gebhart/patrepeval huggingface dataset:
Understanding the lithiation/delithiation mechanism of Si<sub>1−x</sub>Ge<sub>x</sub> alloys (2017)

Ge<sub>x</sub>Si<sub>1−x</sub> alloys have demonstrated synergetic effects as lithium-ion battery (LIB) anodes because silicon brings its high lithium storage capacity and germanium its better electronic and Li ion conductivity.
Surface modification of extrasynovial tendon by chemically modified hyaluronic acid coating (2001)

We investigated a method for chemically binding hyaluronic acid (HA) to extrasynovial tendon and the effect of chemically modified HA on the gliding resistance of tendon. Canine peroneus longus (PL) tendons were immersed into one of three different solutions (saline, 1% HA, or 1% chemically modified HA) for 2 h. The gliding resistance of treated PL tendons was measured at 1, 5, 10, 20, 50, and 100 cycles in a saline bath. After treatment with unmodified HA and chemically modified HA, the gliding resistance of the PL tendons decreased significantly compared with the saline-treated tendons (p < 0.05), and this effect of the two HA treatments persisted through 10 cycles. For cycles 20-100, the gliding resistance of PL tendons treated with chemically modified HA remained significantly lower than that of tendons treated either with saline or unmodified HA (p < 0.01). The effect of paratenon removal on gliding resistance was neither statistically significant for repetitions beyond 10 cycles, nor was it an independent predictor of gliding resistance, as the effect (higher resistance after paratenon removal) was mainly seen in the saline-treated tendons. Chemically modified HA-treated extrasynovial tendons may improve gliding of tendon graft and reduce adhesion postoperatively, compared with traditional grafts.
7+1 to 1 pump/signal combiner for air-clad fiber with 15 Âµm MFD PM single-mode signal feed-through (2010)

A 7+1 to 1 pump/signal combiner with single-mode (SM) polarization maintaining (PM) 15 μm mode-field-diameter (MFD) signal feed-through is demonstrated. The combiner is designed for pulse amplification in an active Yb-doped airclad fiber operated in backward pumped configuration. Signal coupling through the device is realized by a microstructured taper element allowing single-mode guidance and constant MFD at a taper ratio of 3.4.
Differential Gene Expression in Gram-negative and Gram-positive Sepsis (2004)

Sepsis is the most common cause of death in patients in the intensive care unit. Genome-wide gene expression analysis can provide insights into the molecular alterations of sepsis. Total mRNA was extracted from the livers of 6 uninfected control mice and 60 septic mice after infusion of either live Escherichia coli or Staphylococcus aureus. Using a murine complementary DNA microarray system, changes in gene expression were monitored at six time points (uninfected, 2, 8, 24, 48, and 72 hours). Overall, 4.8% of 6,144 assessed genes were differentially regulated with a greater than twofold change across all time points. Most of the genes with altered expression were commonly present in gram-negative and gram-positive sepsis, but the expression levels of 17 genes were different between both types of sepsis at particular time points after infection. The microarray results support the hypothesis that both gram-positive and gram-negative sepsis share a final common pathway involved in the pathogenesis of sepsis, but certain genes are differentially expressed under distinct regulation. These results may provide insights into the pathogenesis of sepsis and may also help identify some altered genes that can serve as new targets for diagnostic tools and therapeutic strategies.
Comparative Evaluation of 11 Scoring Functions for Molecular Docking (2003)

Eleven popular scoring functions have been tested on 100 protein-ligand complexes to evaluate their abilities to reproduce experimentally determined structures and binding affinities. They include four scoring functions implemented in the LigFit module in Cerius2 (LigScore, PLP, PMF, and LUDI), four scoring functions implemented in the CScore module in SYBYL (F-Score, G-Score, D-Score, and ChemScore), the scoring function implemented in the AutoDock program, and two stand-alone scoring functions (DrugScore and X-Score). These scoring functions are not tested in the context of a particular docking program. Instead, conformational sampling and scoring are separated into two consecutive steps. First, an exhaustive conformational sampling is performed by using the AutoDock program to generate an ensemble of docked conformations for each ligand molecule. This conformational ensemble is required to cover the entire conformational space as much as possible rather than to focus on a few energy minima. Then, each scoring function is applied to score this conformational ensemble to see if it can identify the experimentally observed conformation from all of the other decoys. Among all of the scoring functions under test, six of them, i.e., PLP, F-Score, LigScore, DrugScore, LUDI, and X-Score, yield success rates higher than the AutoDock scoring function. The success rates of these six scoring functions range from 66% to 76% if using root-mean-square deviation < or =2.0 A as the criterion. Combining any two or three of these six scoring functions into a consensus scoring scheme further improves the success rate to nearly 80% or even higher. However, when applied to reproduce the experimentally determined binding affinities of the 100 protein-ligand complexes, only X-Score, PLP, DrugScore, and G-Score are able to give correlation coefficients over 0.50. All of the 11 scoring functions are further inspected by their abilities to construct a descriptive, funnel-shaped energy surface for protein-ligand complexation. The results indicate that X-Score and DrugScore perform better than the other ones at this aspect.
Protein Dielectric Constants Determined from NMR Chemical Shift Perturbations (2013)

Understanding the connection between protein structure and function requires a quantitative understanding of electrostatic effects. Structure-based electrostatic calculations are essential for this purpose, but their use has been limited by a long-standing discussion on which value to use for the dielectric constants (ε(eff) and ε(p)) required in Coulombic and Poisson-Boltzmann models. The currently used values for ε(eff) and ε(p) are essentially empirical parameters calibrated against thermodynamic properties that are indirect measurements of protein electric fields. We determine optimal values for ε(eff) and ε(p) by measuring protein electric fields in solution using direct detection of NMR chemical shift perturbations (CSPs). We measured CSPs in 14 proteins to get a broad and general characterization of electric fields. Coulomb's law reproduces the measured CSPs optimally with a protein dielectric constant (ε(eff)) from 3 to 13, with an optimal value across all proteins of 6.5. However, when the water-protein interface is treated with finite difference Poisson-Boltzmann calculations, the optimal protein dielectric constant (ε(p)) ranged from 2 to 5 with an optimum of 3. It is striking how similar this value is to the dielectric constant of 2-4 measured for protein powders and how different it is from the ε(p) of 6-20 used in models based on the Poisson-Boltzmann equation when calculating thermodynamic parameters. Because the value of ε(p) = 3 is obtained by analysis of NMR chemical shift perturbations instead of thermodynamic parameters such as pK(a) values, it is likely to describe only the electric field and thus represent a more general, intrinsic, and transferable ε(p) common to most folded proteins.
Octacoordinate Metal Carbonyls of Lanthanum and Cerium: Experimental Observation and Theoretical Calculation (2014)

The octacoordinate metal carbonyls La(CO)8(+) and Ce(CO)8(+) were observed in laser vaporization of La and Ce in pure CO gas. The peak intensities in the mass spectra, the infrared photodissociation spectra, and the theoretical calculations indicate that all CO ligands in these two complexes are bonded with the central metal atoms. The CO stretching frequencies in La(CO)8(+) and Ce(CO)8(+) are determined to be 2110 and 2108 cm(-1), respectively. Theoretical studies indicate that the most stable structures for La(CO)8(+) and Ce(CO)8(+) are an Oh geometry at its triplet state and a slightly distorted Oh geometry at its quartet state, respectively. These two complexes represent new octacoordinate metal carbonyls after previously determined U(CO)8(+) and Y(CO)8(+).
Hybrid soft computing systems: industrial and commercial applications (1999)

Soft computing (SC) is an association of computing methodologies that includes as its principal members fuzzy logic, neurocomputing, evolutionary computing and probabilistic computing. We present a collection of methods and tools that can be used to perform diagnostics, estimation, and control. These tools are a great match for real-world applications that are characterized by imprecise, uncertain data and incomplete domain knowledge. We outline the advantages of applying SC techniques and in particular the synergy derived from the use of hybrid SC systems. We illustrate some combinations of hybrid SC systems, such as fuzzy logic controllers (FLCs) tuned by neural networks (NNs) and evolutionary computing (EC), NNs tuned by EC or FLCs, and EC controlled by FLCs. We discuss three successful real-world examples of SC applications to industrial equipment diagnostics, freight train control, and residential property valuation.
Determination of RSD921 in human plasma by high‐performance liquid chromatography–tandem mass spectrometry using tri‐deuterated RSD921 as internal standard: application to a phase I clinical trial (2001)

A fast, sensitive and specific method is presented for the quantification of RSD921 in human plasma by liquid chromatography coupled with tandem mass spectrometry using tri-deuterated RSD921 (3d-RSD921) as an internal standard. A single-step liquid/liquid extraction was performed with diethyl ether/hexane (80 : 20, v/v) using 0.5 ml of plasma. The plasma calibration curves were linear from 0.1 to 20 ng ml(-1) (r > 0.999). Between-run precision, based on the percent relative deviation for replicate (n = 40) quality controls, was < or =7.27% (0.5 ng ml(-1)), < or =7.39% (5.0 ng ml(-1)), and < or =5.06% (20.0 ng ml(-1)). Between-run accuracies, based on the relative error, were +/-2.59%, +/-1.23% and +/-1.64% respectively. The method was developed to evaluate the pharmacokinetic profile after 15 min of intravenous stepwise-ascending infusion dose of RSD921 in 18 healthy volunteers. A dissociation study of protonated RSD921 and 3d-RSD921 by collision-induced dissociation using in-source fragmentation and tandem mass spectrometry is also presented.
Up-regulation of Mcl-1 Is Critical for Survival of Human Melanoma Cells upon Endoplasmic Reticulum Stress (2008)

We have previously shown that most melanoma cell lines are insensitive to endoplasmic reticulum (ER) stress-induced apoptosis, and this involves activation of the mitogen-activated protein/extracellular signal-regulated kinase (MEK)/ERK signaling pathway and expression of the apoptosis repressor with caspase recruitment domain (ARC) protein in the cells. In the present study, we show that up-regulation of the antiapoptotic Bcl-2 family member Mcl-1 is another mechanism critical for protection of melanoma cells against ER stress-induced apoptosis. Inhibition of Mcl-1 by small interference RNA (siRNA) rendered melanoma cells sensitive to apoptosis induced by the ER stress inducers thapsigargin and tunicamycin, but this sensitization was partially reversed by siRNA knockdown of PUMA or Noxa, as shown in Mcl-1-deficient melanoma cells. Both PUMA and Noxa were increased by ER stress through transcriptional up-regulation, but only up-regulation of Noxa was dependent on p53, whereas up-regulation of PUMA seemed to be mediated by a p53-independent mechanism(s). Up-regulation of Mcl-1 was also due to increased transcription that involved the IRE1alpha and activating transcription factor 6 signaling pathways of the unfolded protein response. In addition, activation of the MEK/ERK signaling pathway seemed to be necessary for optimal up-regulation of Mcl-1. Taken together, these results reveal the mechanisms of resistance of melanoma cells to apoptosis induction mediated by BH3-only proteins upon ER stress, and identify Mcl-1 as a target for the treatment of melanoma in combination with therapeutics that induce ER stress.
Oncogenes as Therapeutic Targets in Cancer: A Review (2013)

Carcinogenesis is a multi-step process which result in uncontrolled cell growth. Mutations in DNA that lead to cancer disrupt these orderly processes by disrupting the programming regulating the processes.. This results in uncontrolled cell division leading to carcinogenesis. Oncogenes are genes whose protein products stimulate or enhance the division and viability of cells. Oncogenes arise by activating mutation of their precursors, the proto-oncogenes. Proto-oncogenes are often directly involved in growth regulation of normal cells. Advances in molecular studies had led to the identification of many oncogenes in cancer formation. This will help in early detection of many cancers. The action of drugs on oncogenes will help in specific treatment of different types of cancers. An overview of the functions, properties and clinical importance of oncogenes is discussed in this review.
Layered interpolation for interactive avatar control (2011)

Data driven motion interpolation methods have been widely used in interactive avatar control, however, their ability to generalize example database has not been explored very well. This paper aims to discuss this issue in interactive avatar application domain. A new layered interpolation model is presented in this paper, where partial motions in limb subspace are interpolated and then final natural posture is further achieved by compensating the motion correlation between limbs. By comparing previous methods in representative interactive avatar applications such as pose editing and performative user interface, experimental results show that the proposed method outperforms previous ones.
A review of the pharmacology and clinical uses of ivermectin. (1987)

The avermectins were introduced in 1981 and constitute a potent new class of anthelmintic agents. They are naturally-derived products of microbial action displaying an exceptionally wide range of antiparasitic efficacy against internal and external parasites of domestic animals. This paper reviews their isolation and chemistry, mechanism of action, chemical efficacy and safety in cattle, sheep, swine, horses and dogs.
Management of Early- Stage Epithelial Ovarian Cancer (1994)

"Early" epithelial ovarian carcinoma encompasses a spectrum of patients with diseases that have markedly different survivals, ranging from indolent lesions truly confined to the ovary to high-grade lesions that have a significant chance of occult metastasis at the time of diagnosis. The basic principles of management rest on an adequate primary surgical procedure that removes all gross disease and accurately assesses the sites at risk for metastasis with a comprehensive staging laparotomy. After a comprehensive staging laparotomy, patients can be stratified into low-risk and high-risk groups. Those with low-risk disease have such a low risk of recurrence that the toxicity of adjuvant therapy is not warranted. Although patients with high-risk disease have a high enough of a risk of recurrence to justify consideration of adjuvant therapy, their ultimate prognosis may be determined more by an accurate determination of the stage of disease rather than by currently available, marginally effective or ineffective therapy. Patients who are thought to have early stage disease on the basis of inadequate staging procedures either should undergo a restaging laparotomy or receive therapy for the possibility of occult advanced disease.
Low-power fully-testable flow meter in CMOS ASIC (1998)

This paper shows a circuit designed to measure the water flow in private homes and industrial buildings. The circuit was developed with hard constraints in size and in power consumption. It counts pulses coming from a sensor (multipole turbine placed inside the water pipe) operating as a slave of a microprocessor. It measures the period of that signal using an exponential counter (counting integer part and mantissa) to prevent overflows extending the dynamic range. The data is sent to the microprocessor through a bi-directional serial channel, using a protocol similar to the I/sup 2/C standard. The circuit has interrupt generation capabilities. Since it has to be used with a wide range of sensors and in different operating modes, it can be programmed from the microprocessor via command and status registers. It has an adaptive clock to minimize power dissipation when water flow is zero or with small water leaks. Since the circuit will be manufactured in large quantities additional circuitry was added for testing purposes.
Statistical models for the induction and use of selectional preferences (2002)

Abstract Selectional preferences have a long history in both generative and computational linguistics. However, since the publication of Resnik's dissertation in 1993, a new approach has surfaced in the computational linguistics community. This new line of research combines knowledge represented in a pre‐defined semantic class hierarchy with statistical tools including information theory, statistical modeling, and Bayesian inference. These tools are used to learn selectional preferences from examples in a corpus. Instead of simple sets of semantic classes, selectional preferences are viewed as probability distributions over various entities. We survey research that extends Resnik's initial work, discuss the strengths and weaknesses of each approach, and show how they together form a cohesive line of research.
Use of the Scintillation Camera to Reduce Radioisotope Scanning Time (1965)

The scintillation camera, when used either with positron or gamma-ray emitters, will image organs in a much shorter time than the focused-collimator scanner. Frequently, pictures can be taken in one tenth the time required for conventional scanning. As a result, acutely ill, agitated, or uncooperative patients can be examined. In addition, the short exposures encourage obtaining oblique and lateral views. These permit a more precise localization of the lesion and improve the diagnostic accuracy of the scanning procedure. Clinical use of the scintillation camera is expected to become widespread in years to come. It should be particularly valuable for stop-motion studies of dynamic physiological processes.
Broadband graphene electro-optic modulators with sub-wavelength thickness (2012)

Graphene's featureless optical absorption, ultrahigh carrier mobility, and variable optical absorption by an applied gate voltage enable a new breed of optical modulators with broad optical and electrical bandwidths. Here we report on an electro-optic modulator that integrates single-layer graphene in a sub-wavelength thick, reflective modulator structure. These modulators provide a large degree of design freedom, which allows tailoring of their optical properties to specific needs. Current devices feature an active aperture ~100 µm, and provide uniform modulation with flat frequency response from 1 Hz to >100 MHz. These novel, low insertion-loss graphene-based modulators offer solutions to a variety of high-speed amplitude modulation tasks that require optical amplitude modulation without phase distortions, a flat frequency response, or ultra-thin geometries, such as for controlling monolithic, high-repetition rate mode-locked lasers or active interferometers.
Tumor Vascular Maturation and Improved Drug Delivery Induced by Methylselenocysteine Leads to Therapeutic Synergy with Anticancer Drugs (2008)

These results show, for the first time, the antiangiogenic effects of MSC results in tumor growth inhibition, vascular maturation in vivo, and enhanced anticancer drug delivery that are associated with the observed therapeutic synergy in vivo.
An automated platform for high-throughput mouse behavior and physiology with voluntary head-fixation (2017)

Recording neural activity during animal behavior is a cornerstone of modern brain research. However, integration of cutting-edge technologies for neural circuit analysis with complex behavioral measurements poses a severe experimental bottleneck for researchers. Critical problems include a lack of standardization for psychometric and neurometric integration, and lack of tools that can generate large, sharable data sets for the research community in a time and cost effective way. Here, we introduce a novel mouse behavioral learning platform featuring voluntary head fixation and automated high-throughput data collection for integrating complex behavioral assays with virtually any physiological device. We provide experimental validation by demonstrating behavioral training of mice in visual discrimination and auditory detection tasks. To examine facile integration with physiology systems, we coupled the platform to a two-photon microscope for imaging of cortical networks at single-cell resolution. Our behavioral learning and recording platform is a prototype for the next generation of mouse cognitive studies.
Rescue of Female Infertility from the Loss of Cyclooxygenase-2 by Compensatory Up-regulation of Cyclooxygenase-1 Is a Function of Genetic Makeup (2004)

Cyclooxygenase-2 (COX-2), an inducible rate-limiting enzyme in prostaglandin biosynthesis, is implicated in various physiological and pathological processes including female fertility, renal function, angiogenesis, inflammation, and tumorigenesis. We showed previously that targeted deletion of Ptgs2 encoding COX-2, but not Ptgs1 encoding COX-1, in C57BL/6J/129 mice produces complete female infertility resulting from multiple reproductive failures spanning ovulation, fertilization, and implantation. Here we show that Ptgs2 null mice on a CD1 background have dramatically improved female fertility including ovulation, fertilization, and implantation, giving rise to live births. We provide evidence that this improved fertility in CD1 Ptgs2 null mice is the result of a compensatory up-regulation of Ptgs1 which does not occur in C57BL/6J/129 mice missing Ptgs2. These results clearly demonstrate for the first time that COX-1 can replace specific functions of COX-2 in vivo in the context of genetic disparity. In light of this finding, the therapeutic use and efficacy of COX-2-specific inhibitors among human populations without regard for genetic and ethnic diversities should be revisited.
Roots of Sorghum Exude Hydrophobic Droplets Containing Biologically Active Components<sup>1</sup> (1986)

Roots of Sorghum are known to exude materials that exhibit allelochemical activity, but the compounds identified do not completely account for the observed species‐specific allelochemical activities. The purpose of this investigation was to characterize both water‐soluble and water‐insoluble exudates from roots of sorghum [ Sorghum bicolor (L.) Moench] seedlings grown in petri dishes. Hydrophilic exudates included phenols, protein, and 3‐deoxyanthocyanidin derivatives. Hydrophobic droplets, exuded from root hairs, tested positively for phenols and lipids. These hydrophobic exudates strongly inhibit (85%) root elongation in lettuce ( Lactuca sativa cv. Great Lakes) seedlings, but do not affect that of corn ( Zea mays L. cv. B73 Ht ), nor the germination of either of these plants. Associated with these hydrophobic droplets are novel quinones, yet unidentified. The results indicate that these hydrophobic exudate droplets contain components that may have species‐specific biological activities.