gebhart/patrepeval huggingface dataset:
Redox Potentials of Cobalt Corrinoids with Axial Ligands Correlate with Heterolytic Co–C Bond Dissociation Energies (2017)

We investigate the correlations between the redox potentials of nonalkylated cobalt corrinoids and the Co-C bond dissociation energies (BDEs) of the methylated species with an aqua or histidine axial ligand. A set of cobalt corrinoids, cobalamin, and its model systems, which include new version of myoglobin reconstituted with cobalt didehydrocorrin, are investigated. The Co(III)/Co(II) and Co(II)/Co(I) redox potentials of myoglobin reconstituted with cobalt tetradehydrocorrin and didehydrocorrin and the bare cofactors were determined. Density functional theory (DFT) calculations were performed to estimate the Co-C BDEs of the methylated species. It is found that the redox potentials correlate well with the heterolytic BDEs, which are dependent on the electronegativity of the corrinoid frameworks. The present study offers two important insights into our understanding of how enzymes promote the reactions: (i) homolysis is promoted by strong axial ligation and (ii) heterolysis is controlled by the redox potentials, which are regulated by the saturated framework and axial ligation in the enzyme.
Dimerization of DOCK2 Is Essential for DOCK2-Mediated Rac Activation and Lymphocyte Migration (2012)

The migratory properties of lymphocytes depend on DOCK2, an atypical Rac activator predominantly expressed in hematopoietic cells. Although DOCK2 does not contain the Dbl homology domain typically found in guanine nucleotide exchange factors (GEFs), DOCK2 mediates the GTP-GDP exchange reaction for Rac via its DOCK homology region (DHR)-2 (also known as CZH2 or Docker) domain. DOCK2 DHR-2 domain is composed of three lobes, and Rac binding site and catalytic center are generated entirely from lobes B and C. On the other hand, lobe A has been implicated in dimer formation, yet its physiological significance remains unknown. Here, we report that lobe A-mediated DOCK2 dimerization is crucial for Rac activation and lymphocyte migration. We found that unlike wild-type DOCK2, DOCK2 mutant lacking lobe A failed to restore motility and polarity when expressed in thymoma cells and primary T cells lacking endogenous expression of DOCK2. Similar results were obtained with the DOCK2 point mutant having a defect in dimerization. Deletion of lobe A from the DHR-2 domain did not affect Rac GEF activity in vitro. However, fluorescence resonance energy transfer analyses revealed that lobe A is required for DOCK2 to activate Rac effectively during cell migration. Our results thus indicate that DOCK2 dimerization is functionally important under the physiological condition where only limited amounts of DOCK2 and Rac are localized to the plasma membrane.
A Practical Mild, One-Pot, Regiospecific Synthesis of 2,3-Disubstituted Indoles via Consecutive Sonogashira and Cacchi Reactions (2006)

[Structure: see text] A practical one-pot, regiospecific three-component process for the synthesis of 2,3-disubstituted indoles was developed via consecutive Pd-catalyzed Sonogashira coupling, amidopalladation, and reductive elimination.
Super-Homogeneous Saturation of Microwave-Photonic Gain in Optoelectronic Oscillator Systems (2012)

We show that the saturation characteristic of microwave-photonic gain is “super-homogeneous” such that the gain of a weaker tone saturates more rapidly than that of a stronger tone when both signals are transmitted over an intensity-modulated optical link. Using this gain model, we simulate the effect of nonlinear gain saturation on the performance of a slab-coupled optical waveguide (SCOW)-based optoelectronic oscillator (OEO). We verify our simulations with experimental measurements and show that low sidemode levels (<; -110 dBc) can be achieved even when multiple modes can oscillate within the passband of the OEO loop filter.
The semantics of grammar formalisms seen as computer languages (1984)

The design, implementation, and use of grammar formalisms for natural language have constituted a major branch of computational linguistics throughout its development. By viewing grammar formalisms as just a special case of computer languages, we can take advantage of the machinery of denotational semantics to provide a precise specification of their meaning. Using Dana Scott's domain theory, we elucidate the nature of the feature systems used in augmented phrase-structure grammar formalisms, in particular those of recent versions of generalized phrase structure grammar, lexical functional grammar and PATR-II, and provide a denotational semantics for a simple grammar formalism. We find that the mathematical structures developed for this purpose contain an operation of feature generalization, not available in those grammar formalisms, that can be used to give a partial account of the effect of coordination on syntactic features.
Measurement of charged jet cross section in pp collisions at s=5.02  TeV (2019)

The cross section of jets reconstructed from charged particles is measured in the transverse momentum range of $5&lt;{p}_{\mathrm{T}}&lt;100\text{ }\text{ }\mathrm{GeV}/c$ in $pp$ collisions at the center-of-mass energy of $\sqrt{s}=5.02\text{ }\text{ }\mathrm{TeV}$ with the ALICE detector. The jets are reconstructed using the anti-${k}_{\mathrm{T}}$ algorithm with resolution parameters $R=0.2$, 0.3, 0.4, and 0.6 in the pseudorapidity range $|\ensuremath{\eta}|&lt;0.9\ensuremath{-}R$. The charged jet cross sections are compared with the leading-order (LO) and to next-to-leading-order (NLO) perturbative quantum chromodynamics (pQCD) calculations. It is found that the NLO calculations agree better with the measurements. The cross section ratios for different resolution parameters are also measured. These ratios increase from low ${p}_{\mathrm{T}}$ to high ${p}_{\mathrm{T}}$ and saturate at high ${p}_{\mathrm{T}}$, indicating that jet collimation is larger at high ${p}_{\mathrm{T}}$ than at low ${p}_{\mathrm{T}}$. These results provide a precision test of pQCD predictions and serve as a baseline for the measurement in Pb-Pb collisions at the same energy to quantify the effects of the hot and dense medium created in heavy-ion collisions at the LHC.
Selective and Direct Immobilization of Cysteinyl Biomolecules by Electrochemical Cleavage of Azo Linkage (2010)

Controlled orientation and reserved activity of biomolecules, when site-selectively immobilized in a highly integrated manner on a minimal time scale, are crucial in designing biosensors for the multiplex detection. Here, we describe a novel method for the orientation-controlled immobilization of biomolecules based on site-selective electrochemical activation of p-hydroxyazobenzene self-assembled monolayer (SAM) followed by one-step coupling of cysteinyl biomolecules. The p-aminophenol, a product of reductive cleavage of p-hydroxyazobenzene, was subsequently oxidized to yield p-quinoneimine which then conjugated with cysteinyl biomolecules through 1,4-Michael addition, thus obviating additional linker agents and the related time consumption. Using this method, we selectively activated the electrode surface and immobilized laminin peptide IKVAV, a neurite promoting motif. When we cultured hippocampal neurons on the electrode, the extended neurites were found only within the electrochemically activated area. Hence, the proposed method represents a new promising platform for the patterning of functional peptides, active proteins, and live cells.
The Occurrence of Stagnation Bubbles in Supersonic Jet Impingement Flows (1976)

Summary This paper reports an experimental investigation into the stagnation bubbles found in the shock layers of some supersonic jets impinging on perpendicular flat plates at small nozzle-to-plate distances. The experiments used twelve contoured nozzles within the Mach number range 1.42 to 2.83. Surface pressures were measured on the plate and free-jet pitot pressure distributions were obtained at the level of the centre of the plate shock. Schlieren pictures were taken of both impinging and free jets. It was found that the bubbles result from the interaction of the plate shock with very weak shock waves which are produced in the jet either by small imperfections in the nozzle wall or by slight inaccuracies in the design or production of the nozzle contour. The bubbles can be eliminated by suitable improvements to the nozzle. Other anomalous flows produced by shock interactions are described and explanations offered. It is shown that the bubbles sometimes encountered at close plate spacings with conical nozzles are also due to shock waves. However, for wide-angled nozzles, internal shocks can be an inherent part of the flow from the nozzle and the bubbles which they produce are thus an inherent part of the impingement flow. From physical arguments concerning the main factors involved in producing a bubble, a parameter is constructed whose values are shown to be a good criterion for whether a bubble occurs or not.
"Bit rate on demand" using pruned tree-structured hierarchical lookup vector quantization (1999)

We propose a real-time image coding system, which is capable of adapting instantaneously to the available channel bandwidth. The range of operational bandwidths for this system has a finer calibration than ordinary hierarchical vector quantization (HVQ) or wavelet based hierarchical vector quantization (WHVQ) methods suggested in the literature. These properties make it very attractive for networks with fluctuating available bandwidth, like the Internet. All encoder and decoder operations are strictly constant time per pixel, proceeding through table lookups, and are intrinsically suitable for parallel and hardware implementation.
Heterologous expression of Phanerochaete chrysosporium cellobiose dehydrogenase in Trichoderma reesei (2021)

Heterologous production of PcCDH<sub>Tr</sub> is faster and the yield higher than secretion by P. chrysosporium. It also does not need a cellulose-based medium that impedes efficient production and purification of CDH by binding to the polysaccharide. The obtained high uniformity of PcCDH<sub>Tr</sub> glycoforms will be very useful to investigate electron transfer characteristics in biosensors and biofuel cells, which are depending on the spatial restrictions inflicted by high-mannose N-glycan trees. The determined catalytic and electrochemical properties of PcCDH<sub>Tr</sub> are very similar to those of PcCDH and the FAD cofactor occupancy is good, which advocates T. reesei as expression host for engineered PcCDH for biosensors and biofuel cells.
Orphan Disease – Peripartale Kardiomyopathie (2017)

Die peripartale Kardiomyopathie ist eine lebensgefährliche Herzerkrankung, die oft spät erkannt wird, da die klinischen Beschwerden sehr unterschiedlich sein können. In der Regel verläuft die Schwangerschaft zunächst ohne Komplikationen. Die Patientinnen sind jung, gesund und stehen kurz vor der Geburt oder haben sie eben hinter sich gebracht. In den letzten Schwangerschaftswochen bis 6 Monate nach der Geburt macht sich dann eine plötzlich einsetzende Herzinsuffizienz bemerkbar.
Alpha ash transport and ash control (1990)

This paper discusses: thermal {alpha}-particle transport is a crucial issue in ash buildup. The transport will determine if buildup prevents ignition and if external control is necessary. Due to uncertainties in the transport coefficients, 1-1/2-D sensitivity study of the influence on the fusion power density is done using the BALDUR code. The Baldur simulations with varying diffusion coefficients for ash plasma are performed. The results of ash transport in the presence of sawteeth and varying edge conditions are discussed. Also, the nature of the fishbone oscillation in the presence of two hot species consisting of hot alphas and beam injected ions is discussed. The sawteeth and fishbones can be potential mechanisms for enhanced ash transport; the latter will indirectly influence the ash transport.
On the design of sinc interpolator for pilot symbol assisted modulation systems (2006)

This paper investigates the design of practical sine interpolation filters in pilot symbol assisted modulation (PSAM) systems. By closely examining the error mechanism in PSAM channel estimation, we show that the error floor phenomenon is caused by the non-ideal characteristic of the interpolation filter. Based on the use of adjustable window functions, we present a set of design guidelines to determine the shape of window functions, the window/filter length and the pilot insertion rate. The design choices essentially reflect the trade-offs between error performance, implementation complexity and transmission rate.
Ray Tracing Lossy Compressed Grid Primitives (2021)

We propose a new watertight representation of geometry for ray tracing highly complex scenes in a memory efficient manner. Polygon meshes in the scene are first converted into compressed grid primitives, which are represented by a base bilinear patch with quantized displacement vectors. Ray-scene intersections are then computed by efficiently decompressing these grids onthe- fly and intersecting the implicit triangles. Our representation requires just 5:4??6:6 bytes per triangle for the combined geometry and acceleration structure, resulting in a 5-7x reduction in memory footprint compared to indexed triangle meshes. This is achieved with less than 15% increase in rendering time.
Studies on Histaminergic Compounds, IV Non‐isosterism between the Imidazole, Guanidino and Isothiourea Moieties at the H2‐Receptor (1986)

Abstract S,S'‐Alkylenediisothioureas were found to show only weak agonistic or antagonistic H 2 ‐activity, depending on the length of the alkylene chain. Introduction of a substituent in the amidino parts of both isothiourea groups resulted in a complete loss of the agonistic activity; only inactive compounds or weakly active H 2 ‐antagonists were obtained. Replacing one of the isothiourea groups of the alkylenediisothioureas with n = 2, 3 or 4 by a guanidino group has hardly any or no effect at all on the histamine H 2 ‐activity on the guinea‐pig right atrium. However, extending the alkylene chain of these guanidylalkylisothioureas to n = 5 and 6 results in a strong increase in the H 2 ‐agonistic activity.
Influences of pH, Temperature, and Moisture on Gaseous Tritium Uptake in Surface Soils (1982)

In South Carolina surface soils, the uptake of gaseous tritium (T(2), HT, or both) showed a broad optimal temperature response from about 20 to 50 degrees C, with the highest rates at 35 to 45 degrees C. The optimal pH was in the range of 4 to 7. Uptake rates declined at the wet and dry extremes in soil moisture content. Inhibition seen upon the addition of hydrogen or carbon monoxide to the soil atmosphere suggested that hydrogenase may be responsible for T(2)-HT uptake in soil. During the period of most rapid recovery in a 36-day incubation of reinoculated, sterilized soil, T(2)-HT uptake rates doubled every 2 to 4 days. Thus, T(2)-HT uptake appears to be biologically mediated. Soil uptake of T(2)-HT was not severely limited by pH, temperature, or moisture in the soils tested. Thus, rapid exchange of gaseous tritium into soil water must be expected and accounted for in modeling the isotope distributions around nuclear facilities.
5G-ICN : Delivering ICN Services over 5G using Network Slicing (2016)

The challenging requirements of 5G--from both the applications and the architecture perspectives--motivate the need to explore the feasibility of delivering services over new network architectures. As 5G proposes application-centric network slicing, which enables the use of new data planes realizable over a programmable compute, storage, and transport infrastructure, we consider Information-centric Networking (ICN) as a candidate network architecture to realize 5G objectives. This can co-exist with end-to-end IP services that are offered today. To this effect, we first propose a 5G-ICN architecture and compare its benefits (i.e., innovative services offered by leveraging ICN features) to current 3GPP-based mobile architectures. We then introduce a general application-driven framework that emphasizes on the flexibility afforded by Network Function Virtualization (NFV) and Software Defined Networking (SDN) over which 5G-ICN can be realized. We specifically focus on the issue of how mobility-as-a-service (MaaS) can be realized as a 5G-ICN slice, and give an in-depth overview on resource provisioning and inter-dependencies and -coordinations among functional 5G-ICN slices to meet the MaaS objectives.
Effects of Substrate Orientation and Channel Stress on Short-Channel Thin SOI MOSFETs (2010)

We present a study of the effects of substrate orientation and longitudinal channel stress on the performance of extremely thin silicon-on-insulator (ETSOI) MOSFETs with gate lengths down to 25 nm. We find that short-channel electron and hole mobilities follow the long-channel mobility trends versus substrate orientation and longitudinal channel stress. We show that with respect to (100) silicon-on-insulator (SOI) substrates, short-channel ETSOI MOSFETs on (110) SOI substrates lead to 25% enhancement of the p-channel FET drive current at the expense of 12% degradation of the n-channel FET drive current at a fixed off-current of 100 nA/μm and a supply voltage of 1 V. Finally, we estimate that an ETSOI complementary metal-oxide-semiconductor (CMOS) on (110) SOI substrates should lead to 10% faster ring oscillators compared with those on (100) SOI wafers, which also implies that (100)-oriented wafers with (110) sidewalls are a better choice for fabricating nonplanar FinFETs and trigate CMOS circuits.
Preclinical antitumor activity of an Fc domain-optimized HER2 monoclonal antibody (mAb). (2010)

e13135 Background: Response to trastuzumab in metastatic breast cancer correlates with expression of the high affinity allele of the activating Fcγ receptor IIIA (CD16A). We engineered MGAH22, a HER2 mAb with specificity and affinity similar to trastuzumab, to have an optimized Fc domain that confers increased binding to both alleles of CD16A and decreased binding to CD32B (the inhibitory FcγRIIB). Methods: MGAH22 was compared to RES120, an identical mAb except for a wild type Fc domain. Antibody-dependent cell cytotoxicity (ADCC) assays were performed with HER2-expressing cancer cells and human PBMC or purified NK cells. Xenograft studies were conducted in mice with wild-type murine FcγRs; mice lacking murine CD16; or mice lacking mCD16 but transgenic for human CD16A-158F, the low-binding variant. The latter model reproduces the differential binding between wild type and Fc-optimized mAbs for human CD16A. JIMT-1 breast tumor cells were from a patient that progressed on trastuzumab therapy. Results: Compared to RES120, MGAH22 exhibited greater ADCC against HER2-expressing cancer cells with lower EC50. Increased maximal lysis was seen against cells expressing low HER2 levels. With JIMT-1 cells as targets and NK cells as effectors, MGAH22 was more potent than RES120, but an increase in maximal cytotoxicity was only observed with NK cells from CD16-158F carriers. In mouse xenograft models, MGAH22 was active against HER2 expressing breast, ovarian or pancreatic tumors in a manner similar to RES120. MGAH22, however, showed enhanced activity against JIMT-1 xenografts in mCD16-/- hCD16A+ transgenic mouse lines, but not in wild type or mCD16-/- mouse lines. Conclusions: The optimized Fc domain confers enhanced activity against HER2-positive tumor cells, including cells expressing low HER2 levels or resistant to trastuzumab anti-proliferative activity, and enhanced activity against HER2-expressing tumors in hCD16A-158F transgenic mice. MGAH22 may have utility in patients with low HER2 expressing tumors, irrespective of the patient's CD16A genotype. A phase I dose- escalation study to assess the safety and PK of MGAH22 in patients with refractory HER2-positive cancers for whom no standard therapy is available is planned for 2010. Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration MacroGenics, Inc. MacroGenics, Inc.
PROTECTIVE EFFECT OF LORANTHUS LONGIFLORUS ON LEARNING AND MEMORY OF RATS EXPOSED TO ELECTROMAGNETIC RADIATION (EMR) (2013)

The interaction of mobile phone radio-frequency electromagnetic radiation (RF-EMR) with the brain is a serious concern of our society. In this study, we aimed to experiment on the antioxidative property of a parasitic plant Loranthus longiflorus (Loranthaceae) to protect central nervous system against oxidative damages of mobile phone electromagnetic radiation (EMR). Healthy male albino wistar rats were exposed to RF-EMR by giving 5 min calling/ 5min interval for 1 hour per day for two month, Keeping a GSM (0.9 GHz/1.8 GHz) mobile phone in Silent mode (no ring tone) in the cage. After 15, 30, 45, 60 days exposure, three randomly picked animals from both groups were tested with using Morris water maze. Antioxidant compounds and their Neuroprotective action of Loranthus longiflorus bark sample collected from Ficus religiosa host trees were assessed. Rats which have been feed with Ethyl acetate Extract of Loranthus longiflorus (EAL) bark (700mg/kg body weight, p.o.)
Time Course of In Vivo 5-HTT Transporter Occupancy by Fluvoxamine (2006)

The pharmacokinetics of drugs with specific binding sites in the brain needs to be evaluated at these sites. In this study, we measured the time course of the selective serotonin reuptake inhibitor fluvoxamine in the human brain based on serotonin transporter (5-HTT) occupancy by positron emission tomography. Consecutive positron emission tomography scans were performed using [11C]3-amino-4-(2-dimethylaminomethyl-phenylsulfanyl)-benzonitrile before, 5 hours, 26 hours, and 53 hours after 50 mg of fluvoxamine administration in 6 healthy male volunteers (mean, 24.3 +/- 4.8 years). Quantification was performed using the multilinear reference tissue model 2. Mean 5-HTT occupancies were 72.9% +/- 4.9% at 5 hours, 50.3% +/- 11.0% at 26 hours, and 24.7% +/- 15.3% at 53 hours, and plasma concentrations were 13.9 +/- 5.5 ng/mL at 5 hours, 5.1 +/- 3.2 ng/mL at 26 hours, and 1.5 +/- 1.7 ng/mL at 53 hours. The relationship between the plasma concentration of fluvoxamine and 5-HTT occupancy at these different time points was fitted to the law of mass action.
Insulin Analogs ‐ Improving the Therapy of Diabetes (2015)

The treatment of diabetes has exploited protein engineering to generate an array of insulin receptor agonists whose properties can be exploited through subcutaneous exogenous administration to create pharmacokinetic and pharmacodynamic profiles that better approximate endogenously secreted insulin profiles. This chapter describes the nature of these insulin analogs and derivatives and the engineering strategies employed.
A surprising problem in navigation (2011)

Navigation tasks, and particularly robot navigation, are tasks that are closely associated with data collection. Even a tourist on holiday devotes extensive effort to reportage: the collection of images, narratives or recollections that provide a synopsis of the journey. Several years ago, the term vacation snapshot problem was coined to refer to the challenge of generating a sampling and navigation strategy (Bourque and Dudek, 2000). The notion of a navigation summary refers to a class of solutions to this problem that capture the diversity of sensor readings, and in particular images, experienced during an excursion without allowing for active alteration to the path being followed.