present but are unlikely to be useful for quantifying BEHP.
OSIRIS -- A DISTRIBUTED FAULT-TOLERANT CONTROL SYSTEM (1977)

OSIRIS is an Onboard Survivable Integrated Redundant Information System, being developed for a variety of control applications, and in particular for commercial transport aircraft. The system elements include a fault-to-tolerant multiprocessor, a damage-and fault-tolerant network, distributed local processors, and operational software for fault detection, identification, and recovery for the entire system. This article briefly describes the kinds of applications for which OSIRIS is intended, the architecture of the system and the precepts that have guided its development, and the current status of the experimental configuration.
Performance limitations of subband adaptive filters (1998)

In this paper, we evaluate the performance limitations of subband adaptive filters in terms of achievable final error terms. The limiting factors are the aliasing level in the subbands, which poses a distortion and thus presents a lower bound for the minimum mean squared error in each subband, and the distortion function of the overall filter bank, which in a system identification setup restricts the accuracy of the equivalent fullband model. Using a generalized DFT modulated filter bank for the subband decomposition, both errors can be stated in terms of the underlying prototype filter. If a source model for coloured input signals is available, it is also possible to calculate the power spectral densities in both subbands and reconstructed fullband. The predicted limits of error quantities compare favourably with simulations presented.
Preferential association of glycoproteins to the euchromatin regions of cross-fractured nuclei is revealed by fracture-label. (1986)

We used fracture-label to establish ultrastructural localization of glycoproteins in cross-fractured nuclei of duodenal columnar and exocrine pancreatic cells. Mannose residues were detected in cell nuclei by labeling freeze-fractured tissues with concanavalin A-horseradish peroxidase X colloidal gold (Con A-HRP X CG) or direct concanavalin A X colloidal gold (Con A X CG); fucose residues were detected with Ulex Europaeus I X colloidal gold (UEA I X CG) markers. Areas of the three main intranuclear compartments (euchromatin, heterochromatin, and nucleolus) exposed by freeze-fracture were determined by automated image analysis. Colloidal gold particles bound to each nuclear subcompartment were counted and the results expressed in number of colloidal gold particles per square micrometer +/- SEM. Duodenal and pancreatic tissues fractured and labeled with Con A-HRP X CG complex or direct Con A X CG conjugates showed that the vast majority of Con A binding sites was confined to euchromatin regions with only sparse labeling of the heterochromatin and nucleolus. UEA I labeling of duodenal columnar cells showed that colloidal gold particles were almost exclusively confined to cross-fractured areas where euchromatin is exposed. Trypsinization of the fractured tissues before labeling with Con A and UEA I abolished 95-100% of the original label. Our results show that, within the nucleoplasm, mannose and fucose are residues of glycoproteins preferentially located within the regions of euchromatin.
The Membrane Topography of the Diphtheria Toxin T Domain Linked to the A Chain Reveals a Transient Transmembrane Hairpin and Potential Translocation Mechanisms (2009)

The diphtheria toxin T domain helps translocate the A chain of the toxin across membranes. To gain insight into translocation, the membrane topography of key residues in T domain attached to the A chain (AT protein) was compared to that in the isolated T domain using fluorescence techniques. This study demonstrates that residues in T domain hydrophobic helices (TH5-TH9) tended to be less exposed to aqueous solution in the AT protein than in the isolated T domain. Under conditions in which the loop connecting TH5 to TH6/7 is located stably on the cis (insertion) side of the membrane in the isolated T domain, it moves between the cis and trans sides of the membrane in the AT protein. This is indicative of the formation of a dynamic, transient transmembrane hairpin topography by TH5-TH7 in the AT protein. Since TH8 and TH9 also form a transmembrane hairpin, this means that TH5-TH9 may form a cluster of transmembrane helices. These helices have a nonpolar surface likely to face the lipid bilayer in a helix cluster and a surface rich in uncharged hydrophilic residues which in a helix cluster would likely be facing inward (and perhaps be pore-lining). This uncharged hydrophilic surface could play a crucial role in translocation, interacting transiently with the translocating A chain. A similar motif can be found in, and may be important for, other protein translocation systems.
Coordinated control of multiple prefetchers in multi-core systems (2009)

Aggressive prefetching is very beneficial for memory latency tolerance of many applications. However, it faces significant challenges in multi-core systems. Prefetchers of different cores on a chip multiprocessor (CMP) can cause significant interference with prefetch and demand accesses of other cores. Because existing prefetcher throttling techniques do not address this prefetcher-caused inter-core interference, aggressive prefetching in multi-core systems can lead to significant performance degradation and wasted bandwidth consumption.
Segmentation and analysis of the three‐dimensional redistribution of nuclear components in human mesenchymal stem cells (2008)

To better understand the impact of changes in nuclear architecture on nuclear functions, it is essential to quantitatively elucidate the three-dimensional organization of nuclear components using image processing tools. We have developed a novel image segmentation method, which involves a contrast enhancement and a subsequent thresholding step. In addition, we have developed a new segmentation method of the nuclear volume using the fluorescent background signal of a probe. After segmentation of the nucleus, a first-order normalization is performed on the signal positions of the component of interest to correct for the shape of the nucleus. This method allowed us to compare various signal positions within a single nucleus, and also on pooled data obtained from multiple nuclei, which may vary in size and shape. The algorithms have been tested by analyzing the spatial localization of nuclear bodies in relation to the nuclear center. Next, we used this new tool to study the change in the spatial distribution of nuclear components in cells before and after caspase-8 activation, which leads to cell death. Compared to the morphological TopHat method, this method gives similar but significantly faster results. A clear shift in the radial distribution of centromeres has been found, while the radial distribution of telomeres was changed much less. In addition, we have used this new tool to follow changes in the spatial distribution of two nuclear components in the same nucleus during activation of apoptosis. We show that after caspase-8 activation, when centromeres shift to a peripheral localization, the spatial distribution of PML-NBs does not change while that of centromeres did. We propose that the use of this new image segmentation method will contribute to a better understanding of the 3D spatial organization of the cell nucleus.