gebhart/patrepeval huggingface dataset:
Phosphorylation and Cytoskeletal Anchoring of the Acetylcholine Receptor by Src Class Protein-tyrosine Kinases (1999)

Src class protein-tyrosine kinases bind to and phosphorylate the nicotinic acetylcholine receptor of skeletal muscle. This study provided evidence for the functional importance of Src kinases in regulating the nicotinic acetylcholine receptor at the neuromuscular junction. Three Src class kinases, Fyn, Fyk, and Src, each formed a complex with the endplate-specific cytoskeletal protein rapsyn. In addition, cellular phosphorylation by each kinase was stimulated by rapsyn in heterologous transfected cells. Several lines of evidence supported rapsyn as a substrate for Src kinases. Most importantly, rapsyn regulation of Fyn, Fyk, and Src resulted in phosphorylation of the nicotinic acetylcholine receptor beta and delta subunits and anchoring of the receptor to the cytoskeleton. Both nicotinic acetylcholine receptor phosphorylation and cytoskeletal anchoring were blocked by the Src kinase-selective inhibitor herbimycin A. Rapsyn alone also induced a modest increase in nicotinic acetylcholine receptor phosphorylation and cytoskeletal translocation. However, inhibition by herbimycin A and a catalytically inactive dominant negative Src demonstrated that the effects of rapsyn were mediated by endogenous Src kinases. These data support the importance of Src class kinases for stabilization of the nicotinic acetylcholine receptor at the endplate during synaptic differentiation at the neuromuscular junction.
Preparation of Silicon Nanowire Field-effect Transistor for Chemical and Biosensing Applications (2016)

Surveillance using biomarkers is critical for the early detection, rapid intervention, and reduction in the incidence of diseases. In this study, we describe the preparation of polycrystalline silicon nanowire field-effect transistors (pSNWFETs) that serve as biosensing devices for biomarker detection. A protocol for chemical and biomolecular sensing by using pSNWFETs is presented. The pSNWFET device was demonstrated to be a promising transducer for real-time, label-free, and ultra-high-sensitivity biosensing applications. The source/drain channel conductivity of a pSNWFET is sensitive to changes in the environment around its silicon nanowire (SNW) surface. Thus, by immobilizing probes on the SNW surface, the pSNWFET can be used to detect various biotargets ranging from small molecules (dopamine) to macromolecules (DNA and proteins). Immobilizing a bioprobe on the SNW surface, which is a multistep procedure, is vital for determining the specificity of the biosensor. It is essential that every step of the immobilization procedure is correctly performed. We verified surface modifications by directly observing the shift in the electric properties of the pSNWFET following each modification step. Additionally, X-ray photoelectron spectroscopy was used to examine the surface composition following each modification. Finally, we demonstrated DNA sensing on the pSNWFET. This protocol provides step-by-step procedures for verifying bioprobe immobilization and subsequent DNA biosensing application.
Insulin Pump Risks and Benefits: A Clinical Appraisal of Pump Safety Standards, Adverse Event Reporting, and Research Needs (2015)

Insulin pump therapy, also known as continuous subcutaneous insulin infusion (CSII), is an important and evolving form of insulin delivery, which is mainly used for people with type 1 diabetes. However, even with modern insulin pumps, errors of insulin infusion can occur due to pump failure, insulin infusion set (IIS) blockage, infusion site problems, insulin stability issues, user error, or a combination of these. Users are therefore exposed to significant and potentially fatal hazards: interruption of insulin infusion can result in hyperglycemia and ketoacidosis; conversely, delivery of excessive insulin can cause severe hypoglycemia. Nevertheless, the available evidence on the safety and efficacy of CSII remains limited. The European Association for the Study of Diabetes (EASD) and the American Diabetes Association (ADA) have therefore joined forces to review the systems in place for evaluating the safety of pumps from a clinical perspective. We found that useful information held by the manufacturing companies is not currently shared in a sufficiently transparent manner. Public availability of adverse event (AE) reports on the US Food and Drug Administration's Manufacturer and User Facility Device Experience (MAUDE) database is potentially a rich source of safety information but is insufficiently utilized due to the current configuration of the system; the comparable database in Europe (European Databank on Medical Devices [EUDAMED]) is not publicly accessible. Many AEs appear to be attributable to human factors and/or user error, but the extent to which manufacturing companies are required by regulators to consider the interactions of users with the technical features of their products is limited. The clinical studies required by regulators prior to marketing are small and over-reliant on bench testing in relation to "predicate" products. Once a pump is available on the market, insufficient data are made publicly available on its long-term use in a real-world setting; such data could provide vital information to help health care teams to educate and support users and thereby prevent AEs. As well as requiring more from the manufacturing companies, we call for public funding of more research addressing clinically important questions in relation to pump therapy: both observational studies and clinical trials. At present, there are significant differences in the regulatory systems between the US and European Union at both pre- and postmarketing stages; improvements in the European system are more urgently required. This statement concludes with a series of recommended specific actions for "meknovigilance" (i.e., a standardized safety approach to technology) that could be implemented to address the shortcomings we highlight.
Nonlocal In-Plane Resistance due to Vortex-Antivortex Dynamics in High-<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="italic">T</mml:mi></mml:mrow><mml:mrow><mml:mi mathvariant="italic">c</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math>Superconducting Films (1998)

In high- ${T}_{c}$ superconducting ${\mathrm{YBa}}_{2}{\mathrm{Cu}}_{3}{\mathrm{O}}_{7\ensuremath{-}\ensuremath{\delta}}$ films and at no applied magnetic field we found both positive and negative in-plane nonlocal resistance in the vicinity of a vortex-antivortex unbinding transition, as it was predicted recently. The sign of the nonlocal resistance depends on the probed region in the current-temperature diagram. Our results indicate that a negative nonlocal resistance is due to the motion of unbounded vortex-antivortex (V-A), whereas a positive sign is attributed to the motion of a 2D V-A ordered lattice.
Temperature dependence of the electrical resistivity of reactively sputtered TiN films (1993)

The electrical resistivity of reactively sputtered TiN films was measured as a function of film thickness. The effect of directionality of the sputtered atoms, substrate temperature, bias voltage, deposition rate, and film morphology on the electron conductivity in TiN films was studied. The combination of rapid deposition rate and high substrate temperature with bias-collimated sputtering results in TiN films with the lowest resistivity, 45 μΩ cm, the largest temperature coefficient of resistance, 1355 ppm, and the highest superconducting transition temperature, 5.04 K. These films are characterized by small grains with mixed &lt;111≳ and &lt;200≳ orientation and reduced electron scattering with an estimated electron mean-free path of 96 nm.
DOCK 6: Impact of new features and current docking performance (2015)

This manuscript presents the latest algorithmic and methodological developments to the structure-based design program DOCK 6.7 focused on an updated internal energy function, new anchor selection control, enhanced minimization options, a footprint similarity scoring function, a symmetry-corrected root-mean-square deviation algorithm, a database filter, and docking forensic tools. An important strategy during development involved use of three orthogonal metrics for assessment and validation: pose reproduction over a large database of 1043 protein-ligand complexes (SB2012 test set), cross-docking to 24 drug-target protein families, and database enrichment using large active and decoy datasets (Directory of Useful Decoys [DUD]-E test set) for five important proteins including HIV protease and IGF-1R. Relative to earlier versions, a key outcome of the work is a significant increase in pose reproduction success in going from DOCK 4.0.2 (51.4%) → 5.4 (65.2%) → 6.7 (73.3%) as a result of significant decreases in failure arising from both sampling 24.1% → 13.6% → 9.1% and scoring 24.4% → 21.1% → 17.5%. Companion cross-docking and enrichment studies with the new version highlight other strengths and remaining areas for improvement, especially for systems containing metal ions. The source code for DOCK 6.7 is available for download and free for academic users at http://dock.compbio.ucsf.edu/.
On the comparison between Josephson-junction array variations (1991)

Recent work has shown that the expected performance of a given Josephson-junction series array depends greatly on whether the coupling load is a resistor or an inductor-capacitor combination. This raises the question of how arrays using different loads can be compared in a quantitatively meaningful way, for example, with respect to the effects of noise. We show that it is possible to choose the circuit parameters so that the in-phase output for different loads is, though not identical, nearly so. The key lies in the development of a nonlinear generalization of the load impedance.
Molecular mapping of the determinants involved in human Staufen–ribosome association (2002)

The human double-stranded (ds) RNA-binding protein Staufen (hStau) is considered to have a role in RNA transport and its localization. By using sedimentation analysis on sucrose gradients, we showed that the Staufen isoform with an apparent molecular mass of 55 kDa (Stau(55)) co-fractionated with ribosomes and associated with both the 40 and 60 S ribosomal subunits, suggesting that the Staufen isoform hStau(55) plays some role in translation. To map the determinant(s) involved in this association, we generated a series of deletion mutants and analysed their subcellular distribution by cell fractionation and fluorescent immunomicroscopy. Our results demonstrated that multiple determinants promote hStau(55)-ribosome association via both an RNA-binding-dependent mechanism and protein-protein interaction. The RNA-binding activity of the ds RNA-binding protein domain 3 (dsRBD3) but not that of dsRBD4 is the first determinant. Although necessary for stable association with ribosomes, dsRBD3 alone is not sufficient and needs other determinants as co-factors. Consistently, when expressed together, dsRBD4 and the tubulin-binding domain constitute the minimal Stau(55)/ribosome protein-protein association domain. This region of Stau(55) is sufficient to associate with ribosomes independently, but requires the RNA-binding activity of dsRBD3 for complete association. Thus the results are consistent with a putative role for Stau(55) in the regulation of translation.
Induction of apoptosis and modulation of activation and effector function in T cells by immunosuppressive drugs (2002)

Immunosuppressive drugs (ISD) are used for the prevention and treatment of graft rejection, graft-versus-host-disease (GVHD) and autoimmune disorders. The precise mechanisms by which ISD interfere with T cell activation and effector function or delete antigen-specific T cells are defined only partially. We analysed commonly used ISD such as dexamethasone (DEX), mycophenolic acid (MPA), FK506, cyclosporin A (CsA), rapamycin (RAP), methotrexate (MTX) and cyclophosphamide (CP) for apoptosis-induction and modulation of activation and effector function in human peripheral T cells, cytotoxic T cell lines (CTL) and Jurkat T cells. Of all drugs tested only CP and MTX prevented antigen-specific proliferation of T cells and decreased cytotoxicity of alloantigen specific CTL lines by direct induction of apoptosis. MTX and CP also slightly increased activation-induced cell death (AICD) and CD95-sensitivity. In contrast, all other drugs tested did not induce T cell apoptosis, increase CD95-sensitivity or AICD. CsA and FK506 even prevented AICD by down-modulation of CD95L. DEX, MPA, CsA, FK506 and RAP inhibited activation of naive T cells, but were not able to block proliferation of activated T cells nor decrease cytotoxic capacity of CTL lines. These results show that ISD can be classified according to their action on apoptosis-induction and inhibition of proliferation and would favour a rational combination therapy to delete existing reactive T cells and prevent further T cell activation.
The effect of the mixtures of photoinitiators in polymerization efficiencies (2008)

Abstract The photoinitiated polymerization of methyl methacrylate using the mixtures of camphorquinone (CQ) and acylphosphine oxides (monoacylphosphine oxide, MAPO, or bisacylphosphine oxide, BAPO) was studied to determine the possible synergistic effects. The addition of the acylphosphines to CQ resulted in an increase of the polymerization rate compared with CQ alone. On the other hand, a significant decrease of the polymerization quantum yield is observed for the mixtures compared with the pure acylphosphines. Therefore, the increase in the polymerization efficiency of the two mixtures studied, MAPO/CQ and BAPO/CQ (compared with CQ) can be traced to the larger light absorption range, rather than to the onset of new mechanisms. The presence of the coinitiator ethyl 4‐dimethylaminobenzoate, EDB, always present in CQ formulations, has no effect at all on the rates of polymerization photoinitiated by the acylphosphine oxides. From the point of view of photopolymerization quantum yields, an antagonistic effect is observed because of the energy transfer of the more efficient initiator (MAPO or BAPO) to the less efficient one (CQ). © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2009
Automatic recognition of malignant lesions in ultrasound images by artificial neural networks (2002)

A method for the automatic classification of lesions in ultrasound images by artificial neural nets is presented. The parameters used for training of the network are texture related indicators and shape related indicators. Three lesions have been considered: cysts, fibroadenomas and carcinomas. Solid lesions have been separated from cysts in the first step and carcinomas have been separated from fibroadenomas in a second step. A satisfactory classification between cysts and solid lesions can be achieved using texture parameters only, whereas shape parameters appear to be the most significant ones when classifying between carcinomas and fibroadenomas.
Postural abnormalities to multidirectional stance perturbations in Parkinson's disease (2004)

Our results confirm previous findings in ankle muscles, and provide new information on balance impairments in hip, trunk, and arm responses in PD.
HSBP1 Is a Novel Interactor of FIP200 and ATG13 That Promotes Autophagy Initiation and Picornavirus Replication (2021)

ATG13 and FIP200 are two subunits of the ULK kinase complex, a key regulatory component of the autophagy machinery. We have previously found that the FIP200-ATG13 subcomplex controls picornavirus replication outside its role in the ULK kinase complex and autophagy. Here, we characterized HSBP1, a very small cytoplasmic coiled-coil protein, as a novel interactor of FIP200 and ATG13 that binds these two proteins <i>via</i> FIP200. HSBP1 is a novel pro-picornaviral host factor since its knockdown or knockout, inhibits the replication of various picornaviruses. The anti-picornaviral function of the FIP200-ATG13 subcomplex was abolished when HSBP1 was depleted, inferring that this subcomplex negatively regulates HSBP1's pro-picornaviral function during infections. HSBP1depletion also reduces the stability of ULK kinase complex subunits, resulting in an impairment in autophagy induction. Altogether, our data show that HSBP1 interaction with FIP200-ATG13-containing complexes is involved in the regulation of different cellular pathways.
Invariant pattern recognition for range images using the phase Fourier transform and a neural network (1995)

A method for invariant pattern recognition of range images by means of the phase Fourier transform is introduced. The phase Fourier transform may be used for the segmentation of connected planar and quadric surfaces. The method is generalized to nonconnected planar surfaces through the use of the concept of the characteristic normal. An invariant representation under changes of position, scale, and orientation for the characteristic normals is defined. This representation is used as the input for a feedforward neural network. Examples of applications are given, and finally the method is applied to the problems of classification and occlusion.
Chemistry of fragrant substances (1994)

This publication is a monograph with tutorial and reference qualities, providing an in-depth picture of the chemistry of fragrances. The book contains hundreds of original schemes and formulas (a total of more than 1400) and is the result of years of research. The book is intended for professional chemists doing research and development in the perfume industry, in the cosmetics and toiletry industry. The text is also intended for natural-products chemists and organic chemists, in academic and industrial settings.
특집 : 한국의 북한 핵개발에 대한 인식과 대응: 3차 핵실험 이후 (2013)

2013년 2월 12일 북한의 3차 핵실험은 국내외에 커다란 충격을 주었다. 북한의 핵능력이 진전되고 북한은 경제건설과 함께 핵 무력건설을 김정은 시대의 발전전략으로 채택했다. 북핵문제의 패러다임이 변화했다. 한국 사회에서의 북한 핵개발에 대한 인식도 변화하였다. 정부와 정치권은 상당히 단결된 모습을 보여주었고, 국민 여론은 위협의 인식과 대응의 측면에서 보다 강경하게 나타났다. 북한 핵에 대한 대응도 ‘독자적 핵개발론’, ‘전술핵 재도입론’, ‘핵우산 강화론’ 또는 ‘강화된 확장 억지론’, ‘선제 핵타격론’, ‘북한체제 변화론’ 등 이전과는 다른 방식의 대응 방안들이 적극적으로 제시되었다. 그러나 이러한 대응 방안들은 정치성(精緻性)을 결여하고 있으며, 따라서 대안으로서의 실현 가능성, 효과성, 국가이익 차원의 실용적 가치 등을 고려한 냉철한 검토와 평가가 요구된다.이러한 검토를 바탕으로 북핵문제의 평화적 해결을 위한 새로운 대안을 찾아야 할 것이다.
Circular Microstrip Patch Array Antenna for C‐Band Altimeter System (2008)

The purpose of this paper is to discuss the practical and experimental results obtained from the design, construction, and test of an array of circular microstrip elements. The aim of this antenna construction was to obtain a gain of 12 dB, an acceptable pattern, and a reasonable value of SWR for altimeter system application. In this paper, the cavity model was applied to analyze the patch and a proper combination of ordinary formulas; HPHFSS software and Microwave Office software were used. The array includes four circular elements with equal sizes and equal spacing and was planed on a substrate. The method of analysis, design, and development of this antenna array is explained completely here. The antenna is simulated and is completely analyzed by commercial HPHFSS software. Microwave Office 2006 software has been used to initially simulate and find the optimum design and results. Comparison between practical results and the results obtained from the simulation shows that we reached our goals by a great degree of validity.
Edge terminations for SiC high voltage Schottky rectifiers (2002)

A study of floating metal field rings (FMRs) and resistive Schottky barrier field plate (RESP) edge terminations for high-voltage silicon carbide (SiC) Schottky barrier diodes (SBD) is reported. For a drift region doping of 2*10/sup 16/ cm/sup -3/, numerical simulations indicated a breakdown voltage for an unterminated diode of about 225 V as compared to approximately=1125 V for a parallel plane structure. For the FMR termination, simulations indicate a breakdown voltage of approximately=600 V for a three-ring termination with a ring spacing of 0.8 mu m. Experimentally determined breakdown voltages of SiC SBDs fabricated using FMR termination were >400 V as compared to approximately=220 V for unterminated diodes. For the RESP termination, an analytical model was developed to study the effect of various design parameters, such as RESP length and sheet-resistance, on the breakdown voltage. This model was used to optimize various design parameters for SBDs fabricated using RESP termination.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The theory of rubber elasticity (1976)

Abstract This paper attempts to improve several weaknesses in the classical theories of rubber elasticity. It develops a formulation of the statistical thermodynamics of amorphous materials analogous to the Gibbs formalism for conventional statistical mechanics. This then permits the replacement of ‘phantom chains’, i.e. long polymer molecules with the fictitious property that they experience no forces except at cross link points and are transparent to one another, by realistic molecules which do experience forces and which can become entangled. The crosslinked points are no longer assumed to deform affinely with the gross behaviour of the solid. Under the simplest conditions forms like the classical are recovered but with a different coefficient, and the term representing the degrees of freedom lost by crosslinking, over which the classical theories are in dispute, is found to lie between the previous values in a formula which can reproduce the classical results by making different assumptions. The entanglements give rise to more complicated forms than the classical sum of squares of strain ratios, which under certain circumstances can reproduce the Mooney-Rivlin term which when added empirically to the free energy usually improves the fit with experiment. The general expression is complicated, but is nevertheless an explicit function of the density of crosslinks, the density of the rubber and the interchain forces.
Moment-Based Acceleration for Neutral Gas Kinetics with BGK Collision Operator (2014)

In this work, we present a moment-based accelerator algorithm for a Picard iteration applied to a neutral gas dynamics Boltzmann transport equation with a Bhatnagar-Gross-Krook collision operator. Traditional approaches relying on either explicit or Picard iteration schemes (i.e., source iteration) are severely limited for investigating time-scales much larger than the collisional relaxation time-scale, τ. We have developed a nonlinear accelerator algorithm that allows one to step over this stiff collision time scale and follow the hydrodynamic time scale of the problem when appropriate. The new algorithm relies on formulating a nonlinear, coupled system comprised of a high-order (HO) kinetic equation and a low-order (LO) fluid moment equation system. The HO equation provides self-consistent closures to the LO fluid equations, while the latter provides the required implicit-moment variables to evaluate the collision operator. We characterize the performance of the new algorithm on a Sod shock tube and a strong shock tube problem with varying Knudsen number.
Survival of a 30-week baby with congenital myotonic dystrophy initially ventilated for 55 days (1999)

In previous reports, duration of initial ventilation exceeding 1 month almost always predicts non-survival of babies with congenital myotonic dystrophy. However, a baby with this condition survived beyond infancy after 55 days' ventilation. We describe this case in detail, explain why the baby survived and highlight the importance of individualized assessment, in addition to applying general prognostic terms described in the literature.