gebhart/patrepeval huggingface dataset:
Effects of protein-crystal hydration and temperature on side-chain conformational heterogeneity in monoclinic lysozyme crystals (2018)

The modulation of main-chain and side-chain conformational heterogeneity and solvent structure in monoclinic lysozyme crystals by dehydration (related to water activity) and temperature is examined. Decreasing the relative humidity (from 99 to 11%) and decreasing the temperature both lead to contraction of the unit cell, to an increased area of crystal contacts and to remodeling of primarily contact and solvent-exposed residues. Both lead to the depopulation of some minor side-chain conformers and to the generation of new conformations. Side-chain modifications and main-chain r.m.s.d.s associated with cooling from 298 to 100 K depend on relative humidity and are minimized at 85% relative humidity (r.h.). Dehydration from 99 to 93% r.h. and cooling from 298 to 100 K result in a comparable number of remodeled residues, with dehydration-induced remodeling somewhat more likely to arise from contact interactions. When scaled to equivalent temperatures based on unit-cell contraction, the evolution of side-chain order parameters with dehydration shows generally similar features to those observed on cooling to T = 100 K. These results illuminate the qualitative and quantitative similarities between structural perturbations induced by modest dehydration, which routinely occurs in samples prepared for 298 and 100 K data collection, and cryocooling. Differences between these perturbations in terms of energy landscapes and occupancies, and implications for variable-temperature crystallography between 180 and 298 K, are discussed. It is also noted that remodeling of a key lysozyme active-site residue by dehydration, which is associated with a radical decrease in the enzymatic activity of lysozyme powder, arises due to a steric clash with the residue of a symmetry mate.
ChemInform Abstract: Synthesis and Characterization of a Chiral Dendrimer Derived from Pentaerythritol. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Quantitative surface defect analysis of drug-eluting coronary stents by scanning electron microscopy: coating integrity of the CYPHER® Sirolimus-eluting Coronary Stent (2012)

A method was developed to assess the durability of drug-polymer coatings, such as those found on drug-eluting stents (DES). The method is based on scanning electron microscopy (SEM) and intensity threshold detection for converting qualitative SEM images to quantification of defects on a DES surface. Previously, a method was developed to fatigue stents by subjecting them to pulsatile loading conditions. The particles generated during fatigue testing were captured and evaluated for chemistry, size, and quantity. The amount of particulates observed from a commercially available DES product was low and on the same order of magnitude as the blanks/controls after acute and chronic simulated in vitro fatigue testing. These results are confirmed using the method developed in this work by evaluating the stent surface before and after chronic fatigue cycling. The relative change in surface defect area during the entire pulsatile fatigue testing was insignificant (<3%), indicating the polymer coating maintains remarkable durability even when subjected to deployment, overexpansion, and repetitive fatigue cycling. Further chemical analysis by FTIR microscopy of individual particles supports the claim that the polymer coating does not shed appreciably during the testing.
On the evaluation of estimated impulse responses (1998)

We discuss the philosophy of evaluating estimated impulse responses for applications in which the overall scaling or gain is irrelevant, as, for example, in blind channel identification. We argue that no matter how the estimate is obtained, the performance should be independently evaluated using an error measure that is appropriate for a problem of this class. Of several possible error measures, the normalized projection error, which is obtained by minimizing the l/sub 2/ norm over all possible gain values, seems to be the most natural and consistent. An example demonstrates that using an inappropriate error measure can produce misleading results.
Job Strain and Health Behaviors: Results of a Prospective Study (1998)

The effectiveness of smoking cessation may be aided by modification of structural features of the work environment, such as job decision latitude. This study is limited by the small number of subjects who were engaged in high risk behaviors.
Procedures for evaluating multijunction concentrators (2000)

Procedures at NREL and Fraunhofer ISE for evaluating multijunction cells are detailed with a triple-junction GaInP/GaAs/Ge concentrator cell designed and grown at Spectrolab and processed at NREL, and a tandem Fraunhofer ISE Ga/sub 0.35/In/sub 0.85/P/Ga/sub 0.83/In/sub 0.17/As cell as examples. The one-sun efficiency and I/sub sc/ for the triple-junction device measured at Fraunhofer ISE and NREL agreed within 0.2%, well below the /spl plusmn/6% uncertainty estimated by NREL. The procedures for determining the one-sun characteristics involve determining the quantum efficiency and using it for spectral correction during the I-V characterization. The characteristics under concentration are evaluated with a flash simulator.
Abstract 155: TGF-β1 Positively Modulates Cell-Metal Interaction in Cardiovascular Applications (2012)

Introduction: The interaction between a metallic implant and local cells in the cardiovascular system determines the fate of the implant. We have recently developed a hybrid scaffold for tissue engineering of valves, which consists of an extra thin layer of Stainless Steel mesh tightly enclosed by three distinct layers of cells. We have examined the effect of TGF-β1 on degree of cell attachment to the metal mesh. Methods and Results: By using a 3D cell culture method a Stainless Steel mesh with desired size and thickness was enclosed through cultured layers of cells similar to a heart valve leaflet pattern. Human aortic smooth muscle cells and adventitial fibroblast/myofibroblast cells were used to fulfill the role of valvular interstitial cells, and human umbilical vascular endothelial cells were used to cover the construct in place of the valvular endothelial cells. The layers were seeded in sequence on a three dimensional, porous biological scaffold comprised of bovine type I collagen gel mixture. The effect of TGF-β1 supplementation at proper time-steps on the cultured hybrid tissue after two months of cell culture was determined. TGF-β supplementation resulted in significant increase in proliferation, and extra ingrowths into the outer portions of the tissue. DAPI staining of nuclei showed that the number of cells at the surface of the mesh progressively increased due to TGF-β, and eventually formed a thicker tissue around the mesh Conclusions: We have demonstrated the effects of TGF-β1 on cell attachment and tissue development by using a hybrid tissue material that helped us study the direct cell-metal interactions in-vitro.
Intramolecular hydrogen bonding in imidazole‐4(5)‐alkoxycarbonyl‐5(4)‐carboxamide derivatives (1987)

Abstract The ir spectrum of imidazole derivatives, which have an alkoxycarbonyl group and a carboxamide group at the 4‐ and 5‐positions of the imidazole ring respectively, exhibits the shift of the ester carbonyl band to a lower wave number. This phenomenon was investigated by spectroscopic measurements of a group of relevant compounds. The results indicate that the shift is caused by the intramolecular hydrogen bonds between the hydrogen atom of the amide and the carbonyl oxygen of the ester which is enhanced by the resonance stabilization of the imidazole ring.
The brown bear as a translational model for sedentary lifestyle‐related diseases (2019)

Sedentary lifestyle accelerates biological ageing, is a major risk factor for developing metabolic syndrome and is associated with cardiovascular disease, diabetes mellitus, kidney failure, sarcopenia and osteoporosis. In contrast to the linear path to worsening health in humans with metabolic syndrome, brown bears have developed a circular metabolic plasticity enabling these animals to tolerate obesity and a 'sedentary lifestyle' during hibernation and exit the den metabolically healthy in spring. Bears are close to humans physiology wise, much closer than rodents, the preferred experimental animals in medical research, and may better serve as translational model to develop treatments for lifestyle-related diseases. In this review, aspects of brown bear hibernation survival strategies are outlined and conceivable experimental strategies to learn from bears are described.
Multiple sclerosis (1986)

The percentage of interleukin-2-receptor-positive peripheral blood lymphocytes in MS patients was significantly higher in acute relapse than in remission or in controls. After stimulation by phytohemagglutinin, the expression of interleukin-2 receptor on peripheral blood lymphocytes of MS patients was within the range of healthy controls, implying no general impairment of receptor expression. These results confirm other evidence that there is a small population of activated T lymphocytes in acute relapse of MS.
Development of Digital Oil for Heavy Crude Oil: Molecular Model and Molecular Dynamics Simulations (2017)

We constructed a molecular model (digital oil model) for heavy crude oil based on analytical data. Crude oil was separated into four fractions: saturates, aromatics, resins, and asphaltenes (SARA). The digital oil was constructed as a mixture of representative molecules of saturates, aromatics, resins, and lost components (low boiling-point compounds vaporized during drying), while asphaltenes of ∼0.4 wt % in the crude oil being ignored. Representative molecules were generated by quantitative molecular representation (QMR), a technique that provides a set of molecules consistent with analytical data, such as elemental composition, average molecular mass, and the proportions of structural types of hydrogen and carbon atoms, as revealed by 1H and 13C nuclear magnetic resonance. To enable the QMR method to be applicable to saturates, we made two developments: the first was the generation of nonaromatic molecules by a new algorithm that can generate a more branched structure by separating the chain bonding into main and subsidiary processes; the second was that the molecular mass distribution of the model could be fitted to that obtained from experiments. To validate the digital oil thus obtained, we first confirmed the validity of the model for each fraction in terms of plots of double-bond equivalent as a function of carbon number. We then calculated its density and viscosity by molecular dynamics simulations. The calculated density was in good agreement with experimental data for crude oil. The calculated viscosity was higher than experimental values; however, the error appeared systematic, being a factor of ∼1.5 higher than that of experiments. The calculated viscosity as a function of temperature was well described by the Vogel–Fulcher–Tammann equation. Digital oil will be a powerful tool to analyze both macroscopic properties and microscopic phenomena of crude oil under any thermodynamic conditions.
Innate transcriptional networks activated in bladder in response to uropathogenic Escherichia coli drive diverse biological pathways and rapid synthesis of IL-10 for defense against bacterial urinary tract infection (2012)

Early transcriptional activation events that occur in bladder immediately following bacterial urinary tract infection (UTI) are not well defined. In this study, we describe the whole bladder transcriptome of uropathogenic Escherichia coli (UPEC) cystitis in mice using genome-wide expression profiling to define the transcriptome of innate immune activation stemming from UPEC colonization of the bladder. Bladder RNA from female C57BL/6 mice, analyzed using 1.0 ST-Affymetrix microarrays, revealed extensive activation of diverse sets of innate immune response genes, including those that encode multiple IL-family members, receptors, metabolic regulators, MAPK activators, and lymphocyte signaling molecules. These were among 1564 genes differentially regulated at 2 h postinfection, highlighting a rapid and broad innate immune response to bladder colonization. Integrative systems-level analyses using InnateDB (http://www.innatedb.com) bioinformatics and ingenuity pathway analysis identified multiple distinct biological pathways in the bladder transcriptome with extensive involvement of lymphocyte signaling, cell cycle alterations, cytoskeletal, and metabolic changes. A key regulator of IL activity identified in the transcriptome was IL-10, which was analyzed functionally to reveal marked exacerbation of cystitis in IL-10–deficient mice. Studies of clinical UTI revealed significantly elevated urinary IL-10 in patients with UPEC cystitis, indicating a role for IL-10 in the innate response to human UTI. The whole bladder transcriptome presented in this work provides new insight into the diversity of innate factors that determine UTI on a genome-wide scale and will be valuable for further data mining. Identification of protective roles for other elements in the transcriptome will provide critical new insight into the complex cascade of events that underpin UTI.
Luminescence properties of thick InGaN quantum‐wells (2009)

Abstract In this paper, we discuss the physics of recombination in thick InGaN quantum‐well (QW) based structures. Thick InGaN QWs have been suggested as one concept to reduce the typical decrease of internal efficiency of InGaN based light emitters towards high current densities. We show that at typical operation current densities, recombination in such thick QWs mainly originates from excited QW‐states, which exhibit good electron hole overlap and large spatial extent, enabling a reduction of carrier density. We identify these states by comparing current dependent electroluminescence spectra to band structure simulations. The reduction of carrier density is verified by measuring current dependent carrier lifetimes. We find that saturation of efficiency is reduced for increasedQWthickness. However, the same effect can also be achieved using an MQW structure optimized for real MQW emission. We conclude that regardless of the employed concept, a decrease in carrier density is central to improve the high current efficiency of InGaN based light emitters (© 2009 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Technical details for safer venous and biliary anastomoses for liver transplantation in the rat (1998)

Although orthotopic liver transplantation in the rat is a well-established experimental model, no detailed illustrated description of the procedure is available in the literature. As a result, achieving success in the technique without prolonged learning time requires training in specialized centers where the step-by-step details essential to success in the technique can be learnt. The aim of this paper is to provide beginners with the culminative experience of 15 years of improvements made to Kamada's original model, clearly illustrating the necessary steps and fine detail of each anastomosis to help beginners avoid unnecessary complications. We hope that this complete description of orthotopic liver transplantation in the rat, which remains the most difficult rodent transplant model to master, will greatly help microsurgeons acquire this demanding procedure.
Utility of Intraoperative Three-Dimensional Imaging at the Hip and Knee Joints with and without Navigation (2009)

Intraoperative three-dimensional imaging in orthopaedic trauma care has achieved greater importance over the last few years in some specialized hospital centers. For various types of peripheral-extremity trauma, clinical studies have confirmed, on the basis of three-dimensional information, an intraoperative revision rate ranging from 7% to 19%. Three-dimensional C-arm imaging may be used to achieve adequate intraoperative information about the quality of fracture reduction, residual steps, and correct implant placement, and this technique has been described for use in both the hip joint (for acetabular fractures, isolated femoral head [Pipkin-type] fractures, three-dimensional navigated sacroiliac screw or acetabular column screw placements, and, less frequently, for navigated drilling of tumors or osteochondral lesions) and the knee joint (for tibial plateau fractures, complex distal femoral condylar fractures, and navigated targeting of osteochondral lesions in combination with the use of preoperative magnetic resonance imaging scans). Major limitations of this technology include increased intraoperative time requirements, limited image quality compared with that of computed tomographic scans, cost, specific positioning techniques, and the need for radiolucent operating-room tables. Although prospective studies have yet to be conducted, the ways in which the surgeon will benefit from the use of intraoperative three-dimensional imaging are apparent, but indications for combined three-dimensional C-arm navigated procedures at the hip and knee joint are still limited. Future directions may include the use of digital flat-panel detectors and even robotic-controlled C-arm motion.
Collisionless Intramolecular Vibratonal Relaxation in S<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">F</mml:mi></mml:mrow><mml:mrow><mml:mn>6</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math> (1978)

Time-resolved spectroscopy is applied to the problem of collisionless intramolecular relaxation within the ground electronic state of polyatomic molecules. The redistribution of vibrational energy within a molecule may be monitored by the different anharmonic shifts which occur when the energy is localized in the different modes. Picosecond infrared-laser-absorption saturation-recovery measurements on S${\mathrm{F}}_{6}$ show that the relaxation time, for statistical behavior to set in, falls within the limits $1 \mathrm{psec}&lt;{T}_{1}&lt;30 \mathrm{psec}$.
Effect of Amount of Gd and Y Contents on Precipitation in Mg&amp;ndash;Gd&amp;ndash;Y Alloys Aged at 473 K (2013)

Precipitation in Mg–Gd–Y (Gd : Y = 3 : 1) alloys without Zr were investigated by HRTEM and SAED technique, and calculation of HRTEM images and electron density using DV-Xα to understand the relationship between precipitation in these alloys and HRTEM images. The diffuse scattering was obtained in as-quenched samples in each alloy by SAED and the mono-layer zones have been confirmed by HRTEM observation. The β′-phase was confirmed in the 2.9Gd–0.8Y alloy by HRTEM, although the β′′-phase was confirmed in the 2.1Gd–0.6Y alloy before the β′-phase. The β′-phase became predominant after prolonged aging. Zigzag lines were observed at the same time when the β′-phase appeared in the sample. HRTEM images obtained for these precipitates were compared with calculated HRTEM images. The contrast of atomic columns of the matrix in HRTEM image was calculated simplified model of cluster based on the Mg-matrix including one or some atomic columns of RE. This is also corresponded the distribution of electron density of the cluster.
Large Negative Stress Phase Angle (SPA) Attenuates Nitric Oxide Production in Bovine Aortic Endothelial Cells (2006)

Hemodynamics plays an important role in cardiovascular physiology and pathology. Pulsatile flow (Q), pressure (P), and diameter (D) waveforms exert wall shear stress (WSS), normal stress, and circumferential strain (CS) on blood vessels. Most in vitro studies to date have focused on either WSS or CS but not their interaction. Recently, we have shown that concomitant WSS and CS affect EC biochemical response modulated by the temporal phase angle between WSS and CS (stress phase angle, SPA). Large negative SPA has been shown to occur in regions of the circulation where atherosclerosis and intimal hyperplasia are prevalent. Here, we report that nitric oxide (NO) biochemical secretion was significantly decreased in response to a large negative SPA of -180 deg with respect to an SPA of 0 degrees in bovine aortic endothelial cells (BAEC) at 5 h. A new hemodynamic simulator for the study of the physiologic SPA was used to provide the hemodynamic conditions of pro-atherogenic (SPA = -180 deg) and normopathic (SPA = 0 deg) states. The role of complex hemodynamics in vascular remodeling, homeostasis, and pathogenesis can be advanced by further assessment of the hypothesis that a large negative SPA is pro-atherogenic.
The Synergistic Gains of Coded Caching and Delayed Feedback (2016)

In this paper, we consider the $K$-user cache-aided wireless MISO broadcast channel (BC) with random fading and delayed CSIT, and identify the optimal cache-aided degrees-of-freedom (DoF) performance within a factor of 4. The achieved performance is due to a scheme that combines basic coded-caching with MAT-type schemes, and which efficiently exploits the prospective-hindsight similarities between these two methods. This delivers a powerful synergy between coded caching and delayed feedback, in the sense that the total synergistic DoF-gain can be much larger than the sum of the individual gains from delayed CSIT and from coded caching. The derived performance interestingly reveals --- for the first time --- substantial DoF gains from coded caching, even when the (normalized) cache size $γ$ (fraction of the library stored at each receiving device) is very small. Specifically, a microscopic $γ\approx e^{-G}$ can come within a factor of $G$ from the interference-free optimal. For example, storing at each device only a \emph{thousandth} of what is deemed as `popular' content ($γ\approx 10^{-3}$), we approach the interference-free optimal within a factor of $ln(10^3) \approx 7$ (per user DoF of $1/7$), for any number of users. This result carries an additional practical ramification as it reveals how to use coded caching to essentially buffer CSI, thus partially ameliorating the burden of having to acquire real-time CSIT.
Formal Methods in Cyberphysical Systems (2021)

To improve the state-of-theart practice of applying formal methods to cyberphysical systems, we briefly discuss the evolution of these methods and also summarize four research efforts to close the current capability gaps in their application.
Strain and temperature sensor using few-mode fiber, designing guidelines and results (2023)

Strain and temperature sensing based on mode interference in a few-mode fiber is analyzed theoretically and experimentally. The effect of using different mode combinations is explored. A fiber guiding four LP modes is investigated as an example. Good agreement between modeling and experimental results is found for strain sensor. We demonstrate the sensors feasibility by measuring strain ranging from 0 mm to 16 mm with a sensitivity of 3.43 nm/mm and measuring temperature ranging from 30 °C to 100 °C with a sensitivity of 4.8 pm/°C.