gebhart/patrepeval huggingface dataset:
Understanding and Estimating Membrane/Water Partition Coefficients:  Approaches To Derive Quantitative Structure Property Relationships (1998)

In the current study we describe three approaches to derive quantitative structure property relationships (QSPRs) that give insight in the interactions that are important in membrane/water partitioning. In the first model only semiempirically (AM1) calculated descriptors are used to model membrane/water partition coefficients. Additionally, differences between the n-octanol/water and membrane/water partition coefficients are explored using a small selection of calculated descriptors. The results from both these models show that besides the partitioning between an organic phase and water, additional hydrogen-bonding parameters (epsilonLUMO, Q-, and Q+) should be taken into account. Finally, using structural fragment values, a QSPR was derived to correct the n-octanol/water partition coefficient to obtain membrane/water partition coefficients, in case that obtaining AM1 descriptors is not feasible. The QSPRs that are presented here include only alcohols, benzenes, anilines, phenols, nitrobenzenes, quinoline, esters, and amines. Due to the data limitation, the models should be regarded preliminary for other structures, and caution is necessary when modeling charged species.
Erlotinib in Previously Treated Non–Small-Cell Lung Cancer (2005)

Erlotinib can prolong survival in patients with non-small-cell lung cancer after first-line or second-line chemotherapy.
Transcription of RNA templates by T7 RNA polymerase (1998)

Although highly specialized, T7 RNA polymerase seems to possess a large range of DNA- and RNA-dependent properties. To study such flexibility, we determined the ability of T7 RNA polymerase to transcribe chimeric DNA-RNA and RNA templates following initiation at a double stranded DNA promoter. We have found that T7 RNA polymerase is able to initiate on RNA templates, was processive, and was able to use templates containing RNA-RNA duplexes under standard transcription conditions. Implications of remnants of such RNA-dependent activities for T7 DNA-dependent polymerase are discussed.
[Development of prediction models for three in vitro embryotoxicity tests which are evaluated in an ECVAM validation study] (1999)

In 1997 ZEBET started the co-ordination of a study funded by the European Centre for the Validation of Alternative Methods (ECVAM) with the aim of pre-validation and validation of three in vitro embryotoxicity tests. These tests employ the cultivation of post-implantation whole rat embryos (WEC test), cultures of primary limb bud cells of rat embryos (micromass test, MM-Test), and cultures of a pluripotent mouse embryonic stem cell line (embryonic stem cell test, EST). In the current Validation Study each of the tests is evaluated in four laboratories under blind conditions. In an initial phase of the validation study six out of 20 test chemicals comprising different embryotoxic potential (non, weak and strong embryotoxic) were tested. The results were used to improve the prediction models (PM) for the WEC test and the MM-Test in order to identify the embryotoxic potential of test chemicals. In addition, the existing PM for the EST was evaluated using the results from testing of the initial six chemicals. The PM for the EST was developed using the results of a previous pre-validation study (Scholz et al.,1999), in which 94% of the learning sample were classified correctly. Applying this PM to the results of the initial phase of the current validation study, 80% of the experiments were classified correctly according to the embryotoxic potential of the tested chemicals in vivo. Applying the PM for the MM-Test and the WEC test that were developed during the current validation study in both tests, 79% correct classifications were achieved. Since the PM of the WEC-Test took into account only parameters of growth and development, but not cytotoxicity data, a second PM (PM2) for the WEC was developed that was improved by incorporating cytotoxicity data of the differentiated mouse fibroblast cell line 3T3 derived from the EST. This approach, which has previously never been used as an adjunct to the WEC test, resulted in an increase of correct classifications to 96%.
Large signal modeling of HBT's including self-heating and transit time effects (1992)

A physically based, large signal heterojunction bipolar transistor (HBT) model is presented to account for the time dependence of the base, collector, and emitter charging currents, as well as self heating effects. The model tracks device performance over eight decades of current. The model can be used as the basis of SPICE modeling approximations, and to this end, examples are presented. A thesis for the divergence of high frequency large signal SPICE simulations from measured data is formulated, including a requisite empirical equation for the base-collector junction capacitance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
阳极产生的Sn^2＋引发聚合（N,N,N—三甲基—N—2—甲基丙烯酰氧乙基）氯化 … (2000)

研究了使用新的合成技术和引发剂Ｓｎ＾２＋进行ＤＭＡＥＭ－ＭＣ阳离子聚合过程，Ｓｎ＾２＋由牺牲阳极产生。在只有Ｓｎ材作电极的间歇反应器中配制聚合物，获得了电解法制备聚合物转化率和平均分子质量的影响因素。一方面，这些结果表明搅拌速度、初始ｐＨ值、电流密度和电极构成对转化率和聚合物分子质量都有重要影响；另一方面，温度和单体浓度在电化聚合过程中的影响虽是次要的，然而这两种因素在传统化学方法中影响最大。理想
No-Incision Pubovaginal Suspension for Stress Incontinence (1987)

We describe a modified needle suspension for urinary incontinence that eliminates all incisions. The anterior vaginal wall is suspended from the rectus fascia with 2 heavy nonabsorbable monofilament mattress sutures. The sutures pass down through and back up through the full thickness of the vaginal wall, and are tied suprapubically to bury the knot into the fat in the suprapubic puncture site. The technique is based on our laboratory observation that in rats and guinea pigs monofilament mattress sutures that are tied under tension to include the outside abdominal skin will cut through the skin, and become internalized and accepted without any residual inflammation if the knot is buried initially. The simplified technique makes routine use of outpatient surgery and allows for the use of local anesthesia only in selected patients. At 2 1/2 years the continence rate in the first 38 patients exceeded 87 per cent. There were no failures among the last 14 patients after the technique was modified to include an extra full thickness pass of the mattress suture through the vaginal wall. There have been no significant complications.
Pathogenesis and immunity in murine salmonellosis (1989)

Salmonella is traditionally described as a facultative intracellular parasite, and host macrophages are regarded as the primary effector cells in both native and acquired immunity in mouse typhoid. This concept has not been unanimously accepted in the literature. Based on cell culture experiments and electron microscopic examinations of infected tissues, we observed that virulent Salmonella typhimurium is killed within polymorphs and macrophages of guinea pigs and mice. In a systemic disease, the organism propagates primarily in the extracellular locations of sinusoids and tissue lesions and within hepatocytes. Hence, it is more likely to be an extracellular pathogen and its virulence is directly related to its antiphagocytic property. The conspicuous absence of macrophages in the primary lesions of murine salmonellosis disputes the likelihood of their significant role in native resistance to the disease. Acquired cellular immunity is expressed as an enhanced antibacterial activity of macrophages facilitated by cytophilic antibodies rather than as an altered antibacterial action of immune macrophages. It is proposed that acquired immunity in murine salmonellosis is a synergistic manifestation of the innate capacity of polymorphs and macrophages to destroy ingested salmonellae, the activated antibacterial functions of macrophages mediated by cytophilic antibodies, the opsonic and agglutinating actions of antiserum, and the accelerated inflammation associated with delayed hypersensitivity to bacterial antigens. Unlike live attenuated vaccines, nonviable vaccines offer a significant, though not a solid, protection against subsequent challenges.
Confocal‐line microscopy (1992)

The confocal-line (CL) technique combines some of the characteristics of confocal-scanning microscopy with those of conventional-imaging methods. It is based on the introduction of line-shaped illumination and linear image detection, as an alternative to the current confocal-point (CP) approach. Although confocal only in one dimension, the proposed solution offers performance and features adequate to a variety of biological and non-biological applications and is also adaptable to an increased number of microscopical observations and measurements. The absence of moving components in the optical path and the use of electronic linear imagers permits flexible and fast operation that appears particularly relevant in many fields of basic and applied research. For instance, transmission, reflection and emission images can simultaneously be collected from the same area of the specimen, with slight adjustments to the optical setup. Useful extensions of CL microscopy to the field of spectral imaging are obtained with the introduction of a slit, a polychromator and an area detector, substituting for the linear imager. Prototype instrumentation has been constructed working from the cited principles and some tests have been performed on selected applications.
Bone morphogenetic protein receptor II regulates pulmonary artery endothelial cell barrier function (2010)

Mutations in bone morphogenetic protein receptor II (BMPR-II) underlie most heritable cases of pulmonary arterial hypertension (PAH). However, less than half the individuals who harbor mutations develop the disease. Interestingly, heterozygous null BMPR-II mice fail to develop PAH unless an additional inflammatory insult is applied, suggesting that BMPR-II plays a fundamental role in dampening inflammatory signals in the pulmonary vasculature. Using static- and flow-based in vitro systems, we demonstrate that BMPR-II maintains the barrier function of the pulmonary artery endothelial monolayer suppressing leukocyte transmigration. Similar findings were also observed in vivo using a murine model with loss of endothelial BMPR-II expression. In vitro, the enhanced transmigration of leukocytes after tumor necrosis factor α or transforming growth factor β1 stimulation was CXCR2 dependent. Our data define how loss of BMPR-II in the endothelial layer of the pulmonary vasculature could lead to a heightened susceptibility to inflammation by promoting the extravasation of leukocytes into the pulmonary artery wall. We speculate that this may be a key mechanism involved in the initiation of the disease in heritable PAH that results from defects in BMPR-II expression.
Incidence of Nephrogenic Systemic Fibrosis after Adoption of Restrictive Gadolinium-based Contrast Agent Guidelines (2011)

After restrictive guidelines regarding GBCA administration were instituted, no new cases of NSF were identified among 52,954 contrast-enhanced MR examinations, including those performed in patients with an eGFR lower than 60 mL/min/m(2).
Collagen sponge: Theory and practice of medical applications (1977)

Theoretical as well as practical-clinical applications of one form of collagen (collagen sponge) as a biodegradable material is reviewed. The role of porosity of the sponge and surface characteristics of the meshwork in relation to cell ingrowth are considered essential features of collagen sponge. Rate of resorption and antigenicity could be controlled by graded crosslinking of collagenous framework. Four basic examples of clinical use of collagen sponge are presented: as wound (burn) dressing material, as a matrix, for bone and cartilage repair, as an intravaginal contraceptive diaphragm, and as surgical tampons.
Role of Receptor Binding and Gene Transcription for Both of Stimulatory and Inhibitory Effects of Interleukin-1 In Pancreatic β-Cells (1992)

A brief exposure of pancreatic islets to the cytokine interleukin-1 beta (IL-1 beta) induces an initial stimulatory phase, which is followed by inhibition of islet function and eventually beta-cell damage. In the present study we have investigated the effects of IRAP, a blocker of type I IL-1 receptor and actinomycin D, an inhibitor of DNA transcription, on both the stimulatory and inhibitory effects of IL-1 beta on rat pancreatic islets in vitro. The two test agents counteracted the initial stimulatory actions of IL-1 beta on both islet glucose-induced insulin release and glucose oxidation rates. Furthermore, cycloheximide, an inhibitor of protein synthesis, could also prevent the early IL-1 beta-induced stimulation of insulin release. When islets were exposed for 1 hr to IL-1 beta and studied after 12 hr, there was a 75% inhibition of glucose induced insulin release, a 50% decrease in glucose oxidation rates and a 30% decrease in (pro)insulin biosynthesis. These effects were completely counteracted by coincubation with IRAP or actinomycin D, but were not affected by coincubation with pertussis toxin. Islet exposure to IL-1 alpha also induced a 60-80% inhibition of glucose-induced insulin release after 12 hr. As observed with rIL-1 beta, IRAP was also able to block the suppressive effects of IL-1 alpha on islet function. Mouse islets exposed for 2 hr to IL-1 beta and studied after 12 hr presented a 50% decrease in the glucose-induced insulin release. This effect was completely blocked by coincubation with a rat monoclonal antibody generated against the type I mouse IL-1 receptor.(ABSTRACT TRUNCATED AT 250 WORDS)
Theoretical and experimental Raman spectroscopy study of mechanical stress induced by electronic packaging (2005)

The mechanical stress induced in Si chips by the packaging process (effect of die attach, flip chip bumping, etc.) is measured by micro-Raman spectroscopy. The measurements are performed on the [110] cross-section surface of the polished samples. This study shows that the current Raman formula for top-surface measurements cannot be used for cross-section measurements due to the anisotropic property of Si. The new formula for cross-section measurements is introduced in this paper. The experimental results are compared to finite element simulations. The Raman results correlate very well with the FE calculations. It shows that micro-Raman spectroscopy is a very interesting technique to study packaging induced stress in Si chips and to validate finite element calculations.
The Influence of Parental Socialization Factors on Family Farming Plans of Preadolescent Children: An Exploratory Analysis. (2005)

The Illinois Rural Families Project at the University of Illinois Urbana-Champaign, which is funded by the Illinois Council on Food and Agricultural Research and the U.S. Department of Agriculture, provided support for this study. Correspondence concerning this article should be addressed to Angela Wiley, Department of Human and Community Development, University of Illinois, 237 Bevier Hall, Urbana, IL 61801. (awiley@uiuc.edu) Citation: Wiley, A. R., Bogg, T., & Ho, M. R. (2005, December 1). The influence of parental socialization factors on family farming plans of preadolescent children: An exploratory analysis. Journal of Research in Rural Education, 20(11). Retrieved [date] from http://www.umaine.edu/jrre/20-11.pdf
Using Syntactic and Semantic based Relations for Dialogue Act Recognition (2010)

This paper presents a novel approach to dialogue act recognition employing multilevel information features. In addition to features such as context information and words in the utterances, the recognition task utilizes syntactic and semantic relations acquired by information extraction methods. These features are utilized by a Bayesian network classifier for our dialogue act recognition. The evaluation results show a clear improvement from the accuracy of the baseline (only with word features) with 61.9 % to an accuracy of 67.4 % achieved by the extended feature set. 1
Concomitant Formation of N-Heterocyclic Carbene−Copper Complexes within a Supramolecular Network in the Self-Assembly of Imidazolium Dicarboxylate with Metal Ions (2009)

A new building block containing an imidazolium salt was synthesized and used for the construction of supramolecular networks with metal ions. We discovered the concomitant formation of the N-heterocyclic carbene-copper complex (CN = 2) in the self-assembly of imidazolium dicarboxylates and copper nitrates in N,N-dimethylformamide under heating. The proton in the 2 position of the imidazolium salt was abstracted, and Cu(II) was reduced to Cu(I) during the self-assembly process.
Facilitation of Conditioned Fear Extinction by Systemic Administration or Intra-Amygdala Infusions of d-Cycloserine as Assessed with Fear-Potentiated Startle in Rats (2002)

NMDA receptor antagonists block conditioned fear extinction when injected systemically and also when infused directly into the amygdala. Here we evaluate the ability of D-cycloserine (DCS), a partial agonist at the strychnine-insensitive glycine-recognition site on the NMDA receptor complex, to facilitate conditioned fear extinction after systemic administration or intra-amygdala infusions. Rats received 10 pairings of a 3.7 sec light and a 0.4 mA footshock (fear conditioning). Fear-potentiated startle (increased startle in the presence vs the absence of the light) was subsequently measured before and after 30, 60, or 90 presentations of the light without shock (extinction training). Thirty non-reinforced light presentations produced modest extinction, and 60 or 90 presentations produced nearly complete extinction (experiment 1). DCS injections (3.25, 15, or 30 mg/kg) before 30 non-reinforced light exposures dose-dependently enhanced extinction (experiment 2) but did not influence fear-potentiated startle in rats that did not receive extinction training (experiment 3). These effects were blocked by HA-966, an antagonist at the glycine-recognition site (experiment 4). Neither DCS nor HA-966 altered fear-potentiated startle when injected before testing (experiment 5). The effect of systemic administration was mimicked by intra-amygdala DCS (10 microg/side) infusions (experiment 6). These results indicate that treatments that promote NMDA receptor activity after either systemic or intra-amygdala administration promote the extinction of conditioned fear.
Statistical Mechanics of the Combinatorial Synthesis and Analysis of Folding Macromolecules (1997)

Combinatorial chemistry techniques provide a promising route to the design of macromolecules that acquire predetermined folded conformations. A library of sequences based on a pool of different monomer types can be synthesized, where the sequences are partially designed so as to be consistent with a particular target conformation. The library is screened for folding molecules. The number of sequences grows rapidly with the length of the polymer, however, and both the experimental and computational tabulation of sequences become infeasible. For polymers and libraries of arbitrary size, we present a self-consistent, mean-field theory that can be used to estimate the number of sequences as a function of the energy in a target structure. The theory also yields the probabilities that each position in the sequence is occupied by a particular monomer type. The theory is tested using a simple lattice model of proteins, and excellent agreement between the theory and the results of exact enumerations are observed. The theory may be used to quantify particular design strategies and the facility of finding low-energy sequences for particular structures. The theory is discussed with an eye toward protein design and the mutability of particular residues in known proteins.
Harmonizing the Metabolic Syndrome (2009)

A cluster of risk factors for cardiovascular disease and type 2 diabetes mellitus, which occur together more often than by chance alone, have become known as the metabolic syndrome. The risk factors include raised blood pressure, dyslipidemia (raised triglycerides and lowered high-density lipoprotein cholesterol), raised fasting glucose, and central obesity. Various diagnostic criteria have been proposed by different organizations over the past decade. Most recently, these have come from the International Diabetes Federation and the American Heart Association/National Heart, Lung, and Blood Institute. The main difference concerns the measure for central obesity, with this being an obligatory component in the International Diabetes Federation definition, lower than in the American Heart Association/National Heart, Lung, and Blood Institute criteria, and ethnic specific. The present article represents the outcome of a meeting between several major organizations in an attempt to unify criteria. It was agreed that there should not be an obligatory component, but that waist measurement would continue to be a useful preliminary screening tool. Three abnormal findings out of 5 would qualify a person for the metabolic syndrome. A single set of cut points would be used for all components except waist circumference, for which further work is required. In the interim, national or regional cut points for waist circumference can be used.
An integrated system for real-time model predictive control of humanoid robots (2013)

Generating diverse behaviors with a humanoid robot requires a mix of human supervision and automatic control. Ideally, the user's input is restricted to high-level instruction and guidance, and the controller is intelligent enough to accomplish the tasks autonomously. Here we describe an integrated system that achieves this goal. The automatic controller is based on real-time model-predictive control (MPC) applied to the full dynamics of the robot. This is possible due to the speed of our new physics engine (MuJoCo), the efficiency of our trajectory optimization algorithm, and the contact smoothing methods we have developed for the purpose of control optimization. In our system, the operator specifies subtasks by selecting from a menu of predefined cost functions, and optionally adjusting the mixing weights of the different cost terms in runtime. The resulting composite cost is sent to the MPC machinery which constructs a new locally-optimal time-varying linear feedback control law once every 30 msec, while planning 500 msec into the future. This control law is evaluated at 1 kHz to generate control signals for the robot, until the next control law becomes available. Performance is illustrated on a subset of the tasks from the DARPA Virtual Robotics Challenge.
Divalent Ion and Thermally Induced DNA Conformational Polymorphism on Single-walled Carbon Nanotubes (2007)

Various sequences of single and double stranded DNA can wrap and colloidally stabilize single- walled carbon nanotubes in solution. The binding of divalent ions to these complexes results in a 10 meV emission energy red-shift of the photoluminescence of the nanotube. In this work, this optical modulation is linked to specific secondary structure changes in the adsorbed DNA. Dynamic light scattering is used to rule out aggregation and inter-particle effects. It is observed that the transition can also be induced thermally over the temperature range between 0 and 50 °C without ion addition. Interestingly, we find evidence of the dissociation of a DNA duplex at the surface, as confirmed using both selective dialysis and DNA electrophoresis on a 20% PAGE gel. Consistent with several observations is a mechanism that proceeds via a competitive, stepwise process of partial desorption of the DNA along the length of SWNT. A two-state mathematical model quantitatively describes the equilibrium for various divalent ions binding to DNA adsorbed at the nanotube surface.