gebhart/patrepeval huggingface dataset:
Ionic channels in murine macrophages. (1987)

In this paper we examine the different voltage or calcium-dependent currents present in murine peritoneal macrophages, and in a macrophage-like cell line, J774. Three of these are K currents while the fourth is carried by Cl. One K current, activated by hyperpolarization, has all the characteristics of the inward rectifier found in egg or muscle cells. It appears in peritoneal macrophages only after several days in culture. A second K current, activated by depolarization, is a typical delayed rectifier. The amplitude of these currents and, as a consequence, the membrane potential of the cells, can be markedly changed by the movement of fluid around the cells. A third K current is activated by internal calcium levels in the micromolar range. It presents a low-voltage sensitivity and is blocked by 0.1-1 mM quinine. The Cl current flows through large-size channels (180-390 pS) that are active mainly in excised patches. These channels are unlikely to be half gap junctional channels, as suggested in former studies. The second goal of this paper is to examine if the activation of receptors for the Fc fragment of IgGs (Fc receptors) is associated with a change in the electrical properties of the membrane of macrophages. We have observed that the binding of multivalent ligands (the monoclonal antibody 2.4G2, aggregated IgGs, or sheep red blood cells coated with IgGs) to their Fc receptors on adherent macrophages did not trigger any change in resting potential. This is a surprising difference with former results obtained on non-adherent J774 cells (Young, J. D.-E., J. C. Unkeless, H. R. Kaback, and Z. A. Cohn, 1983, Proc. Natl. Acad. Sci. USA., 80:1357-1361) and on human alveolar macrophages (Nelson, D. J., E. R. Jacobs, J. M. Tang, J. M. Zeller and R. C. Bone, 1985, J. Clin. Invest., 76:500-507).
Scattering loss of interface waves at a rough seabed: Theoretical calculations (1986)

Using the Rayleigh method, a boundary perturbation technique, the propagation of interface waves (i.e., Scholte waves) along a randomly rough fluid/solid boundary is studied. It is assumed that the surface has Gaussian statistics and that the autocorrelation function is exp(− r2/L2), in which L is the correlation length. The method assumes that the rms surface height is small compared to the acoustic wavelength λ, and that the surface slopes are also small. There is no restriction on L/λ. The intensity of the average field decays exponentially with range; the energy lost is scattered into interface waves traveling in other directions and into bulk waves carrying energy away from the boundary. For L/λ&amp;lt;1, the loss varies as (L/λ)5 and energy is lost mostly to bulk waves; for L/λ&amp;gt;1, the loss varies as (L/λ)4 and the energy is lost mostly to interface waves; at intermediate values of L/λ, there is a local maximum of energy loss. This behavior is explained qualitatively using wavenumber-space scattering diagrams. Results for the cases of water over sand, chalk, and granite are presented, respectively.
Soy Protein Adhesive Blends with Synthetic Latex on Wood Veneer (2010)

Abstract Environmental pollution has prompted an interest in and a need for bio‐based wood adhesives. Modified soy protein has shown adhesion properties similar to those of formaldehyde based adhesives. The objective of this research was to investigate the compatibility of a modified soy protein (MSP) with six commercial synthetic latex adhesives (SLAs). Four different blending ratios of MSP and SLAs were studied. Adhesion; structural change; and rheological, thermal, and morphological properties of the MSP/SLAs blends were characterized. Dry adhesion strength of MSP, SLAs and their blends were all similar with 100% wood cohesive failure. Water resistance of all six SLAs was improved by blending with MSP in terms of the wet adhesion strength. The wet adhesion strength of MSP/PBG (40/60) blends was 6.416 MPa, as compared to 4.66 MPa of pure PBG (press bond glue, urea formaldehyde based resin). Viscosity of MSP/SLAs blends was reduced significantly and reached the lowest value at 40–60% MSP. Infrared spectra, thermal properties, and morphological images indicated that chemical reactions occurred between soy protein and PBG molecules. The MSP provided some functional groups, such as carboxylic (–COOH), hydroxyl (–OH) and amino groups (–NH 2 ), that cross‐linked with hydroxymethyl groups (–CH 2 –OH) of PBG, and also acted as an acidic catalyst for the self‐polymerization of urea formaldehyde based resin.
Optically active analogues of ebastine: Synthesis and effect of chirality on their antihistaminic and antimuscarinic activity (1994)

A series of optically active analogues of the H1-antihistamine ebastine, with chiral center(s) at the benzhydryl and/or phenylbutyl part of the molecule, have been synthesized. Their in vitro antihistaminic and antimuscarinic activities were investigated, along with a molecular modelling study. It was found that introduction of the benzhydryl chiral center yielded significant stereoselectivity for both antihistaminic and antimuscarinic activities. The steric preferences of the benzhydryl chiral center for antihistaminic and antimuscarinic actions were mirror images of each other. The (-)-isomer of 4-methylebastine (6d) showed more than 10-fold higher in vitro antihistaminic potency than ebastine. Meanwhile the selectivity of 6d for histamine H1-receptors was also increased by more than 20 times in comparison with ebastine. The chirality at the phenylbutyl part of the molecule does not significantly alter the antihistaminic or antimuscarinic activity of the compounds although the (S)-isomers showed slightly but unanimously higher antihistaminic activity than the (R)-isomers. These results have been discussed with existing stereoselectivity data of antihistamines and an asymmetric pharmacophore model for H1-antagonists has been described.
Discovery and Understanding of Transition-Metal-Catalyzed Aromatic Substitution Reactions (2006)

This article presents studies on the development of cross-coupling reactions of aryl halides and sulfonates with amines, alkoxides, and various enolates. Emphasis is placed on the process of developing new catalysts with mechanistic information gained in the author's laboratory.
Cell therapy for ischaemic stroke (2011)

While acute neuroprotection in acute stroke has proven difficult and ended in many failures, there is increasing interest in restorative therapies that target brain remodelling. Cell therapy (transplantation of cells) shows promise, with a growing body of pre-clinical evidence demonstrating improved functional outcomes in animal models; however, questions still remain concerning mechanisms of action. Clinical trials are already underway and will increase in the next few years; their appropriate design and execution along with continued pre-clinical work are necessary for the field to advance and satisfy a large unmet clinical need.
Intramolecular soft modes and intermolecular interactions in liquid acetone (2011)

Resonant inelastic x-ray scattering spectra excited at the $O1{s}^{\ensuremath{-}1}{\ensuremath{\pi}}^{*}$ resonance of liquid acetone are presented. Scattering to the electronic ground state shows a resolved vibrational progression where the dominant contribution is due to the C-O stretching mode, thus demonstrating a unique sensitivity of the method to the local potential energy surface in complex molecular systems. For scattering to electronically excited states, soft vibrational modes and, to a smaller extent, intermolecular interactions give a broadening, which blurs the vibrational fine structure. It is predicted that environmental broadening is dominant in aqueous acetone.
The role of shear forces in arterial branching. (1976)

A new optimality principle for the branching angles of blood vessels in the cardiovascular system is proposed: the principle of minimum drag. The results are examined in the light of general observations and compared with those obtained from the principles of minimum work and minimum volume. It is shown that in some aspects the new principle is equally consistent with observations, and, in other aspects, it is perhaps more plausible than the other two principles.
Motorcycle Lean Angle Variation around a Constant Radius Curve at Differing Speeds and Travel Paths with an Evaluation of Data Measurement Systems (2019)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Recent studies evaluating motorcycle lean angle have compared theoretical lean angle equations with real-world-tested motorcycle lean angles. These studies have considered several factors affecting lean angle, including the simplified assumptions made when calculating theoretical lean angles, the speed of the motorcycle around a curve, and the geometry of the roadway/curve. This study further evaluates motorcycle lean angle as a function of speed, but primarily focuses on the effects of different travel paths selected by the rider around the same constant radius curve. The testing incorporates nine passes around the same curve traveling three different paths at three different speeds. The real-world-tested lean angles were compared to the predicted calculated lean angles for each tested travel path and speed. The theoretical lean angles were calculated using the graphically reconstructed radius of curvature generated through three-dimensional (3D) laser scans of the roadway and aerial video footage and orthomosaic imagery. The orthomosaic imagery was collected via small Unmanned Aerial Vehicle (sUAV) (commonly referred to as a drone). The analyzed curve is a sweeping constant radius left-hand curve with an approximate 670-ft (204-m) radius of curvature. This study also analyzed the variations in lean angle through the transient entrance of the curve, steady-state middle of the curve, and transient exit of the curve. Lean angles were also analyzed utilizing video analysis and 3D camera matching techniques. The accuracy and effectiveness of this data was compared and analyzed. The results of this testing empirically establish that at a given speed on a given curve, motorcycle lean angles vary depending on the travel path selected by the motorcyclist, the motorcyclist’s efforts to maintain lane position, and intended path of travel.&lt;/div&gt;&lt;/div&gt;
TRITYL PERCHLORATE AS AN EFFICIENT CATALYST IN THE ALDOL-TYPE REACTION (1984)

Abstract In the presence of a catalytic amount of trityl perchlorate, silyl enol ethers and ketene silyl acetals react with acetals and methyl orthoformate to give the corresponding aldol-type addition products in good yields.
Molecular hydrogen in globular clusters - A search for carbon monoxide (1978)

Five globular clusters, including the X-ray cluster M15, were observed in the 2.6 mm transition of CO to limits (3 sigma) of T(A)(asterisk) = 0.08-0.4 K, with no detections. Upper limits on the mass of molecular hydrogen deduced from our observations are M(H2) less than 0.2-6.0 solar masses. Model calculations were used to estimate the amount of molecular hydrogen that may be shielded from photoionization, on the basis of estimates for the UV intensity in clusters and observed limits on H II emission. These estimates indicate that unless the neutral gas is in globules which are very small and dense, it will be difficult to shield more than 1 solar mass of molecular hydrogen. It is therefore unlikely that the observed irregularities in the cluster star distribution can be attributed to dark clouds.
Diabetic cardiomyopathy: the need for adjusting experimental models to meet clinical reality (2022)

Diabetic cardiomyopathy (CM), occurring in the absence of hypertension, coronary artery disease, and valvular or congenital heart disease, is now recognized as a distinct, multifactorial disease leading to ventricular hypertrophy and abnormal myocardial contractility that correlates with an array of complex molecular and cellular changes. Animal models provide the unique opportunity to investigate mechanistic aspects of diabetic CM, but important caveats exist when extrapolating findings obtained from preclinical models of diabetes to humans. Indeed, animal models do not recapitulate the complexity of environmental factors, most notably the duration of the exposure to insulin resistance that may play a crucial role in the development of diabetic CM. Moreover, most preclinical studies are performed in animals with uncontrolled or poorly controlled diabetes, whereas patients tend to undergo therapeutic intervention. Finally, whilst type 2 diabetes mellitus prevalence trajectory mainly increases at 40- < 75 years (with a currently alarming increase at younger ages, however), it is a legitimate concern how closely rodent models employing young animals recapitulate the disease developing in old people. The aim of this review is to identify the current limitations of rodent models and to discuss how future mechanistic and preclinical studies should integrate key confounding factors to better mimic the diabetic CM phenotype.
Bathymetry Retrieval from Hyperspectral Imagery in the Very Shallow Water Limit: A Case Study from the 2007 Virginia Coast Reserve (VCR'07) Multi-Sensor Campaign (2010)

We focus on the validation of a simplified approach to bathymetry retrieval from hyperspectral imagery (HSI) in the very shallow water limit (less than 1–2 m), where many existing bathymetric LIDAR sensors perform poorly. In this depth regime, near infra-red (NIR) reflectance depends primarily on water depth (water absorption) and bottom type, with suspended constituents playing a secondary role. Our processing framework exploits two optimal regions where a simple model depending on bottom type and water depth can be applied in the very shallow limit. These two optimal spectral regions are at a local maximum in the near infra-red reflectance near 810 nm, corresponding to a local minimum in absorption, and a maximum in the first derivative of the reflectance near 720 nm. These two regions correspond to peaks in spectral correlation with bathymetry at these depths.
Pseudotumors in Association with Well-Functioning Metal-on-Metal Hip Prostheses (2012)

A periprosthetic cystic pseudotumor was diagnosed commonly (in thirty-four [59%] of the entire study cohort) with use of metal artifact reduction sequence (MARS) magnetic resonance imaging in this series of patients with a metal-on-metal hip prosthesis. The prevalence of pseudotumors was similar in patients with a well-functioning hip prosthesis and patients with a painful hip. Pseudotumors were also diagnosed commonly in patients with a well-positioned acetabular component. Although magnetic resonance imaging is useful for surgical planning, the presence of a cystic pseudotumor may not necessarily indicate the need for revision arthroplasty. Further correlation of clinical and imaging data is needed to determine the natural history of pseudotumors to guide clinical practice.
Incorporating Linear Synchronous Transit Interpolation into the Growing String Method: Algorithm and Applications (2011)

The growing string method is a powerful tool in the systematic study of chemical reactions with theoretical methods which allows for the rapid identification of transition states connecting known reactant and product structures. However, the efficiency of this method is heavily influenced by the choice of interpolation scheme when adding new nodes to the string during optimization. In particular, the use of Cartesian coordinates with cubic spline interpolation often produces guess structures which are far from the final reaction path and require many optimization steps (and thus many energy and gradient calculations) to yield a reasonable final structure. In this paper, we present a new method for interpolating and reparameterizing nodes within the growing string method using the linear synchronous transit method of Halgren and Lipscomb. When applied to the alanine dipeptide rearrangement and a simplified cationic alkyl ring condensation reaction, a significant speedup in terms of computational cost is achieved (30-50%).
Mechanism of protein-primed template-independent DNA synthesis by Abi polymerases (2022)

Abortive infection (Abi) is a bacterial antiphage defense strategy involving suicide of the infected cell. Some Abi pathways involve polymerases that are related to reverse transcriptases. They are unique in the way they combine the ability to synthesize DNA in a template-independent manner with protein priming. Here, we report crystal and cryo-electron microscopy structures of two Abi polymerases: AbiK and Abi-P2. Both proteins adopt a bilobal structure with an RT-like domain that comprises palm and fingers subdomains and a unique helical domain. AbiK and Abi-P2 adopt a hexameric and trimeric configuration, respectively, which is unprecedented for reverse transcriptases. Biochemical experiments showed that the formation of these oligomers is required for the DNA polymerization activity. The structure of the AbiK-DNA covalent adduct visualized interactions between the 3' end of DNA and the active site and covalent attachment of the 5' end of DNA to a tyrosine residue used for protein priming. Our data reveal a structural basis of the mechanism of highly unusual template-independent protein-priming polymerases.
Relating ASME Flaw Evaluation to ASME Task Group on Carbon Fiber Repairs (2017)

As most nuclear power stations in the US have surpassed their initial 40 years of operability, the industry is now challenged with maintaining safe operations and extending the operating life of structures, systems and components. The US Nuclear Regulatory Commission (NRC), Nuclear Energy Institute (NEI), and Electric Power Research Institute (EPRI) have identified safety related buried piping systems as particularly susceptible to degradation. These systems are required to maintain the structural factors of the ASME Construction Codes under pressure and piping loads, which includes seismic wave passage. This paper focuses on evaluation approaches for metallic buried piping that can be used to demonstrate that localized thinning meets the requirements of the Construction Code. The paper then addresses a non-metallic repair option using carbon fiber reinforced polymers (CFRP) as the new pressure boundary.
Exchange of Protein Molecules Through Connections Between Higher Plant Plastids (1997)

Individual plastids of vascular plants have generally been considered to be discrete autonomous entities that do not directly communicate with each other. However, in transgenic plants in which the plastid stroma was labeled with green fluorescent protein (GFP), thin tubular projections emanated from individual plastids and sometimes connected to other plastids. Flow of GFP between interconnected plastids could be observed when a single plastid or an interconnecting plastid tubule was photobleached and the loss of green fluorescence by both plastids was seen. These tubules allow the exchange of molecules within an interplastid communication system, which may facilitate the coordination of plastid activities.
Stable isotope fractionation of strontium in coccolithophore calcite: Influence of temperature and carbonate chemistry (2018)

Marine calcifying eukaryotic phytoplankton (coccolithophores) is a major contributor to the pelagic production of CaCO<sub>3</sub> and plays an important role in the biogeochemical cycles of C, Ca and other divalent cations present in the crystal structure of calcite. The geochemical signature of coccolithophore calcite is used as palaeoproxy to reconstruct past environmental conditions and to understand the underlying physiological mechanisms (vital effects) and precipitation kinetics. Here, we present the stable Sr isotope fractionation between seawater and calcite (Δ<sup>88/86</sup> Sr) of laboratory cultured coccolithophores in individual dependence of temperature and seawater carbonate chemistry. Coccolithophores were cultured within a temperature and a pCO<sub>2</sub> range from 10 to 25°C and from 175 to 1,240 μatm, respectively. Both environmental drivers induced a significant linear increase in coccolith stable Sr isotope fractionation. The temperature correlation at constant pCO<sub>2</sub> for Emiliania huxleyi and Coccolithus braarudii is expressed as Δ<sup>88/86</sup> Sr = -7.611 × 10<sup>-3</sup> T + 0.0061. The relation of Δ<sup>88/86</sup> Sr to pCO<sub>2</sub> was tested in Emiliania huxleyi at 10 and 20°C and resulted in Δ<sup>88/86</sup> Sr = -5.394 × 10<sup>-5</sup> pCO<sub>2</sub> - 0.0920 and Δ<sup>88/86</sup> Sr = -5.742 × 10<sup>-5</sup> pCO<sub>2</sub> - 0.1351, respectively. No consistent relationship was found between coccolith Δ<sup>88/86</sup> Sr and cellular physiology impeding a direct application of fossil coccolith Δ<sup>88/86</sup> Sr as coccolithophore productivity proxy. An overall significant correlation was detected between the elemental distribution coefficient (D<sub>Sr</sub> ) and Δ<sup>88/86</sup> Sr similar to inorganic calcite with a physiologically induced offset. Our observations indicate (i) that temperature and pCO<sub>2</sub> induce specific effects on coccolith Δ<sup>88/86</sup> Sr values and (ii) that strontium elemental ratios and stable isotope fractionation are mainly controlled by precipitation kinetics when embedded into the crystal lattice and subject to vital effects during the transmembrane transport from seawater to the site of calcification. These results provide an important step to develop a coccolith Δ<sup>88/86</sup> Sr palaeoproxy complementing the existing toolbox of palaeoceanography.