gebhart/patrepeval huggingface dataset:
An IgY-based immunoassay to evaluate the biomarker potential of the Tannerella forsythia virulence factor karilysin in human saliva (2019)

Tannerella forsythia is a gram-negative anaerobic bacterium that is associated with the development of destructive periodontal disease. T. forsythia secretes the metalloprotease-like enzyme karilysin. Using in vitro systems karilysin has been shown to modulate the host immune response by degradation of complement system proteins and by inactivation of the antimicrobial peptide LL-37 by proteolytic cleavage. This makes karilysin a highly interesting virulence factor to study in the framework of drug development and diagnostics. However, to date the presence of karilysin in clinical samples has not been demonstrated due to the lack of specific probes. In the present work, a high titer and stable affinity-purified avian IgY antibody against karilysin was developed. By surface plasmon resonance imaging the IgY affinity was found to be in the low nanomolar range. The antibody could be used to detect karilysin in saliva samples by immuno-blotting and was specific when tested towards human MMP-3. Furthermore, an avian IgY-based immunoassay was developed, which demonstrated low intra- and interday assay variability (CV's below 10%). Application of the immunoassay on a well-characterized set of saliva samples from adolescents with or without signs of periodontitis showed that it was possible to detect karilysin in saliva. A significant difference in karilysin concentration was found between saliva from participants with signs of periodontitis and saliva from healthy controls (p = .0024). The median of karilysin levels among periodontitis cases was 957 pg/ml (IQR, 499-2132 pg/ml) and the median for controls was 569 pg/ml (IQR, 210-1343 pg/ml). Collectively our data confirm the presence of karilysin in clinical samples. The described IgY-based immunoassay may prove useful as part of protein-based biomarker screenings in the clinic or in point-of care settings.
Age-Dependent Arterial Mechanics via a Multiscale Elastic Approach (2012)

A multiscale mechanical model for arterial walls is proposed to describe their age-dependent elastic behavior. The model accounts for nanoscale mechanisms related to molecular and cross-link stretching, as well as for micro- and macroscale effects, by employing homogenization techniques. Such a model uses only a few measurable histological parameters, and allows the reproduction of well-established experimental evidence, highlighting that stiffness of collagen fibrils is related to both cross-link density and their mechanical properties. In the case of aortic walls, the model allows to account for histological alterations occurring with age, fully reproducing available experimental results. Proposed evidence also gives a clear mechanical interpretation of the influence of cross-link density and stiffness on arterial tissue elastic modulus and arterial compliance.
Reactive and unreactive pathways in a photochemical ring opening reaction from 2D femtosecond stimulated Raman (2015)

Two-dimensional femtosecond stimulated Raman spectroscopy (2D-FSRS) is used to probe the structural evolution of a modified cyclohexadiene as it undergoes a photoinduced ring opening reaction. Analysis of the excited state stimulated Raman vibrational data reveals oscillations of the center frequencies and amplitudes of 21 high frequency modes. These oscillations in vibrational properties are due to anharmonic couplings between the high frequency finger print modes and the impulsively driven low frequency molecular distortions in the excited state. The largest anharmonic couplings, with intrinsic oscillation magnitudes of up to 40 cm(-1), are observed between the 467 cm(-1) C-C bend and the 1333 cm(-1) C-C stretch with the 191 cm(-1) methyl wag, all of which are centered on the reactive cyclohexadiene moiety. Conversely, motions located on the periphery - the 993 cm(-1) phenyl bend, the 1389 cm(-1) methyl bend and 1580 cm(-1) phenyl C-C stretch - are coupled with the 104 cm(-1) asymmetric bend. These couplings reveal two key energetic pathways: one leading to formation of the ring-opened product and the other reversion back to the ground state. This work is also important because it presents a new powerful method for measuring anharmonicities of potential energy surfaces and determining their role in chemical reactivity.
절대적,상대적 빈곤수준의 결정요인 및 격차 비교분석: 2005-2007년의 수도권과 비수도권의 차이를 중심으로 (2011)

본 연구는 2005-2007년의 수도권과 비수도권의 절대적·상대적 빈곤수준 결정요인 및 격차변화를 비교·분석하였다. 그 결과 첫째, 절대적 빈곤수준(가구연간경상소득)과 상대적 빈곤수준(주관적 빈곤지수)은 수도권과 비수도권 간 차이와 연도별로도 상이한 변화패턴을 보였다. 둘째, 빈곤계층여부, 나이, 학력, 가구형태, 경제활동형태, 가구규모 등의 다양한 요소에 의해서 절대적·상대적 빈곤수준이 영향을 받는 것으로 나타났다. 셋째, 평균적으로 비수도권이 수도권에 비해서 절대적 빈곤수준이 높은 반면, 상대적 빈곤수준은 낮은 것으로 나타났다. 넷째, 연도별로 수도권과 비수도권의 절대적 빈곤수준의 격차는 더 심화된 반면에, 상대적 빈곤수준의 격차는 다소 감소한 것으로 나타났다. 다섯째, Oaxaca 모형을 통해, 절대적빈곤수준은 대체로 지역요인에서 기인하는 비중이 높으나, 상대적 빈곤수준은 주로 지역외의 기타 요인(개인 및 가구특성)에 의해 기인하는 결과임을 알 수 있었다.
Solvent‐Influenced Fragmentations in Free‐Standing Three‐Dimensional Covalent Organic Framework Membranes for Hydrophobicity Switching (2022)

Abstract The ordered open organic frameworks membranes are attractive candidates for flow‐assisted molecular separations. The physicochemical properties of such membranes mostly depend on their selectively chosen functional building blocks. In this work, we have introduced a novel concept of functional switchability of three‐dimensional covalent organic framework (3D‐COF) membranes through a simple solvent‐influenced fragmentation method. This room‐temperature interfacial synthesis provides free‐standing 3D‐COF membranes with distinct physicochemical properties from the same building monomers. Notably, the change of solvent from chloroform to ethyl acetate switches the membrane property from hydrophilic (water contact angle 60°) to hydrophobic (water contact angle 142°) nature. The hydrophobic 3D‐COF membrane selectively passes oil molecules from an oil–water emulsion with a gravitational flux of 1536 L m −2 h −1 .
The Relationship of Actin to Ligament Contraction (1986)

A surgical model of a contracting ligament was established in a Z-Iengthened, rat medial collateral ligament. These lengthened ligaments contracted back to a normal degree of tightness in a three-week period. Immunofluorescent actin staining of cryostat ligament sections was increased in these contracted ligaments, compared with sham-operated ligaments that had not contracted. In vitro culture of ligament fibroblasts confirmed that they (like fibroblasts from other systems) produce large, actin, stress fibers thought to be involved in cell contraction. Transmission electron-microscopic examination of normal ligament demonstrated the cytoplasm of fibroblast cell processes extending out to and surrounding collagen fibrils, indicating a closer involvement with established fibrils than was expected. On the basis of these observations, it is hypothesized that intracellular proteins, such as actin, allow the fibroblast to exert forces and actively contribute to the contraction of ligamentous tissues.
Efficient implementation of a set of lifting based wavelet filters (2002)

Lifting based wavelet transform implementation not only helps in reducing the number of computations but also achieves lossy to lossless performance with finite precision. We first do a precision analysis for the set of seven filters proposed by the JPEG2000 verification model. We determine the precision required to implement the filters using fixed point 2's complement arithmetic for lossless as well as lossy coding. Next we propose a unified architecture for implementing this set of filters for both the forward and the inverse transform.
Simulated Ischemia in Flow-Adapted Endothelial Cells Leads to Generation of Reactive Oxygen Species and Cell Signaling (1999)

We have previously shown that increased reactive oxygen species (ROS) generation occurs with ischemia in the oxygenated lung and have hypothesized that mechanotransduction is the initiating event. In the present study, we developed an in vitro model of oxygenated ischemia by interrupting medium flow to flow-adapted bovine pulmonary artery endothelial cells in an artificial capillary system. Cellular oxygenation during the "ischemic" period was maintained by perfusing medium over the abluminal surface of porous capillaries. Cells were assessed for ROS generation, nuclear factor-kappaB (NF-kappaB) and activator protein-1 (AP-1) binding activities, and DNA synthesis using dichlorofluorescein fluorescence by flow cytometry and spectrofluorometry, electrophoretic mobility shift assay of nuclear extracts with NF-kappaB-specific or AP-1-specific (32)P-labeled oligonucleotides, and (3)H-thymidine incorporation into DNA. Cells that were flow adapted for 2 to 7 days with 1 to 2 dyne/cm(2) shear stress exhibited a 1.6- to 1.9-fold increase in ROS generation during 1 hour of simulated ischemia compared with continuously perfused cells. This effect was abolished by diphenyleneiodonium chloride (DPI), indicating a role for a flavoprotein such as NADPH oxidase. The increase in ROS generation with ischemia was similar for cells from low and high passages. With ischemia, flow-adapted cells exhibited increases of 1.7-fold in nuclear NF-kappaB and 1.5-fold in nuclear AP-1; these changes were abolished by pretreatment with N-acetylcysteine or DPI. Ischemia for 24 hours resulted in a 1.8-fold increase of (3)H-thymidine incorporation into DNA and a significant increase of cells entering the cell cycle, as indicated by flow cytometry with propidium iodide. We conclude that flow-adapted endothelial cells generate ROS with ischemia that results in activation of NF-kappaB and AP-1 and an increase of DNA synthesis. This effect is not mediated by hypoxia, implicating a role for mechanotransduction in ischemia-mediated cell signaling.
Inhibition of Electrolyte Oxidation in Lithium Ion Batteries with Electrolyte Additives (2009)

The incorporation of additives designed to sacrificially react on the surface of cathode materials in lithium ion batteries has been investigated. Addition of low concentrations of either 2,5-dihydrofuran or γ -butyrolactone to 1 M LiPF6 in 1:1:1 ethylene carbonate/diethyl carbonate/dimethyl carbonate improves the capacity retention of Li/Li 1.17Mn0.58Ni0.25O2 cells cycled at 4.9 V vs Li. A surface analysis of the cathode materials (X-ray photoelectron spectroscopy and IR) suggests that the structure of the cathode surface film is modified by the presence of the additives resulting in a decrease in detrimental electrolyte oxidation reactions on the cathode surface. © 2009 The Electrochemical Society.
OH rotational temperature from two-line laser-excited fluorescence (1981)

A two-line laser-excited fluorescence technique has been developed to measure the rotational temperature of the OH molecule. This technique eliminates problems encountered in the application of other laser fluorescence methods for measuring the OH temperature in combustion environments, such as fluorescence trapping, nonequilibrium excited state population, spectral bandwidth sensitivity, and quenching. The technique consists of exciting a specific rotational level of the OH molecule in the A(2)Sigma (upsilon' = 0) excited state from two different rotational levels in the X(2)Pi(upsilon'' = 0) ground state using a tunable dye laser and monitoring the broadband fluorescence. An example of the implementation of this technique in an atmospheric pressure methane-air flat flame is included. The possible application of this technique in turbulent combustion is also evaluated.
Anomalous excitations of atomically crafted quantum magnets (2022)

High-energy resolution spectroscopic studies of quantum magnets proved extremely valuable in accessing magnetodynamics quantities, such as energy barriers, magnetic interactions, and lifetime of excited states. Here, we investigate a previously unexplored flavor of low-energy spin excitations for quantum spins coupled to an electron bath. In sharp contrast to the usual tunneling signature of two steps symmetrically centered around the Fermi level, we find a single step in the conductance. Combining time-dependent and many-body perturbation theories, magnetic field-dependent tunneling spectra are explained as the result of an interplay between weak magnetic anisotropy energy, magnetic interactions, and Stoner-like electron-hole excitations that are strongly dependent on the magnetic states of the nanostructures. The results are rationalized in terms of a noncollinear magnetic ground state and the dominance of ferro- and antiferromagnetic interactions. The atomically crafted nanomagnets offer an appealing model for the exploration of electrically pumped spin systems.
Synthesis, characterization, and photoluminescence of Er2O3–Er2SO2 nanoparticles on reduced graphene oxide (2017)

Thermal reduction of erbium nitrate and S-doped reduced graphene oxide (rGO) mixture resulted in the formation of small (∼3-18 nm sized) Er<sub>2</sub>O<sub>3</sub>-Er<sub>2</sub>SO<sub>2</sub> nanoparticles with a high degree of surface coverage on the reduced GO support. The morphology, structure, and the chemical composition of the synthesized nanoparticles have been studied by scanning and transmission electron microscopy, x-ray photoelectron spectroscopy, x-ray diffraction, and by optical spectroscopies. The rGO-supported Er<sub>2</sub>O<sub>3</sub>-Er<sub>2</sub>SO<sub>2</sub> nanoparticles (Er<sub>2</sub>O<sub>3</sub>-Er<sub>2</sub>SO<sub>2</sub>/rGO) demonstrate sufficiently strong light emission (luminescence and upconversion) in the visible and near-infrared range via intra-4f Er<sup>3+</sup> optical transitions. The reported synthetic approach demonstrates a novel method for synthesizing Er-containing nanoparticles for sensor applications.
Supplementary Table 2 from PD-1 and Tim-3 Regulate the Expansion of Tumor Antigen–Specific CD8<sup>+</sup> T Cells Induced by Melanoma Vaccines (2023)

&lt;p&gt;PDF file - 76K, Ex vivo frequencies of cytokine-producing NY-ESO-1 157-165-specific CD8+ T cells before and after vaccination with either MHC class I peptide alone (arm 1), or both MHC class I and class II peptides (arm 2).&lt;/p&gt;
Affordable Sequence Decoding Techniques for High Speed SerDes (2019)

Higher data rate requirements in data centers have motivated more spectrum efficient modulation to combat additional ISI at higher frequencies. But this also leads to significant SNR penalty. In addition to that technology scaling is shifting equalization from analog domain to the digital domain. Therefore, recent trend is to explore ADC-DSP based receiver where higher performance equalization such as viterbi decoder can be implemented. But the power consumption and complexity have limited their adoption in conventional SerDes applications. In this work we will introduce several low power implementation techniques such as analog to sequence conversion and direct branch matric estimation to explore possibility of sequence decoding in SerDes domain. Implemented prototype validates that the proposed sequence decoding is capable of compensating 35+ dB loss at 10 Gb/s with better than 10 pJ/bit energy efficiency.
Embedding positional-independent hidden data into hardcopy (2011)

We propose an approach for embedding of imperceptible hidden data into printed text document with ability to extract this data during scanning. Our approach is based on intrusion of cluster of small black dots (patterns) with predefined positional-independent structure into the document. Such intrusion will not visibly deteriorate document itself. Proposed multiple duplications of embedded information and statistical approach during hidden message extraction provide method with high immunity against document modification or noise.
Polycarboxylate crown ethers from meso-tartaric acid (1991)

The synthesis of crown ethers derived from meso-tartaric acid was investigated. The sodium salt of the bis(dimethylamide) of meso-tartaric acid reacted with diethylene glycol ditosylate to give a mixture of 18-crown-6 tetraamide and 27-crown-9 hexaamide crown ethers. The 2R,3S,11S,12R 18-crown-6 isomer crystallized in triclinic space group [Formula: see text] (a = 7.557(2), b = 8.866(2), c = 10.4133(13) Å, α = 94.13(2), β = 95.86(2), γ = 99.26(2)°, R = 0.040 for 2090 observed of 3129 unique reflections). The structures of the remaining products were then assigned from the NMR spectra. The solution conformations of the amide crown ethers were examined by NMR, and provide a rationale for the product distribution obtained. One of the 18-crown-6 isomers and a mixture of the two 27-crown-9 isomers were hydrolyzed to the respective crown ether carboxylic acids, and the stability constants for complexation of cations were determined by potentiometric titration. The meso tetra- and hexacarboxylates are remarkably nonselective and inefficient cation complexing agents, compared to related crown ethers from R,R-(+)-tartaric acid, due to the unfavorable conformational control exerted by the tartaro units. Key words: crown ether synthesis, complexation, crown ether conformation, meso-tartaric acid, crystal structure.
Enhanced AP-1 and NF-κB activities and stability of interleukin 8 (IL-8) transcripts are implicated in IL-8 mRNA superinduction in lung epithelial H292 cells (1998)

Inhibition of protein synthesis may result in superinduction of short-lived transcripts and has been attributed variably to stabilization of transcripts and/or increased gene transcription. Little is known about the kinetics of these processes and relevant transcriptional elements have not been identified. In this study, we describe superinduction of interleukin 8 (IL-8) mRNA, an important inflammatory mediator, in lung epithelial-like H292 cells and identify the underlying molecular mechanisms and their kinetics. Cycloheximide (CHI, 10 microg/ml), an inhibitor of protein synthesis, maximally increased IL-8 mRNA levels 30-fold in H292 cells. Tumour necrosis factor alpha (TNF-alpha), which induced IL-8 mRNA 3-fold, synergized with CHI causing a 150-fold increase at 6 h. CHI early on increased the stability of IL-8 mRNA (from 40 min in cells cultured with medium to more than 4 h with CHI). CHI also increased transcription as shown by transfection with IL-8 promoter constructs. Truncated and mutated constructs identified NF-kappaB and AP-1 binding sites as primary cis-acting elements in IL-8 gene transcription and IL-8 mRNA superinduction. Electrophoretic mobility shift assays indicated that CHI increased NF-kappaB and prolonged AP-1 DNA-binding activities and that the synergism of TNF-alpha and CHI on IL-8 mRNA expression was paralleled by a further increase of AP-1 DNA-binding activity. This synergism was still noticed when 4 h elapsed between the addition of CHI and that of TNF-alpha. Taken together, our results indicate that CHI interferes with both post-transcriptional and transcriptional repressive mechanisms of IL-8 mRNA expression.
Intermittent androgen suppression for prostate cancer: Canadian Prospective Trial and related observations. (2000)

The Canadian Prospective Trial of intermittent androgen suppression was a prototype therapeutic initiative started in 1995 for the management of patients in biochemical relapse after radiation for localized prostate cancer. An interim analysis has yielded several observations on the relations between baseline serum prostate specific antigen (PSA), nadir serum PSA, Gleason score, and time off-treatment. In a typical androgen-dependent tumor, the response of serum PSA to androgen withdrawal is biphasic, but with early tumor progression, plateauing of serum PSA is observed. Ligand-independent activation of the androgen receptor, a mechanism subserving the initiation of androgen independence, can be counteracted experimentally with decoy molecules and clinically with nonsteroidal antiandrogens. In some patients, it is possible to lengthen the off-treatment interval by inhibiting the enzyme 5 alpha-reductase, an effect that can be reinforced by lowering serum testosterone with an antigonadotropin. Serial measurements of serum PSA indicate that intermittent androgen suppression engenders a more diverse range of hormone-related responses than previously appreciated. These include: (1) repeated differentiation of tumor with recovery of apoptotic potential; (2) inhibition of tumor growth by rapid restoration of serum testosterone; and (3) restraint of tumor growth by subnormal levels of serum testosterone. These responses are aspects of regulation that should be taken into account when planning long-term treatment of prostate cancer with intermittent androgen suppression.
Local fields and optical properties of metal-dielectric films (2001)

Optical response of metal-dielectric inhomogeneous films is considered. The generalized Ohm's law is formulated that relates electric and magnetic fields outside to the currents inside the film. Computer simulations, with the use of the generalized Ohm's law show that the local electric and magnetic fields experience giant spatial fluctuations. The fields are localized in small spatially separated peaks: electric and magnetic hot spots. In these hot spots the local fields (both electric and magnetic) exceed the applied field by several orders of magnitude. It is also shown that transmittance of a regular modulated metal film is strongly enhanced when the incident wave is in resonance with surface polaritons in the film. A new optical switch based on this effect is proposed.
Mad cows meet mad yeast: the prion hypothesis. (1996)

Obscure work on the inheritance of two peculiar genetic traits in yeast has recently collided with work on infectious, neurodegenerative diseases in mammals. The impact illuminates both fields. The yeast work reveals a new mechanism of genetic variation that is based on differences in protein conformation rather than differences in nucleic acid. In the light of this work the prion hypothesis for transmissible neurodegenerative disease no longer seems so bizarre. Indeed, the mammalian prion hypothesis is now placed within a larger framework that is likely to be of universal importance in biology. Yeast prions, as the genetic elements are called, can be cured, offering new insights into the molecular processes involved in protein-based inheritance and new hope for the treatment of neurodegenerative diseases in man.
Learning Curves in the Arthroscopic Latarjet Procedure: A Multicenter Analysis of the First 25 Cases of 5 International Surgeons (2019)

Level IV, retrospective cohort study.
Theoretical Analysis of the CW Doppler Ultrasonic Flowmeter (1974)

The widespread application of ultrasonic techniques for the measurement of pulsatile blood flow has been hampered by the lack of a detailed theoretical understanding of the Doppler ultrasonic flowmeter. A general model for the Doppler flowmeter based upon stochastic considerations of the scattering of ultrasound by blood is introduced in this paper. The model characterizes the back- scattered ultrasound as a Gaussian random process and the expression for the autocovariance function is derived. For the CW Doppler flowmeter, the power spectral density function is computed, and its significance is emphasized: measurement of blood flow velocity corresponds to estimation of the average frequency of the Doppler power spectrum.