gebhart/patrepeval huggingface dataset:
Development of a New Pharmacophore Model That Discriminates Active Compstatin Analogs (2008)

Compstatin and its active peptide analogs can potentially be used for therapeutic purposes because their binding to the third component of complement prohibits its conversion into the proteolytically activated form of the third component of complement, thus inhibiting complement cascades in all three complement pathways. Mallik and Morikis built three quasi-dynamic pharmacophore models for compstatin peptide analogs before, but only nine compstatin peptide analogs were incorporated in their study and the most active compstatin analog had only medium inhibitory activity. Since then, many more compstatin analogs have been synthesized and their inhibitory activities tested. Furthermore, the X-ray structure of AcCompNH2-V4W-H9A bound to the third component of complement has become available (PDB ID: 2QKI). In this paper, we utilized all the new information and built a new pharmacophore model using a distinct approach. Our model demonstrated good performance in a separate test set of 82 compstatin analogs: it accurately identified 70% of the analogs of medium or high inhibitory activities and misclassified only 8.5% of the analogs of low or no inhibitory activities. The results proved our pharmacophore model to be a filter of great sensitivity and specificity.
Negative refraction and omnidirectional total transmission at a planar interface associated with a uniaxial medium (2004)

The conditions for yielding negative refraction as well as omnidirectional total transmission at planar interfaces between uniaxial media have been analyzed. It is found that both phenomena can occur at a wide variety of interfaces associated with uniaxial media. In particular, when certain conditions are satisfied, even an interface between isotropic and uniaxial media can also exhibit negative refraction and omnidirectional total transmission, adding considerably to the flexibility in potential device applications.
Performance enhancement of respiratory tumor motion prediction using adaptive support vector regression: Comparison with adaptive neural network method (2014)

ABSTRACT The breathing motion moves internal organs and targeted regions determined by radiation therapy planning. For the radiation therapy, accurate prediction for breathing motion is of great interest as the outer targeted region treatment could endanger sensitive tissue. In this study, the use of a prediction algorithm with adaptive support vector regression (aSVR) was proposed and compared with the adaptive neural network (ANN) algorithm considering the prediction accuracy and training and predicting time. Respiration data from 87 patients treated by radiation therapy, were acquired with an optical marker at 30 Hz. Five types of prediction filters with the ANN or aSVR filters, were implemented and their performance was compared according to the size of the sliding window (2.5 and 5.0 sec), and the prediction latencies (100, 200, 300, 400, and 500 msec). Training and testing of the prediction algorithms with aSVR and ANN were performed. The root mean square error (RMSE) was used as the accuracy metric. The aSVR with an RBF kernel outperformed other prediction filters, including not only various types of ANN filters but also the aSVR with a linear kernel. A sliding window of 2.5 sec significantly and independently enhanced the overall accuracy. Otherwise, the training and prediction testing times were significantly prolonged in case of aSVR with an RBF kernel. The aSVR filter with the RBF kernel is in all cases superior to other filters regarding its accuracy; it also shows clinically applicable results from the viewpoint of training and predicting time, which may be effective for predicting patient breathing motion and thus enhancing the efficacy of radiation therapy.
A combination of chemical derivatisation and improved bioinformatic tools optimises protein identification for proteomics (2001)

The identification of individual protein species within an organism's proteome has been optimised by increasing the information produced from mass spectral analysis through the chemical derivatisation of tryptic peptides and the development of new software tools. Peptide fragments are subjected to two forms of derivatisation. First, lysine residues are converted to homoarginine moieties by guanidination. This procedure has two advantages, first, it usually identifies the C-terminal amino acid of the tryptic peptide and also greatly increases the total information content of the mass spectrum by improving the signal response of C-terminal lysine fragments. Second, an Edman-type phenylthiocarbamoyl (PTC) modification is carried out on the N-terminal amino acid. The renders the first peptide bond highly susceptible to cleavage during mass spectrometry (MS) analysis and consequently allows the ready identification of the N-terminal residue. The utility of the procedure has been demonstrated by developing novel bioinformatic tools to exploit the additional mass spectral data in the identification of proteome proteins from the yeast Saccharomyces cerevisiae. With this combination of novel chemistry and bioinformatics, it should be possible to identify unambiguously any yeast protein spot or band from either two-dimensional or one-dimensional electropheretograms.
Stearoyl-CoA Desaturase Is Involved in the Control of Proliferation,Anchorage-independent Growth, and Survival in Human TransformedCells (2005)

Saturated and monounsaturated fatty acids are the most abundant fatty acid species in mammalian organisms, and their distribution is regulated by stearoyl-CoA desaturase, the enzyme that converts saturated into monounsaturated fatty acids. A positive correlation between high monounsaturated fatty acid levels and neoplastic transformation has been reported, but little is still known about the regulation of stearoyl-CoA desaturase in cell proliferation and apoptosis, as well as in cancer development. Here we report that simian virus 40-transformed human lung fibroblasts bearing a knockdown of human stearoyl-CoA desaturase by stable antisense cDNA transfection (hSCDas cells) showed a considerable reduction in monounsaturated fatty acids, cholesterol, and phospholipid synthesis, compared with empty vector transfected-simian virus 40 cell line (control cells). hSCDas cells also exhibited high cellular levels of saturated free fatty acids and triacylglycerol. Interestingly, stearoyl-CoA desaturase-depleted cells exhibited a dramatic decrease in proliferation rate and abolition of anchorage-independent growth. Prolonged exposure to exogenous oleic acid did not reverse either the slower proliferation or loss of anchorage-independent growth of hSCDas cells, suggesting that endogenous synthesis of monounsaturated fatty acids is essential for rapid cell replication and invasiveness, two hallmarks of neoplastic transformation. Moreover, apoptosis was increased in hSCDas cells in a ceramide-independent manner. Finally, stearoyl-CoA desaturase-deficient cells were more sensitive to palmitic acid-induced apoptosis compared with control cells. Our data suggest that, by globally regulating lipid metabolism, stearoyl-CoA desaturase activity modulates cell proliferation and survival and emphasize the important role of endogenously synthesized monounsaturated fatty acids in sustaining the neoplastic phenotype of transformed cells.
Antonio de los Reyes (1729-1789): un Bartolomé de las Casas alicantino en el siglo XVIII (1999)

El estudio trata de enfatizar la importancia del obispo Antonio de los
Reyes en el contexto de las exploraciones e incursiones espanolas de la
segunda mitad del siglo XVIII al noroeste del continente americano y la
relevancia de sus informes para determinar la critica que externaban
algunos sectores de la iglesia sobre los metodos de colonizacion practicada
por las autoridades civiles y militares. El articulo tambien tiene
como apendice uno de estos informes Manifiesto estado de las Provincias
Sonora y un estudio textual introductorio.
<i>N</i> -Acetylaspartate and <i>N</i> -acetylaspartylglutamate (2008)

N -Acetylaspartate (NAA) and its derivative, N -acetylaspartylglutamate (NAAG), are synthesized in neurons and present in very high concentrations in the CNS. NAA is a marker of the functional integrity of neuronal mitochondrial metabolism and may be critical for myelinogenesis,1 whereas NAAG modulates glutamatergic transmission and may have a role in neuroprotection and synaptic plasticity.2 Regional reduction of NAA levels measured by magnetic resonance spectroscopy (MRS) has been used as a marker of neuronal or axonal loss in several neurologic disorders, including traumatic brain injury, stroke, epilepsy, and multiple sclerosis, but may also reflect reversible metabolic impairment. Elevation of NAA levels is a hallmark of Canavan disease, a severe demyelinating disorder of infancy.1 Inhibitors of NAAG peptidase provide neuroprotection in experimental models of stroke, head trauma, and amyotrophic lateral sclerosis (ALS), presumably by increasing endogenous NAAG signaling.2 Thus, elucidation of the neurobiology of NAA and NAAG provides insight into the role of these molecules in the pathophysiology of several neurologic disorders and their potential as a therapeutic target for these conditions.

NAA and NAAG participate in important mechanisms of signaling among neurons and glial cells (figure).





Figure Interactions among neurons and glial cells mediated by N -acetylaspartate (NAA) and N -acetylaspartylglutamate (NAAG)

In neurons, NAA is synthesized in the mitochondria and is then transported to oligodendrocytes, when it is metabolized by the aspartoacylase (ASPA) to acetate. Acetate serves as a precursor for synthesis of myelin lipids. In neurons, NAA is combined to glutamate to produce NAAG, which is released from synaptic vesicles and acts as a cotransmitter with several other neurotransmitters, including l-glutamate. NAAG, acting via presynaptic type 3 metabotropic glutamate receptors (mGluR3), blocks presynaptic calcium (Ca2+) channels, thus inhibiting glutamate release. NAAG may also bind to N -methyl-d-aspartate receptors, blocking their function. NAAG, …
Binocular fusion and rivalry (1996)

Abstract This chapter begins with a discussion of binocular fusion. It then discusses dichoptic color mixture, stimulus determinants of rivalry, binocular suppression selectivity, rivalry and stereopsis, binocular suppression, models of binocular rivalry, and cognition and binocular rivalry.
Pathogenesis of Diabetic Neuropathy (1998)

Diabetes mellitus affects over 14 million people in the United States and the number of diabetics is increasing by 5% per year. Diabetic neuropathy (DN) is a common complication of diabetes and occurs in approximately 50% of diabetic patients over time. Clinical trials have proven that hyperglycemia almost certainly conditions the development of DN. Despite this fact, we still do not understand the mechanism(s) underlying DN. Several possible etiologies have been proposed including altered metabolism of polyol, lipids, or amino acids, vascular insufficiency, increased superoxide-induced free radical formation, impaired axonal transport or reduced neurotrophism. Accumulating evidence suggests that these defects are likely interrelated and that their interaction(s) within the diabetic milieu are responsible for the development and progression of DN. In this review we will discuss these theories, their interrelationships and how, collectively, these ideas may begin to explain the etiology of DN.
Effect of the Solvent Flow Rate on the Ionization Efficiency in Atmospheric Pressure Photoionization-Mass Spectrometry (2005)

In the novel atmospheric pressure photoionization-mass spectrometry the ionization efficiency has been observed to decrease when the solvent flow rate is increased. The effect of the flow rate on the ionization efficiency was studied by comparing the behavior of two analytes, one of which is ionized through charge exchange, the other through proton transfer. Additional information about the ion loss mechanisms was obtained by comparing results obtained with two different APPI ion sources: a Sciex prototype and the Agilent/Syagen APPI source. In addition to the measurements done by using the mass analyzer, the total ion current in the ion source was obtained by measuring the currents of the ions arriving at curtain/end plate and orifice/capillary of the two mass spectrometers. The total ion current measurements showed a significant decrease at high solvent flow rates. Loss of dopant radical cations was thought to be the reason for the signal decrease of the analytes formed through charge exchange. Analytes formed through proton transfer were not as seriously ected by the high solvent flow rates, but some saturation of their signal was nevertheless observed. Loss of photons through absorption by solvent vapor is another mechanism that can be held responsible for a reduction of the total number of ions produced by the APPI source.
Tyrosine Sulfation of the Glycoprotein Ib-IX Complex: Identification of Sulfated Residues and Effect on Ligand Binding (1994)

Here, we present evidence that glycoprotein (GP) Ib alpha, one of three polypeptides that make up the GP Ib--IX complex--the receptor for von Willebrand factor (vWf) on the surface of unactivated platelets--is modified by sulfation of tyrosine residues. Only GP Ib alpha was found to incorporate 35S when the GP Ib--IX complex was immunoprecipitated from [35S]sulfate metabolically labeled L and CHO cells that express the recombinant complex. The occurrence of sulfation on tyrosine residues of the polypeptide backbone was determined by removing O- and N-linked oligosaccharides. Limited proteolytic digestion of metabolically labeled GP Ib alpha revealed that sulfated tyrosine residues are located in the 45-kDa globular region containing the vWf binding site. By mutating potentially sulfated tyrosine residues to phenylalanine and comparing the stoichiometry of sulfate incorporation of these mutants to the incorporation in wild-type GP Ib alpha, three clustered tyrosine residues--Tyr-276, Tyr-278, and Tyr-279-were identified that undergo the modification. Culturing cells in sulfate-depleted medium containing sodium chlorate and guaiacol completely inhibited GP Ib alpha sulfation but did not decrease GP Ib-IX expression on the cell surface. Similarly, transiently transfected CHO cells expressed the mutant GP Ib alpha polypeptide on their surfaces at the same levels as they expressed wild-type GP Ib alpha. These results suggest that tyrosine sulfation of GP Ib alpha has little or no effect on the synthesis, assembly, and surface expression of the GP Ib-IX complex. Nevertheless, inhibiting sulfation of GP Ib alpha reduced the binding of 125I-labeled vWf in the presence of ristocetin by up to 37%.(ABSTRACT TRUNCATED AT 250 WORDS)
Analog filtering methods improve leading edge timing performance of multiplexed SiPMs (2016)

Multiplexing many SiPMs to a single readout channel is an attractive option to reduce the readout complexity of high performance time of flight (TOF) PET systems. However, the additional dark counts and shaping from each SiPM cause significant baseline fluctuations in the output waveform, degrading timing measurements using a leading edge threshold. This work proposes the use of a simple analog filtering network to reduce the baseline fluctuations in highly multiplexed SiPM readouts. With 16 SiPMs multiplexed, the FWHM coincident timing resolution for single [Formula: see text] mm LYSO crystals was improved from 401 ± 4 ps without filtering to 248 ± 5 ps with filtering. With 4 SiPMs multiplexed, using an array of [Formula: see text] mm LFS crystals the mean time resolution was improved from 436 ± 6 ps to 249 ± 2 ps. Position information was acquired with a novel binary positioning network. All experiments were performed at room temperature with no active temperature regulation. These results show a promising technique for the construction of high performance multiplexed TOF PET readout systems using analog leading edge timing pickoff.
Integration of autopatching with automated pipette and cell detection in vitro (2016)

Patch clamp is the main technique for measuring electrical properties of individual cells. Since its discovery in 1976 by Neher and Sakmann, patch clamp has been instrumental in broadening our understanding of the fundamental properties of ion channels and synapses in neurons. The conventional patch-clamp method requires manual, precise positioning of a glass micropipette against the cell membrane of a visually identified target neuron. Subsequently, a tight "gigaseal" connection between the pipette and the cell membrane is established, and suction is applied to establish the whole cell patch configuration to perform electrophysiological recordings. This procedure is repeated manually for each individual cell, making it labor intensive and time consuming. In this article we describe the development of a new automatic patch-clamp system for brain slices, which integrates all steps of the patch-clamp process: image acquisition through a microscope, computer vision-based identification of a patch pipette and fluorescently labeled neurons, micromanipulator control, and automated patching. We validated our system in brain slices from wild-type and transgenic mice expressing channelrhodopsin 2 under the Thy1 promoter (line 18) or injected with a herpes simplex virus-expressing archaerhodopsin, ArchT. Our computer vision-based algorithm makes the fluorescent cell detection and targeting user independent. Compared with manual patching, our system is superior in both success rate and average trial duration. It provides more reliable trial-to-trial control of the patching process and improves reproducibility of experiments.
Ichthyophthiriasis in carp, <i>Cyprinus carpio</i> L.: fate of parasites in immunized fish (1992)

Abstract. The host‐parasite relationship between O‐group carp and the ciliatc Ichthyophthirius multifiliis Fouquet was investigated, with the specific aim of characterizing the fate of parasites encountering immunized fish. Carp were immunized by repeated controlled infections; immunized fish and control fish naive to I. multifiliis were then infected in the caudal fin epidermis by a single controlled exposure to theronts, which were applied in a droplet suspension to the tail surface. The number of parasites present within the caudal fin was monitored over a subsequent 5‐day period by means of in situ parasite mapping. Results indicated that, contrary to previous reports, theronts penetrated the skin of immunized fish in numbers comparable to those of fish receiving a primary infection. However, the majority of parasites which penetrated immune skin did not complete normal development; 79% of the parasites which had initially penetrated the immune skin were not relocated within 2h of exposure, and since no parasite material was detected at penetration sites, it was concluded that these parasites had prematurely exited the skin rather than been killed in situ. Subsequently, these sites became populated by leucocytes, predominantly macrophages, and the infiltrations continued for up to 5 days after the initial exposure. In contrast, at sites where mature trophonts had exited the skin of fish following a primary infection, more diffuse leucocytic infiltrations were recorded, and these were predominated by neutrophils. Differences in the response to parasite exit from immunized and previously unexposed control fish skin are discussed, with particular reference to the mode of protection and the fate of parasites encountering immune fish.
Synthesis of 1,2‐Diaryl‐ and 1‐Aryl‐2‐alkylimidazoles with Sterically Demanding Substituents (2013)

Abstract 1,2‐Diarylimidazoles are an important class of compounds. They are frequently used as ligands for photophysically active metal complexes and also display physiological activity. We developed a new, high‐yielding procedure for the synthesis of 1,2‐diaryl‐substituted imidazoles with sterically demanding substituents at the respective ortho positions by starting from commercially available anilines and benzoic acids through the corresponding acid chlorides. The metal‐free method provides access to a variety of different substituents on the phenyl rings at N‐1 and C‐2 as well as at the 4,5‐positions of the imidazole backbone. Our new method is also suitable for the preparation of 1‐aryl‐2‐alkylimidazoles.
Professional Augmented Reality Browsers for Smartphones: Programming for junaio, Layar and Wikitude (2011)

Create amazing mobile augmented reality apps with junaio, Layar, and Wikitude!Professional Augmented Reality Browsers for Smartphones guides you through creating your own augmented reality apps for the iPhone, Android, Symbian, and bada platforms, featuring fully workable and downloadable source code. You will learn important techniques through hands-on applications, and you will build on those skills as the book progresses.Professional Augmented Reality Browsers for Smartphones:Describes how to use the latitude/longitude coordinate system to build location-aware solutions and tells where to get POIs for your own augmented reality applicationsDetails the leading augmented reality platforms and highlights the best applicationsCovers development for the leading augmented reality browser platforms: Wikitude, Layar, and junaioShows how to build cross-platform location-aware content (Android, iPhone, Symbian, and bada) to display POIs directly in camera viewIncludes tutorials for building 2D and 3D content, storing content in databases, and triggering actions when users reach specific locationswrox.comProgrammer ForumsJoin our Programmer to Programmer forums to ask and answer programming questions about this book, join discussions on the hottest topics in the industry, and connect with fellow programmers from around the world.Code DownloadsTake advantage of free code samples from this book, as well as code samples from hundreds of other books, all ready to use.Read MoreFind articles, ebooks, sample chapters, and tables of contents for hundreds of books, and more reference resources on programming topics that matter to you.Wrox Professional guides are planned and written by working programmers to meet the real-world needs of programmers, developers, and IT professionals. Focused and relevant, they address the issues technology professionals face every day. They provide examples, practical solutions, and expert education in new technologies, all designed to help programmers do a better job.
Possible function of Ah receptor nuclear translocator (Arnt) homodimer in transcriptional regulation. (1995)

Arnt (Ah receptor nuclear translocator) is a member of a transcription factor family having characteristic motifs designated bHLH (basic helix-loop-helix) and PAS and was originally found as a factor forming a complex with Ah receptor (AhR) to bind the specific xenobiotic responsive element (XRE) sequence for induction of drug-metabolizing P4501A1. We have examined interaction of Arnt with other PAS proteins--Drosophila Per, Sim, and AhR--by the coimmunoprecipitation method. Arnt formed a homodimer with itself as well as heterodimers with the others by means of the PAS and HLH domains in a cooperative way. The Arnt homodimer binds the sequence of adenovirus major late promoter (MLP) with the E box core sequence CACGTG, suggesting that the CAC half of the XRE, CACGCN(A/T), recognized by the AhR-Arnt heterodimer is a target for Arnt. Cotransfection experiments using CV-1 cells with an Arnt expression plasmid and a MLP chloramphenicol acetyltransferase (CAT) reporter plasmid revealed that Arnt markedly activated CAT expression, indicative of a newly discovered regulatory role of Arnt.