gebhart/patrepeval huggingface dataset:
Identification of a Possible Secondary Picrotoxin-Binding Site on the GABA<sub>A</sub>Receptor (2013)

The type A GABA receptors (GABARs) are ligand-gated ion channels (LGICs) found in the brain and are the major inhibitory neurotransmitter receptors. Upon binding of an agonist, the GABAR opens and increases the intraneuronal concentration of chloride ions, thus hyperpolarizing the cell and inhibiting the transmission of the nerve action potential. GABARs also contain many other modulatory binding pockets that differ from the agonist-binding site. The composition of the GABAR subunits can alter the properties of these modulatory sites. Picrotoxin is a noncompetitive antagonist for LGICs, and by inhibiting GABAR, picrotoxin can cause overstimulation and induce convulsions. We use addition of picrotoxin to probe the characteristics and possible mechanism of an additional modulatory pocket located at the interface between the ligand-binding domain and the transmembrane domain of the GABAR. Picrotoxin is widely regarded as a pore-blocking agent that acts at the cytoplasmic end of the channel. However, there are also data to suggest that there may be an additional, secondary binding site for picrotoxin. Through homology modeling, molecular docking, and molecular dynamics simulations, we show that binding of picrotoxin to this interface pocket correlates with these data, and negative modulation occurs at the pocket via a kinking of the pore-lining helices into a more closed orientation.
Study of Detection Limits and Quantitation Accuracy Using 300 Mhz NMR (2003)

The analytical precision and accuracy of 300 MHz nuclear magnetic resonance (NMR) spectrometers was determined. The instruments that were used include a Bruker AC-300, a Bruker Avance 300, and a Varian 300. The minimum detection limits for proton (H1) and phosphorus (P31) were determined and compared for different instruments. The Minimum Detection Limits (MDL) for proton measurements were in the range of 3-10 microg/g. The MDL for phosphorus measurements were in the range of 50-70 microg/g. The quantitation accuracy for purity determinations was measured to be in the range of 1% relative to an internal standard. Specific MDL values should be determined for each particular matrix, internal standard, and instrument conditions.
Can observers judge future circular path relative to a target from retinal flow? (2011)

We investigated the ability of observers to judge whether they will pass left or right of a visible target from simulated motion along a circular path. Strategies based on optic flow would generally require compensation for pursuit eye movements. J. P. Wann and D. K. Swapp (2000) proposed an alternative strategy that requires only retinal flow. The experiments compared three conditions that provide the same retinal flow but different observer-relative optic flow. In the heading-relative view condition, simulated view direction rotated with change in heading, as naturally occurs when driving a car. In target-relative view condition, simulated view direction rotated to keep the direction of the target constant. In world-relative view condition, the simulated view direction was fixed relative to the environment. If an observer fixates the target, these conditions produce the same retinal flow. The initial heading direction of simulated motion was varied across trials, and responses were used to compute PSEs representing perceptual bias. Judgments were most accurate in the heading-relative condition. In the target-relative and world-relative view conditions, PSEs indicated large biases consistent with underestimation of path curvature. The large biases suggest that retinal flow is not sufficient to judge future circular path relative to a target.
Analytic solution for the birefringence produced by thermal stress in polarization-maintaining optical fibers (1983)

Polarization-maintaining optical fibers are usually made by inducing a large anisotropic thermal stress in the core so that it appears highly birefringent. A simple analytic solution has been found for the birefringence in terms of the cross-sectional distribution of the high-expansion material used to create the thermal stress. The analysis is able to predict optimal structures which efficiently utilize the available stress and thus maximize the birefringence. It is shown that the optimum structure has a cross-sectional geometry resembling a bow-tie. Design rules are given whereby the dimensions may be chosen and these are verified in a simple experiment.
Analysis of the site-specific N-glycosylation of  1,6 N-acetylglucosaminyltransferase V (2004)

N-acetylglucosaminyltransferase V (GnT-V) catalyzes the addition of a beta1,6-linked GlcNAc to the alpha1,6 mannose of the trimannosyl core to form tri- and tetraantennary N-glycans and contains six putative N-linked sites. We used mass spectrometry techniques combined with exoglycosidase digestions of recombinant human GnT-V expressed in CHO cells, to identify its N-glycan structures and their sites of expression. Release of N-glycans by PNGase F treatment, followed by analysis of the permethylated glycans using MALDI-TOF MS, indicated a range of complex glycans from bi- to tetraantennary species. Mapping of the glycosylation sites was performed by enriching for trypsin-digested glycopeptides, followed by analysis of each fraction with Q-TOF MS. Predicted tryptic glycopeptides were identified by comparisons of theoretical masses of peptides with various glycan masses to the masses of the glycopeptides determined experimentally. Of the three putative glycosylation sites in the catalytic region, peptides containing sites Asn 334, 433, and 447 were identified as being N-glycosylated. Asn 334 is glycosylated with only a biantennary structure with one or two terminating sialic acids. Sites Asn 433 and 447 both contain structures that range from biantennary with two sialic acids to tetraantennary terminating with four sialic acids. The predominant glycan species found on both of these sites is a triantennary with three sialic acids. The appearance of only biantennary glycans at site Asn 433, coupled with the appearance of more highly branched structures at Asn 334 and 447, demonstrates that biantennary acceptors present at different sites on the same protein during biosynthesis can differ in their accessibility for branching by GnT-V.
Distribution of protectin (CD59), a complement membrane attack inhibitor, in normal human tissues. (1991)

Protectin (CD59) is a recently discovered 18-20 kDa glycoprotein that effectively inhibits lysis by the membrane attack complex of the homologous complement system. This glycoprotein is widely distributed on the membranes of human blood cells (erythrocytes and leukocytes). By using immunofluorescence microscopy, protectin was observed in vascular endothelia throughout the body and in extravascular tissues. Cells expressing protectin were also found in ductal epithelia of pancreatic, biliary, and salivary systems, bronchi, and kidney collecting ducts. Furthermore, protectin was expressed in the epidermis and in the syncytiotrophoblast of placenta. The expression of protectin in endothelia, in various epithelial cells, and in placenta presumably protects autologous tissues and the fetoplacental unit from complement-mediated damage.
Ultrastructural organisation of HCV from the bloodstream of infected patients revealed by electron microscopy after specific immunocapture (2016)

Twenty-five years after the discovery of HCV, this study finally provides information about the precise morphological organisation of viral particles. It is truly remarkable that our TEM images fully confirm the ultrastructure of LVPs predicted by several authors, almost exclusively from the results of molecular biology studies.
Effects of shivering prevention on haemodynamic and metabolic demands in hypothermic postoperative neurosurgical patients (2001)

We evaluated the haemodynamic and metabolic effects of prevention of shivering after prophylactic nefopam administration in neurosurgical patients undergoing craniotomy and mild systemic hypothermia (33-35 degrees C). Forty patients were enrolled in a randomised, double-blind study. Before extubation, patients received intravenously either nefopam 0.12 mg.kg-1 or an equal volume of saline 0.9%. Left ventricular systolic work index, oxygen consumption index and systemic lactate concentration were recorded before, immediately after and every 20 min for 2 h after extubation. Shivering appeared in two patients treated with nefopam and in all control patients (p < 0.001). Both left ventricular systolic work index and oxygen consumption index were similar in the two groups before extubation, increased after extubation, and further increased in control patients showing a statistical difference compared to patients treated with nefopam. Our results suggest that nefopam is effective in preventing postoperative shivering in patients undergoing neurosurgery and mild hypothermia and attenuates the haemodynamic effects of shivering during rewarming.
Solvent‐Ligated Copper(II) Complexes for the Homopolymerization of 2‐Methylpropene (2008)

Copper(II) complexes with weakly coordinating counter anions can be utilized as highly efficient catalysts for the synthesis of poly(2-methylpropene) ("polyisobutene") with a high content of terminal double bonds. These copper(II) compounds are significantly more active than the manganese(II) complexes described previously, can be applied in chlorine-free solvents such as toluene, are easily accessible, and can be handled at room temperature and in laboratory atmospheres for brief periods, but they are sensitive to excess water, thereby losing their catalytic activity. Replacing the acetonitrile ligands by benzonitrile ligands improves the solubility and catalytic activity in nonpolar and nonchlorinated solvents. However, the benzonitrile copper(II) compounds have lower thermal stability than their acetonitrile congeners.
Role of Myofibroblasts at the Invasion Front (2002)

Tumor progression occurs within a microecosystem, where cancer cells and myofibroblasts exchange proteinases and cytokines that promote growth directly through stimulation of proliferation and survival, as well as invasion through local proteolysis of the extracellular matrix and stimulation of motility. Myofibroblasts maintain the capacity of fibroblasts to induce differentiation. Fibroblasts are the main source of tumorassociated myofibroblasts. The transition to myofibroblasts also occurs in noncancerous situations. This transition is modulated by mechanical stress and cytokines, amongst which transforming growth factorβ. The crosstalk between cancer cells and myofibroblasts illustrates the microecosystem of tumor invasion. In order to consider myofibroblasts as a possibly new target for cancer therapy, further characterization of the molecular crosstalk between myofibroblasts and cancer cells is required.
Multi‐<scp>UAV</scp>Cooperation (2015)

This chapter discusses architectures for multi‐UAV cooperation. It focuses mainly on systems in which the UAVs have a certain degree of autonomy and that present intentional cooperation (thus swarming techniques and low‐level formations are not covered). The chapter discusses the main elements of such architectures, with special emphasis on cooperative perception and decision making. For each of these topics, the main approaches considered in the literature are discussed. An application of a cooperative team of UAVs tracking firemen in a disaster management scenario that was developed by the authors is shown.
Improving DNA Quality using FFPE tissues for Array Comparative Genomic Hybridization to find Single Nucleotide Polymorphisms (SNPs) in Melanoma (2015)

The hypothesis of the project is that the quality of the DNA does have an effect on how successfully the samples can hybridize onto array CGH microarrays.Therefore, improving the quality of the DNA will improve the aCGH data to efficiently find SNPs that cause/predispose to malignant melanoma, which can be useful for finding prognostic/diagnostic markers. PROJECT AIMS1. Optimize the quality of extracted genomic DNA from formalin-fixed paraffin embedded tissues for DNA fragment length, yield, and PCR performance.2. Improve the performance of SNP 6.0 microarrays for FFPE DNA and generate raw array data.3. Detect the novel SNPs that predispose to malignant melanoma.vi
Lessons learned from building a terabyte digital video library (1999)

The Informedia Project at Carnegie Mellon University has created a terabyte digital video library in which automatically derived descriptors for the video are used for indexing, segmenting and accessing the library contents. Begun in 1994, the project presented numerous challenges for library creation and deployment, valuable information covered in this article. The authors, developers of the project at Carnegie Mellon University, addressed these challenges by: automatically extracting information from digitized video; creating interfaces that allowed users to search for and retrieve videos based on extracted information; and validating the system through user testbeds. Through speech, image, and natural language processing, the Informedia Project has demonstrated that previously inaccessible data can be derived automatically and used to describe and index video segments.
A Regioselective Biocatalyst for Alkane Activation under Mild Conditions (2011)

Going green: Chemical methods for the hydroxylation of alkanes involve toxic, dangerous reagents and are not very selective. In a biochemical alternative route based on an artificial self-sufficient cytochrome P450, the highly selective and efficient terminal hydroxylation of n-alkanes is possible under mild conditions (see scheme; NADPH is the reduced form of nicotinamide adenine dinucleotide phosphate (NADP+)).
BPA's experience of Implementing Remedial Action Schemes in power flow for operation studies (2013)

This paper discusses the BPA experience of implementing Remedial Action Schemes (RAS) in operations studies. The previous methodology of manually including each RAS action as part of the applicable contingency definition is both time consuming and error prone. A more holistic approach was chosen with the goal of allowing automatic deployment of RAS based upon the initial conditions and changes in topology caused by contingency actions. This allows any power flow condition to be simulated without the need to modify the contingency files. This method has been tested and works well with both regional planning case bus-branch model and the breaker oriented real-time State Estimator model. It has proven to save time, reduce work load and minimize errors. A step by step modeling approach is presented.
Inside Linux (2000)

From the Publisher:
With in-depth, complete coverage on the Linux operating system, Inside Linux is the only book Linux users and system administrators will need. This text is just the right reference for any experienced computer user wanting an understanding of Linux. Tobler leaves the monotonous steps to a minimum and instead fits readers' sophisticated needs in a thought-provoking manner.
Centering balloon to improve esophageal photodynamic therapy (1992)

A cylindrical balloon was developed to improve delivery of circumferential light for photodynamic therapy (PDT) of esophageal carcinoma. The balloon consisted of a 36-mm-long clear cylindrical membrane and a central tube to hold a cylindrical diffuser in the center of the lumen. Three isotropic probes were placed on the outside of the balloon to allow measurement of delivered light dose to the esophageal mucosa. The balloon was tested in the normal esophagus of 8 dogs that were injected with 4.0 mg/kg of PHOTOFRINR. Endoscopy was performed 48 hours following the injection, and under endoscopic observation the balloon assembly was passed, fixed in place, and inflated. A 1-cm cylindrical diffuser was passed into the central tube and 150, 300, and 600 Joules/cm of 630 nm laser light was delivered at 25 cm, 15 cm, and 5 cm proximal to the gastroesophageal junction. One control dog was illuminated using the cylindrical diffuser alone at doses of 300 and 600 Joules/cm of diffuser. Complete circumferential tissue response was obtained when the balloon was used. Relatively uniform light intensities were measured around the lumen. In contrast, noncircumferential and unpredictable PDT responses were generated when the cylindrical diffuser was used without the balloon.
Pulse sequence and parameter choice in NMR imaging as a problem of constrained multidimensional nonlinear optimization (1988)

The advantage of the multiparametric nature of NMR imaging is connected with the problem of finding optimum pulse sequences and sequence parameters, which ensure a high contrast-to-noise ratio. For a given imaging task with m (m greater than or equal to 2) regions characterized by sets of NMR parameters (e.g., rho, T1, T2) two functions are proposed, which can be used to transform the search for an optimum pulse sequence into a problem of constrained multidimensional nonlinear optimization. The numerical algorithm is described and the results of two examples are presented and discussed. A short description of useful extensions of the proposed optimization approach, which are currently implemented, is given.
Hardware/software co-synthesis with memory hierarchies (1998)

Article Free Access Share on Hardware/software co-synthesis with memory hierarchies Authors: Yanbing Li Department of Electrical Engineering, Princeton University, Princeton, NJ Department of Electrical Engineering, Princeton University, Princeton, NJView Profile , Wayne Wolf Department of Electrical Engineering, Princeton University, Princeton, NJ Department of Electrical Engineering, Princeton University, Princeton, NJView Profile Authors Info & Claims ICCAD '98: Proceedings of the 1998 IEEE/ACM international conference on Computer-aided designNovember 1998 Pages 430–436https://doi.org/10.1145/288548.289066Published:01 November 1998Publication History 9citation253DownloadsMetricsTotal Citations9Total Downloads253Last 12 Months15Last 6 weeks2 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
SgrA, a Nidogen-Binding LPXTG Surface Adhesin Implicated in Biofilm Formation, and EcbA, a Collagen Binding MSCRAMM, Are Two Novel Adhesins of Hospital-Acquired <i>Enterococcus faecium</i> (2009)

Hospital-acquired Enterococcus faecium isolates responsible for nosocomial outbreaks and invasive infections are enriched in the orf2351 and orf2430 genes, encoding the SgrA and EcbA LPXTG-like cell wall-anchored proteins, respectively. These two surface proteins were characterized to gain insight into their function, since they may have favored the rapid emergence of this nosocomial pathogen. We are the first to identify a surface adhesin among bacteria (SgrA) that binds to the extracellular matrix molecules nidogen 1 and nidogen 2, which are constituents of the basal lamina. EcbA is a novel E. faecium MSCRAMM (microbial surface component recognizing adhesive matrix molecules) that binds to collagen type V. In addition, both SgrA and EcbA bound to fibrinogen; however, SgrA targeted the alpha and beta chains, whereas EcbA bound to the gamma chain of fibrinogen. An E. faecium sgrA insertion mutant displayed reduced binding to both nidogens and fibrinogen. SgrA did not mediate binding of E. faecium cells to biotic materials, such as human intestinal epithelial cells, human bladder cells, and kidney cells, while this LPXTG surface adhesin is implicated in E. faecium biofilm formation. The acm and scm genes, encoding two other E. faecium MSCRAMMs, were expressed at the mRNA level together with sgrA during all phases of growth, whereas ecbA was expressed only in exponential and late exponential phase, suggesting orchestrated expression of these adhesins. Expression of these surface proteins, which bind to extracellular matrix proteins and are involved in biofilm formation (SgrA), may contribute to the pathogenesis of hospital-acquired E. faecium infections.
Filling the Concept with Data: Integrating Data from Different In Vitro and In Silico Assays on Skin Sensitizers to Explore the Battery Approach for Animal-Free Skin Sensitization Testing (2008)

Tests for skin sensitization are required prior to the market launch of new cosmetic ingredients. Significant efforts are made to replace the current animal tests. It is widely recognized that this cannot be accomplished with a single in vitro test, but that rather the integration of results from different in vitro and in silico assays will be needed for the prediction of the skin sensitization potential of chemicals. This has been proposed as a theoretical scheme so far, but no attempts have been made to use experimental data to prove the validity of this concept. Here we thus try for the first time to fill this widely cited concept with data. To this aim, we integrate and report both novel and literature data on 116 chemicals of known skin sensitization potential on the following parameters: (1) peptide reactivity as a surrogate for protein binding, (2) induction of antioxidant/electrophile responsive element dependent luciferase activity as a cell-based assay; (3) Tissue Metabolism Simulator skin sensitization model in silico prediction; and (4) calculated octanol-water partition coefficient. The results of the in vitro assays were scaled into five classes from 0 to 4 to give an in vitro score and compared to the local lymph node assay (LLNA) data, which were also scaled from 0 to 4 (nonsensitizer/weak/moderate/strong/extreme). Different ways of evaluating these data have been assessed to rate the hazard of chemicals (Cooper statistics) and to also scale their potency. With the optimized model an overall accuracy for predicting sensitizers of 87.9% was obtained. There is a linear correlation between the LLNA score and the in vitro score. However, the correlation needs further improvement as there is still a relatively high variation in the in vitro score between chemicals belonging to the same sensitization potency class.
CELL WALL DEGRADING ENZYMES AND THE SOFTENING OF SENESCENT STRAWBERRY FRUIT (1976)

ABSTRACT The changes in enzyme activity occurring during the ripening of strawberry fruit on the plant and the development of senescence after picking have been studied. Pectinesterase is found to increase from the green to early ripe stages but to decrease during the senescent “overripe” stage. Polygalacturonase and polymethylgalacturonase activity were not found. A C x ‐type cellulolytic activity was observed in ripe fruit and increases in the “over‐ripe” fruit. These observations tie used to provide a possible explanation for the loss of firmness after strawberry fruit has been picked and becomes senescent.